@article {pmid41787133, year = {2026}, author = {Katzke, J and Hita Garcia, F and Lösel, PD and Azuma, F and Faragó, T and Aibekova, L and Casadei-Ferreira, A and Gautam, S and Richter, A and Toulkeridou, E and Bremer, S and Hamann, E and Hein, J and Odar, J and Sarkar, C and Zuber, M and Boomsma, JJ and Feitosa, RM and Schrader, L and Zhang, G and Csősz, S and Dong, M and Evangelista, O and Fischer, G and Fisher, BL and Florez-Fernandez, JA and ,  and García, F and Gómez, K and Grasso, DA and de Greef, S and Guénard, B and Hawkes, PG and Johnson, RA and Keller, RA and Larsen, RS and Linksvayer, TA and Liu, C and Matte, A and Ogasawara, M and Ran, H and Rodriguez, J and Schifani, E and Schultz, TR and Shik, JZ and Sosa-Calvo, J and Tong, C and Tozetto, L and Yoon, S and Yoshimura, M and Zhao, J and Baumbach, T and Economo, EP and van de Kamp, T}, title = {High-throughput phenomics of global ant biodiversity.}, journal = {Nature methods}, volume = {}, number = {}, pages = {}, pmid = {41787133}, issn = {1548-7105}, support = {21K06326//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 22KJ3077//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 24K01785//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; IC 180100008//Department of Education and Training | Australian Research Council (ARC)/ ; K 147781//Ministry of Science, Technology and Innovation | Conselho Nacional de Desenvolvimento Científico e Tecnológico (National Council for Scientific and Technological Development)/ ; 502787686//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DEB-1932467//National Science Foundation (NSF)/ ; IOS-2128304//National Science Foundation (NSF)/ ; DEB 1927161//National Science Foundation (NSF)/ ; DEB 1927161//National Science Foundation (NSF)/ ; DEB 1927161//National Science Foundation (NSF)/ ; ECF 137/2020//Environment and Conservation Fund (ECF)/ ; UIDB/00329/2020//NOVA | Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa (FCT/UNL)/ ; 05K2022//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 05K2019//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; }, abstract = {The big data era in biology is underway, but the study of organismal form has been slow to capitalize on advances in imaging and computation. Imaging approaches can digitize whole organisms, but low throughput has limited the effort to document morphological diversity. Here, within the open science initiative 'Antscan', we applied high-throughput synchrotron X-ray microtomography to capture phenotypes across a diverse and ecologically dominant insect group: ants. At https://www.antscan.info , we provide 2,193 whole-body three-dimensional ant datasets from 212 genera and 792 species to broadly cover the ant phylogeny with a global scope, also pairing phenomic data with genome sequencing projects. Scans acquired with standardized parameters facilitate automated analysis, and free access to data can broaden the audience and incentivize methods development. Antscan presents a scalable approach to create libraries of diverse anatomies, heralding an era of studies on the evolution, structure and function of organismal phenotypes.}, }
@article {pmid41786578, year = {2026}, author = {Xu, N and Zhang, Z and Xu, H and Yao, J and Lu, H and Cai, W and Ou, Y and Luan, H and Gong, P and Tu, W and Li, Q}, title = {Multifaceted assessment of recent saltwater intrusion along China's coasts.}, journal = {Science bulletin}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.scib.2026.02.021}, pmid = {41786578}, issn = {2095-9281}, }
@article {pmid41779789, year = {2026}, author = {Gonzalez, A and August, T and Bailey, S and Bobiwash, K and Boersch-Supan, PH and Burgess, ND and Daru, BH and Elphick, CS and Freckleton, RP and Frick, WF and Hughes, AC and Isaac, NJB and Jones, JPG and Lambertini, M and Mac Aodha, O and Madhavapeddy, A and Milner-Gulland, EJ and Purvis, A and Salafsky, N and Sutherland, WJ and Tanshi, I and Vijay, V and Woodard, SH and Williams, DR}, title = {From data to decisions: Toward a Biodiversity Monitoring Standards Framework.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {10}, pages = {e2519347123}, doi = {10.1073/pnas.2519347123}, pmid = {41779789}, issn = {1091-6490}, support = {101133983//European Union/ ; }, mesh = {*Biodiversity ; *Conservation of Natural Resources/methods ; *Environmental Monitoring/methods/standards ; Decision Making ; }, abstract = {Achieving the goals of the Kunming-Montreal Global Biodiversity Framework (GBF) requires monitoring systems that can transform heterogeneous observations into consistent, decision-relevant knowledge. Yet current biodiversity data are fragmented, uneven in quality, and seldom comparable across space or time. Existing standards such as Darwin Core, Findable, Accessible, Interoperable, and Reusable (FAIR) and Collective Benefit, Authority to Control, Responsibility, and Ethics (CARE) principles provide important foundations, but they do not connect the full chain from field observation to policy reporting. We introduce the Biodiversity Monitoring Standards Framework (BMSF)-a unifying architecture that links ethical principles, standardized data collection, accredited analytical workflows, and transparent reporting into a single auditable "chain of evidence." The framework's novelty lies in its tiered and federated design, enabling national agencies, Indigenous knowledge holders, local communities, and private-sector actors to operate under shared principles while maintaining data sovereignty. By integrating Essential Variables, accredited analytical methods, and open-source implementation pathways, the BMSF allows locally generated data to be aggregated into credible, comparable indicators aligned with GBF targets. Concrete application, such as a national forest-connectivity assessment, demonstrates how the BMSF improves reproducibility, transparency, and policy relevance relative to existing approaches. Implemented generally, this framework would convert fragmented monitoring efforts into a coordinated, scalable system capable of tracking and guiding collective progress toward halting and reversing biodiversity loss.}, }
@article {pmid41762296, year = {2026}, author = {Vohra, R and Mishra, P}, title = {Sustainable mapping identification of municipal solid waste disposal zones using RS-GIS-basedMCDA techniques: a case study in Darjeeling, West Bengal.}, journal = {Environmental monitoring and assessment}, volume = {198}, number = {3}, pages = {}, pmid = {41762296}, issn = {1573-2959}, mesh = {*Geographic Information Systems ; *Environmental Monitoring/methods ; India ; *Refuse Disposal/methods ; *Solid Waste/statistics & numerical data/analysis ; *Remote Sensing Technology ; Cities ; Decision Support Techniques ; }, abstract = {Demographic expansion together with fast-paced urbanization within hilly terrain of ecologically fragile areas such as Darjeeling in West Bengal complicated the process of managing municipal solid waste (MSW). A study develops a comprehensive geospatial method which combines remote sensing (RS) and geographic information systems (GIS) with multi-criteria decision analysis (MCDA) to locate sustainable zones for municipal solid waste disposal. The study examines the Darjeeling Municipality area alongside its 2-km surrounding zone which demonstrates steep topography and density as well as ecological risks. A spatial decision support system (SDSS) is developed using a multi-criteria RS-GIS framework to determine the suitable areas for municipal solid waste disposal site suitability (MSWDSS). The framework standardizes geospatial and urban planning criteria through quantitative evaluation of slope, elevation, land use/land cover, and areas around roads, water bodies, and settlements which are weighted using analytic hierarchy process (AHP). The weighted linear combination (WLC) technique is used to compute a composite suitability index, ensuring proportional influence from each criterion after normalization. For proximity-sensitive factors, a Gaussian decay function is applied to model nonlinear reductions in suitability near sensitive infrastructure. The parameters were weighted using AHP based on their influence on landfill site suitability, with land value (0.184), distance to settlement (0.135), and distance to road (0.123) receiving the highest weights. These reflect the prioritization of economic feasibility, public health, and operational efficiency. Spatial data layers were generated, reclassified, and overlaid in a GIS environment to produce a composite suitability map. The final map classified land into three suitability zones: high, moderate, and low, highlighting that high suitability zones are located in the southern and southwestern parts of Darjeeling Municipality, characterized by low population density, low land value, greater distance from sensitive sites, gentle slopes, and poor access to existing waste services. The composite MSWDSS index is classified using natural breaks (Jenks) into three suitability categories: high (≥ 0.66), moderate (0.33-0.65), and low (≤ 0.32), to support informed site selection under constrained urban conditions. Findings reveal that only a limited portion of the study area meets the environmental and infrastructural criteria for landfill development, owing to Darjeeling's challenging topography and dense urban fabric. Nevertheless, the model successfully identifies zones with optimal accessibility, minimal ecological disruption, and reduced risks of leachate contamination and landslides. The findings show that the analysis produced the best results when applied to the study area, optimizing the balance between environmental, infrastructural, and economic factors.}, }
@article {pmid41760678, year = {2026}, author = {Leiva, FP and Molina-Venegas, R and Alter, K and Freire, CA and Hendriks, AJ and Hermaniuk, A and Serre-Fredj, L and Shokri, M and Czarnoleski, M and Mark, FC}, title = {ErythroCite: a database on red blood cell size of fishes.}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {}, pmid = {41760678}, issn = {2052-4463}, mesh = {Animals ; *Fishes/blood ; *Erythrocytes/cytology ; Female ; Male ; *Cell Size ; *Databases, Factual ; }, abstract = {Size is a fundamental trait in biology, and cell size plays a key role in cellular functions, influencing physiological adaptations and evolutionary processes in living organisms. For decades, scientists have been fascinated by the considerable variation in cell sizes among animals, yet systematic efforts to compile such data have been scarce. To address this gap, we employed a systematic map approach to create ErythroCite, an open-source database of fish erythrocyte sizes. This comprehensive resource encompasses 1,764 records from 660 species among four major lineages: Actinopterygii, Chondrichthyes, Dipnoi, and Cyclostomata. Our findings reveal a remarkable 414-fold range in cell volume, with most studies on bony fishes and limited data on juveniles and earlier life stages. Life stage and sex were infrequently reported, but available data showed equal representation of adult of females and males. ErythroCite offers valuable insights for studies in macroecology, macrophysiology, comparative physiology, evolutionary biology and cell biology. We anticipate this resource will facilitate comparative approaches and meta-analyses, globally driving further exploration of erythrocyte diversity and function in fish.}, }
@article {pmid41755684, year = {2026}, author = {Li, H and Li, S}, title = {Computer-Assisted Performance-Based Assessment for Mental Health: A Scoping Review.}, journal = {PsyCh journal}, volume = {15}, number = {2}, pages = {e70086}, pmid = {41755684}, issn = {2046-0260}, support = {2021YFC3340800//National Key Research and Development Program of China/ ; }, mesh = {Humans ; Adolescent ; *Mental Health ; *Mental Disorders/diagnosis ; *Diagnosis, Computer-Assisted/methods ; Reproducibility of Results ; }, abstract = {Adolescent mental health is foundational to personal development, yet it faces escalating challenges globally. While traditional assessment methods lack objectivity and ecological validity, integrating computer-assisted technology (CAT) into performance-based assessments (PBAs) offers a promising pathway. This review, following the PRISMA-ScR reporting standard, analyzed 89 articles (2015-2025) to map the assessed components, CAT applications, and scenario diversity in mental health PBAs. Analysis revealed a research emphasis on mental disorders, with critical domains for adolescent development remaining significantly understudied. CATs significantly enhanced PBAs through data analysis, data acquisition, scenario creation, and tool digitization. PBA scenarios are diverse, demonstrating the adaptability of PBAs for multidimensional mental health assessment. Prioritizing the design of PBAs for social-emotional and adaptive assessment is critical for the early identification of adolescent mental health issues. Furthermore, advancing predictive analytics and leveraging large language models for feedback generation are promising ways to unlock CAT's potential in enhancing PBAs. Importantly, integrating and adapting scenarios from validated scales by CATs into PBAs could further enhance assessment typicality and reliability.}, }
@article {pmid41741096, year = {2026}, author = {Weingarden, H and Holstein, V and Jonathan, GK and Armey, M and Onnela, JP and Wilhelm, S}, title = {Low-Burden Detection of Clinical Worsening in Body Dysmorphic Disorder Using Smartphone Sensor and Demographic Data.}, journal = {Behavior therapy}, volume = {57}, number = {2}, pages = {220-233}, pmid = {41741096}, issn = {1878-1888}, support = {K23 MH119372/MH/NIMH NIH HHS/United States ; }, mesh = {Humans ; *Smartphone ; Female ; Male ; *Body Dysmorphic Disorders/diagnosis/psychology ; Adult ; *Ecological Momentary Assessment ; Young Adult ; Machine Learning ; Adolescent ; Suicidal Ideation ; Middle Aged ; Accelerometry ; Geographic Information Systems ; Wearable Electronic Devices ; }, abstract = {Body dysmorphic disorder (BDD) is characterized by distressing preoccupations with perceived appearance flaws, leading to functional impairment and suicidal ideation (SI). Traditional approaches for monitoring clinical deterioration in BDD include self-reports and clinician assessments, which can miss acute changes in risk due to infrequent administration and recall biases. Alternatively, real-time monitoring via smartphones and wearable devices can enable low-burden early detection of deterioration, identifying intervention opportunities before someone's condition critically worsens. This study tests the feasibility of using smartphone sensor and demographic data to predict daily clinical acuity. Eighty-two participants with BDD completed ecological momentary assessments (EMA) over 28 days, reporting levels of SI, BDD-related avoidance, and time spent on BDD-related concerns. Smartphone sensor data were collected for 3 months that overlapped with EMA. Machine learning models were trained to predict same-day levels of SI, avoidance, and time spent on BDD using the Global Positioning System (GPS), accelerometer, and demographic data. We evaluated model performance using mean absolute error, Pearson and Spearman correlations, and permutation tests. Random forest (RF) models using time and random split validation outperformed dummy regressor models across outcomes (maximum SI, mean SI, maximum avoidance, mean avoidance, time spent on BDD-related behaviors). Pearson correlations for RF models showed strong predictive performance for BDD-related time (r = .74-.75) and mean and max SI (r = .70-.73). Mean and max avoidance was moderately well predicted (r = .56-.62). Step count and demographic factors (e.g., education, living situation) were the most consistent and important features. This study provides initial evidence that smartphone sensor and demographic data can be used to monitor real-time clinical worsening in BDD, without burdening the patient. This work has potential for building just-in-time interventions that are delivered as deterioration onsets, to prevent its escalation. Future research should test these models in real-world datasets collected over longer periods and subsequently explore integration into interventions and clinical decision making. Trial Registration: ClinicalTrials.gov Identifier: NCT04254575.}, }
@article {pmid41662977, year = {2026}, author = {Kaya, C}, title = {Metabolomics-guided engineering of drought-resilient crops: Integrating multi-omics and AI for climate-smart agriculture.}, journal = {Plant science : an international journal of experimental plant biology}, volume = {365}, number = {}, pages = {113025}, doi = {10.1016/j.plantsci.2026.113025}, pmid = {41662977}, issn = {1873-2259}, mesh = {*Metabolomics/methods ; *Crops, Agricultural/genetics/metabolism/physiology ; *Droughts ; *Artificial Intelligence ; *Agriculture/methods ; Plant Breeding ; Gene Editing ; Stress, Physiological ; Multiomics ; }, abstract = {Drought stress is among the most critical threats to global food security, and its complex impact on plant physiology often exceeds the reach of traditional breeding approaches. Metabolomics has emerged as a transformative tool for dissecting drought responses, enabling dynamic, systems-level characterization of primary and secondary metabolites that mediate osmotic balance, redox homeostasis, and stress acclimation. Building on earlier reviews that primarily focused on stress-associated metabolites, this article emphasizes the integration of metabolomics with cutting-edge technologies, CRISPR-based genome editing, pathway engineering, synthetic biology, and artificial intelligence, to establish a translational framework for drought-resilient cropimprovement. Recent advances in analytical platforms, bioinformatics pipelines, and crop-specific case studies are critically examined to demonstrate how metabolomic signatures can be translated into predictive biomarkers and incorporated into breeding pipelines. In addition, emerging frontiers such as single-cell and spatial metabolomics, ecological metabolomics, and AI-driven predictive modeling are highlighted as promising directions for connecting laboratory discoveries with field-scale applications. By synthesizing technological and biological advances, this review outlines how metabolomics can evolve from a diagnostic tool into a predictive and prescriptive platform, positioning it as a key component of climate-smart agriculture and next-generation crop improvement.}, }
@article {pmid41662342, year = {2026}, author = {Chen, J and Feng, Y and Zhang, Y and Gao, J and Ou, J and Wu, W and Li, C and Song, S and Tai, L and Rifat, MH and Akhter, D and Hu, J and Feng, P and Shen, XX and Pan, R}, title = {Structure-guided discovery of protein functions in plants.}, journal = {The Plant cell}, volume = {38}, number = {2}, pages = {}, doi = {10.1093/plcell/koag022}, pmid = {41662342}, issn = {1532-298X}, support = {32470287//National Natural Science Foundation of China/ ; 32500235//National Natural Science Foundation of China/ ; 32200231//National Natural Science Foundation of China/ ; R26C130007//Zhejiang Provincial Natural Science Foundation of China/ ; QN26C020005//Zhejiang Provincial Natural Science Foundation of China/ ; LZ23C020002//Zhejiang Provincial Natural Science Foundation of China/ ; 2025SZRJJ0918//Natural Science Foundation of Hangzhou/ ; 2024SZRYBC130003//Natural Science Foundation of Hangzhou/ ; 2022YFD1401600//National Key Research and Development/ ; 2024YFD1200401//National Key Research and Development/ ; 2024M762901//China Postdoctoral Science Foundation/ ; 2025T180747//China Postdoctoral Science Foundation/ ; 2025M782775//China Postdoctoral Science Foundation/ ; 2025M772587//China Postdoctoral Science Foundation/ ; }, mesh = {*Plant Proteins/metabolism/chemistry/genetics ; Databases, Protein ; Magnoliopsida/metabolism/genetics ; }, abstract = {Protein structure serves as a critical bridge between sequence and functional annotation, particularly in establishing functional links among distantly homologous proteins with low sequence similarities. However, systematic protein structure-based functional annotations have been lacking in plants, where functions for a significant portion of the proteomes are still elusive. In this study, we leveraged protein structural data from 17 angiosperms to uncover previously unannotated protein functions in plants. After structural clustering, we used the plant clusters to query the UniProtKB/Swiss-Prot database (the expertly curated component of UniProtKB), a repository of expertly curated and reliably annotated proteins, and identified structural matches for thousands of plant clusters that were undetectable by sequence-based BLAST searches. We further selected 120 clusters, which are highly reliable in structural quality and alignment and are well-conserved across plant species, and uncovered various protein functions that are potentially widely important in plants. Finally, we experimentally analyzed one plant cluster structurally resembling the yeast peroxisomal peroxin 8 (PEX8) protein and verified that plant PEX8-like proteins can functionally complement yeast pex8 mutants. Our findings highlight the power of structural comparison in uncovering protein functions in plants.}, }
@article {pmid41643351, year = {2026}, author = {Itzkovitch, A and Sulami, I and Efroni, RD and Shahar, M and Levy, O}, title = {From big data to small scales: Machine learning enhances microclimate model predictions.}, journal = {Journal of thermal biology}, volume = {136}, number = {}, pages = {104387}, doi = {10.1016/j.jtherbio.2026.104387}, pmid = {41643351}, issn = {0306-4565}, mesh = {*Machine Learning ; *Microclimate ; *Big Data ; *Climate Models ; Climate Change ; Ecosystem ; }, abstract = {Microclimates are critical for understanding how organisms interact with their environments, influencing behaviour, physiology, and species distributions. However, traditional physical heat-balance models for predicting ground temperatures in microhabitats often exhibit biases due to unaccounted environmental complexities and poorly constrained parameters. These limitations can hinder ecological research and conservation planning, particularly in the context of climate change. In this study, we demonstrate how high-resolution drone-based mapping and machine learning can improve the accuracy of microclimate models. Using drone imagery, we generated detailed environmental maps, including solar radiation, vegetation indices, and skyview factors, to parameterize a physical heat-balance model. Validation with thermal maps derived from drone-mounted infrared cameras revealed systematic errors in the physical model's predictions, including over- and underestimations under specific environmental conditions. To address these errors, we applied a random forest machine learning model to predict and correct biases in new prediction maps. Our results show that machine learning reduced mean absolute errors by over 30% and mean square errors by 50%, while consistently narrowing the range of prediction inaccuracies. Key factors driving biases, such as vegetation cover, solar radiation, and height above ground, were identified, offering valuable insights for improving physical models. The machine learning corrections not only improved accuracy but also highlighted parameters and processes that were previously underrepresented or oversimplified in traditional models. These findings illustrate the potential of machine learning to improve microclimate predictions. While our drone-based approach is most applicable to open, sparsely vegetated habitats, the principle of machine learning bias correction can be extended to other systems as well. Correcting microclimate models with machine learning and observational data provides ecologists and conservation practitioners with a powerful framework for generating more accurate microclimate estimates. Such improvements deepen our understanding of species' responses to climate change and support climate-resilient management strategies.}, }
@article {pmid41620065, year = {2026}, author = {Zhou, Y and Wang, Y and Si, P and Zhao, X and Kong, Q and Zhang, H}, title = {Naphthenic acid exposure disrupts mitochondrial function and locomotor behavior in marine medaka (Oryzias melastigma) via G protein-coupled receptor signaling: A multi-omics perspective.}, journal = {Environmental research}, volume = {295}, number = {}, pages = {123919}, doi = {10.1016/j.envres.2026.123919}, pmid = {41620065}, issn = {1096-0953}, mesh = {Animals ; *Oryzias/physiology ; *Water Pollutants, Chemical/toxicity ; *Receptors, G-Protein-Coupled/metabolism ; *Mitochondria/drug effects ; Signal Transduction/drug effects ; *Carboxylic Acids/toxicity ; *Locomotion/drug effects ; Oxidative Stress/drug effects ; Multiomics ; }, abstract = {Naphthenic acids (NAs) are a class of toxic petroleum-derived carboxylic acids that are being increasingly detected in marine environments at ecologically concerning concentrations. However, the molecular initiating events underlying NA toxicity and the adaptive responses of marine organisms during prolonged exposure remain poorly defined. In this study, juvenile marine medaka (Oryzias melastigma) were exposed to environmentally relevant NA concentrations for up to 28 days. Multi-omics and molecular docking analyses indicated that the NAs interacted with G-protein coupled receptors (GPCRs) in marine medaka, disrupting mTOR and FoxO signaling and enhancing oxidative stress. Antioxidant depletion was associated with mitochondrial damage and apoptosis, leading to dysfunction. Combined with the disturbance of lipid metabolism (glycerophospholipids, ether lipids, and sphingolipids), this disrupted the energy supply and induced abnormal locomotor behavior. Notably, low-level NA exposure initially elicited stimulatory responses, which transitioned to inhibitory effects over time. This temporal shift likely results from the progressive accumulation of oxidative stress, ultimately amplifying the ecological risks associated with prolonged exposure. Overall, this study elucidates a previously uncharacterized receptor-mediated pathway underlying NA toxicity and establishes a quantitative framework for evaluating the long-term ecological risks posed by petrochemical pollutants. These findings provide mechanistic and predictive insights for assessing environmental health risks from chronic low-dose NA exposure in marine ecosystems.}, }
@article {pmid41580412, year = {2026}, author = {Draisma, A and Loureiro, C and Louwen, NLL and Kautsar, SA and Navarro-Muñoz, JC and Doering, DT and Mouncey, NJ and Medema, MH}, title = {BiG-SCAPE 2.0 and BiG-SLiCE 2.0: scalable, accurate and interactive sequence clustering of metabolic gene clusters.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41580412}, issn = {2041-1723}, support = {OSF.23.1.044//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; }, mesh = {*Multigene Family ; *Software ; Microbiota/genetics ; Databases, Genetic ; Cluster Analysis ; *Computational Biology/methods ; Metabolic Networks and Pathways/genetics ; }, abstract = {Microbial metabolic gene clusters encode the biosynthesis or catabolism of metabolites that facilitate ecological specialization, mediate microbiome interactions and constitute a major source of medicines and crop protection agents. Here, we present BiG-SCAPE and BiG-SLiCE 2.0, next-generation methods that facilitate scalable, accurate and interactive gene cluster analyses. BiG-SCAPE 2.0 updates its classification, alignment methods, and visualizations, enabling more accurate analysis, up to 8x faster runtimes and halved memory requirements. BiG-SLiCE 2.0 updates its distance metric, pHMM database, and classification logic, resulting in increased sensitivity nearing that of BiG-SCAPE. Analysis of 260,630 biosynthetic gene clusters from publicly available genomes reveals that both tools generate concurring estimates of gene cluster diversity, thus providing significantly extended methodological support for recent evidence indicating that the vast majority of natural product diversity remains unexplored. Together, these updates will facilitate global genome mining efforts for natural product discovery and microbiome analyses scalable with current data sizes.}, }
@article {pmid41563008, year = {2026}, author = {Karatzas, E and Beracochea, M and Baltoumas, FA and Aplakidou, E and Richardson, L and Fellows Yates, JA and Lundin, D and ,  and Buluç, A and Kyrpides, NC and Georgakopoulos-Soares, I and Pavlopoulos, GA and Finn, RD}, title = {nf-core/proteinfamilies: a scalable pipeline for the generation of protein families.}, journal = {GigaScience}, volume = {15}, number = {}, pages = {}, pmid = {41563008}, issn = {2047-217X}, support = {//European Union/ ; DE-AC02-05CH11231//Hellenic Foundation for Research and Innovation/ ; }, mesh = {*Proteins/chemistry/genetics/classification ; *Software ; *Computational Biology/methods ; Databases, Protein ; Metagenomics/methods ; Sequence Alignment ; Molecular Sequence Annotation ; }, abstract = {The growth of metagenomics-derived amino acid sequence data has transformed our understanding of protein function, microbial diversity, and evolutionary relationships. However, the vast majority of these proteins remain functionally uncharacterized. Grouping the millions of such uncharacterized sequences with the few experimentally characterized ones allows the transfer of annotations, while the inspection of conserved residues with multiple sequence alignments can provide clues to function, even in the absence of existing functional information. To address the challenges associated with this data surge and the need to group sequences, we present a scalable, open-source, parametrizable Nextflow pipeline (nf-core/proteinfamilies) that generates nascent protein families or assigns new proteins to existing families. The computational benchmarks demonstrated that resource usage scales approximately linearly with input size, and the biological benchmarks showed that the generated protein families closely resemble manually curated families in widely used databases.}, }
@article {pmid41547155, year = {2026}, author = {Liu, X and Zhang, H and Su, T and Arshad, M and Gao, W and Zhang, S and Wu, J and Li, H}, title = {Multi-omics analysis reveals immune responses in tobacco leaves treated with polyethylene nanoparticles.}, journal = {Plant physiology and biochemistry : PPB}, volume = {231}, number = {}, pages = {111026}, doi = {10.1016/j.plaphy.2026.111026}, pmid = {41547155}, issn = {1873-2690}, mesh = {*Nicotiana/immunology/drug effects/metabolism/microbiology/genetics ; *Plant Leaves/immunology/drug effects/metabolism ; *Nanoparticles/chemistry ; *Polyethylene/pharmacology/chemistry ; Reactive Oxygen Species/metabolism ; *Plant Immunity/drug effects ; Gene Expression Regulation, Plant/drug effects ; Pseudomonas syringae ; Transcriptome/drug effects ; Plant Proteins/metabolism/genetics ; Proteome/metabolism ; Multiomics ; }, abstract = {As an emerging contaminant, nanoplastics (NPs) could enter plant tissues through roots and leaves, posing threats to plant growth. Majority of the earlier studies have focused on the toxic effects of NPs after their uptake and the potential non-toxicological biological impacts. We found that 20 nm polyethylene NPs (PE-NPs) could rapidly induce stomatal closure in tobacco leaves after 1 h of exposure, along with increased reactive oxygen species levels and up-regulated expression of pathogenesis-related genes. These responses were similar to those induced by pathogen-associated molecular patterns (PAMPs), as in case of response to pathogen recognition. Subsequent multi-omics integration analyses of transcriptome, proteome, metabolome, and phosphoproteome revealed convergent and divergent responses of tobacco leaves to PE-NPs and the tobacco pathogen Pseudomonas syringae pattern-triggered immunity (PTI) responses. Tobacco leaves responded to both elicitors in a similar manner at the transcriptome and proteome levels, exhibiting numerous similar PTI response patterns, but distinct at the metabolome levels. The differences might arise from elicitor-specific phosphorylation events during post-translational modification, which reshaped gene expression by modulating enzyme activity, leading to distinct metabolite profiles. Our multi-level regulatory network revealed the molecular framework by which NPs as abiotic stressors activated plant innate immunity, providing a novel perspective for understanding the ecological impacts of NPs.}, }
@article {pmid41528732, year = {2026}, author = {Ivancevic, A and Sankovitz, M and Allen, H and Joyner, O and Chuong, EB and Ramsey, SD}, title = {Whole-genome sequences of the dwarf honey bee subgenus Micrapis: Apis andreniformis and Apis florea.}, journal = {G3 (Bethesda, Md.)}, volume = {16}, number = {3}, pages = {}, pmid = {41528732}, issn = {2160-1836}, support = {//Study of Honey Bee Pest Diversity to Support Development of Emergency Response Plan/ ; //United States Department of Agriculture Animal Plant Health Inspection Service/ ; //National Geographic Wayfinder Award/ ; 2R35GM128822/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bees/genetics/classification ; *Genome, Insect ; Molecular Sequence Annotation ; *Whole Genome Sequencing ; Genomics/methods ; Computational Biology/methods ; }, abstract = {The Micrapis subgenus, which includes the black dwarf honey bee (Apis andreniformis) and the red dwarf honey bee (Apis florea), remains underrepresented in genomic studies despite its ecological significance. Here, we present high-quality de novo genome assemblies for both species, generated using a hybrid sequencing approach combining Oxford Nanopore Technologies long reads with Illumina short reads. The final assemblies are highly contiguous, with contig N50 values of 5.0 Mb (A. andreniformis) and 4.3 Mb (A. florea), representing a major improvement over the previously published A. florea genome. Genome completeness assessments indicate high quality, with BUSCO scores exceeding 98.5% using the Hymenoptera database and k-mer analyses supporting base-level accuracy. Repeat annotation revealed a relatively low repetitive sequence content (∼6%), consistent with other Apis species. Using RNA sequencing data, we annotated 12,189 genes for A. andreniformis and 12,207 genes for A. florea, with ∼98% completeness in predicted proteomes. These genome assemblies provide a valuable resource for comparative and functional genomic studies, with the potential to offer new insights into the genetic basis of dwarf honey bee adaptations.}, }
@article {pmid41455431, year = {2026}, author = {Pazhamala, L and Pandey, M and Deveshwar, P and Ghatak, A and Weckwerth, W and Chaturvedi, P and Giri, J}, title = {Network-based multiomics and transgenic validation reveal that OsPHR3 modulates phosphate-carbon metabolic trade-offs during rice seed development.}, journal = {Plant physiology and biochemistry : PPB}, volume = {231}, number = {}, pages = {110981}, doi = {10.1016/j.plaphy.2025.110981}, pmid = {41455431}, issn = {1873-2690}, mesh = {*Oryza/metabolism/genetics/growth & development ; *Seeds/metabolism/growth & development/genetics ; *Phosphates/metabolism ; *Plant Proteins/genetics/metabolism ; Plants, Genetically Modified/metabolism ; *Carbon/metabolism ; Gene Expression Regulation, Plant ; Phytic Acid/metabolism ; Starch/metabolism ; Multiomics ; }, abstract = {Phosphate (Pi) allocation during the grain-filling stage is a major determinant of crop yield, supporting macromolecule synthesis, energy metabolism, and nutrient storage. However, its storage as phytic acid (PA) reduces nutritional quality by chelating essential minerals. Despite its importance, a comprehensive understanding of the molecular mechanisms integrating Pi transport, carbohydrate metabolism, and PA biosynthesis during seed development remains incomplete. To address this gap, we investigated stage-specific phosphate regulatory networks in rice by integrating transcriptomic, proteomic, and metabolomic approaches. Temporal expression profiling and gene coexpression network analyses of phosphate regulators and transporter genes revealed their distinct roles during early and mid-grain filling stages. PHOSPHATE STARVATION RESPONSE 3 (OsPHR3) emerged as a central regulatory hub, coordinating the balance of Pi, sugar, starch and phytate, along with other metabolites. Network-based multiomics integration further identified 126 genes involved in nutrient storage and stress tolerance, with myo-inositol-1-phosphate synthase (OsMIPS1) and starch synthase 3 (OsSSIII) as key genes. CRISPR/Cas9-generated osphr3 knockout lines confirmed the critical role of OsPHR3 in regulating these target genes. Mutants exhibited significantly reduced seed starch, PA, and total phosphorus contents, while scanning electron microscopy revealed aberrant starch granule morphology. Loss-of-function of OsPHR3 lowered PA levels by 19.46-22.50 %, with moderate trade-offs in yield-related traits. Although, OsPHR3 is known to contribute to nitrogen and phosphorus homeostasis, our findings establish it as a key regulator orchestrating a stage-specific phosphate-carbon allocation during seed development. These insights provide key targets for refining nutrient partitioning to achieve increased yields, reduced phytic acid, and enhanced phosphorus use efficiency for agricultural sustainability.}, }
@article {pmid41242981, year = {2026}, author = {Andonotopo, W and Bachnas, MA and Dewantiningrum, J and Adi Pramono, MB and Bernolian, N and Yeni, CM and Putra Wiradnyana, AAG and Hariyasa Sanjaya, IN and Akbar, MIA and Darmawan, E and Sulistyowati, S and Stanojevic, M and Kurjak, A}, title = {The fetal exposome and preterm birth: a systematic synthesis of environmental exposures and multi-omics evidence.}, journal = {Journal of perinatal medicine}, volume = {54}, number = {2}, pages = {391-407}, pmid = {41242981}, issn = {1619-3997}, mesh = {Humans ; Female ; Pregnancy ; *Premature Birth/etiology/epidemiology ; *Exposome ; *Environmental Exposure/adverse effects ; Infant, Newborn ; *Maternal Exposure/adverse effects ; Multiomics ; }, abstract = {OBJECTIVES: Preterm birth (PTB), defined as delivery before 37 weeks of gestation, is a leading cause of neonatal mortality and long-term developmental impairment. Its complex etiology, spanning environmental, genetic, psychosocial, and socio-economic domains, limits effective prediction and prevention. We systematically synthesized evidence on how environmental exposures influence PTB risk through multi-omic disruptions within a fetal exposome framework.<br><br>METHODS: A comprehensive literature search was conducted in major biomedical databases, following PRISMA guidelines. Ninety-five human studies published through May 2025 were included, encompassing exposures such as ambient air pollution, endocrine-disrupting chemicals, maternal stress, nutrition, occupational hazards, climate variability, and microbiome alterations. Two reviewers independently extracted data (exposure type, omics platform, biospecimen, PTB subtype) with inter-rater reliability assessment, and study quality was evaluated using the Newcastle-Ottawa Scale. Findings were narratively stratified by exposure category, study design, and spontaneous vs. indicated PTB.<br><br>RESULTS: Environmental exposures were consistently associated with disruptions in oxidative stress, inflammation, immune regulation, hormonal signaling, placental aging, and microbial ecology, mediated by multi-omic signatures in maternal, placental, and fetal tissues. Candidate biomarkers show promise for early risk stratification but lack validation and population-level predictive performance due to heterogeneous exposure assessment and study design.<br><br>CONCLUSIONS: Integrating fetal exposome concepts with multi-omics enhances mechanistic insight into PTB risk and may support biomarker discovery and precision-guided prenatal interventions. Clinical translation requires standardized exposure measurement, biomarker validation, and equity-focused implementation.}, }
@article {pmid41215744, year = {2026}, author = {Wei, Y and Lin, Z and Xie, Q and Gao, J and Jin, J and Li, J and Lu, C and Ye, G and Li, W and Huang, C and Yang, D and Liu, Q and Zhu, G and Yang, F}, title = {OrchidMD: An Integrated and User-Interactive Orchid Multi-Omics Database for Mining Genes and Biological Research.}, journal = {Plant biotechnology journal}, volume = {24}, number = {3}, pages = {1885-1897}, pmid = {41215744}, issn = {1467-7652}, support = {2023YFD2300904//National Key Research and Development Program of China/ ; CYZX202406//Guangdong Academy of Agricultural Sciences Project/ ; R2020PY-JX018//Guangdong Academy of Agricultural Sciences Project/ ; R2023PY-JG023//Guangdong Academy of Agricultural Sciences Project/ ; XTXM202201//Guangdong Academy of Agricultural Sciences Project/ ; XT202212//Guangdong Academy of Agricultural Sciences Project/ ; 2024B1212060012//Science and Technology Planning Project of Guangdong Province/ ; 2024CXTD12//Innovation Team of Modern Agriculture Industry Technology System in Guangdong Province/ ; 2024-NPY-00-035//Seed Industry Revitalization Project of the Special Fund for the Rural Revitalization Strategy of Guangdong Province/ ; 2024A1515013187//Guangdong Basic and Applied Basic Research Foundation/ ; 2024A1515011604//Guangdong Basic and Applied Basic Research Foundation/ ; 2025010//Ex Situ Conservation and Artificial Propagation of National Key Protected Orchids and Ferns/ ; R2021YJ-XD001//Special Foundation for Introduction of Scientific Talents of GDAAS/ ; //Modern Seed Industry Innovation Capability Enhancement Project of Guangdong Academy of Agricultural Sciences/ ; }, mesh = {*Orchidaceae/genetics/metabolism ; *Data Mining ; *Genomics/methods ; *Databases, Genetic ; Metabolomics ; Proteomics ; Phenomics ; Multiomics ; }, abstract = {The Orchidaceae family, with its unparalleled species diversity among angiosperms, is integral to ornamental, medicinal, cultural, and ecological value. Multi-omics techniques have proven invaluable for the identification of candidate genes and the advancement of functional genomics research. Nevertheless, the application of these technologies in Orchidaceae remains severely limited due to the lack of effective platforms that can integrate and analyze multi-omics data, especially in understanding the mechanisms underlying key traits such as distinctive floral morphology. In this study, we present OrchidMD, the Orchid Multi-omics Database (www.orchidcomics.com), a resource platform that integrates data from five omics layers: genomics, transcriptomics, proteomics, metabolomics, and phenomics, encompassing a total of 213 species. OrchidMD is equipped with 18 specialized statistical and analytical tools, and features a user-friendly interface that facilitates efficient gene mining, multi-omics data exploration, and integrative interactive analysis. A case study on the comprehensive identification of the pan-ARF gene family across Orchidaceae species demonstrates the effectiveness and convenience of OrchidMD. Furthermore, experimental validation further shows that transgenic overexpression of CsiARF04 promotes the differentiation and budding of orchid rhizomes. In addition, another case study using gene editing in orchids, CRISPR Design was employed to predict the CsiPDS target site in Cymbidium sinense. Effective editing was subsequently achieved via Agrobacterium-mediated delivery of the CRISPR/Cas9 vector into leaves. These results underscore OrchidMD's formidable capacity to discern candidate genes associated with salient traits and elucidate their regulatory mechanisms. Thus, OrchidMD serves as a pivotal platform advancing multi-dimensional biological research and functional genomics in orchids.}, }
@article {pmid41726913, year = {2026}, author = {Chalar, R and Khatri, N and Obeid, J and Downey, E and Song, JH and Xiao, Y and Samad, S and Chen, A and Resnick, A and Karbalaei, K and Allopenna, JJ and Mao, C and Clarke, C and Velazquez, F and Luberto, C and Chen, B and Canal, D and Hannun, Y and Damaghi, M}, title = {Metabolic plasticity of sphingolipids governs cancer cell fitness in acidic tumor ecosystems.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41726913}, issn = {2692-8205}, abstract = {Cancer cells must adapt to harsh tumor microenvironments, including acidic stress, to survive and thrive. Understanding how cancer cells achieve this adaptation can uncover new biomarkers and therapeutic strategies. In this study, we investigated the spatial metabolic phenotypic heterogeneity of breast cancer cells in acidic habitats using spatial multi-omics approaches on 3D spheroids. We found that cancer cells dynamically regulate sphingolipid metabolism to fine-tune their cell state to cope with acidic selection pressures. Cancer cells evolve mechanisms to deal with initially accumulating toxic ceramides but later adapt to it by rerouting SL metabolic pathways to eliminate them. Using advanced MALDI image analysis, and SL inhibitors on patient derived organoids, we demonstrated that cancer cells can switch between metabolic routes when key pathways are blocked, showcasing remarkable cell state plasticity. These insights highlight the potential to target metabolic plasticity as a novel therapeutic strategy to disrupt cancer adaptation and evolution, offering new avenues for cancer treatment.}, }
@article {pmid41779788, year = {2026}, author = {Sutherland, WJ and Burgess, ND and Edwards, SV and Jones, JPG and Soltis, PS and Tilman, D and Allen, JM and Andrianandrasana, HT and Armour, CJ and August, T and Bawa, KS and Bailey, S and Birch, T and Boersch-Supan, PH and Cavender-Bares, J and Blaxter, M and Chaplin-Kramer, R and Daru, BH and De Palma, A and Eisenberg, C and Elphick, CS and Freckleton, RP and Frick, WF and Gonzalez, A and Goetz, SJ and Greenspoon, L and Grozingeree, CM and Hankins, DL and Hazell, J and Isaac, NJB and Lambertini, M and Lewin, HA and Mac Aodha, O and Madhavapeddy, A and Milner-Gulland, EJ and Milo, R and O'Dwyer, J and Purvis, A and Salafsky, N and Tallis, H and Tanshi, I and Vijay, V and Wikelski, M and Williams, DR and Woodard, SH and Robinson, GE}, title = {Nine changes needed to deliver a radical transformation in biodiversity measurement.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {10}, pages = {e2519345123}, doi = {10.1073/pnas.2519345123}, pmid = {41779788}, issn = {1091-6490}, support = {101133983//More4nature/ ; }, abstract = {Biodiversity is declining in many parts of the world. Biological diversity measurement and monitoring are fundamental to the assessment of the causes and consequences of environmental changes, identification of key areas for the protection of biodiversity or ecosystem services, determining the effectiveness of actions, and the creation of decision-support tools critical to maintaining a sustainable planet. Biodiversity measurement is rapidly changing due to advances in citizen science, image recognition, acoustic monitoring, environmental DNA, genomics, remote sensing, and AI. In this perspective, we outline the exciting opportunities these developments offer but also consider the challenges. Our key recommendations are to 1) Capitalize on the ability of novel technology to integrate data sources 2) agree to standard methods for data collection 3) ensure new technologies are calibrated with existing data; 4) fill data gaps by using emerging technologies and increasing capacity, especially in the tropics; 5) create living safeguarded databases of trusted information to reduce the risk of poisoning by AI hallucinated, or false, information; 6) ensure data generation is valued; 7) ensure respectful incorporation of Indigenous Knowledge; 8) ensure measurements enable the quantification of effectiveness of actions, and 9) increase the resilience of global datasets to technical and societal change. Radical new collaborations are needed between computer scientists, engineers, molecular biologists, data scientists, field ecologists, citizen scientists, Indigenous peoples, policymakers, and local communities to create the rigorous, resilient, accessible biodiversity information systems required to underpin policies and practices that ensure the maintenance and restoration of ecological systems.}, }
@article {pmid41779521, year = {2026}, author = {Laguna, GGC and Gusmão, ALF and Gusmão, ABF and Fernandes, JSG and Fonseca, YS and Azevedo, KMR}, title = {Silent wounds: an epidemiological analysis of self-inflicted injuries among youths in Brazil (2013-2023).}, journal = {Cadernos de saude publica}, volume = {42}, number = {}, pages = {e00062525}, doi = {10.1590/0102-311XEN062525}, pmid = {41779521}, issn = {1678-4464}, abstract = {This study aimed to describe the epidemiological profile of self-inflicted injuries among children and adolescents in Brazil over the past decade (2013-2023). This ecological study had a nationwide coverage and was based on data from the Brazilian Health Informatics Department (DATASUS). Descriptive and inferential statistical analysis were applied (t-test, ANOVA, Tukey, and Friedman), with normality assessment (Shapiro-Wilk), using Jamovi software. From 2013 to 2023, 18,382 hospitalizations and 261 deaths due to self-inflicted injuries were recorded among children and adolescents in Brazil, with a total hospital cost of approximately BRL 10 million. The Southeast accounted for the highest number of hospitalizations (55.45%) and deaths (60.1%), while the North reported the lowest figures. The most affected age group was 15-19 years. Hospitalizations were more frequent among females, whereas deaths predominated among males, with a significant impact on the Black population. During the study period, hospitalizations increased by 44.28% and deaths by 26.31%, with the highest hospital costs occurring in 2022 and 2023. These findings reveal significant regional and demographic disparities and underscore the need for targeted prevention strategies and specific public health policies.}, }
@article {pmid41779489, year = {2026}, author = {Moura, PH and Carvalho, LDG and Godoy, PH and Salis, LHA and Paez, MS and Alves, MB and Maia, LFPG and Santos, RLD and Silva, NASE}, title = {Impact of PM2.5 Air Pollution on Mortality from Circulatory System Diseases in the Neighborhoods of the City of Rio de Janeiro (2000-2019).}, journal = {Arquivos brasileiros de cardiologia}, volume = {123}, number = {1}, pages = {e20250459}, doi = {10.36660/abc.20250459}, pmid = {41779489}, issn = {1678-4170}, abstract = {BACKGROUND: Air pollution by fine particulate matter with an aerodynamic diameter ≤ 2.5 μm (PM2.5) is the main environmental risk factor associated with diseases of the circulatory system (DCS), ischemic heart disease (IHD), and cerebrovascular diseases (CBVD).<br><br>OBJECTIVE: To estimate mortality rates from DCS, IHD, and CBVD (2000-2019) among residents of the 164 neighborhoods of Rio de Janeiro, according to PM2.5 levels.<br><br>METHODS: This retrospective ecological study used georeferenced satellite data classified into three PM2.5 levels and mortality records from the Department of Information and Informatics of the Unified Health System for DCS, IHD, and CBVD among individuals of both sexes aged &#x2265; 20 years from 2000 to 2019. Age-adjusted mortality rates per 1,000 inhabitants were calculated, and comparative statistical analyses were performed by sex, PM2.5 level, and age group (5% significance).<br><br>RESULTS: Approximately 91% of the 4.7 million residents (&#x2265; 20 years) live in areas with high or extreme PM2.5 pollution. Deaths occurred up to 3.4 years earlier among men living in highly polluted areas compared with those in moderately polluted areas. The highest DCS mortality rates were observed in neighborhoods with high and extreme pollution (female = 3.9 &#xb1; 1.7; 95% CI = 3.5-4.2; male = 4.6 &#xb1; 2.1; 95% CI = 4.1-4.9), particularly in individuals aged &#x2265; 70 years. Significant associations were found between mortality rates and pollution levels for DCS (p = 0.019), IHD (p = 0.025), and CBVD (p = 0.002) in the 50-69-year age group when comparing moderately and extremely polluted areas. Intermediate/high social vulnerability was identified in 71% of neighborhoods, with an increasing socioenvironmental gradient linking higher vulnerability to higher PM2.5 concentrations (R = 0.354; p = 0.001).<br><br>CONCLUSION: Mean PM2.5 concentrations in the neighborhoods of Rio de Janeiro exceeded the World Health Organization's recommended standard by a factor of four. Mortality from DCS is significantly higher and occurs earlier in areas with high or extreme levels of pollution.}, }
@article {pmid41388798, year = {2026}, author = {Haahtela, T and O'Mahony, L and Traidl-Hoffmann, C and Akdis, M and Ceylan, O and Chaslaridis, P and Damialis, A and Del Giacco, S and Lauerma, A and Nadeau, KC and Paciência, I and Pali-Schöll, I and Palomares, O and Renz, H and Schwarze, J and Urrutia-Pereira, M and Venter, C and Vercelli, D and Winders, T and Akdis, CA and Jutel, M and Agache, I}, title = {EAACI Guidelines on the Importance of Green Space in Urban Environments for Allergy and Asthma Prevention.}, journal = {Allergy}, volume = {81}, number = {3}, pages = {635-650}, pmid = {41388798}, issn = {1398-9995}, support = {43205//European Academy of Allergy and Clinical Immunology/ ; }, abstract = {The allergy and asthma epidemic in urban societies following World War II is mostly caused by changes in the environment, diet and lifestyle. Disconnection of urban populations from the wider environment has reduced the protective factors building up immunological resilience. The European Academy of Allergy and Clinical Immunology (EAACI) guidelines on greenness impact on allergy and asthma follow the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) approach and provide eight recommendations encouraging greenness exposure to support immune health. Controlled follow-up studies are still scarce, and the strength of evidence is generally low or moderate at best. For primary prevention of allergy and asthma, most of the evidence indicates beneficial effects. Exposure is also useful for secondary prevention. Asthma patients may feel better and need less medication by combining green space exposure with physical activity. During the high-pollen season, effective seasonal medication is necessary for patients with pollen allergy. In urban planning, implementing appropriate green infrastructure and easy access to green space promotes immune health and reduces risks of air pollution and heatwaves. These EAACI guidelines are the first recommendations highlighting the importance of urban green spaces on immune health and call for prioritising innovative research in this field.}, }
@article {pmid41775999, year = {2026}, author = {Steindorff, AS and Cai, FM and Ding, M and Jiang, S and Atanasova, L and Baker, SE and Barbosa-Filho, JR and Bayram Akcapinar, G and Brown, DW and Chaverri, P and Chen, P and Chenthamara, K and Daum, C and Drula, E and Dubey, M and Brandström Durling, M and Flatschacher, D and Ebner, T and Emri, T and Gao, R and Georg, RC and Henrissat, B and Hermosa, R and Herrera-Estrella, A and Hinterdobler, W and Kainz, P and Karlsson, M and Kredics, L and Kubicek, CP and Kuo, A and LaButti, K and Lipzen, A and Lorito, M and Mach, RL and Manganiello, G and Marik, T and Martinez-Reyes, N and Mayrhofer-Reinhartshuber, M and Miskei, M and Moisan, MC and Mondo, S and Monte, E and Ng, V and Pang, G and Pangilinan, J and Peng, M and Piombo, E and Pócsi, I and Rahimi, MJ and Reddy, SK and Riley, R and Sarrocco, S and Schmal, M and Schmoll, M and Szűcs, A and Woo, SL and Yarden, O and Zeilinger, S and Zimmermann, C and Shelest, E and Tsang, A and Berka, R and de Vries, RP and Grigoriev, IV and Druzhinina, IS}, title = {Phenogenomics reveals the ecology and evolution of Trichoderma fungi for sustainable agriculture.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {41775999}, issn = {2058-5276}, support = {32470020//National Natural Science Foundation of China (National Science Foundation of China)/ ; DEB-1638976//National Science Foundation (NSF)/ ; DEB-1019972//NSF | National Science Board (NSB)/ ; }, abstract = {Trichoderma fungi support sustainable agriculture by suppressing plant diseases and improving crop performance. However, emerging pathogenicity of Trichoderma warrants further ecological and genetic characterization. Here we used machine learning to correlate genomic data from 37 Trichoderma strains with over 140 phenotypic traits, spanning metabolic versatility, biotic interactions, stress tolerance and reproductive strategies. We determined Trichoderma to be an ancient, genetically cohesive and physiologically diverse genus with spores capable of germination in water and dispersal via air and water droplets. Metabolic preferences indicate universal adaptation to mycoparasitism and to niches like arboreal microbial mats, alongside broader saprotrophic versatility. Our analyses are consistent with character displacement among close relatives and convergent evolution in distant lineages, with both processes shaping ecological plasticity and traits including dispersal modes, terrestrialization or endophytism. Our findings reveal that while some Trichoderma species show traits of biosafety concern, its vast ecophysiological diversity enables the development of safe, targeted bioeffectors.}, }
@article {pmid41768530, year = {2026}, author = {Ross-Adelman, M and Aalbers, G and Matcham, F and Leightley, D and Oetzmann, C and Carr, E and Siddi, S and Haro, JM and Annas, P and Dalby, M and Narayan, VA and Hotopf, M and Myin-Germeys, I and Lamers, F and Penninx, BWJH and , }, title = {Sleep, Steps, and Screens: Between- and within-person effects of digital markers of daily life behaviors on smartphone-based assessments of cognitive functioning in depression.}, journal = {Neuroscience applied}, volume = {5}, number = {}, pages = {106985}, pmid = {41768530}, issn = {2772-4085}, abstract = {Cognitive impairment represents a core feature of major depressive disorder (MDD), often persisting after mood symptoms remit and not addressed by usual antidepressant treatments. Despite its relevance, cognition is typically assessed with infrequent tests in clinical settings, overlooking its contextual nature. Smartphones and wearables enable ecologically valid, repeated measurements of cognition and daily life behaviors that may impact it. We examined whether sleep duration, step count, and smartphone screen time are associated with cognitive functioning in MDD. We conducted secondary analyses of RADAR-MDD, a multicenter study following individuals with recurrent MDD. Cognitive functioning - self-reported and performance-based - was assessed with the THINC-it® app. Sleep duration and step count were measured with Fitbit devices, and screen time with the RADAR-Base app. Cognitive assessments (outcomes) were linked to behavioral measures (predictors) from the day of and the day preceding each assessment. Two-level multilevel models estimated between-person (differences in participant means) and within-person (deviations from participant means) effects. The sample included 502 participants, further subdivided by behavior-cognitive outcome pair. For performance-based cognitive assessments, positive associations at the between-person level were found for step count (β = 0.104, SE = 0.031, p < 0.001) and screen time (β = 0.075, SE = 0.036, p = 0.038), and sleep duration showed a quadratic negative effect (β = -0.080, SE = 0.018, p < 0.001). No within-person effects were detected. For self-reported cognitive functioning, step count showed positive associations both between (β = 0.161, SE = 0.037, p < 0.001) and within persons (β = 0.027, SE = 0.010, p = 0.005), while screen time was negatively associated within persons (β = -0.033, SE = 0.011, p = 0.002). Our findings illustrate that smartphones and wearables can collect meaningful daily life data of MDD patients that can be used to support cognitive health. Step count emerges as a promising behavioral target as it is simple to track and is correlated with better cognitive outcomes.}, }
@article {pmid41768099, year = {2023}, author = {Boyes, D and Phillips, D and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Dusky Thorn moth, Ennomos fuscantarius (Haworth, 1809).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {505}, doi = {10.12688/wellcomeopenres.20174.2}, pmid = {41768099}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Ennomos fuscantarius (the Dusky Thorn; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 444.9 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.49 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,173 protein coding genes.}, }
@article {pmid41765545, year = {2026}, author = {Xiong, H and Yin, Y and Cui, X and Dai, W and Dong, J and Wang, X and Duan, G}, title = {Impacts of coal mining on heavy metal concentration and microbial community composition in surrounding soils.}, journal = {Journal of environmental sciences (China)}, volume = {162}, number = {}, pages = {465-475}, doi = {10.1016/j.jes.2025.05.060}, pmid = {41765545}, issn = {1001-0742}, abstract = {Coal mining activities have been demonstrated to result in substantial environmental contamination, posing severe risks to surrounding soil ecosystems. However, the interaction between microbial community structure and environmental factors in coal mining areas remains poorly understood. In this study, we evaluated the health status of soils and the effects of heavy metals on microbial community structure in coal mining areas through comprehensive soil health assessments and sequencing. Our findings revealed that soils impacted by mining activities exhibited low soil health index values, with health grades ranging from moderate to poor. Active biomarkers including Gemmatimonadota (phylum), Patescibacteria (phylum), and Saccharimonadia were highly enriched in mine soils, with some developing metal tolerance. Additionally, potential pathogenic bacteria, including MND1, Bacillus, and Pannonibacter, and potential pathogenic fungi including Fusarium and Alternaria, showed significantly higher abundance in these soils. Heavy metal concentrations, particularly Cu and As, were strongly correlated with the distribution of certain bacterial genera, alongside variations in soil physicochemical properties, including C/N ratios and organic matter content. These findings demonstrate complex relationships among heavy metal pollution, soil properties, and microbial communities, underlining the potential risks posed by mining activities to soil health and agricultural productivity in affected regions.}, }
@article {pmid41764794, year = {2026}, author = {Wang, Z and Zhang, G and Lu, X and Lei, R and Zhou, W and Tian, Y and Lu, Y and Tu, L and Li, S}, title = {Transforming mine dump waste soil into biogeo-composites with vegetation growth regulation function through bio-mediated treatment.}, journal = {Journal of hazardous materials}, volume = {506}, number = {}, pages = {141630}, doi = {10.1016/j.jhazmat.2026.141630}, pmid = {41764794}, issn = {1873-3336}, abstract = {Valorization of mine waste soils into sustainable materials provides both ecological protection and recycling benefits. This study develops a calcium lignosulfonate (CLS)-enzyme-induced calcium carbonate precipitation (EICP)-driven biogeo-composite that simultaneously enhances mechanical stability, regulates hydraulic behavior, and promotes vegetation growth. Laboratory tests demonstrated that CLS-EICP treatment increased shear strength of soils through cohesion enhancement driven by rigid CaCO3 bonding and ductile CLS bridging. Hydraulic conductivity reduced by two orders of magnitude and slaking resistance significantly enhanced. Microstructural analyses confirmed a dense organic-inorganic hybrid network formation, enabling a transition from surface to volumetric cementation and promoting structural densification. Field trials further validated these findings, as biogeo-composite-treated slopes resisted gully erosion, delayed pore water pressure build-up, and maintained overall stability while supporting uniform vegetation growth. These results highlight the dual role of CLS-EICP composites in slope reinforcement and eco-functional regulation, offering a scalable pathway for the valorization of waste soils.}, }
@article {pmid41764240, year = {2026}, author = {Alice, S and Pierangela, P and Giuseppe, B and Fabio, P and Stefania, P}, title = {Ecosystem structure influences human health outcomes as the basis for green prescriptions.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-40752-8}, pmid = {41764240}, issn = {2045-2322}, abstract = {The role of Nature [**][**] in supporting human life, health, and well-being has been recognized and appreciated since ancient times, and has become a topic of scientific investigation with early studies dating back several decades. In recent years, this field has gained renewed attention and methodological refinement, driven by interdisciplinary frameworks and advances in environmental psychology, ecology, and health sciences, including new ecosystem-based approaches that highlight the deep human dependence on Nature for both mental and physical health. Among Nature-based Interventions that aim at exposing people to the natural environment, Green Prescriptions (GRx) represent a promising strategy to address human health challenges in ways that can also support environmental sustainability, in line with the Planetary Health framework. However, significant gaps remain in our understanding of the specific ecological factors that influence health outcomes during therapeutic activities in natural settings; in particular, it remains unclear how ecosystem structure and functions modulate health responses in individuals. This nine-month pilot study examined the therapeutic efficacy of GRx within a Mediterranean woodland ecosystem, to assess if and how variations in ecosystem structure influence health outcomes in individuals with complex chronic conditions. Using a novel aggregated index to characterize four distinct woodland patches, we identified a gradient in structural complexity where greater ecosystem functionality was consistently associated with greater alleviation of psychological and physical symptoms. Notably, health outcomes were independent of weather conditions and participants' baseline connectedness to Nature, whereas temporal dynamics and the presence of peaks in the productivity of some species influenced both perceptions and physical responses. This underscores the intrinsic role of ecosystem properties and dynamic functions in modulating human health responses, while also suggesting the potential presence of a complex set of signals pervading complex ecosystems that is worth further exploration. The results demonstrated cumulative health benefits, including significant reductions in medication use over time, particularly among individuals with respiratory challenges and chronic pain. Furthermore, participants showed improved environmental awareness and behavior, embracing the interconnectedness principle, which is integral to effective environmental conservation. This study highlights the potential of well-functioning ecosystems to serve as co-effectors in healthcare interventions, advancing the goals of Planetary Health while reinforcing the importance of preserving ecological integrity. (**In this paper, "Nature" is written with a capital "N" to indicate the living biosphere and the abiotic matrices (soil, air, and water) in which life is embedded, including the ecological processes they sustain. This capitalization reflects the scientific perspective of Nature not merely as a passive backdrop, but as an active ecological system that interacts and influences human health. It also avoids confusion with "nature" as the intrinsic quality of a phenomenon**).}, }
@article {pmid41762592, year = {2026}, author = {Salarzaei, S and Shiri, F and Ahmadi, S}, title = {A global Quasi-SMILES model based on the Monte Carlo algorithm for assessing the multi-organism aquatic ecotoxicity of personal care products.}, journal = {Ecotoxicology and environmental safety}, volume = {312}, number = {}, pages = {119948}, doi = {10.1016/j.ecoenv.2026.119948}, pmid = {41762592}, issn = {1090-2414}, abstract = {Personal care products (PCPs) are widely used for external applications on the body, and their increased consumption has raised concerns about their potential environmental impact, particularly in aquatic ecosystems. Evaluating the aquatic ecotoxicity of PCPs is essential, but the process is a long and difficult task. Thus, it is crucial to employ tools for rapid screening. The quantitative structure-activity relationship (QSAR) approach can leverage existing data to identify potentially hazardous PCPs quickly. This study uses QSAR models to assess the aquatic ecotoxicity of 159 PCPs across three organisms' algae, crustaceans, and fish providing a broader ecological perspective than traditional methods, which typically focus on a single organism. A QSAR model was implemented using CORAL software, which utilizes the SMILES format to predict aquatic toxicity. However, traditional SMILES do not incorporate experimental context, limiting prediction accuracy. To address this, the Quasi-SMILES method extends the traditional SMILES notation by incorporating experimental conditions related to three key organisms of the aquatic trophic level algae (Pseudokirchneriella subcapitata), crustacean (Daphnia magna), and fish (Pimephales promelas) thus enabling more accurate predictions of chemical behavior under diverse environmental conditions. Using random data splitting and multiple objective functions, 40 models were developed based on the Monte Carlo method. The model that combined the Ideal Correlation Index (IIC) and the Correlation Intensity Index (CII) as dual objective functions achieved the best predictive performance for split 4, with rm[2] = 0.7396, R[2]= 0.7757, and Q[2] = 0.7509 for validation set highlighting the effectiveness of multi-objective optimization strategies.}, }
@article {pmid41760830, year = {2026}, author = {Abraham, AJ and Duvall, ES and Leese, C and Abraham, K and le Roux, E and Riond, B and Ortmann, S and Terranova, M and Leese, G and Bailey, MA and Clauss, M}, title = {Preliminary evidence of extrarenal sodium storage in a large mammal: implications for comparative physiology and hypertension research : Running: Sodium storage in cattle.}, journal = {Pflugers Archiv : European journal of physiology}, volume = {478}, number = {3}, pages = {}, pmid = {41760830}, issn = {1432-2013}, abstract = {Under conditions of dietary sodium (Na[+]) excess, the kidneys may fail to adequately excrete Na[+], potentially compromising blood pressure homeostasis. Body tissues, such as skin, can offer sites of short-term extrarenal Na[+] storage and previous research has shown that this can help guard against hypertension in small mammals (e.g., rodents). Large mammals have relatively greater Na[+] storage potential, but whether extrarenal Na[+] storage occurs for this group is unknown. Here, we report preliminary evidence of extrarenal Na[+] storage in cattle. We provided a large pulse-dose of NaCl to four cattle (body mass: ~720 kg) and measured excretion of Na[+] and potassium (K[+]) in urine and faeces for a period of 7-days. Following NaCl administration, Na[+] excretion spiked in both urine and faeces for ~ 48 h before returning to baseline measurements. After ~ 96 h, however, Na[+] excretion increased again; a consistent physiological phenomenon across all individuals studied. We did not observe a pattern in urinary K[+] excretion, indicating that the mechanism of Na[+] storage does not appear to involve exchange for K[+]. However, faecal K[+] excretion was reciprocal to that of Na[+], presumably reflecting exchange of Na[+]/K[+] across the walls of the large intestine. We infer that during the initial period of Na[+] stress, short-term extrarenal Na[+] storage occurred and the stored Na[+] was later released only when the body had returned to Na[+] homeostasis. Additional experiments are required to understand how patterns of Na[+] regulation changes across body sizes and the specific body compartments involved. Cattle may be a useful model system for examining the impact of high Na[+] intake in mammals larger than humans.}, }
@article {pmid41758169, year = {2026}, author = {Sun, Y and Jaiswal, A and Kargarandehkordi, A and Slade, C and Benzo, RM and Phillips, KT and Washington, P}, title = {Barriers to Designing Inclusive Ecological Momentary Assessment and Wearable Data Collection Protocols for AI-Driven Substance Use Monitoring in Hawai'i.}, journal = {Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing}, volume = {31}, number = {}, pages = {566-579}, doi = {10.1142/9789819824755_0041}, pmid = {41758169}, issn = {2335-6936}, abstract = {Ecological momentary assessment (EMA) and wearable sensors offer unprecedented opportunities to capture the dynamics of substance use through real-time, high-resolution behavioral and physiological data. These data streams are increasingly used to train AI/ML models for digital phenotyping and predictive intervention, raising critical questions about fairness, bias, and inclusivity in model development. However, the adoption of these technologies, or the lack thereof, among diverse and historically marginalized groups raises questions and challenges of equity, cultural relevance, and participant trust. In this study, we conducted a four-week observational study with adults in Hawai.i where we combined continuous Fitbit monitoring and daily EMA surveys to document substance use patterns and cravings. Through semi-structured interviews and grounded theory analysis, we identified six primary barriers to study participation and adherence: (1) disruptions to daily routines, (2) physical and psychosocial discomfort associated with wearing the Fitbit device, (3) concerns about aesthetic compatibility and professional appearance, (4) phonerelated issues, (5) challenges related to substance use and cravings, and (6) socially sensitive contexts. We also highlight participant-identified facilitators, such as the value of participant-driven scheduling, motivational feedback, and contextually adaptive protocols. Drawing on these collective findings, we propose a set of design guidelines aimed at advancing the inclusivity, engagement, and fairness of wearable-based EMA research.}, }
@article {pmid41755163, year = {2026}, author = {Hu, Q and Hou, R and Kou, Y and Wang, P and Liu, Z and Li, H and Liu, W and Wang, X and Yi, S and Zhang, F and Zhou, Z and Zhang, M and Li, X and Wu, Q}, title = {Investigating Mining-Induced Surface Subsidence in Mountainous Areas Using Integrated InSAR and GNSS Monitoring.}, journal = {Sensors (Basel, Switzerland)}, volume = {26}, number = {4}, pages = {}, pmid = {41755163}, issn = {1424-8220}, support = {42277478//National Natural Science Foundation of China/ ; U21A20109//National Natural Science Foundation of China/ ; 52274165//National Natural Science Foundation of China/ ; 2024YFC3212200//National Key Research and Development Program of China/ ; 242300421041//Henan Science Foundation for Distinguished Young Scholars of China/ ; 25IRTSTHN008//Henan Provincial University Science and Technology Innovation Team Support Program/ ; 241111321100//Henan Key Research and Development Program of China/ ; }, abstract = {Leveraging the complementary advantages of InSAR and GNSS, this study proposes a refined method for monitoring mining-induced surface subsidence by integrating both technologies. The method begins with calculating the time-series cumulative subsidence basin from InSAR. Subsequently, a constraint condition is established to identify large-gradient deformations, thereby distinguishing the subsidence edge from the subsidence center. For the subsidence edge with minor deformation, the InSAR results are retained. For the large-gradient subsidence center, the subsidence basin around the mining panel is reconstructed by integrating InSAR and GNSS models. Continuous surface deformation information in a geographic coordinate system is then obtained through spatial interpolation, ultimately yielding comprehensive surface subsidence results across the mining area. Taking a mining area in Shanxi Province as the study region, the feasibility and accuracy of the proposed method were validated using 35 SAR images acquired between April 2016 and September 2017, along with leveling measurement data from the mining panel. The maximum surface subsidence rate of the settlement basin obtained from the solution is -186.68 mm/year, and the maximum surface subsidence amount is 248 mm. Compared with the InSAR monitoring results, the root mean square error of the data collaborative monitoring is reduced by 96.8%, and it is reduced by 64.4% compared with the GNSS probability integral method. The results demonstrate that the proposed method can achieve subsidence results consistent with the actual situation. Its monitoring capability is significantly superior to that of using either InSAR or GNSS alone, effectively compensating for the limitations inherent in each individual technology when applied to mining subsidence monitoring. Consequently, this integrated approach provides more accurate and reliable information on surface subsidence in mining areas.}, }
@article {pmid41750773, year = {2026}, author = {Ștefârță, A and Brătoiu, MR and Rădoi, MA and Mercuț, V and Ionescu, M and Scrieciu, M and Petcu, IC and Mărășescu, PC and Amărăscu, MO and Popescu, AM and Vlăduțu, DE}, title = {Assessment of Salivary Parameters-pH, Buffering Capacity and Flow-Associated with Caries Susceptibility.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {16}, number = {4}, pages = {}, pmid = {41750773}, issn = {2075-4418}, abstract = {Background/Objectives: Saliva plays an essential role in maintaining the oral ecological balance, and its quantitative and qualitative characteristics may influence susceptibility to dental caries. The aim of this study was to determine susceptibility to dental caries based on the DMFT index and to establish a correlation between caries experience and salivary parameters in a group of young adults. Methods: This cross-sectional study was conducted between July and November 2025 on a sample of 87 fourth-year students from the Faculty of Dentistry in Craiova. Each participant underwent an intraoral clinical examination to determine the DMFT index. The salivary parameters assessed included unstimulated salivary flow rate, saliva consistency, salivary pH, stimulated salivary flow rate, and buffering capacity, using the GC Saliva-Check Buffer kit. Statistical analyses were performed using SPSS (Statistical Package for Social Sciences) software, version 26 (SPSS Inc., Armonk, NY, USA). Results: The mean DMFT index value for the entire sample was 8.26 ± 4.481, with higher values observed among female participants. Low salivary pH was significantly associated with higher DMFT values. Participants with low or very low buffering capacity exhibited higher DMFT values compared to those with normal capacity, indicating that a reduced ability to neutralize salivary acidity is associated with increased caries activity. Conclusions: The results indicate that salivary pH and buffering capacity are important factors in dental caries susceptibility among young adults. The integration of salivary testing into the diagnostic assessment of caries risk may contribute to personalized and effective preventive strategies.}, }
@article {pmid41749705, year = {2026}, author = {Caragață, AV and Hnatiuc, M and Geman, O and Halunga, S and Tulbure, A and Iov, CJ}, title = {Smart Devices and Multimodal Systems for Mental Health Monitoring: From Theory to Application.}, journal = {Bioengineering (Basel, Switzerland)}, volume = {13}, number = {2}, pages = {}, pmid = {41749705}, issn = {2306-5354}, abstract = {Smart devices and multimodal biosignal systems, including electroencephalography (EEG/MEG), ECG-derived heart rate variability (HRV), and electromyography (EMG), increasingly supported by artificial intelligence (AI), are being explored to improve the assessment and longitudinal monitoring of mental health conditions. Despite rapid growth, the available evidence remains heterogeneous, and clinical translation is limited by variability in acquisition protocols, analytical pipelines, and validation quality. This systematic review synthesizes current applications, signal-processing approaches, and methodological limitations of biosignal-based smart systems for mental health monitoring. Methods: A PRISMA 2020-guided systematic review was conducted across PubMed/MEDLINE, Scopus, the Web of Science Core Collection, IEEE Xplore, and the ACM Digital Library for studies published between 2013 and 2026. Eligible records reported human applications of wearable/smart devices or multimodal biosignals (e.g., EEG/MEG, ECG/HRV, EMG, EDA/GSR, and sleep/activity) for the detection, monitoring, or management of mental health outcomes. The reviewed literature after predefined inclusion/exclusion criteria clustered into six themes: depression detection and monitoring (37%), stress/anxiety management (18%), post-traumatic stress disorder (PTSD)/trauma (5%), technological innovations for monitoring (25%), brain-state-dependent stimulation/interventions (3%), and socioeconomic context (7%). Across modalities, common analytical pipelines included artifact suppression, feature extraction (time/frequency/nonlinear indices such as entropy and complexity), and machine learning/deep learning models (e.g., SVM, random forests, CNNs, and transformers) for classification or prediction. However, 67% of studies involved sample sizes below 100 participants, limited ecological validity, and lacked external validation; heterogeneity in protocols and outcomes constrained comparability. Conclusions: Overall, multimodal systems demonstrate strong potential to augment conventional mental health assessment, particularly via wearable cardiac metrics and passive sensing approaches, but current evidence is dominated by proof-of-concept studies. Future work should prioritize standardized reporting, rigorous validation in diverse real-world cohorts, transparent model evaluations, and ethics-by-design principles (privacy, fairness, and clinical governance) to support translation into practice.}, }
@article {pmid41742940, year = {2026}, author = {Mendes, L and Oliveira, J and Simões, M and Pinto, M and Castelo-Branco, M}, title = {Remote cognitive training for older adults using tablets: A pilot trial.}, journal = {Digital health}, volume = {12}, number = {}, pages = {20552076261417771}, pmid = {41742940}, issn = {2055-2076}, abstract = {BACKGROUND: Cognitive decline significantly affects the functional and intrinsic capacities of older adults, highlighting the need for effective interventions. Evidence suggests that mentally stimulating activities, particularly those supported by digital technologies, can promote cognitive health and quality of life in aging populations.<br><br>OBJECTIVE: This pilot trial examined the feasibility and preliminary effectiveness of GameAAL, a multidomain Cognitive Training programme delivered via tablet and television, in older adults with cognitive impairment or dementia.<br><br>METHODS: The intervention targeted key cognitive domains including attention, reaction time, memory, language, and executive functioning. Forty-one older adults (aged 60-93), living in nursing homes, participated in a 6-month programme. The tablet intervention group (n&#x2009;=&#x2009;10) completed 30 sessions using a tablet device, while the TV intervention group (n&#x2009;=&#x2009;31) completed nine sessions using a TV interface. All participants engaged with six serious games designed around cognitive tasks related to activities of daily living.<br><br>RESULTS: Pre- and post-intervention assessments included the Montreal Cognitive Assessment (MoCA) and the Hospital Anxiety and Depression Scale (HADS). The Tablet group showed a trend towards improved MoCA scores following the intervention, whereas the TV group did not show significant changes. At the post-intervention, the Tablet group demonstrated significantly better cognitive performance compared to the TV group (p&#x2009;=&#x2009;0.044). No significant between-group differences were observed in HADS scores.<br><br>CONCLUSION: The findings suggest that the GameAAL Cognitive Training programme may help improve cognitive function in older adults with cognitive impairment by combining computer-based exercises with ecologically valid tasks.}, }
@article {pmid41741663, year = {2026}, author = {Pankararu, CJ and Teixidor-Toneu, I and Odonne, G and Asante, F and Bandeira, SO and Barrera-Bello, &#xc1;M and Benitez-Capistros, FJ and Dahdouh-Guebas, F and Dalcin, E and Dennehy-Carr, ZH and Diallo, K and Drouet-Cruz, HT and Fonseca-Kruel, VS and Gallois, S and Gnansounou, SC and Hamza, AJ and Hugé, J and Jordan, FM and Kalle, R and Khan, NI and Kuijper, I and Levis, C and Lima, AS and Mattalia, G and Milliken, W and Munga, CN and Narchi, NE and Ngeve, MN and Ofori, SA and Phartyal, SS and Peroni, N and Pironon, S and Polanía, J and Prakofjewa, J and Silva, MT and Sõukand, R and Thomas, MB and Ulian, T and Uprety, Y and Vandebroek, I and Ximenes, AC and Zank, S and Hanazaki, N}, title = {A global biodiversity use data infrastructure acknowledging indigenous and local knowledge.}, journal = {npj biodiversity}, volume = {5}, number = {1}, pages = {}, pmid = {41741663}, issn = {2731-4243}, abstract = {Many global biodiversity datasets overlook or misrepresent the knowledge of Indigenous Peoples, Local Communities, and Afro-Descendants (IPLCAD). We propose minimum data and metadata standards for a global data infrastructure on biodiversity knowledge and use, co-designed with IPLCAD, including information on language, community attribution and consent, to ensure data traceability and ethical use. This initiative integrates ancestral and academic sciences to advance inclusive biodiversity governance, addressing historical inequities for global sustainability.}, }
@article {pmid41741145, year = {2026}, author = {Watanabe, F and Muramatsu, K and Tokutsu, K and Okawara, M and Fushimi, K and Matsuda, S}, title = {Functional Differentiation Among Medical Institutions During COVID-19 State of Emergency Periods: Autoregressive Integrated Moving Average Analysis of Percutaneous Coronary Intervention Using Diagnosis Procedure Combination Data.}, journal = {The Tohoku journal of experimental medicine}, volume = {}, number = {}, pages = {}, doi = {10.1620/tjem.2026.J016}, pmid = {41741145}, issn = {1349-3329}, }
@article {pmid41741097, year = {2026}, author = {Tamm, J and Takano, K and Just, L and Ehring, T and Rosenkranz, T and ,  and Kopf-Beck, J}, title = {Early Improvement Predicts Treatment Response in Depression: An Ecological Momentary Assessment Study in an Inpatient and Day Clinic Setting.}, journal = {Behavior therapy}, volume = {57}, number = {2}, pages = {234-249}, doi = {10.1016/j.beth.2025.08.002}, pmid = {41741097}, issn = {1878-1888}, abstract = {Predicting treatment response through early improvement can reduce patients' time in ineffective treatments before considering alternatives. However, for psychological interventions, there is no consensus on what time window and improvement rate early in the treatment is the most informative for distinguishing treatment responders from nonresponders. This study investigated these aspects in an inpatient and day clinic setting among severe depressed patients who perceived intensive psychological treatment and compared Weekly Questionnaire Assessments (WQA) and Ecological Momentary Assessment (EMA) regarding their power to predict treatment response through early improvement. Fifty-two depressed patients were randomly assigned to one of three intensive 7-week psychological interventions (two individual and two group sessions per week) applied in an inpatient or day clinic setting. Early improvement was assessed three times daily using EMA and weekly using questionnaires (BDI-II). Linear Regression Models and Receiver Operating Characteristic Analyses were conducted to predict treatment response (BDI-II improvement from pre- to postintervention ≥50%) in patients who received a full course of treatment. Moreover, ratios of true negative/false negative predictions were calculated to explore the predictive value of different early improvement definitions: 10%, 20%, 30%, or 40% improvement after 1, 2, 3, or 4 treatment weeks. Both EMA and WQA significantly predicted treatment response after 3 weeks with AUC values of 73% (EMA) and 77% (WQA). A WQA-assessed 10% improvement after 4 weeks yielded the highest ratio of true negative/false negative predictions, with a true negative rate of 22% and a false negative rate of 0%. 10% improvement in depressive symptoms assessed with WQA after 3 to 4 weeks of treatment was the best predictor in our study. Further research is needed to validate the results. This trial design is registered with osf.io/9fuhn.}, }
@article {pmid41740147, year = {2026}, author = {Rowland, BW and Sexton, V and Mill, A and Rushton, S and Sanderson, R and Grundy, C and de Lusignan, S and Cunliffe, NA and Hungerford, D and Hopkins, M and Gharbia, S and Jenkins, C and Godbole, G and Vivancos, R and Elliot, AJ and Mellor, DJ and Larkin, L and Chalmers, R and O'Brien, S and , }, title = {The Third Study of Infectious Intestinal Disease (IID3 Study) in the Community: Protocol for UK-Based Prospective Cohort Studies Investigating the Disease Burden.}, journal = {JMIR research protocols}, volume = {15}, number = {}, pages = {e88759}, doi = {10.2196/88759}, pmid = {41740147}, issn = {1929-0748}, abstract = {BACKGROUND: There is a significant hidden burden of infectious intestinal disease (IID) in the UK community, which has increased over time. In the late 2000s, the Second Study of Infectious Intestinal Disease (IID2 study) estimated 17 million IID cases annually in the United Kingdom. However, only a small proportion of cases present to health care, and even those are often not tested for causative organisms.<br><br>OBJECTIVE: The Third Study of Infectious Intestinal Disease (IID3 study) aims to determine the IID burden in the UK community, estimate the underreporting level in routine practice and the general population, and recalibrate UK national surveillance based on the new incidence rates.<br><br>METHODS: We will follow methods of previous studies, along with modern pathogen detection methods and digital platforms for recruitment and follow-up. Participants will be recruited to three population-based prospective cohorts: cohort 1 (the general population), cohort 2 (patients with IID presenting to general practices [GPs]), and cohort 3 (enumeration study of IID cases presenting to GPs). Microbiological analysis of stool samples in cohorts 1 and 2 will include testing for a wide range of causative organisms using molecular assays, including pathogen targets not routinely sought by National Health Service (NHS) laboratories. Additional characterization of pathogens will be conducted at national reference laboratories. The incidence rates of IID and organisms detected in cohorts 1-3 will be compared to national surveillance systems, both laboratory and syndromic. Descriptive statistics and analysis will allow comparison of IID rates within each cohort, estimate the overall burden of disease caused by different pathogens, and compare findings to earlier IID studies.<br><br>RESULTS: A favorable ethical opinion was obtained from the UK Health Research Authority on August 4, 2022. A pilot phase to test the sampling process was conducted from January to August 2023. Participant recruitment commenced on September 1, 2023, for cohort 2 and on March 16, 2024, for cohort 1; recruitment ceased on August 31, 2025. Data collection is complete, and data analysis is to begin. The study is expected to end in September 2026.<br><br>CONCLUSIONS: Since the first and second IID studies, changes have occurred within national surveillance systems, the NHS structure, and public recommendations about when to consult a GP and where to seek health care advice, which may have altered the extent of IID reporting and the perceived burden in the community, creating greater uncertainty about the representativeness of IID rates. The IID3 study results will provide insight into trends in disease incidence over time and help quantify inequalities in IID in the UK community. Revised estimates can inform policy related to prevention, including food standards and disease management. Furthermore, advances in molecular diagnostics will significantly enhance pathogen detection, increasing our understanding of the causes of IID.<br><br>DERR1-10.2196/88759.}, }
@article {pmid41739554, year = {2026}, author = {Echigoya, S and Ohmura, T and Sato, K and Nakagaki, T and Nishigami, Y}, title = {Geometrical preference of anchoring sites in the unicellular organism Stentor coeruleus.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {9}, pages = {e2518816123}, doi = {10.1073/pnas.2518816123}, pmid = {41739554}, issn = {1091-6490}, support = {2021-6029//Japan Science Society (JSS)/ ; None//Promotion Project for Young Investigators in Hokkaido University/ ; JPMJFS2101//Establishment of University Fellowships towards the Creation of Science Technology Innovation/ ; 2300464//Sumitomo Foundation (SF)/ ; JP21H05303//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP21H05308//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP21H05310//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP23H04300//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP24K09388//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP24K23220//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP25K17535//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; }, mesh = {*Ciliophora/physiology ; Hydrodynamics ; Movement/physiology ; Calcium/metabolism ; }, abstract = {Organisms often inhabit environments comprising complex structures across various scales. Animals rely on visual information from surrounding geometrical structures for navigation. Even at the microscale, various microsediments form complex structures in microbial habitats. The movement of microorganisms is passively affected by collisions and hydrodynamic interactions with surrounding structures. However, the influence of microenvironmental geometry on behavioral changes of unicellular organisms that lack visual perception remains unclear. Here, we developed geometrically structured chambers to investigate anchoring site preferences in the swimming ciliate Stentor coeruleus. Our experiments revealed that S. coeruleus preferentially anchored in narrow regions characterized by specific geometrical features, including corner angle, depth, and curvature at the corner end. Before anchoring, free-swimming S. coeruleus changed its behavior to move along the boundary wall of the chambers, accompanied by Ca[2+]-induced asymmetrical body deformation. To further investigate how S. coeruleus moves along the wall continuously, we conducted a hydrodynamic simulation and revealed that the asymmetric morphology causes asymmetric propulsive forces, explaining wall-following behavior through physical interactions with a wall. Thus, morphological change near a wall causes wall-following behavior, facilitating the identification of these narrow anchoring sites. Our findings indicate that environmental geometry drives behavioral transitions in S. coeruleus through simple biophysical processes, enabling spatial selection without visual cues. Overall, these results suggest that microgeometry plays a key role in shaping ecological niches for unicellular microorganisms.}, }
@article {pmid41738306, year = {2026}, author = {Baalsrud, HT and Tørresen, OK and Danneels, B and Ferrari, G and Tooming-Klunderud, A and Skage, M and Kollias, S and Arnyasi, M and Svensen, E and Kuklinski, P and Jakobsen, KS and Liow, LH}, title = {Chromosomal Fusions Shaped the Genome of the Greater Hornwrack Bryozoan (Flustra Foliacea) (Linnaeus, 1758).}, journal = {The Journal of heredity}, volume = {}, number = {}, pages = {}, doi = {10.1093/jhered/esag013}, pmid = {41738306}, issn = {1465-7333}, abstract = {The phylum Bryozoa is an understudied, yet commonly-occurring, globally distributed bilaterian metazoan organismal group. They have a colonial lifestyle and an evolutionary history that spans at least 480 million years but likely longer. Despite their contentious phylogenetic affinities among metazoans, disproportionately few genomic investigations have been performed thus far. Here, we describe the first chromosome-level genome assembly of an individual Flustra foliacea colony belonging to the order Cheilostomatida, collected in southern Norway. The haplotype-resolved assembly of F. foliacea contains two pseudo-haplotypes spanning 956 megabases and 880 megabases, respectively. Both assemblies are highly complete both in terms of scaffolding (>90% of sequences placed in 8 autosomal chromosomal pseudomolecules), and gene content (BUSCO completeness scores > 90%). We also present gene and repeat annotations of the two assemblies. A comparison of our newly sequenced F. foliacea with five previously published bryozoan genomes supports the hypothesis that the group has undergone extensive genome rearrangements. This includes multiple chromosomal fusions in F. foliacea since their split with other cheilostome bryozoans. These fusions were enriched with long terminal repeat (LTR) retrotransposons, highlighting the complex interplay between genome organization and genomic repeats. Our study contributes to a deeper understanding of bryozoan genome evolution and the role of repeats in metazoan genome organization.}, }
@article {pmid41733649, year = {2026}, author = {Liang, X and Guo, J and Lei, W and Wang, H and Fan, Q and He, S}, title = {Spatial Distribution and Environmental Risk Assessment of Neonicotinoids, Antibiotics, and Heavy Metals in the Yellow River Riparian Soils.}, journal = {Environmental management}, volume = {76}, number = {4}, pages = {}, pmid = {41733649}, issn = {1432-1009}, support = {52300244//National Natural Science Foundation of China/ ; }, mesh = {*Neonicotinoids/analysis ; *Anti-Bacterial Agents/analysis ; *Soil Pollutants/analysis ; Rivers/chemistry ; Environmental Monitoring ; Risk Assessment ; *Metals, Heavy/analysis ; Soil/chemistry ; China ; Insecticides/analysis ; Water Pollutants, Chemical/analysis ; }, abstract = {Co-occurring contaminants in riparian soils posed a growing threat to the sustainable development of the Yellow River Basin. However, understanding of the co-occurrence patterns and key drivers of heavy metals (HMs), antibiotics, and neonicotinoid insecticides (NNIs) at the watershed scale remains limited. Therefore, we selected surface soil along the Yellow River to analyze its content characteristics, spatial patterns, and interrelationships. Detection rates of NNIs, antibiotics, and HMs in soils exceeded 99%. The average content of total NNIs (∑8NNIs) was 5.118 ng/g, with thiacloprid (1.667 ng/g) being the predominant component (32.5%). Total antibiotics averaged 0.412 ng/g, dominated by quinolones (47.8%) and macrolides (30.9%). The concentrations of As, Cr, and Zn among the HMs were 5.7-18.0 μg/g, 53.4-91.1 μg/g, and 35.6-94.3 μg/g, respectively, exceeding their background values at 36%, 21%, and 37% of the sampling sites, respectively. Soil organic matter content and pH negatively correlated with NNIs but positively with HMs, while fine soil particles positively correlated with both. Furthermore, ∑8NNIs (7.680 ng/g) and the contents of thirteen antibiotics (∑13ABX, 13.956 ng/g) in corn-cultivated soils were higher than in other cropped types, while ∑8NNIs (0.780 ng/g) and ∑13ABX (0.003 ng/g) in reed marshes were lower than in other cultivated soils. Health and ecological risks were generally low across the study area, but some specific sites posed potential integrated contamination risks. The study provided scientific data on the environmental fate and risks of NNIs, antibiotics, and HMs in riparian soils of large-scale watersheds, and underscored the need for more efficient usage practices and integrated watershed management strategies.}, }
@article {pmid41730638, year = {2026}, author = {Okui, T and Fukushima, H and Maeda, M and Oda, F and Nakashima, N and Fukuda, H}, title = {A short-term association between hospitalizations for mental disorders and ambient temperature in Japan: an ecological study using the LIFE Study data.}, journal = {Environmental health and preventive medicine}, volume = {31}, number = {}, pages = {12}, doi = {10.1265/ehpm.25-00377}, pmid = {41730638}, issn = {1347-4715}, mesh = {Japan/epidemiology ; Humans ; *Hospitalization/statistics &amp; numerical data ; Male ; Female ; Middle Aged ; *Mental Disorders/epidemiology/etiology ; Aged ; Adult ; *Temperature ; Young Adult ; Cities/epidemiology ; Aged, 80 and over ; Adolescent ; }, abstract = {BACKGROUND: Few studies have investigated the association between ambient temperature and the risk of mental disorders in Japan. In this study, we investigated a short-term association between the risk of hospitalizations for mental disorders and ambient temperature using municipal health insurance data.<br><br>METHODS: We used the data of the Longevity Improvement &amp; Fair Evidence Study in Japan, and the data of 17 municipalities were employed in the analysis. The daily number of hospitalizations for schizophrenia, depressive disorders, and anxiety disorders was used as the outcome variable. The time-stratified case-crossover design was employed in this ecological time-series study, and a distributed-lag non-linear model using a conditional quasi-Poisson regression model was employed to investigate an association between ambient temperature and hospitalizations for the abovementioned mental disorders. The model was applied to each municipality, and a multivariate meta-analysis was conducted to pool the results of municipalities. In addition, subgroup analyses by sex and age groups were conducted, and temperature-related attributable fractions of the mental disorders were also calculated.<br><br>RESULTS: The results of the overall cumulative effect of ambient temperature on hospitalizations for mental disorders indicated that the risk ratio (RR) tended to increase with an increase in temperature regardless of the type of mental disorder. An analysis by sex indicated that the RR tended to increase with an increase in temperature regardless of sex. In addition, an analysis by age group indicated that an increase in RR with increasing temperature was more evident in persons aged <65 years compared to those aged &#x2265;65 years regardless of mental disorders, and that the temperature-related attributable fractions were also higher in persons aged <65 years.<br><br>CONCLUSIONS: Higher temperatures were associated with a higher risk of hospitalization for mental disorders in Japan, while the degree of the association differed by age group.}, }
@article {pmid41728910, year = {2026}, author = {Liu, Y and Niu, B and Zhang, T and Wang, J and Lin, X and Zhu, L and Lv, J and Yu, R and Li, X and Zhu, J and Hu, J and Jin, LN and Chan, LL and Li, Y and Zhang, L}, title = {Environmental Drivers and Trophic Transfer of Domoic Acid in a Eutrophic Subtropical Estuary: Linking Toxigenic Pseudonitzschia Dynamics to Ecosystem Risks.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c00346}, pmid = {41728910}, issn = {1520-5851}, abstract = {Domoic acid (DA), a neurotoxin produced by certain diatoms of Pseudonitzschia, poses significant risks to marine ecosystems and human health, yet its dynamics in subtropical eutrophic estuaries remain poorly understood. This study investigates DA production and trophic transfer in the Pearl River Estuary, combining chemotaxonomy, morphological identification, ITS1 metabarcoding, and HPLC-MS/MS analysis. We revealed strong seasonal and spatial heterogeneity in Pseudonitzschia assemblages, identifying Pseudonitzschia cuspidata Clade III as a dominant DA producer with an estimated in situ cellular quota of 0.1-0.8 pg cell[-1] for the community. DA was ubiquitously detected across trophic levels, with summer maxima in phytoplankton to zooplankton, crustaceans, and mollusks, exceeding safety thresholds with 24.1 mg kg[-1] in scallops. Baseline DA contamination persisted year-round, with this chronic risk amplified by increased summer diatom biomass. Crucially, DA production was governed by optimal salinity and temperature and linked to nutrient stoichiometry rather than absolute nutrient concentration; chronic high nutrient levels showed a negative correlation with DA production. These environmental drivers also influenced DA transfer efficiency, with summer conditions amplifying contamination despite sub-bloom cell densities. These findings reveal underestimated risks in subtropical estuaries, providing a critical framework for monitoring and managing DA contamination under climate variability.}, }
@article {pmid41722362, year = {2026}, author = {Mimura, H and Osaki, T and Takamori, S and AlSaleh, MA and Antony, B and Takeuchi, S}, title = {Cell-based biohybrid sensing of a volatile aggregation pheromone component associated with the invasive red palm weevil.}, journal = {Biosensors &amp; bioelectronics}, volume = {302}, number = {}, pages = {118537}, doi = {10.1016/j.bios.2026.118537}, pmid = {41722362}, issn = {1873-4235}, abstract = {The red palm weevil (Rhynchophorus ferrugineus, RPW) is a highly destructive invasive pest of palm trees, causing severe agricultural and economic losses worldwide. Adult males release an aggregation pheromone, primarily (4RS,5RS)-4-methylnonan-5-ol (ferrugineol), which mediates colony formation and infestation within palm trunks. Because all life stages of this weevil are hidden inside the tree and remain undetected until fatal damage occurs, rapid and sensitive detection of pheromone emissions from the weevil colony is crucial for early detection and monitoring. However, practical sensor technologies capable of detecting this pheromone have not yet been established. Here, we report a cell-based biohybrid sensor capable of detecting pheromones in the vapor phase. This sensor employs HEK293 cells transiently co-expressing the RPW pheromone receptor RferOR1, its co-receptor RferOrco, and the genetically encoded fluorescent calcium indicator GCaMP. The specificity and sensitivity of these cells were first validated for ferrugineol in aqueous solution (0.1-10 μM), showing decreased responses at 100 μM indicative of non-monotonic behavior. The cells were then encapsulated in hydrogel matrices and integrated into a microwell array. We found that the resulting cell-based sensor exhibited a monotonic fluorescence response to ferrugineol across a broader concentration range (0.1-100 μM), likely due to moderated diffusion of ferrugineol within the hydrogel. Furthermore, the sensor successfully detected ferrugineol in the vapor phase at sub-ppm concentrations (0.1-100 ppm). These findings demonstrate that the developed sensor provides a technological basis for pheromone-detection systems for RPW monitoring, thereby extending the applicability of biohybrid sensing to ecologically relevant odorants.}, }
@article {pmid41716623, year = {2026}, author = {Robinson, M and Letovsky, S and Liu, AH and Weber, RW and Rafalko, JM and Valcour, A}, title = {Tree pollen allergen sensitization: Prevalence, risk factors, and geographic variation in the United States.}, journal = {The journal of allergy and clinical immunology. Global}, volume = {5}, number = {3}, pages = {100642}, pmid = {41716623}, issn = {2772-8293}, abstract = {BACKGROUND: Many tree pollens are associated with the pathogenesis of allergic disease.<br><br>OBJECTIVE: Our aim was to investigate prevalence, risk factors, and geographic variation of tree pollen sensitization in the United States.<br><br>METHODS: Results of specific IgE testing for pollen of 31 tree species were obtained from a single United States-wide clinical laboratory by physicians' requests submitted in 2014-2023. Tree pollen sensitization data were statistically analyzed with respect to prevalence, patterns, and relationship with demographic characteristics, clinical diagnoses, and geographic regions.<br><br>RESULTS: A total of 23,932,544 specific IgE tests, originating from 3,067,173 unique patients ranging in age from 0 to 85 years were identified. Males showed higher positivity rates across all tree species and age groups. In both sexes, positivity was highest in individuals aged 10 to 19 years and in patients with atopic dermatitis and asthma. Patients living in urban areas had higher rates of sensitization than patients in rural areas. Considerable differences in top sensitizers were identified across ecoregions, even among different ecoregions present within the same US state. Rates of cosensitization to allergen pairs were generally associated with phylogenetic proximity of species.<br><br>CONCLUSION: Factors associated with higher rates of tree pollen sensitization included being male, being a teenager, having atopic dermatitis, having asthma, and living in a specific ecologic region. Results from this study may be helpful to clinicians in counseling patients, as well as to laboratories designing geographically based allergen testing panels.}, }
@article {pmid41715878, year = {2026}, author = {Sun, H and Radicchi, F and Bianconi, G}, title = {Triadic percolation on multilayer networks.}, journal = {Physical review. E}, volume = {113}, number = {1-1}, pages = {014313}, doi = {10.1103/yvtg-wnn4}, pmid = {41715878}, issn = {2470-0053}, abstract = {Triadic interactions are special types of higher-order interactions that occur when regulator nodes modulate the interactions between other two or more nodes. In the presence of triadic interactions, a percolation process occurring on a single-layer network becomes a full fledged dynamical system, characterized by period doubling and a route to chaos. Here we generalize the model to multilayer networks and name it as the multilayer triadic percolation (MTP) model. We find a much richer dynamical behavior of the MTP model than its single-layer counterpart. MTP displays a Neimark-Sacker bifurcation, leading to oscillations of arbitrarily large period or pseudoperiodic oscillations. Moreover, MTP admits period-two oscillations without negative regulatory interactions, whereas single-layer systems only display discontinuous hybrid transitions. This comprehensive model offers new insights on the importance of regulatory interactions in real-world systems such as brain networks, climate, and ecological systems.}, }
@article {pmid41714061, year = {2026}, author = {Ramesh, B and Freisthler, B and Ye, Y and Kieninger, K and Barboza-Salerno, G and Thurston, H}, title = {Relationship between time spent in outdoor recreational areas and stress among parents during the COVID-19 lockdown - A spatial temporal analysis of GPS traces from geographical EMA.}, journal = {Spatial and spatio-temporal epidemiology}, volume = {56}, number = {}, pages = {100782}, doi = {10.1016/j.sste.2026.100782}, pmid = {41714061}, issn = {1877-5853}, mesh = {Humans ; *COVID-19/epidemiology/prevention &amp; control/psychology ; Male ; Female ; *Parents/psychology ; Adult ; Spatio-Temporal Analysis ; *Stress, Psychological/epidemiology ; *Recreation/psychology ; Geographic Information Systems ; Ecological Momentary Assessment ; Time Factors ; SARS-CoV-2 ; *Quarantine/psychology ; Middle Aged ; Parks, Recreational ; Self Report ; }, abstract = {BACKGROUND: The early COVID-19 period, with stay-at-home orders, was particularly stressful for parents. Outdoor recreation areas (ORAs), such as green spaces, may have helped alleviate stress.<br><br>AIM: To estimate the association between ORA visits and self-reported stress using geographical ecological momentary assessment (gEMA) with refined multi-sourced ORA boundaries.<br><br>METHODS: Self-reported stress was collected from a cohort of 286 participants via EMA three times daily over 14 days, alongside continuous GPS tracking. ORA visit durations were derived by spatio-temporal clustering of GPS tracks. Generalized ordinal logistic regression model supporting partial proportional odds was used to estimate the association between ORA visit duration stress, adjusting for baseline covariates and weather.<br><br>RESULTS: A minute-wise increase in ORA visit duration was not significantly associated with stress (Odds Ratio=0.99; 95% CI: 0.99 to 1.00). However, when the duration was categorized, ORA visits lasting between 15 and 35 min were associated with a 40% reduction in the odds of reporting higher stress (95% CI: 10% to 60%). A similar association was observed for shorter ORA visits (&#x2264; 5 min), though the effect varied across stress levels. The odds of reporting higher stress were also associated with whether the parent was with their focal child, parental sex, marital status, work status, the time of day, and weekday/weekend.<br><br>CONCLUSION: Spending 15-35 min in ORAs may be optimal for parents to manage stress during challenging periods, such as the stay-at-home phase of the COVID-19 pandemic. Even brief ORA visits (< 5 min) may help parents experiencing high stress.}, }
@article {pmid41713447, year = {2026}, author = {Song, P and Jiang, D and Zhou, J and Zhu, Y and Manaf, RA and Bojude, DA and Agbre-Yace, ML and Ali, S and Allen, O and Anyasodor, AE and Aranda, Z and Bahattab, A and Bodomo, A and Borrescio-Higa, F and Buchtova, M and Buljan, N and Deshmukh, V and Díaz-Castro, L and Cheema, S and Ekezie, W and Ganasegeran, K and Ganesan, B and Glasnović, A and Graham, CJ and Htay, MNN and Igwesi-Chidobe, C and Iversen, PO and Islam, MM and Karim, AJ and Kalpič, B and Kanma-Okafor, O and Lanza, G and Luz, S and Mahikul, W and Mladenić, D and Manyara, AM and Munipalli, B and Myburgh, N and Ng, ZX and Nikolopoulos, G and Park, C and Park, JJ and Peprah, P and Rudan, K and Shah, SA and Shi, T and Tiglic, G&#x160; and Sutan, R and Tsanas, A and Tibble, H and Khpalwak, AT and Tomlinson, M and Vento, S and Glasnović, JV and Wang, L and Xu, J and Zhang, J and Zhang, Y and Sheikh, E and Ozoh, OB and Tsiachristas, A and Adeloye, D and Kerr, S and Sanwalka, M and Orešković, S and Sheikh, A and Rudan, I}, title = {Research priorities for data science and artificial intelligence in global health: an international consensus exercise.}, journal = {The Lancet. Global health}, volume = {14}, number = {3}, pages = {e455-e465}, doi = {10.1016/S2214-109X(25)00473-5}, pmid = {41713447}, issn = {2214-109X}, mesh = {Humans ; *Artificial Intelligence ; *Global Health ; *Data Science ; Consensus ; *Research ; Developing Countries ; }, abstract = {Applications of data science and artificial intelligence (AI) in global health are expanding, yet research remains fragmented and often misaligned with the needs of low-income and middle-income countries (LMICs). To address this misalignment, we conducted a global research priority-setting exercise using the Child Health and Nutrition Research Initiative (CHNRI) method. 155 research ideas were scored by 51 experts based on feasibility, potential impact on disease burden, paradigm shift potential, implementation potential, and equity. Top-ranked priorities focused on epidemic preparedness, including AI-based outbreak prediction, improved diagnostics for infectious diseases, and early-warning systems. Other highly ranked topics included AI-assisted resource allocation, telemedicine, culturally adapted mobile health services, and chronic disease management tools. Experts from LMICs prioritised infectious disease control and diagnostic equity, whereas experts from high-income countries emphasised infrastructure and climate-related analytics. The resulting agenda provides a roadmap for aligning AI and data science research with global health priorities, particularly in LMICs.}, }
@article {pmid41712942, year = {2026}, author = {Thompson, DA and Kaizer, LK and Schmiege, SJ and Cabrera, NJ and Clark, L and Ringwood, H and Miramontes Valdes, E and Jimenez-Zambrano, A and Gorman, C and Babiak, M and Tschann, JM}, title = {Maternal Screen-Related Behaviors, Toddler Screen Use, and Toddler BMI in Mexican American Families: Cross-Sectional Study.}, journal = {JMIR pediatrics and parenting}, volume = {9}, number = {}, pages = {e76873}, pmid = {41712942}, issn = {2561-6722}, abstract = {BACKGROUND: Parents, as the most proximal influence on young children, play an important role in shaping toddler behaviors. Yet, evidence on how parents shape toddler screen use is limited. Little is also known about the relationship between toddler screen use and BMI. Given existing disparities in screen use and early childhood obesity, a focus on Mexican American families with toddlers is warranted.<br><br>OBJECTIVE: This study aimed to evaluate the independent contributions of both maternal screen use and screen-related parenting practices with toddler screen use duration, for both TV viewing and mobile device use, and examine the relationship between toddler screen use duration and BMI.<br><br>METHODS: This cross-sectional study enrolled 384 Mexican American mother-toddler dyads recruited from safety net clinics. Enrolled mothers completed 7-day screen use diaries and surveys on screen-related parenting practices, and toddler anthropometrics were obtained. Negative binomial regression models estimated the relationships between screen-related parenting practices and maternal screen use (predictors) with child duration of daily TV use and mobile device use (outcomes). Spearman correlations were calculated to estimate the relationship between toddler screen use duration and age- and sex-specific BMI z scores.<br><br>RESULTS: Maternal duration of daily TV and mobile device use were associated with toddler duration of daily TV (adjusted rate ratios [aRRs] 1.27-1.28; all P<.001) and mobile device use (aRRs 1.17-1.18; all P<.001), respectively, even after adjusting for maternal screen-related parenting practices. Specific parenting practices, including restriction of TV time (aRR=0.86; P=.01), restriction of mobile device time (aRR=0.80; P=.02), use of TV (aRR=1.27; P=.003) and mobile devices (aRR=1.78; P<.001) for child behavior regulation, and coviewing of mobile devices (aRR=1.51; P<.001), were associated with toddler duration of daily screen use, adjusted for maternal duration of daily screen use. Neither toddler duration of daily TV viewing nor daily mobile device use was correlated with toddler BMI z scores.<br><br>CONCLUSIONS: Both the duration of maternal screen use and screen-related parenting practices, for both TV and mobile devices, should be considered when promoting healthy screen use in toddlers in Mexican American families. Interventionists should consider the family ecology when designing interventions promoting healthy screen use in early childhood.}, }
@article {pmid41707187, year = {2026}, author = {Kong, J and Bragazzi, NL}, title = {Framing the Convergence of One Health and Digital Health in the Global South With a Gender-Sensitive Foresight Perspective: Delphi Study Using Latent Semantic Analysis.}, journal = {Journal of medical Internet research}, volume = {28}, number = {}, pages = {e78702}, doi = {10.2196/78702}, pmid = {41707187}, issn = {1438-8871}, mesh = {Delphi Technique ; Humans ; Female ; *Global Health ; Male ; Semantics ; Artificial Intelligence ; Sex Factors ; *Digital Technology ; Digital Health ; }, abstract = {BACKGROUND: The convergence of digital health and One Health represents an emergent paradigm in global health governance. While widely discussed in high-income settings, there is limited understanding of how this convergence is conceptualized in the Global South, particularly when viewed through a gender- and equity-sensitive foresight lens.<br><br>OBJECTIVE: This study aimed to map and classify expert discourse on digital health, One Health, and their convergence in the Global South using latent semantic analysis, with particular attention to structural drivers, emerging issues, weak signals, and gendered patterns of anticipation.<br><br>METHODS: A 3-round online Delphi survey was conducted with 45 experts from 19 countries across the Global South. Open-ended responses were analyzed using latent semantic analysis and stratified by gender. A foresight framework was applied to categorize topics as structural drivers, emerging issues, or weak signals, based on their temporal persistence, salience, and consensus.<br><br>RESULTS: In digital health, structural drivers included the systemic integration of digital technologies into public health systems, strategic alignment, and infrastructure development. Emerging issues comprised the adoption of artificial intelligence, chronic disease management via mobile health, and concerns about digital inclusion and interoperability. Weak signals included feminist digital ethics, trust in digital systems, and relational accountability-more frequently emphasized by female experts. In One Health, structural drivers were centered on intersectoral coordination, ecological integration, and the institutionalization of health-environment frameworks. Emerging issues encompassed anticipatory risk governance, food system sustainability, and the integration of environmental and population-level data. Weak signals included indigenous knowledge systems, subnational antimicrobial resistance governance, and structural underinvestment in ecological public health, with gendered divergence in framing. In the convergence discourse (digital health and One Health), structural drivers focused on the integration of digital surveillance systems, data infrastructures, and health information platforms to operationalize One Health. Emerging issues included climate-triggered system redesign, artificial intelligence and ecological monitoring, and the governance of cross-sectoral data. Weak signals pointed to algorithmic bias in zoonotic prediction, digital sovereignty in environmental health, and feminist critiques of convergence-all thematically rich but peripheral in consensus.<br><br>CONCLUSIONS: This study revealed a multilayered and gender-influenced foresight architecture shaping the future of digital health and One Health in the Global South. Structural drivers denote maturing domains of implementation, while emerging issues and weak signals highlight latent, often overlooked opportunities and tensions. Incorporating equity-sensitive and gender-aware foresight methods is essential for crafting inclusive and anticipatory health governance strategies.}, }
@article {pmid41706338, year = {2026}, author = {Semwal, P and Majhi, B and Shivhare, R and Mishra, SK and Misra, S and Chauhan, PS}, title = {Harnessing endophytes and Multi-Omics for sustainable Colchicine biosynthesis.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {3}, pages = {92}, pmid = {41706338}, issn = {1573-0972}, support = {OLP116//CSIR/ ; }, mesh = {*Colchicine/biosynthesis ; *Endophytes/metabolism/genetics ; Metabolic Engineering ; Metabolomics/methods ; Proteomics ; Biosynthetic Pathways ; Metabolic Networks and Pathways ; Multiomics ; }, abstract = {Gloriosa superba, an endangered medicinal plant, serves as the principal natural source of colchicine, a vital alkaloid used for treating gout, arthritis, cancer, and various inflammatory disorders. However, its conventional extraction from plant tissues is constrained by low yield, ecological degradation, and conservation concerns, necessitating sustainable production alternatives. Emerging evidence indicates that colchicine biosynthesis is not solely plant-autonomous but is strongly influenced by endophytic microorganisms that function as active metabolic partners. Endophytic fungi and bacteria associated with G. superba enhance colchicine accumulation through elicitor-mediated signaling, transcriptional reprogramming, metabolic complementation, and modulation of pathway flux. This review presents a systems-level synthesis that integrates endophyte biology with multi-omics technologies and synthetic biology to redefine colchicine biosynthesis as a coordinated plant-microbe metabolic network. Integrated transcriptomic, proteomic, and metabolomic analyses have enabled mechanistic resolution of the colchicine pathway, including identification of key enzymes, regulatory nodes, and bottlenecks such as the cytochrome P450-mediated oxidative ring expansion central to tropolone alkaloid formation. These insights underpin rational metabolic engineering, CRISPR-based genome editing, and synthetic pathway reconstruction in heterologous microbial hosts. By explicitly linking mechanistic understanding with pathway engineering and biomanufacturing design, this review advances a coherent framework for eco-efficient, scalable colchicine production while supporting conservation of G. superba.}, }
@article {pmid41705859, year = {2026}, author = {Medeiros, WB and Centurion, VB and Silva, JB and Duarte, AW and Hidalgo-Martinez, KJ and Dos Santos, JA and Penna, DDPS and Bagci, C and Ziemert, N and Oliveira, VM}, title = {Antarctic soil prokaryotic diversity: a dataset of 319 metagenome-assembled genomes from Deception and Livingston Islands.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0134625}, doi = {10.1128/mra.01346-25}, pmid = {41705859}, issn = {2576-098X}, abstract = {A total of 319 bacterial metagenome-assembled genomes (MAGs) were recovered from soil samples collected on the Antarctic Peninsula (Deception and Livingston Islands). These MAGs reveal microbial life's phylogenetic diversity and functional potential in extreme polar environments, providing resources for advancing microbial ecology, evolution, and Antarctic biotechnology.}, }
@article {pmid41702871, year = {2026}, author = {Wen, M and Ma, X and Chen, J and Wu, J and Wu, F and Ma, R and Peng, R}, title = {Composition, Structure, and Diversity of Rhizosphere Soil Microbial Community in Saffron (Crocus sativus) Affected by Root Bulb Rot.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-07-25-1456-RE}, pmid = {41702871}, issn = {0191-2917}, abstract = {Fusarium oxysporum, first identified in Yunnan Province as the causal agent of saffron corm rot, causes a destructive soil-borne disease that has become a devastating threat to saffron cultivation in Shangri-La, causing over 50% mortality. This pathogen infects saffron corms, leading to vascular browning and rot, ultimately causing plant death and severe production losses. Given the crucial role of the rhizosphere microbiome in plant immunity and soil ecology, deciphering pathogen-microbiome interactions is essential for developing sustainable disease-control strategies. High-throughput sequencing of ITS/16S rRNA (Illumina MiSeq) was combined with arbuscular mycorrhizal fungi (AMF) analysis to compare the community structures of fungi, bacteria, and AMF in the rhizosphere of healthy and diseased saffron. The effects of soil physicochemical factors on microbiome assembly were systematically evaluated. The rhizosphere microbiome of diseased plants was significantly dysregulated: (1) pathogen-related taxa (e.g., Lauriomyces) proliferated, while saprotrophic functional taxa (e.g., Mortierella elongata) underwent community restructuring; (2) disease-suppressive taxa (e.g., fususidium) were enriched, while symbiotic mycorrhizal fungi (AMF) essential for nutrient acquisition sharply declined; (3) the soil parameter-microbiome relationship changed under different health conditions:available phosphorus (AP) and available potassium (AK) drove the aggregation of pathogenic soil fungi, while pH/organic matter (OM) dominated the aggregation of healthy soil fungi; (4) Knufia and Phomopsis were important taxa regulating soil ammonia oxidation and plant vitality. Fusarium infection disrupts the rhizosphere balance by inhibiting beneficial symbionts and promoting the colonization of pathogenic or saprotrophic microorganisms, ultimately compromising the innate resistance of saffron. Our findings reveal the rhizosphere ecological mechanism underlying corm rot progression and provide a microbiome informatics framework for the selection of biocontrol agents and rhizosphere engineering. Moreover, the worker safety benefits from the reductions in psychic emanations mandate industry adoption.}, }
@article {pmid41702108, year = {2026}, author = {Ma, D and Yu, Y and Wang, Y and Wang, Q and Lin, Z}, title = {Multi-scale analysis of ecosystem service values and their driving factors based on MGWR: A case study of Yellow River Delta efficient ecological economic zone.}, journal = {Ecotoxicology and environmental safety}, volume = {311}, number = {}, pages = {119886}, doi = {10.1016/j.ecoenv.2026.119886}, pmid = {41702108}, issn = {1090-2414}, abstract = {The Yellow River basin has recently experienced intensified pressures from climate change and anthropogenic activities, causing severe ecological degradation and compromised ecosystem security. Enhanced ecological protection is critically important for maintaining regional equilibrium and sustainable development. The Yellow River Delta High-Efficiency Economic Development Zone was examined to investigate multi-grid-scale ecosystem service value (ESV) spatial patterns and drivers (2005-2020). ESV was first calculated using the equivalent factor method at 3 km, 7 km, and 10 km scales. Spatial distribution characteristics were subsequently revealed through autocorrelation analysis. Finally, spatial heterogeneity induced by natural and socio-economic drivers was analyzed using MGWR local regression coefficients. The results indicate that: (1) During 2005-2020, land-use ESV ranked: water bodies > farmland > grassland > forest > unutilized land > construction land, with eastern high-ESV zones expanding and southern low-ESV areas increasing; (2) Significant positive spatial autocorrelation (Moran's I > 0, Z > 2.58) was observed, weakening with scale. High-high clusters occurred in ecological-economic zones, contrasting low-low clusters in human activity areas, with stable overall patterns despite scale variations; (3) Significant spatial heterogeneity was driven by natural (DEM, slope; p < 0.05) and socio-economic factors, with GDP and population density gaining prominence by 2020; (4) Significant drivers increased dynamically from 9 (2005) to 12 (2020), confirming temporal evolution. This work establishes a scientific foundation for deltaic ecological restoration and informs precision conservation policies, with broader implications for global ecosystem sustainability.}, }
@article {pmid41701933, year = {2026}, author = {MacLellan, A and Takano, K}, title = {Exploring the Cognitive and Behavioral Risks and Maintenance Factors of Hikikomori: Protocol for an Ecological Momentary Assessment Study.}, journal = {JMIR research protocols}, volume = {15}, number = {}, pages = {e81384}, pmid = {41701933}, issn = {1929-0748}, mesh = {Humans ; Adult ; *Ecological Momentary Assessment ; Adolescent ; Young Adult ; Male ; Middle Aged ; Female ; Japan ; *Cognition ; *Social Isolation/psychology ; Internet Addiction Disorder/psychology ; Anxiety/psychology ; Affect ; Depression/psychology ; }, abstract = {BACKGROUND: Hikikomori is a state of social withdrawal first identified in Japan and is gaining interest globally. Classically, hikikomori is described as a state of isolation within one's home, though recent conceptualizations have proposed a continuum of severity. Hikikomori frequently shares symptoms with depression, social anxiety, autism, and schizophrenia, as well as internet and gaming disorders. Clinical case studies and cross-sectional studies suggest that dysfunctional emotion regulation, familial support, and internet behaviors are proposed to contribute to the onset and maintenance of a withdrawn state, though they have not been explored longitudinally.<br><br>OBJECTIVE: This study aims to investigate affective, behavioral, and cognitive correlates of hikikomori symptoms, and how daily mood, social enjoyment, familial support, and internet usage may maintain a socially withdrawn state.<br><br>METHODS: A minimum of 84 participants aged between 18 and 60 years will complete self-report measures of hikikomori symptoms, internet addiction, depression, anxiety, autism, and fear of offending others before participating in 14 days of ecological momentary assessment surveys. Surveys will be delivered 5 times per day from 8 AM to 10 PM, measuring mood, internet behavior, familial relationships, social interaction frequency, anticipatory and consummatory enjoyment, sleep quality, and physical activity. Participants will repeat the self-report measure of hikikomori symptoms postmonitoring period.<br><br>RESULTS: Recruitment began in November 21, 2025. Data collection and analysis are scheduled to be completed by summer 2026, with the results also scheduled to be available by the end of summer 2026. Correlation and multiple regression analyses will investigate whether internet addiction, social anxiety, expressive suppression, fear of offending others, daily mood, internet use, social enjoyment, and familial support predict hikikomori symptoms. Time-lagged network analyses will explore the temporal dynamics of these relationships, and how these differ in those with high and low levels of hikikomori symptoms. Finally, time-lagged logistic regressions will explore which factors predict future social behavior.<br><br>CONCLUSIONS: This study will be the first to investigate currently proposed mechanisms underlying hikikomori, while also exploring the time-varying relationships between affect and social behavior. The results will provide initial evidence for factors that predict hikikomori symptoms, explore candidate mechanisms underlying hikikomori, and identify potential maintenance factors as targets for intervention.}, }
@article {pmid41700573, year = {2026}, author = {Fifield, K and Thomas, R and Dawe-Lane, E and Kusosa, R and O'Connor, E and Cummins, N and Pollak, TA and Wykes, T and Easton, A and Simblett, SK}, title = {COPE-EMBRACE: Coping with stress after encephalitis using real-time assessment.}, journal = {Neuropsychological rehabilitation}, volume = {}, number = {}, pages = {1-35}, doi = {10.1080/09602011.2026.2619548}, pmid = {41700573}, issn = {1464-0694}, abstract = {Encephalitis can cause acquired brain injury due to inflammation, leading to cognitive issues and fatigue, exacerbating daily stress. Knowledge of real-time stress coping mechanisms among people post-encephalitis and how this relates to depression is limited. Ecological momentary assessment (EMA) may address limitations in standardized cross-sectional self-report assessments. This study evaluates the feasibility and acceptability of collecting EMA data on mood and coping. Twenty adults post-encephalitis (12 women, age range 26:67) completed daily and self-initiated EMA for mood and coping over 4 months, and post-study interviews explored acceptability using framework analysis. Average daily compliance rate was 79.3% (range 37.3-97.5%), showing EMA's feasibility, though low self-initiated EMA usage indicated challenges. Linear mixed-effects model revealed significant relationships between coping style and depression levels within individuals and over time. Framework analysis categorized two themes: "Encephalitis experience and its relationship to stress response" and "Experience of EMA: barriers and facilitators'. Qualitative analysis indicated acceptability for the m-Path app and measuring daily mood. Results suggest long-term daily EMA is feasible for collecting mood and coping in adults with encephalitis. However, patient and public involvement should be utilized to establish suitability. Following adaptations, EMA may serve as a psychological intervention targeting stress coping in daily life.}, }
@article {pmid41699677, year = {2026}, author = {Prakofjewa, J and Conte, L and Ludwig, D and Šarka, P and Centorrino, P and Kalle, R and Sõukand, R}, title = {"I know a lot about medicinal plants. I read, I watch, and I search": towards hybrid knowledge systems in the modern era.}, journal = {Journal of ethnobiology and ethnomedicine}, volume = {22}, number = {1}, pages = {14}, pmid = {41699677}, issn = {1746-4269}, support = {grant agreement N&#xb0; 714874//Horizon 2020 Framework Programme/ ; }, mesh = {*Plants, Medicinal ; Humans ; Female ; Male ; Adult ; Middle Aged ; Ethnobotany ; Lithuania ; *Knowledge ; Aged ; *Health Knowledge, Attitudes, Practice ; Medicine, Traditional ; }, abstract = {BACKGROUND: Hybrid knowledge systems are central to community negotiations of environmental, social, and epistemic pressures. In multilingual borderland areas, interactions between local ecological knowledge (LEK), formal, and popular knowledge systems remain underexplored, despite their importance for the persistence and transformation of medicinal plant use today.<br><br>METHODS: We conducted 67 semi-structured interviews and participant observation in 21 rural settlements of the Vilnius region (Lithuania), an area bordering Belarus, focusing on the two largest local groups, Lithuanians (LT) and Poles (PL). Detailed Use Reports (n&#x2009;=&#x2009;1446) on medicinal plant use were coded by the origin of knowledge, classified as local, formal, or popular, and the degree of hybridisation was quantified using the Shannon-Wiener diversity index and hybridisation metrics. Sociodemographic variables (age, gender, education, and multilingualism) were tested for associations with hybridisation using Spearman's &#x3c1; and Student's t-tests.<br><br>RESULTS: A total of 139 medicinal taxa were recorded, of which 68 (49%) were shared between the two groups. Overall, recorded medicinal plant knowledge remained primarily grounded in LEK, sustained through intergenerational transmission. Compared with PL, LT interviewees drew on a broader mix of knowledge-origin domains (H'&#x2009;=&#x2009;0.97 vs 0.52) and combined them more often (HD&#x2009;=&#x2009;0.195 vs 0.059). In total, 39 taxa showed hybrid use, predominantly in the LT group. Hybridisation was negatively associated with age but positively correlated with the number of listed plants and their reported uses, while multilingualism showed a near-significant positive trend.<br><br>CONCLUSIONS: The study suggests that medicinal plant knowledge has evolved here through hybridisation, a process whose consequences are context-dependent, offering opportunities for revitalisation but also a risk of displacement. Dialogic exchanges across families, communities, languages, and media expand people's plant repertoire and strengthen community adaptive capacity. Yet when these exchanges lead to excessive standardisation, they risk eroding the diversity of local traditions. Ethnobotanical research must therefore go beyond documenting popular and formal knowledge sources to interrogate how linguistic and sociopolitical contexts condition the emergence of hybrid knowledge systems, privileging certain forms while rendering others transformed or marginalised.}, }
@article {pmid41698967, year = {2026}, author = {Osada, Y and Miya, M and Araki, H and Doi, H and Kasai, A and Masuda, R and Minamoto, T and Seino, S and Takahara, T and Yamamoto, S and Yamanaka, H and Aizu-Hirano, M and Fukaya, K and Fukuchi, T and Gotoh, RO and Hori, M and Iida, M and Imaizumi, T and Kajita, T and Kanbe, T and Kenta, T and Kobayashi, Y and Matsuura, T and Mizumoto, H and Motomura, H and Murakami, H and Nohara, K and Oka, SI and Sado, T and Senou, H and Shibukawa, K and Sunobe, T and Takahashi, H and Takayama, K and Tanaka, K and Yamakawa, H and Yokoyama, S and Yoon, S and Kondoh, M}, title = {Large-scale environmental DNA survey reveals niche axes of a regional coastal fish community.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {3276}, pmid = {41698967}, issn = {2045-2322}, support = {19H05641//JSPS KAKENHI Grants/ ; 20H03311//JSPS KAKENHI Grants/ ; JPMJCR13A2//JSPS CREST program/ ; }, mesh = {Animals ; *Fishes/genetics ; Biodiversity ; *Ecosystem ; *DNA, Environmental/analysis/genetics ; Japan ; }, abstract = {The concept of the ecological niche, defined as the basic habitat requirements for a species, is central to understanding species geographic distributions and predicting their responses to environmental change. However, identifying the essential niche for large regional communities remains a challenge because niche axes can be "hidden" by the complexity of the underlying ecological processes. Here, applying advanced species distribution modelling to nationwide environmental DNA survey data, we identified hidden niche axes of the Japanese coastal fish community and investigated the response diversity to these axes. Our survey detected 1,220 coastal fish species. The hidden niche axes collectively explained most of the variation in fish biodiversity and revealed five biogeographic boundaries for the regional community. These niches of the Japanese fish community may primarily relate to several processes due to ocean currents, such as environmental filters, transport from source areas and dispersal barriers. We also found that the response diversity to niche axes was positively correlated with species richness, although local communities with particularly high response diversity were geographically biased. A better understanding of the niche axes of the regional ecological community should help to mitigate the loss of biodiversity and ecosystem services caused by ongoing environmental change.}, }
@article {pmid41695296, year = {2025}, author = {Crowley, LM and Barclay, MVL and Smith, MN and Brown, PMJ and Roy, HE and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the 24-spot ladybird, Subcoccinella vigintiquattuorpunctata (Linnaeus, 1758) (Coleoptera: Coccinellidae).}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {698}, pmid = {41695296}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Subcoccinella vigintiquattuorpunctata (24-spot ladybird; Arthropoda; Insecta; Coleoptera; Coccinellidae). The genome sequence has a total length of 532.03 megabases. Most of the assembly (97.41%) is scaffolded into 15 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled, with a length of 18.91 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.}, }
@article {pmid41690269, year = {2026}, author = {Paton, L and Kiesel, S and Elinkmann, M and Clases, D and Fernandez-Mendoza, F and Feldmann, J}, title = {The formation of bioavailable Hg in a pipeline: An initial investigation into Hg bioaccumulation resulting from oil and gas decommissioning.}, journal = {The Science of the total environment}, volume = {1019}, number = {}, pages = {181526}, doi = {10.1016/j.scitotenv.2026.181526}, pmid = {41690269}, issn = {1879-1026}, abstract = {Mercury (Hg) released during offshore pipeline decommissioning may pose ecological risks, yet little is known about its chemical form and biological impact. We examined how Hg[0] can react on and subsequently be released from laboratory-generated steel pipeline material to interact with marine algae, focusing on chemical speciation, transformation, and cellular uptake. Laboratory exposures of the marine algae, Isochrysis galbana, to pipeline-derived Hg showed accumulation up to 109 mg kg[-1] dry weight, as determined by cold vapour atomic fluorescence spectrometry (CV-AFS). Single-cell inductively coupled plasma mass spectrometry (SC ICP-MS) confirmed substantial cell-associated Hg, with bimodal distributions suggesting distinct uptake or surface-association pathways. Although classical growth and photosynthetic parameters did not consistently reveal toxicity, Hg exposure altered cell populations and aggregation behaviour, indicating sublethal but ecologically relevant effects. Our findings demonstrate that through interactions with pipeline material Hg[0] can be transformed into species which have an increased likelihood of bioaccumulation.}, }
@article {pmid41687859, year = {2026}, author = {Spagnesi, A and Gilardoni, S and Salzano, R and Feltracco, M and Ulgelmo, B and Maetzke, R and Ardini, F and Grotti, M and Coppolaro, VLM and Viglezio, T and Montaguti, S and Scoto, F and Spolaor, A and Gambaro, A and Barbante, C and Barbaro, E}, title = {Emerging contaminants during arctic rain-on-snow events: A case study from the 2023-24 Ny-Ålesund campaign.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {395}, number = {}, pages = {127790}, doi = {10.1016/j.envpol.2026.127790}, pmid = {41687859}, issn = {1873-6424}, abstract = {The Svalbard Archipelago has undergone rapid warming in recent decades, increasing the frequency and intensity of Rain-on-Snow (ROS) events. While the physical and ecological consequences of ROS in the Arctic have been extensively documented, their role in modulating the atmospheric fate of emerging contaminants remains poorly understood. This study investigates the chemical signature of four ROS events during the 2023-24 field campaign in Ny-Ålesund (Kongsfjorden, Svalbard, Norway), focusing on the behaviour of emerging pollutants across pre-, during-, and post-event phases. By combining aerosol and wet deposition data with meteorological variables and air mass back-trajectories, we explore the potential of ROS to act as removal mechanisms for benzothiazole derivatives, tris(2-carboxyethyl) phosphine (TCEP) as flame retardant, pesticides, and haloacetic acids. The results highlight a substantial variability in contaminant patterns across events and suggest the influence of synoptic-scale air mass origin and local meteorological conditions. Diagnostic ratios and inorganic ion proxies provide insight into possible atmospheric transformation pathways and transport processes. This study provides the first detailed chemical characterisation of aerosol and depositions during Rain-On-Snow events, establishing a preliminary framework to better understand the complex interactions between ROS and contaminant cycling in a warming Arctic. This work contributes to ongoing efforts to clarify the mechanisms of atmospheric scavenging under changing climate conditions.}, }
@article {pmid41686497, year = {2026}, author = {Wu, Z and Liu, Y and Zhu, M and Zeng, J and Labat, D and Meng, F}, title = {SWAT-WASP coupled modeling of ammonia nitrogen in rare earth mining watersheds.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {93}, number = {3}, pages = {273-295}, pmid = {41686497}, issn = {0273-1223}, support = {41861002//National Natural Science Foundation of China/ ; 2022A15150112010//Natural Science Foundation of Guangdong Province/ ; //2023 Annual Guangdong Provincial Higher Education Teaching Reform Project/ ; }, mesh = {*Mining ; *Nitrogen/analysis ; *Metals, Rare Earth ; *Ammonia/analysis ; *Water Pollutants, Chemical ; *Environmental Monitoring/methods ; China ; Rivers/chemistry ; Models, Theoretical ; }, abstract = {High concentrations of ammonia nitrogen (NH4[+]-N) are a dominant water pollutant in ionic rare earth mining basins, threatening aquatic ecosystems and drinking-water safety. To quantify these dynamics, this study developed a coupled SWAT-WASP model for the upper Dongjiang River Basin (UDRB), integrating remote sensing and long-term monitoring data; the model was calibrated and validated with 2016-2018 monthly observations, and quantitative evaluation via Nash-Sutcliffe Efficiency (NSE) and Percent Bias (PBIAS) showed good performance (runoff: NSE = 0.77-0.80; NH4[+]-N: SWAT NSE = 0.56-0.61, SWAT-WASP NSE = 0.65-0.87), confirming its reliability. 2022 simulations revealed strong NH4[+]-N spatial heterogeneity, with concentrations >1.8 mg L[-1] near mining zones versus <0.5 mg L[-1] in upstream natural areas; geodetector analysis identified population density combined with industrial-agricultural activity as the top driver of spatial differentiation (q > 0.40), while interactions between precipitation, temperature, and land use further amplified variability. Overall, the SWAT-WASP framework provides a robust tool for evaluating NH4[+]-N dynamics and supports targeted pollution control and ecological restoration in rare earth mining watersheds.}, }
@article {pmid41683863, year = {2026}, author = {Ren, S and Lv, G}, title = {A Transcriptome Study on Seed Germination of Nitraria roborowskii Kom.}, journal = {International journal of molecular sciences}, volume = {27}, number = {3}, pages = {}, pmid = {41683863}, issn = {1422-0067}, mesh = {*Germination/genetics ; Gene Expression Regulation, Plant ; *Transcriptome ; *Seeds/genetics/growth &amp; development ; Gene Expression Profiling ; Plant Dormancy/genetics ; Gene Ontology ; Computational Biology/methods ; Plant Proteins/genetics ; Molecular Sequence Annotation ; }, abstract = {Nitraria roborowskii Kom. seeds possess pronounced deep dormancy traits. Analyzing changes in gene expression before and after dormancy release is of great significance for elucidating the mechanisms underlying seed dormancy. In this study, transcriptome sequencing and bioinformatics analysis were conducted on N. roborowskii seeds both before and after dormancy release using high-throughput Illumina NovaSeq 6000 sequencing technology. The key findings are as follows: (1) A total of 215,303 transcripts and 84,450 unigenes were obtained through de novo assembly. (2) Comparative analysis revealed 16,130 significantly differentially expressed unigenes during germination, with 10,776 upregulated and 5354 downregulated. Gene Ontology (GO) enrichment analysis indicated that these differentially expressed genes (DEGs) were primarily associated with biological processes and molecular functions, mainly involved in metabolic processes and catalytic activities. (3) Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that the DEGs were predominantly enriched in pathways such as plant hormone signal transduction and starch and sucrose metabolism. Specifically, among the downregulated genes, 126 were linked to plant hormone signal transduction, 110 to phenylpropanoid biosynthesis, 108 to starch and sucrose metabolism, 27 to flavonoid biosynthesis, 20 to plant hormone signal transduction, 6 to phenylpropanoid metabolism, 14 to starch and sucrose metabolism, and none to flavonoid biosynthesis.}, }
@article {pmid41683590, year = {2026}, author = {Li, F and Jin, W and Cheng, H and Wu, F and Pan, Y and Zhu, D and Xu, S and Zhou, C and Zhang, B and Chakraborty, A and Roy, A and He, S}, title = {Transcriptomic Responses of Sclerodermus alternatusi Yang to Ultraviolet (UV) Stress of Different Wavelengths.}, journal = {International journal of molecular sciences}, volume = {27}, number = {3}, pages = {}, pmid = {41683590}, issn = {1422-0067}, support = {CSTB2025NSCQ-GPX0267//the Natural Science Foundation Project of Chongqing/ ; CSTB2024NSCQ-MSX0676//the Natural Science Foundation Project of Chongqing/ ; }, mesh = {Animals ; *Ultraviolet Rays/adverse effects ; *Transcriptome/radiation effects ; *Stress, Physiological/radiation effects/genetics ; Gene Expression Profiling ; *Wasps/genetics/radiation effects ; Gene Ontology ; }, abstract = {Ultraviolet (UV) radiation is a significant environmental stressor that exerts profound impacts on insect physiology, behaviour and survival. Although some insects can use UV light for spatial orientation and navigation, it can induce DNA damage, oxidative stress, and impair critical biological functions, ultimately reducing ecological fitness. Sclerodermus alternatusi Yang (Hymenoptera: Bethylidae) is a dominant ectoparasitoid of the early instar larvae of Monochamus alternatus and plays a key role in the biological control of this pest in forestry systems; however, it faces intense UV exposure in the field environment. Despite its ecological importance, the molecular mechanisms underlying its responses to UV-induced stress remain poorly understood. In this study, newly emerged adult wasps (within 24 h post-eclosion) were exposed to UVA (365 nm) and UVC (253.7 nm) radiation for 9 h under controlled laboratory conditions. Total RNA was extracted from treated and control individuals for transcriptomic analysis using RNA-Seq. A total of 505 differentially expressed genes (DEGs) were identified; gene ontology enrichment analysis revealed that UVA exposure significantly upregulated genes involved in cellular respiration and oxidative phosphorylation, suggesting an enhanced metabolic response. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that UV stress modulates energy metabolism through the activation of oxidative phosphorylation and thermogenesis-related pathways, highlighting the reallocation of energy resources in response to UV-induced stress. To validate the RNA-Seq data, four representative DEGs were selected for quantitative real-time PCR (RT-qPCR) analysis. The qPCR results were consistent with the transcriptomic trends, confirming the reliability of the sequencing data. Collectively, this study provides a comprehensive overview of the molecular response mechanisms of S. alternatusi to UV stress, offering novel insights into its environmental adaptability and laying a theoretical foundation for its application in biological pest control under field conditions.}, }
@article {pmid41683461, year = {2026}, author = {Chen, H and Li, Y and Chen, Q and Chen, C and Hu, Y}, title = {Methodologies for Assessing Chemical Toxicity to Aquatic Microorganisms: A Comparative Review.}, journal = {Molecules (Basel, Switzerland)}, volume = {31}, number = {3}, pages = {}, pmid = {41683461}, issn = {1420-3049}, mesh = {*Aquatic Organisms/drug effects ; Microalgae/drug effects ; Bacteria/drug effects ; *Toxicity Tests/methods ; *Water Pollutants, Chemical/toxicity ; Fungi/drug effects ; Viruses/drug effects ; }, abstract = {Aquatic ecological issues have garnered significant attention in recent years, driving the demand for convenient, effective, and systematic assessment methods in environmental risk evaluation. This review provides a comprehensive introduction to methodologies for assessing the toxicity of chemicals toward aquatic microorganisms, which include viruses, bacteria, fungi, protozoa, and algae. Among these, microalgae are commonly used as model organisms due to their relative simplicity. The article details conventional biological methods, general chemical techniques, modern instrumental analyses, and informatics approaches, with a particular focus on algae and bacteria as model organisms for toxicity assessment. The principles, advantages, and limitations of each method are discussed, along with examples of their application in various contexts. Biological methods offer direct visualization, convenience, and rapid results, while modern instrumental techniques enable mechanistic insights at molecular and biochemical levels. Informatics methods facilitate toxicity evaluation in complex systems. While aquatic microorganisms encompass viruses, fungi, protozoa, bacteria, and algae, this review primarily focuses on bacteria and algae as model organisms due to their ecological relevance, sensitivity, and widespread use in standardized assays.}, }
@article {pmid41683185, year = {2026}, author = {Song, D and Song, L and Zhong, X and Wu, Y and Zhang, Y and Yang, L}, title = {Integrated Molecular Informatics and Sensory-Omics Study of Core Trace Components and Microbial Communities in Sauce-Aroma High-Temperature Daqu from Chishui River Basin.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, pmid = {41683185}, issn = {2304-8158}, support = {MTXYTD202501//Science and Technology Innovation Team of Moutai Institute/ ; QianKeHeJiChu-ZD[2025]018//Guizhou Provincial Basic Research Program (Natural Science)/ ; ZunShiKeHe HZ Zi[2023]112//The Fund of Zunyi Technology and Big data Bureau, Moutai Institute Joint Science and Technology Research and Development Project/ ; mygccrc[2022]011, mygccrc[2022]013//Research Foundation for Scientific Scholars of Moutai Institute/ ; XYNJ20240104//Moutai Institute &amp; Guangdong Li'er'an Chemical Industry Group Co., Ltd/ ; }, abstract = {Flavor-relevant trace volatiles and microbial communities were examined in six sauce-aroma high-temperature Daqu samples. Headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME-GC-MS) quantified 210 trace volatile compounds across 14 chemical classes. Orthogonal partial least squares discriminant analysis (OPLS-DA) with variable importance in projection (VIP) screening was integrated with sensory scoring, correlation analysis, and molecular docking to an olfactory receptor model. Volatile profiles showed clear stratification in total abundance. Pyrazines dominated the high-total group. Tetramethylpyrazine served as a major driver. Sensory evaluation indicated that aroma explained overall quality best. (E)-2-pentenal and dimethyl trisulfide showed significant positive associations with aroma and overall scores. In the olfactory receptor, the polar residue module that provides directional constraints for Daqu odor activation was formed by Ser75, Ser92, Ser152, Ser258, Thr74, Thr76, Thr98, Thr200, Gln99, and Glu94. The hydrogen-bond or charge network was further reinforced by Arg150, Arg262, Asn194, His180, His261, Asp182, and Gln181. The core discriminant set comprised acetic acid, hexanoic acid, (E)-2-pentenal, nonanal, decanal, dimethyl trisulfide, trans-3-methyl-2-n-propylthiophane, 2-hexanone oxime, ethyl linoleate, propylene glycol, 2-ethenyl-6-methylpyrazine, 4-methylquinazoline, 5-methyl-2-phenyl-2-hexenal, and 1,2,3,4-tetramethoxybenzene. Sequencing revealed higher bacterial diversity than fungal. Bacillus and Kroppenstedtia were dominant bacterial genera. Aspergillus, Paecilomyces, Monascus, and Penicillium were major fungal genera. Correlation patterns suggested that Bacillus and Monascus were positively linked to acetic acid and 1,2,3,4-tetramethoxybenzene. Together, these results connected chemical fingerprints, sensory performance, receptor-level plausibility, and microbial ecology. Concrete targets are provided for quality control of high-temperature Daqu.}, }
@article {pmid41682587, year = {2026}, author = {Sandeep, A and Jayarathna, S and Sandaruwan, S and Samarappuli, V and Meedeniya, D and Perera, C}, title = {Context-Aware Multi-Agent Architecture for Wildfire Insights.}, journal = {Sensors (Basel, Switzerland)}, volume = {26}, number = {3}, pages = {}, pmid = {41682587}, issn = {1424-8220}, abstract = {Wildfires are environmental hazards with severe ecological, social, and economic impacts. Wildfires devastate ecosystems, communities, and economies worldwide, with rising frequency and intensity driven by climate change, human activity, and environmental shifts. Analyzing wildfire insights such as detection, predictive patterns, and risk assessment enables proactive response and long-term prevention. However, most of the existing approaches have been focused on isolated processing of data, making it challenging to orchestrate cross-modal reasoning and transparency. This study proposed a novel orchestrator-based multi-agent system (MAS), with the aim of transforming multimodal environmental data into actionable intelligence for decision making. We designed a framework to utilize Large Multimodal Models (LMMs) augmented by structured prompt engineering and specialized Retrieval-Augmented Generation (RAG) pipelines to enable transparent and context-aware reasoning, providing a cutting-edge Visual Question Answering (VQA) system. It ingests diverse inputs like satellite imagery, sensor readings, weather data, and ground footage and then answers user queries. Validated by several public datasets, the system achieved a precision of 0.797 and an F1-score of 0.736. Thus, powered by Agentic AI, the proposed, human-centric solution for wildfire management, empowers firefighters, governments, and researchers to mitigate threats effectively.}, }
@article {pmid41678735, year = {2026}, author = {Jjingo, D and Walakira, A and Hashim, S and Cheickna, C and Galiwango, R and Kibet, C and Kivunike, FN and Mboowa, G and Kakembo, FE and Ayodele, B and Entfellner, JD and de Villiers, S and Wambui, K and Fatumo, S and Chikowore, T and Mukisa, J and Ssekagiri, A and Bbosa, N and Mulindwa, J and Kyobe, S and Nsubuga, M and Kebirungi, G and Katagirya, E and Mwesigwa, S and Lujumba, I and Kamulegeya, R and Kirimunda, S and Kanyerezi, S and Kiyaga, S and Sserwadda, I and Kiberu, D and Bagaya, BS and Okwir, J and Nabisubi, P and Nabakooza, G and Atwine, MT and Sserunjogi, R and Julius, R and Quiñones, M and McCarthy, M and Cruz, P and Noble, K and Whalen, CJ and Hurt, D and Giovanni, MY and Tartakovsky, M and Ssemwanga, D and Kitayimbwa, JM and Reynolds, SJ and Whalen, CC and Kambugu, A and Hanchard, NA and Jian, L and Amoako-Yirenkyi, P and Mardon, G and Jordan, IK and Salifu, SP and Wele, M and Adebiyi, E and Shaffer, JG and Doumbia, S and Kateete, DP and Skelton, M and Mulder, N and Kayondo, JK and Masiga, D and , }, title = {Pathways, outputs and impact of NIH-supported bioinformatics and genomics graduate trainees in Africa.}, journal = {Briefings in bioinformatics}, volume = {27}, number = {1}, pages = {}, pmid = {41678735}, issn = {1477-4054}, mesh = {*Computational Biology/education ; *Genomics/education ; United States ; Africa ; Humans ; *National Institutes of Health (U.S.) ; *Education, Graduate ; Biomedical Research ; }, abstract = {Global biomedical and health research is increasingly relying on genomic and computational approaches, largely driven by the increasing volumes of nucleic acid sequencing. Concurrently, epidemiological studies and clinical records are generating enormous amounts of data amenable to disease modeling, machine learning, and artificial intelligence techniques. Bioinformatics and data science expertise is therefore essential for improved population health. Accordingly, in 2012, the US National Institutes of Health (NIH) in partnership with the Wellcome Trust, and with support from the African Society for Human Genetics, initiated the H3Africa (Human Heredity and Health in Africa) consortium. One of its key goals was to build capacity among African scientists to lead research on genetic and environmental contributors to health and disease across the continent. In 2017, the NIH provided funding to support the establishment of four graduate bioinformatics training programs across five African universities. Over seven years, these programs enrolled multiple trainees (n > 270), with >110 earning Master's degrees and >20 completing PhDs in Bioinformatics. It is thus timely to evaluate the outcomes and impact of these programs, particularly regarding graduation rates, career trajectories, and the institutions and research domains their alumni are serving. We also assess employment outcomes and the nature of the research they are enabling (n > 110 peer-reviewed articles). We additionally include the progress and outputs of the programs' instructors, which were partially enabled by program resources, networks, and trainees. Overall, this review paints valuable insights into the pioneering role of NIH extramural support in shaping Africa's biomedical research landscape.}, }
@article {pmid41678582, year = {2026}, author = {Cleanclay, WD and Kernyuy, FB and Kintung, IF and Yensii, NG and Chick, JA and Obi, AMM}, title = {Evaluating paratransgenesis using engineered symbiotic bacteria for Plasmodium inhibition in mosquito vectors: A systematic review.}, journal = {PLoS neglected tropical diseases}, volume = {20}, number = {2}, pages = {e0013654}, pmid = {41678582}, issn = {1935-2735}, mesh = {Animals ; *Mosquito Vectors/parasitology/microbiology ; *Anopheles/parasitology/microbiology ; *Symbiosis ; *Bacteria/genetics/metabolism ; *Malaria/prevention &amp; control/transmission ; Mosquito Control/methods ; Plasmodium falciparum/drug effects ; *Plasmodium ; }, abstract = {Malaria is a significant health problem in the world and has been increased by the emerging resistance to insecticides and antimalarial drugs. New measures must therefore be implemented as an emergency to break the cycle of Plasmodium parasite transmission by the Anopheles mosquitoes. This systematic review assessed the effectiveness of paratransgenesis, an engineering approach that utilizes symbiotic microbes to deliver antiplasmodial molecules into the midgut of the mosquito as a transmission-blocking agent. PubMed, ScienceDirect, and Web of Science were searched in accordance with the PRISMA guidelines, yielding 1,289 records. Ten eligible studies were then included after screening. The chosen articles studied bacterial and fungal symbionts, such as Asaia, Serratia, Pantoea, Enterobacter, and Aspergillus oryzae, that have been engineered to produce effector proteins, such as Scorpine, EPIP, Defensin, and SM1-2 peptides. The delivery of oral sugar meals was always associated with colonization of the mosquito midguts, and results reported high levels of inhibition of oocysts or sporozoites in the mosquitoes. Scorpine was the strongest and most commonly used effector with a high level of up to 97.8% inhibition of P. falciparum oocysts in various microbial systems. The combination of two or multiple-effector approaches increased the efficacy in some cases, surpassing 89% parasite inhibition. The risk of bias measurement showed moderate variation in the methods, yet it was in favor of the sound findings. All evidence suggests that paratransgenesis is a potentially important malaria control tool, complementing existing approaches to malaria control. Nevertheless, ecological safety, microbial stability, and field validation are the key obstacles before the translation to large-scale use.}, }
@article {pmid41678209, year = {2026}, author = {Colnaghi, M and Santos, FP and Van Lange, PAM and Balliet, D}, title = {The ecological origins of collectivism and individualism.}, journal = {Psychological review}, volume = {}, number = {}, pages = {}, doi = {10.1037/rev0000610}, pmid = {41678209}, issn = {1939-1471}, support = {//European Research Council; Horizon Europe/ ; }, abstract = {Interdependent subsistence styles, such as rice farming, are thought to underlie the evolution of collectivistic cultures, which emphasize collective welfare over individual gains. Rice farming can produce mutual dependence within communities but also create conflicting interests, as people cooperate to provide valuable public goods. However, current theories of the origins of collectivism fail to address the interplay between mutual dependence and conflict. As a consequence of these limitations, the evolutionary dynamics of collectivism and its association with cooperation are still unclear. We advance a theoretical model to study the evolution of cultural traits that enhance people's valuations of collective welfare, one of the key features of collectivistic cultures. Our model investigates the evolutionary dynamics of cooperation and cultural evolution in ecologies with distinct interdependence structures. We find evidence that higher degrees of mutual dependence facilitate the evolution and persistence of collectivism. However, the degree of conflicting interests also plays a crucial role in driving the diffusion and maintenance of collectivistic norms. In particular, the selective advantage of collectivism is strongest when people experience some degree of conflict of interests, an effect that is magnified by heightened mutual dependence. These results clarify how variation in interdependence could underlie the ecological origins of collectivism, lending support to and expanding the scope of current theories of the cultural evolution of cooperation. More broadly, the framework presented here elucidates how fitness interdependence can be influenced by different ecological factors, and, in turn, influence the evolution of social behaviors. (PsycInfo Database Record (c) 2026 APA, all rights reserved).}, }
@article {pmid41676438, year = {2025}, author = {Liu, Y and Ise, Y and Takami, H and Urakawa, R and Tateno, R and Toyoda, A and Ohte, N and Shi, W and Jiang, L and Isobe, K}, title = {Soil pH modulates microbial nitrogen allocation in soil via compositional and metabolic shifts across forests in Japan.}, journal = {iMetaOmics}, volume = {2}, number = {4}, pages = {e70054}, pmid = {41676438}, issn = {2996-9514}, abstract = {Ammonium release (ammonification) and uptake (immobilization) by soil microbial communities are fundamental processes of forest nitrogen (N) cycling, representing major N fluxes that influence plant productivity and ecosystem N retention. However, because these processes involve diverse metabolic pathways distributed across many taxa, they are difficult to evaluate using gene- or taxon-specific approaches, and it remains unclear how microbial community structure governs the patterns of these processes. In this study, we examined how the abundance, taxonomic composition, richness, and metabolic capabilities of microbial communities regulate ammonium-related N cycling processes across a wide range of forests in Japan, using rRNA gene sequencing and quantification, shotgun metagenomics, and [[15]]N tracer assays. Across the full gradients of soil pH and N content, microbial abundance was primarily correlated with the absolute rates of N cycling processes, while taxonomic composition and richness were more strongly correlated with N allocation-that is, the balance among ammonium release, ammonium uptake, and subsequent nitrification. Soils with higher pH supported taxonomic compositions linked to enhanced ammonium release and nitrification, whereas lower-pH soils hosted compositions associated with greater ammonium uptake and retention. Notably, the regulatory influence of taxonomic composition on N allocation was pronounced within the higher-pH range but diminished within the lower-pH range. Despite this environmental dependency, N allocation by soil microbial communities was ultimately constrained by their overall metabolic capabilities. In higher-pH soils, microbial communities were enriched in metabolic functions related to nutrient acquisition and respiratory N transformations, supporting increased ammonium release and N mobility. By contrast, microbial communities in lower-pH soils were enriched in stress-adaptive functions, which promoted ammonium retention and limited N transformations-thereby diminishing the regulatory influence in N cycling. Together, our findings provide a mechanistic understanding of how microbial community structure and metabolic capabilities regulate ammonium-related N cycling processes across forests under varying environmental conditions.}, }
@article {pmid41671148, year = {2026}, author = {Buczek, DJ and Kabir, W and Lindstedt, K and Mäklin, T and Thorpe, HA and Suzuki, Y and Corander, J and Samuelsen, &#xd8; and Sundsfjord, A}, title = {Sequence type and strain-level detection of Klebsiella pneumoniae in culture-enriched bacterial metagenomes: comparative performance of mSWEEP and StrainGE bioinformatic tools.}, journal = {Microbial genomics}, volume = {12}, number = {2}, pages = {}, pmid = {41671148}, issn = {2057-5858}, mesh = {*Klebsiella pneumoniae/genetics/classification/isolation &amp; purification ; *Computational Biology/methods ; *Metagenome ; Humans ; Whole Genome Sequencing ; Phylogeny ; Klebsiella Infections/microbiology ; Genome, Bacterial ; }, abstract = {Klebsiella pneumoniae is a major cause of human infections and is frequently associated with antimicrobial resistance (AMR). Carriage of K. pneumoniae in the gut is a major risk factor for infection and a reservoir for the spread of high-risk clonal lineages and associated AMR determinants. Accurate detection of K. pneumoniae at the subspecies level is therefore essential to better understand K. pneumoniae gut colonization ecology and clonal dissemination. We analysed two recently developed bioinformatic tools, mSWEEP and StrainGE, for sequence type (ST) detection of K. pneumoniae in culture-enriched sweep metagenomes compared to single-colony whole-genome sequencing (WGS). We show that both mSWEEP and StrainGE perform highly accurate ST detection, concordant with culture in 46/49 and 44/49 samples with WGS-detected single STs, respectively, as well as in 2/3 samples with two WGS-detected STs. Within-sample ST diversity was detected in 19 and 15 samples by mSWEEP and StrainGE, respectively, highlighting a major advantage of these tools over conventional single-colony WGS. StrainGE could also reconstruct accurate phylogenetic relationships between strains of the same ST for 2/3 different STs tested. Additionally, assembly of the genomes provides better resolution of ST detection by mSWEEP. Together, our results show that both mSWEEP and StrainGE are accurate tools for the detection and analysis of K. pneumoniae STs from mixed bacterial samples.}, }
@article {pmid41669161, year = {2026}, author = {Akre-Bhide, S and Cohen, ZD and Welborn, A and Zbozinek, TD and Craske, MG and Bui, A}, title = {Detecting momentary reward and affect with real-time passive digital sensor data.}, journal = {JAMIA open}, volume = {9}, number = {1}, pages = {ooag005}, pmid = {41669161}, issn = {2574-2531}, abstract = {OBJECTIVES: This study explores the capability of passive digital sensor data from smartphones and smartwatches to predict self-reported ecological momentary assessments (EMA) of affect, motivation, interest, and pleasure in activities in an unseen test sample.<br><br>MATERIALS AND METHODS: Data were collected from 245 depressed participants with high-to-low anhedonia (195 train, 50 test) generating 23 812 EMA sessions. Machine learning models were used to assess the ability of behavioral and physiological features, aggregated over windows of 15 minutes to 3 hours, to predict momentary subjective states.<br><br>RESULTS: For 12 of 15 EMA questions asked, machine learning models exceeded random chance in the fully-held-out test sample, suggesting detectable signals between passive measures and subjective states. Dependent on the sensor type, the optimal aggregation periods ranged from 15 minutes to 3 hours, with generally at least two hours of data being required. Subgroup analyses revealed variations in model performance by demographics, depression severity, and anhedonia severity.<br><br>CONCLUSION: This study establishes the feasibility of using passive digital sensing to detect momentary subjective states, providing a baseline for scalable, non-invasive mental health monitoring.}, }
@article {pmid41668731, year = {2025}, author = {Gao, H and Li, J and Liu, L and Gu, Z and Yu, H and Xing, D and Zhao, T and Li, C}, title = {Multi-omics profiling reveals associations between gut microbiota and olfactory gene expression in mosquitoes.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1745848}, pmid = {41668731}, issn = {2235-2988}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; *Culex/microbiology/genetics/physiology ; Metagenomics ; *Smell/genetics ; Gene Expression Profiling ; Arthropod Antennae/metabolism ; Transcriptome ; Computational Biology ; Multiomics ; }, abstract = {INTRODUCTION: The interplay between gut microbiota and host physiological processes has been extensively studied in vertebrates, where it plays a crucial role in regulating appetite, emotion, immunity, and other physiological functions. However, whether a similar regulatory mechanism exists in insects remains unclear, especially regarding the long-distance regulation of olfactory function. This study focused on three Culex subspecies (Culex quinquefasciatus, Culex pipiens pallens, and Culex pipiens molestus) that are closely related but exhibit significant differences in olfaction-dependent ecological habits. By integrating antennal transcriptomic and gut metagenomic data, we systematically analyzed the expression characteristics of olfactory-related genes, the structure of gut microbial communities, and their intrinsic associations.<br><br>METHODS: We integrated antennal transcriptomic and gut metagenomic sequencing to analyze olfactory-related gene expression, gut microbial community structure, and their intrinsic associations in male and female individuals of the three Culex subspecies. Bioinformatics analyses included differential gene screening, functional enrichment, microbial taxonomic annotation, and Spearman correlation analysis.<br><br>RESULT: The results showed that a large number of sex-specific and species-specific differentially expressed genes (DEGs) were identified in the antennae of the three Culex subspecies. Among these, 345 DEGs were shared sex-specific genes across species, which were significantly enriched in pathways such as odor binding, signal transduction, and xenobiotic metabolism. At the phylum level, the&#xa0;gut microbial composition was dominated by Proteobacteria, Bacteroidetes, and Firmicutes, showing a conserved structure; at the genus level, 11 dominant&#xa0;genera (including Wolbachia, Elizabethkingia, and Asaia) exhibited distinct species-specific distribution patterns. Diversity analysis revealed that&#xa0;the gut&#xa0;microbial richness of male individuals was significantly higher than that of&#xa0;females, and the &#x3b2;-diversity showed an obvious "sex clustering" pattern.Correlation analysis further indicated that 152 DEGs were significantly correlated with 107 microbial genera. Among them, olfactory-related genes were closely associated with several core genera (e.g., Wolbachia, Asaia, Serratia). Gut microbes may remotely regulate the expression and function of&#xa0;olfactory genes in antennae through metabolites or signaling molecules, thereby influencing mosquito behaviors such as host localization, mating, and oviposition.<br><br>DISCUSSION: This study reveal the intrinsic association between gut microbes and olfactory function in Culex mosquitoes, providing a new perspective for understanding the "microbe-host" cross-organ regulatory mechanism and laying a theoretical foundation for the development of novel mosquito vector control strategies based on microbial or olfactory interference.}, }
@article {pmid41667953, year = {2026}, author = {Guccione, C and Sfiligoi, I and Gonzalez, A and Shaffer, JP and Kazachkova, M and Weng, Y and McDonald, D and Shah, SC and Minot, SS and Paulson, TG and Grady, WM and Alexandrov, LB and Knight, R and Curtius, K}, title = {Community assembly modeling of the microbiome within Barrett's esophagus and esophageal adenocarcinoma.}, journal = {BMC genomics}, volume = {27}, number = {1}, pages = {}, pmid = {41667953}, issn = {1471-2164}, support = {R01 CA270235/NH/NIH HHS/United States ; 5K12GM068524-17/NH/NIH HHS/United States ; P30 CA023100/NH/NIH HHS/United States ; RG103468//University of California, San Diego/ ; 2019-67013-29137//National Institute of Food and Agriculture/ ; ICX002027A//U.S. Department of Veterans Affairs/ ; AGA2022-13-05//AGA Research Foundation/ ; P30 DK120515/DK/NIDDK NIH HHS/United States ; R01 CA270235/NH/NIH HHS/United States ; 5K12GM068524-17/NH/NIH HHS/United States ; P30 CA023100/NH/NIH HHS/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; }, abstract = {UNLABELLED: Computational modeling of somatic evolution, a process shaped by ecology and impacting both host cells and microbial communities in the human body, can capture important dynamics driving carcinogenesis. Here we considered models for esophageal adenocarcinoma (EAC), a cancer that has dramatically increased in incidence over the past few decades in Western populations, with high case fatality rates due to late-stage diagnoses. Despite advancements in genomic analyses of the precursor Barrett’s esophagus (BE), prevention of late-stage EAC remains a significant clinical challenge. Previous microbiome studies in BE/EAC have focused on quantifying static microbial abundance differences rather than determining population dynamics. Using whole genome sequencing data from a total of 505 esophageal samples, we first applied a robust bioinformatics pipeline to extract non-host DNA reads, mapped these putative reads to microbial taxa, and retained those taxa with high genomic coverage. When applying mathematical models of demographic stochasticity to sequential stages of progression to EAC, we observed evidence of neutral dynamics in community assembly within normal esophageal tissue and BE, but not EAC. In a large case–control study of BE patients who progressed to EAC versus BE patients with non-cancer outcomes (NCO) during follow-up (mean = 10.5 years), we found that Helicobacter pylori deviated significantly from the neutral expectation in BE NCO only, suggesting that factors related to H. pylori or H. pylori infection itself may influence EAC risk. Additionally, stochastic simulations incorporating selection recapitulated non-neutral behaviors observed. Formally modeling dynamics during progression holds promise in clinical applications by offering a deeper understanding of microbial involvement in cancer development.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-026-12545-w.}, }
@article {pmid41666339, year = {2026}, author = {Liu, Y and Wu, X and Le, X and Cheng, H and Peng, Q and Wen, L and Hou, H and Hayat, K and Liu, W and Yin, S}, title = {Multiomics Insights into the Ecotoxicological Effects of Soil Microplastics on Crop Plants.}, journal = {Journal of agricultural and food chemistry}, volume = {74}, number = {7}, pages = {5832-5844}, doi = {10.1021/acs.jafc.5c11305}, pmid = {41666339}, issn = {1520-5118}, mesh = {*Soil Pollutants/toxicity/metabolism ; *Crops, Agricultural/metabolism/drug effects/genetics/chemistry/growth &amp; development ; *Microplastics/toxicity/metabolism ; Ecotoxicology ; Metabolomics ; Soil/chemistry ; Multiomics ; }, abstract = {Microplastics (MPs) have become pervasive contaminants. This is due to plastic mulching, wastewater irrigation, and sludge application. Concentrations of MPs in intensive farming regions have been recorded at 41,741 particles/kg. MPs are absorbed by crop roots and leaves and then travel to reproductive organs. In these organs, they cause oxidative stress, genotoxicity, and toxicity, which disrupts nutrient uptake, photosynthesis, and crop yield. This review summarizes 20 years (2003-2024) of studies on MP-distribution in soil-crop systems and their phytotoxicity mechanisms, highlighting the pioneering role of multiomics methods. Genomic analyses show that MPs cause DNA damage and change the expression levels of stress-response genes. Transcriptomics identifies disrupted pathways. These pathways are in carbohydrate metabolism, plant hormones, and antioxidant defense. Proteomics uncovers post-translational modifications. These affect nutrient transporters. Metabolomics further highlights disturbances in glycolysis, amino acid synthesis, and ROS-scavenging metabolites. Despite these advances, integrating multiomics data sets to elucidate systemic "gene-protein-metabolite" networks remains challenging. Key knowledge gaps include MP-protein binding mechanisms, the development of crop-specific biomarkers, and the interaction of MPs with costressors. Future research should prioritize integrated transcriptomic-metabolomic profiling to identify stress-response pathways, use X-ray crystallography to map MP-protein interactions, and develop MP-resilient crop varieties. Multiomics integration is essential for decoding the toxicity of the MPs and formulating mitigation strategies to safeguard the sustainability of agriculture.}, }
@article {pmid41666224, year = {2026}, author = {Yang, B and Molton, I and Humbert, A and Baylor, C and Gregg, E and Ehde, D and Sullivan, J and Lanz, E and Schiller, M and Hurvitz, P and Lee, D}, title = {Environmental influences on community participation among people with multiple sclerosis: A mixed methods study.}, journal = {PloS one}, volume = {21}, number = {2}, pages = {e0342678}, doi = {10.1371/journal.pone.0342678}, pmid = {41666224}, issn = {1932-6203}, mesh = {Humans ; *Multiple Sclerosis/psychology ; Female ; Male ; Middle Aged ; Adult ; *Community Participation ; Focus Groups ; Geographic Information Systems ; *Environment ; Aged ; }, abstract = {OBJECTIVE: To examine the influence of environmental factors (EFs) and personal factors (PFs) on community participation among people with multiple sclerosis (PwMS) and identify areas for improvement.<br><br>METHODS: A mixed methods explanatory sequential design was used. A secondary data analysis of patient-reported outcomes and Global Positioning System (GPS) data was completed using multiple linear regression analysis to examine associations between five EFs, five PFs, and six community participation outcomes in 100 PwMS. Four focus groups were completed with 12 PwMS who use mobility aids and 12 who do not to understand how EFs affected community participation experiences. Thematic analysis was used.<br><br>RESULTS: Regression results showed significant associations between PFs and five community participation outcomes (R2&#x2009;=&#x2009;13% - 48%, p&#x2009;<&#x2009;0.05), and EFs explained an additional 11% variation in satisfaction with participation and 11% in GPS-derived measures of activity space, after adjusting for PFs (&#x394;R&#xb2;&#x2009;=&#x2009;0.11, p&#x2009;<&#x2009;0.05). Among individual EFs, after accounting for PFs, perceived financial resources was associated with ability to participate (B&#x2009;=&#x2009;1.46, p&#x2009;=&#x2009;0.018), and satisfaction with participation (B&#x2009;=&#x2009;3.12, p&#x2009;<&#x2009;0.001). Social support (B&#x2009;=&#x2009;-1.05, p&#x2009;=&#x2009;0.022) and neighborhood safety (B&#x2009;=&#x2009;1.3, p&#x2009;=&#x2009;0.007) were associated with activity space. Qualitative findings revealed that mobility aid users experienced increased challenges in the built environment, and non-users reported more concerns about the attitudinal environment. They also described how environmental support enabled participation despite functional declines. Acceptance and adaptation were useful strategies, but participants called for improvements in the built environment, information access, MS specialty care, and public attitudes towards disability.<br><br>CONCLUSION: Community participation among PwMS is influenced by both PFs and EFs. Statistically, EFs uniquely affected participation satisfaction and activity space, while qualitative findings revealed major barriers and highlighted needs for improvement in physical, social, and attitudinal environments.}, }
@article {pmid41664417, year = {2026}, author = {De Camargo, E and Schindler, S and Zülke, AE and Glaesmer, H and Hinz, A and Engel, C and Wirkner, K and Riedel-Heller, SG and Schomerus, G and Sander, C}, title = {Rest Assured: The Association of Structural, Functional Support, and Loneliness With Subjective Sleep Health.}, journal = {Journal of sleep research}, volume = {}, number = {}, pages = {e70303}, doi = {10.1111/jsr.70303}, pmid = {41664417}, issn = {1365-2869}, support = {713-241202//Freistaat Sachsen/ ; 14505/2470//Freistaat Sachsen/ ; }, abstract = {Sleep is increasingly understood as a socially embedded phenomenon. This study examined how structural and functional aspects of social support, as well as loneliness, relate to sleep health in a German sample of middle-aged adults (N = 5388). Drawing on the socio-ecological model of sleep health, we assessed the contributions of social support dimensions while accounting for age, sex, and socioeconomic status, as well as psychological covariates. The results of the binary logistic regression showed that functional support (ESSI), friend network size (LSNS6), and loneliness (CES-D item 14) significantly (p < 0.001) predicted sleep health (PSQI), while family network size did not. The portion of explained variance was small (4%-5%). Results remained robust after adjusting for age, sex, and socioeconomic status, but no longer when including psychological covariates (GAD-7, SWLS, CES-D), in which case only the friend network size remained significant (p = 0.019). Women were significantly more affected by poor sleep health than men, and with higher socioeconomic status, fewer people reported suffering from poor sleep (all: p < 0.001). Additional subgroup analysis revealed higher age as a risk factor for worse sleep health in women only, while the friend network was only relevant in men. Our findings highlight the importance of distinguishing between structural and functional dimensions of social support in sleep health research and interventions, and suggest a potential sex-by-age interaction. Future research should promote equity by including diverse populations and longitudinally examine how social support, especially friend networks, affects sleep across genders, ages, and contexts.}, }
@article {pmid41664026, year = {2026}, author = {Kim, H and Heo, SJ and Park, S and Lee, J and Do, G and Park, JY}, title = {Predicting suicidal and self-harm ideation using ecological momentary assessment: deep learning analysis in a general population sample.}, journal = {BMC psychiatry}, volume = {26}, number = {1}, pages = {192}, pmid = {41664026}, issn = {1471-244X}, support = {RS-2023-KH135442//Ministry of Health and Welfare/ ; }, abstract = {BACKGROUND: Suicidal and self-harm ideation are major risk factors for suicide but are often difficult to detect, particularly in non-clinical populations. Ecological Momentary Assessment (EMA) offers a real-time, low-burden method for monitoring psychological states, yet its predictive value outside clinical settings remains unclear.<br><br>OBJECTIVE: To evaluate whether brief, indirect daily EMA data collected via a smartphone app can predict suicidal and self-harm ideation two weeks later in a general population sample.<br><br>METHODS: A total of 499 adults in Korea completed 28 days of EMA using the BIG4&#x2009;+&#x2009;app, reporting on seven daily items related to mood, sleep, appetite, concentration, fatigue, and loneliness. Suicidal and self-harm ideation were assessed using the CESD-R at baseline, 2 weeks, and 4 weeks. A recurrent neural network with Long Short-Term Memory (LSTM) architecture was trained on two-week EMA sequences, using 10-fold cross-validation.<br><br>RESULTS: The combined model using EMA and baseline data achieved an AUC of 0.873 for suicidal ideation and 0.821 for self-harm ideation. Predictive accuracy exceeded an AUC of 0.75 by day 6. Participants with ideation consistently showed lower scores on all EMA items. The study achieved a 94% compliance rate.<br><br>CONCLUSIONS: Brief, indirect EMA data can predict near-term suicidal and self-harm ideation in a general population. These findings support the feasibility of smartphone-based EMA as a scalable and non-intrusive tool for early detection of suicide risk.<br><br>CLINICAL TRIAL NUMBER: Not applicable.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12888-026-07815-6.}, }
@article {pmid41662068, year = {2026}, author = {Sacco, MJ and Divita, G and Coale, K and Goldman, HH and Rosé, CP}, title = {An ecological model in support of an ontology of mental functioning.}, journal = {PLOS mental health}, volume = {3}, number = {1}, pages = {e0000407}, pmid = {41662068}, issn = {2837-8156}, abstract = {Health records contain rich sources of mental health data that can be used to evaluate disability and health care outcomes. However, a lack of behavioral health ontologies focused on daily life activity functioning has impeded development of clinical informatic tools to extract mental functioning information. We aim to present the theoretical foundation and conceptual model upon which the Ecological Mental Functioning Ontology (EMFO) was built to facilitate natural language processing (NLP) to extract mental functioning information in free-text clinical records. Subject matter experts operationally defined mental functioning, and a related theoretical perspective was established. Face validity of a proposed model was obtained using an iterative grounded theory approach. An annotation schema based on the model was constructed and tested using manual annotation and consensus on datasets of real and synthetic clinical notes. An annotation schema, based on the Ecological Model of Mental Functioning (EMMF), was shown to be robust when using NLP methods to identify and extract mental functioning information in real and synthetic behavioral health clinical notes. Mental functioning is a complex phenomenon that is fully conceptualized within an ecological milieu encompassing the dynamic transactive relationship between the person, the nature and demands of activities the person participates in, and the external contextual and environmental factors within which the activities take place. By operationalizing mental functioning, the EMMF provided a conceptual roadmap to develop the EMFO and NLP methods that identify and extract mental functioning activity information in clinical records.}, }
@article {pmid41661144, year = {2026}, author = {Miller-Viacava, N and Apoux, F and Ferriere, R and Friedman, NR and Mullet, TC and Sueur, J and Willie, J and Lorenzi, C}, title = {Modulation statistics of natural soundscapesa).}, journal = {The Journal of the Acoustical Society of America}, volume = {159}, number = {2}, pages = {1263-1289}, doi = {10.1121/10.0039892}, pmid = {41661144}, issn = {1520-8524}, mesh = {*Acoustics ; Animals ; *Ecosystem ; *Sound ; Time Factors ; Sound Spectrography ; *Vocalization, Animal ; Signal Processing, Computer-Assisted ; Biodiversity ; }, abstract = {Modulation statistics of "natural soundscapes" were estimated by calculating the modulation power spectrum (MPS) of a database of acoustic samples recorded in nine pristine terrestrial habitats for four moments of the day and two contrasting periods, differing in precipitation level. In particular, a set of statistics estimating low-pass quality, starriness, separability, asymmetry, modulation depth, and 1/ftα temporal-modulation power-law relationships were calculated from the MPS of the samples and related to geographical, meteorological factors and diel variations. MPS were found to be generally low-pass in shape in the modulation domain with most of their modulation power restricted to low temporal (<10-20 Hz) and spectral modulations (<0.5-1 cycle/kHz). Modulation statistics were distinguished between habitats irrespective of moment of the day and precipitation period with a greater role of modulation depth and starriness. Separability and starriness were found to be related to the global biodiversity decrease from tropical to polar regions, suggesting that the lack of joint high spectral and fast temporal modulations and MPS complexity are important features that may characterise "biophony," the collective sound produced by animals in a given habitat. These findings may help guide research on monitoring auditory behaviours and underlying mechanisms expected to exploit regularities of natural scenes.}, }
@article {pmid41660072, year = {2026}, author = {Katapally, TR and Elsahli, N and Ibrahim, ST and Bhawra, J}, title = {Human-centered AI to promote youth mental health: a serendipitous natural experiment enabled by a digital health platform.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e20772}, pmid = {41660072}, issn = {2167-8359}, mesh = {Humans ; Adolescent ; *Mental Health ; Male ; Female ; *Artificial Intelligence ; *Health Promotion/methods ; Rural Population ; Mobile Applications ; Longitudinal Studies ; Digital Health ; }, abstract = {BACKGROUND: Health systems are struggling to deliver timely preventive care, particularly for marginalized populations, necessitating integration across health, education, and social services. For Indigenous youth in rural communities, fragmented services, isolation, and limited culturally safe options worsen mental health disparities. Interactive technologies, particularly human-centered artificial intelligence (AI)-enabled digital health platforms grounded in human-computer interaction (HCI), can enable remote interaction with citizens and decision-makers. This study investigated a serendipitous natural experiment to assess varying levels of platform nudging on Indigenous youth compliance in a longitudinal intervention.<br><br>METHOD: This study emerged from the final year of a 5-year initiative embedding a culturally appropriate digital health intervention into school curricula in rural Indigenous communities. While the broader aim was to assess long-term mental health outcomes, an unexpected system disruption assessment of digital nudging on compliance. The platform featured two interfaces: a citizen-facing mobile app for ecological assessments and nudges, and a scientist dashboard for monitoring engagement and triggering nudges. Youth received three nudges: (1) daily system-triggered reminders to complete assessments, (2) weekly non-personalized messages (e.g., land-based activity reminders), and (3) weekly personalized "Best Picture" messages showcasing youth-submitted images. The disruption created four phases: Phase 1 included all nudges; Phase 2 removed non-personalized and personalized nudges; Phase 3 reintroduced them; Phase 4 removed only personalized nudges. Data were analyzed using one-way analysis of variance (ANOVA) with Tukey post hoc tests in R 4.4.2.<br><br>RESULTS: Compliance, measured by completed mobile ecological prospective assessments (mEPAs), varied significantly across most phases. Comprehensive nudging (Phase 1) yielded the highest completion rates and fastest response times, which declined following the removal of personalized scientist-triggered nudges. Loss of personalized scientist-triggered nudges had the most substantial impact on compliance.<br><br>CONCLUSIONS: Consistent system-triggered reminders and personalized "Best Picture" nudges were most effective in sustaining compliance. Findings highlight the importance of integrating personalized, two-way communication features into digital health platforms to strengthen engagement in rural Indigenous communities. By enabling real-time interaction between youth and scientists, the platform supported integration across health, education, and research sectors. Its human-controlled backend and customizable citizen-facing interface reflect principles of human-centered AI, emphasizing trust and autonomy. This approach offers a scalable model for ethical, effective digital interventions that balance technological precision and participant agency.}, }
@article {pmid41659429, year = {2026}, author = {Vallecillo-Zuniga, ML and Akeefe, A and Brown, DG and Wahlig, TA and Marchetti, M and Heiner, T and Davis, KL and Nieznanski, C and Flynn, A and Leung, DT}, title = {Longitudinal Changes in Nasal and Oral Microbiome and Antimicrobial Resistance Gene Profiles in Response to Human Fecal Microbiota Transplantation.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41659429}, issn = {2692-8205}, support = {UM1 TR004409/TR/NCATS NIH HHS/United States ; UL1 TR002538/TR/NCATS NIH HHS/United States ; S10 OD034321/OD/NIH HHS/United States ; T32 HG008962/HG/NHGRI NIH HHS/United States ; S10 OD021644/OD/NIH HHS/United States ; T32 HL105321/HL/NHLBI NIH HHS/United States ; P30 CA042014/CA/NCI NIH HHS/United States ; }, abstract = {The gut-lung axis describes interactions between intestinal and respiratory mucosal systems through microbial, metabolic, and immune pathways, but the systemic impact of gut-targeted therapies on upper respiratory tract (URT) communities remains underexplored. We conducted a longitudinal study in adult patients undergoing fecal microbiota transplantation (FMT) for recurrent Clostridioides difficile infection (CDI) alongside healthy controls. Fecal, nasal, and oral samples were collected at baseline (Day 0) and on Days 14 and 56 following FMT. Shotgun metagenomic sequencing was performed to quantify microbial diversity, taxonomic composition, and the abundance of antimicrobial resistance genes (ARGs). FMT was associated with increased gut diversity and decreased levels of key intestinal taxa commonly considered pathobionts, including Klebsiella spp., Escherichia spp., Shigella spp., and Klebsiella pneumoniae. At the phylum level, fecal Bacteroidota increased, while Mucoromycota decreased following treatment. Post-FMT nasal microbiome changes included reduced richness and diversity, expansion of Moraxella, and decreases in taxa linked with respiratory colonization, including Staphylococcus aureus and Streptococcus pneumoniae. By Day 56, nasal communities partially recovered toward healthy profiles. Baseline nasal ARG abundance decreased following FMT, particularly among β-lactam, aminoglycoside, and fluoroquinolone resistance genes, and remained comparable to healthy controls by Day 56. In contrast, the oral microbiome and oral resistome remained largely stable, with only minor fluctuations, and no consistent increases in respiratory pathobiont-associated taxa. In summary, FMT was associated with broader effects beyond the gut, including changes in the URT microbial ecology and antimicrobial resistance profiles. Together, these findings are consistent evidence of gut-lung microbial interactions, linking intestinal dynamics with respiratory microbial composition and antimicrobial resistance patterns.}, }
@article {pmid41655849, year = {2026}, author = {Losiewicz, OM and Wen, A and Cohen, ZD and Akre, S and Bui, AAT and Craske, MG}, title = {Negative emotional inflexibility underlies biological inflexibility: An ecological momentary assessment and passive digital sensing study.}, journal = {Journal of affective disorders}, volume = {402}, number = {}, pages = {121352}, doi = {10.1016/j.jad.2026.121352}, pmid = {41655849}, issn = {1573-2517}, mesh = {Humans ; *Ecological Momentary Assessment ; Male ; Female ; Adult ; *Emotions/physiology ; *Heart Rate/physiology ; Middle Aged ; Bayes Theorem ; Young Adult ; *Major Depressive Disorder/physiopathology/psychology ; }, abstract = {Emotional flexibility, thought to reflect the ability to adapt to internal and external environmental stimuli, is associated with psychological well-being. Emotional inertia and network density, defined as stability and interconnectedness, respectively, of emotions, are aspects of emotion dynamics that represent low emotional flexibility. Studies examining biological substrates of emotional persistence are largely limited to emotional inertia and non-depressed samples. Heart-rate variability (HRV) is a transdiagnostic biomarker for psychopathology thought to be associated with emotional flexibility. This study examined whether emotional inertia and network density were associated with HRV in adults with moderate-to-severe depression (N = 315). Participants completed three 8-day epochs of ecological momentary assessment (EMA) five times daily. Smartwatches measured HRV throughout the study. Emotional inertia and idiographic networks were calculated separately for EMA-rated negative and positive affect. Bayesian dynamic structural equation models with noninformative prior distributions examined the association between emotional inertia and HRV; hierarchical linear modeling examined associations between network density and HRV. Both daytime and bedrest HRV were inversely associated with contemporaneous network density of negative emotions. HRV was not associated with inertia, positive network density, or average EMA-reported affect, though it was associated with age, antidepressant medication, and physical exercise. This was the first study to examine HRV in relation to these emotion dynamics in a depressed sample. The results suggest that experiencing a variety of negative emotions within a short period of time may be associated with underlying biological inflexibility. Future studies should examine the directionality and mechanisms behind this effect and explore potential clinical interventions.}, }
@article {pmid41653831, year = {2026}, author = {Jano, T and Sayed, AN and Hossen, MM and Sardianos, C and Hamila, R and Bensaali, F and Varlamis, I and Dimitrakopoulos, G}, title = {Closing the loop: A systematic review of artificial intelligence in circular e-waste management.}, journal = {Waste management (New York, N.Y.)}, volume = {214}, number = {}, pages = {115392}, doi = {10.1016/j.wasman.2026.115392}, pmid = {41653831}, issn = {1879-2456}, abstract = {The proliferation of technological advancements, knitted with volatile consumption patterns and poor end-of-life management of discarded electronics, is currently outpacing sustainability transitions, putting increasing strain on finite material resources and heightening ecological vulnerability. This, in turn, has made electronic waste a stealth contributor to climate change with adverse impacts on the environment, economy, and society at large. This reality underscores the urgent need for a strategic shift from linear waste-disposal methods to circular pathways, where Artificial Intelligence (AI) can build more sustainable feedback loops. At the nexus of AI and circular e-waste management, this study systematically reviews 147 articles from 2019 to October 2025. The analysis reveals a steady increase in AI adoption, particularly in deep learning-based detection and classification applications. To structure the evidence from the literature, a six-tier taxonomy is proposed, encompassing AI methods, lifecycle stages, data, waste types, limitations, challenges, and future pathways and opportunities. Beyond technical interventions, systemic and operational barriers that demand strategic levers to address regulatory ambiguities, legislative gaps, managerial inefficiencies, and logistical fragmentation are elucidated. These challenges underpin data availability and generalizability, as well as the lack of standardization, interoperability gaps, and barriers to the ethical and regulatory adoption of AI. In practice, these constraints limit the development of uncertainty-aware electronic waste systems capable of functioning under realistic operational dynamics. To this end, the paper reframes AI-based systems from terminal sinks to regenerative loops, aligning technological progress with sustainable electronic waste management.}, }
@article {pmid41653553, year = {2026}, author = {Ghosh, A and Bhakta, S and Kapse, N and Dhakephalkar, PK and Patra, C and Gorain, B}, title = {Micro/nanoplastic-mediated gut dysbiosis and its impact on cardiac and neuroimmune function in zebrafish model: A multi-omics approach.}, journal = {The Science of the total environment}, volume = {1017}, number = {}, pages = {181443}, doi = {10.1016/j.scitotenv.2026.181443}, pmid = {41653553}, issn = {1879-1026}, mesh = {Animals ; *Zebrafish ; *Dysbiosis/chemically induced ; *Gastrointestinal Microbiome/drug effects ; *Microplastics/toxicity ; *Water Pollutants, Chemical/toxicity ; Heart/drug effects ; Multiomics ; }, abstract = {The pervasive distribution of micro- and nanoplastics (M/NPs) across ecosystems necessitates a mechanistic investigation into their toxicological consequences. Chronic exposure to M/NPs through combined intestinal uptake and branchial contact in aquatic animals disrupts epithelial barrier integrity, alters gastric secretions and luminal pH, and induces microbial dysbiosis, evidenced by the depletion of commensal taxa and expansion of pathogenic strains. These local perturbations trigger systemic sequelae, including neurotoxicity and cardiotoxicity. Consequences on cross-species analyses demonstrate translational concordance, as human studies similarly link M/NP bioaccumulation with inflammatory bowel disease, cognitive decline, and cardiovascular dysfunction. Integrative multi-omics approaches, encompassing transcriptomic, metabolomic, and microbiome analyses, have begun to elucidate the molecular cascades underpinning M/NP toxicity, providing high-resolution insights into host-microbe-environment interactions. Notwithstanding these advances, critical gaps remain in chronic exposure modelling, capturing particle heterogeneity, and ensuring ecological realism. In this context, zebrafish (Danio rerio) provide a uniquely tractable system for gnotobiotic rearing, microbial transplantation, and live imaging, thereby enabling causal inference and functional validation in real-time. Collectively, this review establishes zebrafish as a pivotal model for elucidating M/NP-induced gut dysbiosis, neurotoxicity, and cardiotoxicity. Multi-omics analyses and translational evidence reveal systemic inflammation, immune-metabolic disruptions, and mechanistic links to human health, providing a foundation for targeted research, regulatory frameworks, and interventions to mitigate environmental M/NP exposure.}, }
@article {pmid41652929, year = {2026}, author = {Pérez-Granados, C and Morant, J and Darras, KFA and Marín-Gómez, OH and Mendoza, I and Muñoz-Mohedano, MA and Santamaría-García, E and Bastianelli, G and Márquez-Rodríguez, A and Budka, M and Bota, G and De la Peña-Rubio, JM and de la Morena, ELG and Santa-Cruz, M and de la Nava, P and Fernández-Tizón, M and Sánchez-Mateos, H and Barrero, A and Traba, J and Osiejuk, TS and Hart, PJ and Navine, AK and Montoya Muñoz, AF and de Araujo, CB and Rosa, GLM and Denóbile Torres, IM and Camargo Catalano, AL and Simões, CR and Llusia, D and Morales, MB and Acebes, P and Medina, JA and Brown, N and Astaras, C and Karmiris, I and Navarrete, E and Cauchoix, M and Barbaro, L and Funosas, D and Arend, D and Müeller, S and González-García, F and González-Romero, A and Mammides, C and Pontikis, M and Jacuzzi, G and Olden, JD and Bombaci, SP and Marcacci, G and Jacot, A and Zurano, JP and Gangenova, E and Varela, D and Di Sallo, F and Zurita, GA and Atemasov, A and Tremblay, JA and Lamarre, V and Hutschenreiter, A and Monroy-Ojeda, A and Díaz-Vallejo, M and Chaparro-Herrera, S and Briers, RA and Sousa-Lima, R and Pinheiro, T and da Silva, WC and Calvente, A and Molin, AD and Antonelli, A and Gogoleva, S and Palko, I and Trọng, HV and Lage Duarte, MH and Dos Santos Saturnino, N and Silva, SR and Rainho, A and Lopes, P and Schuchmann, KL and Marques, MI and de Oliveira, AS and Littlewood, NA and Tuanmu, MN and Cheng, YR and Chao, H and Kepfer-Rojas, S and Aguilera, AL and Brotons, L and Feldman, MJ and Imbeau, L and Panwar, P and Weed, AS and Deshwal, A and da Paz, RV and Salustio-Gomes, C and Oliveira-Júnior, DD and Lima-Santos, CS and Pichorim, M and Pan, W and Goodale, E and Attisano, A and Theuerkauf, J and Sebastián-González, E}, title = {WABAD: A world annotated bird acoustic dataset for passive acoustic monitoring.}, journal = {Ecology}, volume = {107}, number = {2}, pages = {e70317}, pmid = {41652929}, issn = {1939-9170}, mesh = {Animals ; *Birds/physiology ; *Vocalization, Animal/physiology ; *Acoustics ; *Environmental Monitoring/methods ; *Databases, Factual ; }, abstract = {Under the current global biodiversity crisis, there is a need for automated and noninvasive monitoring techniques that can gather large amounts of data cost-effectively at various ecological scales, from local to large spatial scales. These data can then be analyzed to inform stakeholders and decision-makers. One such technique is passive acoustic monitoring, which is commonly coupled with automatic identification of animal species based on their sound. Automated sound analyses usually require the training of sound detection and identification algorithms. These algorithms are based on annotated acoustic datasets which mark the occurrence of sounds of species inside sound recordings. However, compiling large annotated acoustic datasets is time-consuming and requires experts, and therefore, they normally cover reduced spatial, temporal, and taxonomic scales. This data paper presents WABAD, the World Annotated Bird Acoustic Dataset for passive acoustic monitoring. WABAD is designed to provide the public, the research community, and conservation managers with a novel and globally representative annotated acoustic dataset. This database includes 5047 min of audio files annotated to species-level by local experts with the start and end time and the upper and lower frequencies of each identified bird vocalization in the recordings. The database has a wide taxonomic and spatial coverage, including information on 91,931 vocalizations from 1192 bird species recorded at 72 recording sites in 29 recording locations (mainly countries) and distributed across 13 biomes. WABAD can be used, for example, for developing and/or validating automatic species detection algorithms, answering ecological questions, such as assessing geographical variations on bird vocalizations, or comparing acoustic diversity indices with species-based diversity indices. The dataset is published under a Creative Commons Attribution 4.0 International license that permits redistribution and reuse on the condition that the original work is properly credited.}, }
@article {pmid41649635, year = {2026}, author = {Zhou, L and Qian, J and Liu, Y and Zhang, J and Zhang, K and Zhu, X}, title = {Simulation and optimization of multiple permeable reactive barriers (multi-PRBs) for acid mine drainage (AMD) based on machine learning.}, journal = {Environmental geochemistry and health}, volume = {48}, number = {3}, pages = {143}, pmid = {41649635}, issn = {1573-2983}, support = {No. 2022YFC3702203//National Key R&amp;D Program of China/ ; }, mesh = {*Machine Learning ; *Mining ; *Water Pollutants, Chemical/chemistry ; Neural Networks, Computer ; Computer Simulation ; Models, Theoretical ; Drainage ; }, abstract = {Multiple permeable reactive barriers (multi-PRBs) are an effective in-situ technology for acid mine drainage (AMD) treatment. However, their practical implementation is hindered by unclear mechanisms and a lack of decision models. In this study, a coupled processes numerical model was developed to simulate the synergistic removal of TFe and SO42[-] through multi-PRBs with the optimized sequence of limestone, followed by biochar and then D201 resin. Machine learning integrated with the Non-dominated Sorting Genetic Algorithm (ML-NSGAII) was proposed for optimization, in which a Backpropagation Neural Network (BPNN) served as a highly accurate surrogate model (R[2] > 0.99) to predict system performance, reducing the computational load by 99.7% compared to conventional methods. Spearman correlation analysis and SHAP model interpretation revealed hydraulic load and filler size as the most influential parameters. Application of the TOPSIS-entropy weight method to the Pareto-optimal solution set yielded a final design that significantly enhanced system service life and treatment capacity while reducing costs. This research provides a practical and computationally efficient strategy for designing multi-PRBs for AMD treatment.}, }
@article {pmid41649413, year = {2026}, author = {Jo, S and Lee, HG and Nam, DH and Park, C}, title = {Use of metabarcoding detects the rapid onset of cultivation bias in the culture-based profiling of marine sediment bacterial communities.}, journal = {Letters in applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/lambio/ovag020}, pmid = {41649413}, issn = {1472-765X}, abstract = {When cultivation-based microbiology is used to isolate strains from environmental samples, the cultured populations may not represent ecologically relevant taxa in the source community. To address this, we employed pre-cultivation metabarcoding to establish a baseline community profile and detect cultivation bias. Using time-resolved cultivation of marine sediment bacteria, we demonstrated the need for initial community characterization. Sediment-derived microbiomes were cultured in Marine Broth 2216 and analyzed using 16S rRNA gene metabarcoding at 0, 6, 12, 18, and 24 h. A rapid 10-fold reduction in alpha diversity was observed within the 6 h (from 1029 amplicon sequence variants to 34-106), with the genus Vibrio reaching near-complete dominance (>95%) from 18 to 24 h, while environmentally dominant taxa such as Acinetobacter were quickly excluded. This dramatic shift illustrates that, without baseline characterization, cultivation-induced artifacts cannot be clearly distinguished from ecologically meaningful patterns. Fast-growing generalists can quickly outcompete ecologically significant taxa, distorting isolation outcomes and hindering the recovery of functionally important microorganisms. We show that metabarcoding at 0 h can identify cultivation biases, help interpret isolation results, and suggest targeted strategies for recovering ecologically relevant taxa. This integrated approach facilitates more accurate recovery and analysis of functionally significant microbial diversity.}, }
@article {pmid41648310, year = {2026}, author = {Szenei, J and Burke, A and Liong, A and Korenskaia, A and Lukowski, AL and Ziemert, N and Nikel, PI and Leão, PN and Moore, BS and Weber, T and Blin, K}, title = {Computational pipeline reveals nature's untapped reservoir of halogenating enzymes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41648310}, issn = {2692-8205}, support = {R01 GM085770/GM/NIGMS NIH HHS/United States ; R35 GM159745/GM/NIGMS NIH HHS/United States ; }, abstract = {Microbial halogenated natural products (hNPs) hold ecological, agricultural, and biomedical relevance. The hNP-producing potential of the organism can be assessed by the precise prediction of biosynthetic enzymes, yet the detailed annotations of halogenases are often missing from genomic and metagenomic data. We created a manually curated database (https://halogenases.secondarymetabolites.org/) containing information on the halide-specificity, role, and position of verified catalytic residues and results of the mutagenesis studies of more than 120 experimentally validated or in silico inferred halogenases. The collection of experimental data supports a computational pipeline that allows the family-, substrate-, and halide-scope-level annotation of halogenating enzymes by relying on catalytic residues, conserved motifs, and profile Hidden Markov Models (pHMMs). Our analysis with sequence similarity networks (SSNs) highlighted several underexplored clusters in the UniRef50 database. Such finding was a halogenase from Rhodopirellula baltica (RhobaVHPO) previously labelled as a hypothetical chloroperoxidase, which clustered apart from the known chloroperoxidases and bromoperoxidases, but accepted chloride and preferred bromide. Our database and workflow provide extensive and scalable solutions for the systematic and precise annotation of halogenating enzymes in genomic and metagenomic data. The in-depth categorization of halogenases will improve the chemical structure prediction of microbial hNPs, supporting ecological assessments and natural product discovery.}, }
@article {pmid41648011, year = {2025}, author = {Rappazzo, AC and Lo Giudice, A and Giannarelli, S and Rizzo, C and Tomei, A and Ghezzi, L and Cairns, WRL and Azzaro, M and Papale, M}, title = {Diverging contaminant profiles and prokaryotic assemblages in Arctic and Antarctic lake sediments.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1722478}, pmid = {41648011}, issn = {1664-302X}, abstract = {INTRODUCTION: Persistent organic pollutants (POPs) and trace metals are increasingly recognized as critical drivers of ecological change in polar environments. However, their combined impact on sediment microbial communities remains largely unexplored.<br><br>METHODS: We analyzed sediments from 12 high-latitude lakes and ponds, five from the Arctic (Svalbard) and seven from the Antarctic (South Shetland Islands/Deception Island), to examine contaminant profiles (polychlorinated biphenyls [PCBs] and trace metals) and prokaryotic community structure using 16S rRNA gene amplicon sequencing. Finally, we assessed the associations between the identified communities and detected pollutants, and compared these associations across lakes and sites.<br><br>RESULTS: The results revealed distinct chemical signatures between poles: Arctic sediments were mainly contaminated by polycyclic aromatic hydrocarbons (&#x2211;PAHs, 18.5-685.7 ppb; phenanthrene was the most abundant), whereas Antarctic sediments showed relatively higher concentrations of chlorobenzenes (&#x2211;CBs, 1.9-3.6 ppb) and polychlorinated biphenyls (&#x2211;PCBs, 0.9-1.4 ppb), with 2-methylnaphthalene as the most abundant PAH. Manganese was the most abundant metal in both regions, reaching 760 ppm in the Arctic, while elevated arsenic and lead characterized specific Antarctic sites. Amplicon sequencing identified five dominant phyla (i.e., Actinobacteriota, Bacteroidota, Alpha- and Gammaproteobacteria, and Desulfobacterota) with significant compositional shifts between poles.<br><br>DISCUSSION: Notably, the distinct contaminant signatures between regions appeared to be associated with shifts in microbial community composition, suggesting that both the type and intensity of POP and metal exposure may influence bacterial diversity and ecological functions in polar lake sediments. These findings provide a robust baseline for Arctic-Antarctic comparisons, positioning polar lakes as sensitive sentinels of contaminant-driven ecological change. They also underscore the urgent need for functional studies and long-term monitoring to evaluate ecosystem resilience under accelerating climate change.}, }
@article {pmid41644669, year = {2026}, author = {White, SL and Brasher, MS and Pattee, J and Zhou, W and Chapman, S and Jee, YH and Bell, CC and Jamil, TL and Barrio, M and Arehart, CH and Evans, LM and Hirbo, J and Cox, NJ and Straub, P and Namba, S and Bertucci-Richter, E and Guare, L and Edris, A and Morris, S and Mulford, AJ and Zhang, H and Fennessy, B and Tobin, MD and Chen, J and Williams, AT and John, C and van Heel, DA and Mathur, R and Finer, S and Moksnes, MR and Brumpton, BM and Åsvold, BO and Peculis, R and Rovite, V and Konrade, I and Wang, Y and Crooks, K and Chavan, S and Fisher, MJ and Rafaels, N and Lin, M and Shortt, JA and Sanders, AR and Whiteman, DC and MacGregor, S and Medland, SE and Thorsteinsdóttir, U and Stefánsson, K and Karaderi, T and Egan, KM and Bocklage, T and McCrary, HC and Riedlinger, G and Salhia, B and Shriver, C and Phan, MD and Farlow, JL and Edge, S and Kaur, V and Churchman, ML and Rounbehler, RJ and Brock, PL and Ringel, MD and Pividori, M and Schweppe, R and Raeburn, CD and Walters, RG and Chen, Z and Li, L and Matsuda, K and Okada, Y and Zöllner, S and Verma, A and ,  and Preuss, MH and Kenny, E and Hendricks, AE and Fishbein, L and Kraft, P and Daly, MJ and Neale, BM and ,  and ,  and ,  and ,  and Martin, AR and Cole, JB and Haugen, BR and ,  and Gignoux, CR and Pozdeyev, N}, title = {Global multi-ancestry genome-wide analyses identify genes and biological pathways associated with thyroid cancer and benign thyroid diseases.}, journal = {Nature genetics}, volume = {58}, number = {2}, pages = {307-316}, pmid = {41644669}, issn = {1546-1718}, support = {R00HG011898//U.S. Department of Health &amp; Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; R00 HG011898/HG/NHGRI NIH HHS/United States ; I01 BX006252/BX/BLRD VA/United States ; CO-J-24-170//Colorado University | UC Denver | Colorado Clinical and Translational Sciences Institute (CCTSI)/ ; R21 CA282380/CA/NCI NIH HHS/United States ; R01 AG046938/AG/NIA NIH HHS/United States ; NNF20OC0062294//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; /WT_/Wellcome Trust/United Kingdom ; UL1 TR002535/TR/NCATS NIH HHS/United States ; R00 HG012222/HG/NHGRI NIH HHS/United States ; 1R21CA282380//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; }, mesh = {Humans ; *Genome-Wide Association Study ; *Thyroid Neoplasms/genetics/pathology ; *Genetic Predisposition to Disease ; *Thyroid Diseases/genetics ; Multifactorial Inheritance/genetics ; Polymorphism, Single Nucleotide ; Graves Disease/genetics ; }, abstract = {Thyroid diseases are common and highly heritable. We performed a meta-analysis of genome-wide association studies from 19 biobanks for five thyroid diseases: thyroid cancer (ThC), benign nodular goiter, Graves' disease, lymphocytic thyroiditis and primary hypothyroidism. We analyzed genetic association data from ~2.9 million genomes and identified 313 known and 570 new independent loci linked to thyroid diseases. We discovered genetic correlations between ThC, benign nodular goiter and autoimmune thyroid diseases (rg = 0.16-0.97). Telomere maintenance genes contributed to benign and malignant thyroid nodular disease risk, whereas cell cycle, DNA repair and damage response genes were associated with ThC. We propose a paradigm that explains genetic predisposition to benign and malignant thyroid nodules. We found polygenic risk score associations with ThC risk of structural disease recurrence, tumor size, multifocality, lymph node metastases and extranodal extension. Polygenic risk scores identified individuals with aggressive ThC in a biobank, creating an opportunity for genetically informed population screening.}, }
@article {pmid41643370, year = {2026}, author = {Jiajun, C and Xiaojuan, X and Shiyan, C and Xiaoli, Y and Yan, Z and Junfang, Z and Zhiliang, Z and Daqiang, Y and Yanling, Q}, title = {PFOA and co-exposure with PFOS induce AMPK-dependent hypoglycemia in mice: integrated evidence from physiology, multi-omics, and molecular docking.}, journal = {Environment international}, volume = {208}, number = {}, pages = {110076}, doi = {10.1016/j.envint.2026.110076}, pmid = {41643370}, issn = {1873-6750}, mesh = {*Fluorocarbons/toxicity ; Animals ; Molecular Docking Simulation ; Mice ; *Alkanesulfonic Acids/toxicity ; Male ; *Caprylates/toxicity ; Mice, Inbred C57BL ; *Hypoglycemia/chemically induced ; *Environmental Pollutants/toxicity ; AMP-Activated Protein Kinases/metabolism ; Multiomics ; }, abstract = {Per- and polyfluoroalkyl substances, notably perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS), are persistent environmental contaminants with increasing evidence of metabolic toxicity. However, their effects on glucose homeostasis and the underlying mechanisms remain unclear. In this study, we investigated the metabolic consequences of PFOA, PFOS and co-exposure in male C57BL/6 mice for 28 days. Physiological indicators, including fasting blood glucose and hepatic glycogen, were evaluated, followed by transcriptomic, metabolomic, and molecular docking analyses. We found that PFOA and PFOS co-exposure significantly induced hypoglycemia and reduced hepatic glycogen content. Transcriptomic and metabolomic profiling revealed enriched pathways related to glucose metabolism, with the AMPK signaling pathway identified as a central mediator. Notably, PFOA and co-exposure upregulated glycolytic and fatty acid oxidation genes, while suppressing glycogen synthesis regulators. Molecular docking further indicated that both PFOA and PFOS could bind to adiponectin receptors (AdipoR1/2), potentially disrupting normal receptor-mediated AMPK activation. Together, these findings establish an AdipoR1/2-AMPK-mediated mechanism for PFAS-induced glucose metabolic disruption, particularly under PFOA or co-exposure. We provide the integrated physiological and mechanistic evidence linking PFAS exposure to AMPK-dependent hypoglycemia, highlighting the need for metabolic health risk assessments of PFAS mixtures in the environment.}, }
@article {pmid41642108, year = {2026}, author = {Venkatraman, S and Pongchaikul, P and Balasubramanian, B and Anurathapan, U and Meller, J and Tohtong, R and Hongeng, S and Chutipongtanate, S}, title = {Transcriptomic Correlation Identifies Cell Model Representatives for MYCN-Amplified Pediatric Neuroblastoma, Downstream Impact of Model Choice on Functional Interpretation, and Potential Drug Repositioning Candidates.}, journal = {Omics : a journal of integrative biology}, volume = {}, number = {}, pages = {15578100261419486}, doi = {10.1177/15578100261419486}, pmid = {41642108}, issn = {1557-8100}, abstract = {Neuroblastoma (NB) is the most common extracranial solid malignancy of children, and MYCN amplification defines a high-risk subtype with poor outcomes. Although widely used in preclinical drug discovery, NB cell lines are often selected based on availability rather than the molecular characteristics of patient-derived tumors, leading to a critical translational gap between experimental outcomes and clinical relevance. To address this, we developed a rank-based transcriptomic correlation framework to assess the concordance between patient-derived tumors (n = 642; combined from the SEQC/MAQC-III and TARGET cohorts) and publicly available NB cell lines (n = 39). This system-level analysis enabled the identification of cell model representatives (CMRs) that closely recapitulate the gene expression landscapes of clinical tumors. COG-N-557, SMS-KAN, and NB-SD emerged as the top CMRs for MYCN-amplified tumors, whereas COG-N-549, FELIX, and SK-N-SH were identified for MYCN-nonamplified tumors. Pathway enrichment analyses indicated that MYCN-amplified CMRs retain key transcriptional programs involved in neuronal development and tumor proliferation, supporting their biological relevance. Leveraging these models, we integrated pharmacogenomic connectivity mapping and drug-gene network analyses to uncover kinase inhibitors and epigenetic modulators as promising therapeutic candidates capable of targeting MYCN-driven transcriptional programs, despite MYCN being an undruggable oncogene. In conclusion, this study addresses a fundamental systems biology and translational research gap by establishing a data-driven framework for selecting NB cell lines that accurately reflect patient-derived tumor biology with direct implications for prioritizing therapeutically relevant drug candidates. Future studies should prioritize the top CMRs as in vitro models to enhance translational relevance and accelerate precision drug discovery in high-risk pediatric NB.}, }
@article {pmid41640395, year = {2026}, author = {Deane, DC and Hui, C and McGeoch, M}, title = {An Ecological Definition and Objective Threshold for Differentiating Small Fragments.}, journal = {Ecology and evolution}, volume = {16}, number = {2}, pages = {e73054}, pmid = {41640395}, issn = {2045-7758}, abstract = {In an increasingly fragmented natural world, understanding how different ecological phenomena vary with patch size has many motivations. Examples include the assembly of biodiversity, ecosystem service provision and the suitability of fragments for habitat specialist species. A common approach to such questions divides fragments into small and large size classes for separate analysis. However, lack of an objective definition and means to differentiate 'small' from 'large' patches limits our ability to compare findings across studies, arguably impeding progress toward any unified views. Because larger and smaller fragments tend, on average, to respectively over-represent narrow- and wide-range species, an 'area for unbiased species representation' (AUSR) can be defined at some intermediate fragment size predicted to contain species at incidence frequencies approximating that of the overall landscape. A central tendency for AUSR has previously been estimated for patchy habitats (islands, habitat islands and fragments), providing a benchmark to compare this threshold of small fragment size between studies. However, if AUSR can be readily determined within individual study systems, it would also provide an objective threshold to separate small and large fragments under the AUSR definition. Here we assess this potential for 138 published datasets from various fragmented landscapes using an index comparing species incidence frequencies in each fragment with that of the overall landscape. Regressing this index on fragment area yielded an estimate for AUSR in over 90% of cases, suggesting broad applicability as an objective way to separate fragments into two size classes. Regression slopes provide further information on the relative representation of narrow- vs. wide-range species, with ~80% being numerically consistent with the overall negative trend. Requiring only the same data as the island species-area relationship, AUSR can provide useful insights on the relative importance of narrow- vs. wide-ranging species for studies of patch-size dependence in ecological phenomena.}, }
@article {pmid41639126, year = {2026}, author = {Molino, RJEJ and Van Weerd, M and Torreno, VPM and Rellin, KFB and Mondragon, MV and Parungao, L and Manila-Fajardo, AC and Santos, DMC and Junio, HA}, title = {Multi-omics and palynology of selected Philippine forest honey.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {5359}, pmid = {41639126}, issn = {2045-2322}, support = {ORG 2021-0013//Forest Foundation Philippines/ ; }, mesh = {*Honey/analysis ; Philippines ; *Forests ; *Metabolomics/methods ; Bees ; Mass Spectrometry ; Animals ; Chromatography, Liquid ; Multiomics ; }, abstract = {The Sierra Madre Mountains, which happen to be the longest mountain range in the Philippines, is home to lush floral and faunal species as well as forest-based indigenous communities actively involved in preserving local biodiversity. With active reforestation efforts ongoing for decades, the locals are further encouraged to continue their long-standing practice of honey gathering as a form of cultural manifestation and as an important source of livelihood. To further inspire ongoing conservation efforts, we aim to show that the small molecule diversity in Sierra Madre forest honey reflects the local floral composition and is reflective of the positive impact of previous reforestation initiatives. In order to do this, liquid chromatography-mass spectrometry (LC-MS) based metabolomics was used to profile and compare metabolite diversity in honey produced by Apis cerana, Apis breviligula Maa. and Tetragonula biroi (Friese) honey from Palaui Island and Laiban in Northern and Southern Sierra Madre, respectively. Surprisingly, the Philippine National Tree and unfortunately endangered Pterocarpus indicus Willd (loc. Narra) proved to be important, especially in Palaui Island where honey from A. cerana is close to being monofloral. Aside from P. indicus and its small molecule marker hypaphorine, caffeine was detected in Palaui honey beautifully reflecting the way of life of native Agtas who manage a small coffee plantation. The abundance of caffeine, however, is higher in stingless honey samples from Tanay, Rizal where Coffea trees have been extensively included in restoration activities over the past few decades. Our results imply the possibility of using honey as an ecological monitoring tool while generating baseline chemical information that reflects the state of Philippine forests. Furthermore, the identification of unique chemical components in forest honey can be further used in programs that assist indigenous communities in safeguarding the ownership and origin of forest honey sources.}, }
@article {pmid41638723, year = {2026}, author = {Holzer, KJ and Alaverdyan, H and Xu, Z and Frumkin, MR and Frey, KA and Gregory, SH and Rodebaugh, TL and Lu, C and King, CR and Head, D and Kannampallil, T and Haroutounian, S}, title = {Protocol for Personalised Prediction of Persistent Postsurgical Pain.}, journal = {BMJ open}, volume = {16}, number = {2}, pages = {e107055}, pmid = {41638723}, issn = {2044-6055}, mesh = {Humans ; *Postoperative Pain/diagnosis/psychology ; Adult ; Prospective Studies ; Middle Aged ; Aged ; Female ; Adolescent ; Young Adult ; Male ; Pain Measurement ; Ecological Momentary Assessment ; *Precision Medicine ; Quality of Life ; Machine Learning ; Analgesics, Opioid/therapeutic use ; }, abstract = {INTRODUCTION: Persistent postsurgical pain (PPSP) affects up to 15% of patients after major surgery, impairing physical function, quality of life and increasing risk for long-term opioid use. Current PPSP prediction models rely on static or retrospective data and fail to incorporate dynamic perioperative factors. The Personalised Prediction of Persistent Postsurgical Pain (P5) study aims to develop individualised, multimodal prediction models by integrating preoperative behavioural, psychophysical and neurocognitive assessments and high-frequency symptom monitoring.<br><br>METHODS AND ANALYSIS: P5 is a prospective, single-centre cohort study enrolling 2500 adults aged 18-75 undergoing major surgery at a tertiary academic hospital. Participants complete baseline surveys, cognitive testing and quantitative sensory testing preoperatively. Ecological momentary assessments (EMAs) are collected via smartphone three times per day through 30 days postoperatively, capturing pain, mood, catastrophising and medication use. Participants are assessed on postoperative day 1 and complete online surveys at 3 and 6 months, evaluating pain persistence, interference, neuropathic symptoms and related outcomes. Clinical and perioperative data are extracted from the electronic health record. The primary outcome is PPSP at 3 months. Predictive models will be developed using supervised machine learning and dynamic structural equation modelling to extract latent features from EMA data. Model performance will be assessed using area under the receiver operating characteristic curve, area under the precision-recall curve and SHapley Additive exPlanations for interpretability.<br><br>ETHICS AND DISSEMINATION: This study has received ethics approval from the Washington University School of Medicine Institutional Review Board #202101123. Informed consent is required. Results will be submitted for publication in peer-reviewed journals and presented at research conferences.<br><br>TRIAL REGISTRATION NUMBER: NCT04864275.}, }
@article {pmid41638375, year = {2026}, author = {Liu, Y and Wang, C and Wang, C and Fu, L and Zhang, Y and Gao, Z and Yang, Z and Meng, F}, title = {High-concentration polyethylene and polystyrene microplastics co-exposure shorten insect lifespan and impose ecological risk: Multi-omics evidence from Drosophila melanogaster.}, journal = {Comparative biochemistry and physiology. Toxicology &amp; pharmacology : CBP}, volume = {303}, number = {}, pages = {110474}, doi = {10.1016/j.cbpc.2026.110474}, pmid = {41638375}, issn = {1532-0456}, mesh = {Animals ; *Drosophila melanogaster/drug effects/metabolism/genetics/physiology ; *Longevity/drug effects ; *Microplastics/toxicity ; *Polyethylene/toxicity ; *Polystyrenes/toxicity ; Metabolomics ; Transcriptome/drug effects ; Risk Assessment ; *Environmental Pollutants/toxicity ; Multiomics ; }, abstract = {Microplastics (MPs) are pervasive environmental pollutants, accumulating in ecosystems and posing a long-term exposure risk to both the entire ecosystem and human health. However, the combined impact of such high doses on insect longevity and the consequent ecological consequences remain understudied. Here we used Drosophila melanogaster as a model to quantify lifespan shortening under environmentally realistic and extreme concentrations of Polyethylene (PE) and Polystyrene (PS) co-exposures and to unravel the molecular bases of the observed toxicity. Furthermore, we delved into the underlying mechanism through metabolomics and transcriptomics analysis. Our results demonstrated PE and PS MPs co-exposure with greatly high concentrations significantly reduced the lifespan of Drosophila and influenced age-related phenotypes such as climbing ability, intestinal barrier and hunger resistance. We found that differential metabolites were engaged in various metabolic pathways, including ABC transporters, alanine, aspartate and glutamate metabolism. Differentially expressed genes (DEGs) were closely related to Toll and Imd signaling pathway and Longevity regulating pathway. Gram-level PE and PS co-exposure triggers immune-metabolic crosstalk failure and represents a realistic terrestrial risk factor for insect longevity. Our data highlight the urgent need to include high-dose microplastic mixtures in terrestrial ecotoxicological risk assessments and biodiversity conservation strategies. SYNOPSIS: Co-exposure to PE and PS MPs with high concentrations induces changes in gene expression and metabolites associated with immune system and energy metabolism in Drosophila, thereby affecting their lifespan.}, }
@article {pmid41635465, year = {2026}, author = {Bell, KM and Alfikri, Z and Anderst, W and Clark, WW and Cook, HA and Darwin, J and Dicianno, BE and Greco, CM and Hoydick, J and Jakicic, JM and McKernan, GP and Parmanto, B and Patterson, CG and Piva, SR and Roos, RE and Schneider, MJ and Sundaram, M and Vo, NV and Zhou, L and Sowa, GA}, title = {In-Field Ecological Momentary Assessment From Wearable Motion Sensors and Self-Report in a Chronic Low Back Pain Cohort.}, journal = {JOR spine}, volume = {9}, number = {1}, pages = {e70156}, pmid = {41635465}, issn = {2572-1143}, support = {U19 AR076725/AR/NIAMS NIH HHS/United States ; }, abstract = {BACKGROUND: Chronic low back pain (cLBP) is a prevalent and debilitating condition. Gaining insight into the daily experiences of those with cLBP is crucial for developing effective management. Pain and activity are typically assessed at a single time point and often rely on retrospective self-reports, which can be prone to recall bias and may not reflect the day-to-day variability of these experiences. As a part of the University of Pittsburgh LB[3]P Mechanistic Research Center, this study used ecological momentary assessment (EMA) and wearable devices to collect real-time data in a large cohort of adults with cLBP. The primary aims were to collect and characterize pain and activity profiles of individuals with cLBP.<br><br>METHODS: This study enrolled 1007 adults with cLBP who met the National Institutes of Health defined criteria. Over 7&#x2009;days, participants were assessed in their own environment. EMA was gathered in real-time via a custom mobile app, prompting participants three times daily to provide their perceptions of current pain intensity (0-10), pain interference (0-10), and activity level (very light to vigorous). Time of falling asleep and waking was also reported. Participants wore ActiGraph GT9X devices on their wrist and waist. A custom back sensor was also adhered to the skin over the lumbar (L5) segment. Activity counts, wear time, and step counts were calculated, utilizing algorithms provided by ActiGraph. Sensor data were filtered to include at least 4&#x2009;days of 10 or more hours each. Activity counts were categorized into sedentary, light, and moderate-to-very-vigorous based on Freedson Adult cutpoints.<br><br>RESULTS: Out of 1007 participants, 989 submitted EMA data (58.8&#x2009;&#xb1;&#x2009;16.5&#x2009;years old; 40% male and 60% female; mean pain intensity at enrollment of 5.4 (SD 2.1) and a median of 5 (interquartile range [IQR] 3) on a 0-10 scale; mean PROMIS Pain Interference T-score at enrollment of 60.5 (SD 7.5) and a median of 61.2 (IQR 9.6)). The median reported pain intensity level from the EMA was 1 (IQR&#x2009;=&#x2009;3), while pain interference was 3 (IQR&#x2009;=&#x2009;3). More than half of the participants reported a median pain intensity of either 0 or 1 (54.0%) and a median pain interference between 0 and 3 (57.4%). Most participants self-reported their activity levels as moderate (36%) or light (33%). Based on pain ratings during each day, most participants had their pain intensity (30%) and pain interference (40%) peaking in the evening. ActiGraph data from 884 wrist-worn and 785 waist-worn devices were analyzed. Wrist data showed a median of 1&#x2009;765&#x2009;325 (IQR 796&#x2009;995) activity counts/day and 9575 (IQR 4228) steps/day. Waist data showed 358&#x2009;390 (IQR 223&#x2009;758) activity counts/day and 4114 (IQR 3146) steps/day. The percentage of daily sedentary activity was 47.3% for wrist and 72.8% for waist. The back sensor data from 586 participants showed a median of 340&#x2009;345 (IQR&#x2009;=&#x2009;223&#x2009;399) activity counts/day and a median of 3695 (IQR&#x2009;=&#x2009;2743) steps/day. The percentage of time spent in daily sedentary activity was 82.6%. Both ActiGraph devices and the back sensor indicated that the majority of the time was spent in sedentary activity level, which is lower than the activity level reported in the EMA.<br><br>CONCLUSIONS: Despite having cLBP with self-reported moderate pain levels, participants generally reported periods of relatively low levels of pain intensity and interference in their EMA. In addition, their EMA-reported activity levels differed from the sensor data. Participants self-reported higher levels of activity compared to the activity levels calculated by the wearable sensors. This suggests that participants overestimated their activity levels on EMA, or that the activity level cut-points may need to be re-evaluated for the cLBP population. Additionally, sensors placed on different body locations showed varying activity and step counts. The activity counts calculated from the waist ActiGraph and the back sensor from this cohort were lower than the average activity counts in the US adult population. Further research is needed to better quantify these differences for people with cLBP to develop a more comprehensive understanding of the pain experience.}, }
@article {pmid41629941, year = {2026}, author = {Aziz, MA and Malik, A and Hasan, M and Abidullah, S and Ullah, A and Ullah, Z and Abbasi, AM and Pieroni, A}, title = {Displacement threatens local knowledge: plant foraging in a cross-cultural context in the Gomal area, NW Pakistan.}, journal = {Journal of ethnobiology and ethnomedicine}, volume = {22}, number = {1}, pages = {12}, pmid = {41629941}, issn = {1746-4269}, mesh = {Pakistan ; Humans ; *Plants, Edible ; *Ethnobotany ; *Knowledge ; Female ; Male ; Cross-Cultural Comparison ; Adult ; Middle Aged ; Ethnicity ; }, abstract = {In the context of human displacement, it is essential to study how local knowledge is reshaped, eroded, or transformed. This study sheds light on how wild plant reports are articulated after migration, retained, and kept; the research explores specifically the ethnobotanical knowledge linked to wild food plants of five ethnic communities, namely the Bettani, Ormur, Mehsud, and Miani populations living in the Gomal area of NW Pakistan, of which three are displaced communities. The study aims to record the knowledge of wild food plants and their use among generations in these communities. To better determine the impact of displacement, we have analysed the data along two trajectories: (a) cross-geographically comparing the recorded wild food plant reports with the available published literature in NW Pakistan and (b) conducting a cross-cultural comparison of the local plant knowledge among the considered groups (displaced ones: Mehsud, Ormur, and Powanda; autochthonous: Bettani and Miani) residing in the Gomal area. Via semi-structured interviews with a hundred study participants (twenty for each ethic group), the study revealed the use of 69 wild food taxa, showing a remarkable diversity of food uses, with Ormur and Powanda exhibiting several idiosyncratic reports. The research highlights that displacement may have disrupted potential pathways of knowledge transmission among the Mehsud, Ormur, and Powanda; however, local plant knowledge about their past environment remains part of the collective memory of these communities. Moreover, post-migration exposure to a new ecological system has become a challenge for the newcomers, necessitating adaptation to rearticulate their relationship with nature and plants. The broken paths have a profound impact on plant knowledge transmission to youngsters, as social structures and gatherings have been significantly altered or disrupted; these were the primary means of interaction between youngsters and their elders. The exposure to urbanisation compounds the issue of displacement, and the erosion of knowledge systems has come at the expense of hands-on experiences among the selected groups. Notably, the local plant nomenclature of Ormur is also highly threatened. We advocate incorporating local plant knowledge into local educational curricula, which may be crucial for the sustainability of natural knowledge and have profound impacts on mitigating the effects of socioecological change.}, }
@article {pmid41629448, year = {2026}, author = {Tschimmel, D and Saeed, M and Milani, M and Waldherr, S and Hucho, T}, title = {Computational epitope heterogeneity analysis in immunostainings from antibody-dilution series.}, journal = {Communications biology}, volume = {9}, number = {1}, pages = {238}, pmid = {41629448}, issn = {2399-3642}, support = {459759629//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {*Epitopes/immunology/chemistry ; Humans ; *Antibodies/immunology ; *Fluorescent Antibody Technique/methods ; *Computational Biology/methods ; Animals ; }, abstract = {Antibodies are widely used in life sciences and medical therapy. Broadly applicable methods to determine epitope heterogeneity in immunostaining systems are missing. Here, we present a simple-to-use approach to characterize and quantify antibody binding properties that constitute the staining directly in the system of choice. We determine an epitope heterogeneity on the basis of a computational analysis of antibody-dilution immunofluorescence stainings. This allows us to choose signal-specificity maximizing dilutions and to improve signal quantification. Furthermore, the computational analysis provides approaches to obtain a single-channel antibody multiplexing. Our approach could help improving immunostainings in many laboratories by guiding the choice of antibody dilution, by increasing the possibility of antibody-multiplexing in the same color-channel and by allowing for the analysis of binding targets of multi-specific antibodies.}, }
@article {pmid41629371, year = {2026}, author = {Xiao, L and Xiang, J and Liu, X and Zhao, L and Li, Y and Chen, S}, title = {Unveiling scale effects in human settlement environment suitability through a novel multi-factor weighting approach.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {6952}, pmid = {41629371}, issn = {2045-2322}, support = {24C0383//Scientific Research Project of Hunan Provincial Department of Education of China/ ; 2026JJ90040//the Industry-Education Integration Project of the Ministry of Education of China/ ; }, mesh = {Humans ; China ; *Rural Population ; *Conservation of Natural Resources/methods ; Geographic Information Systems ; Spatial Analysis ; Sustainable Development ; Environment ; }, abstract = {Rural human settlement environment suitability is a key indicator for guiding land-use planning and promoting sustainable rural revitalization. This study develops a refined framework for evaluating the natural suitability of rural human settlement environments in central Hunan, China, using GIS-based spatial analysis. We propose an enhanced factor-weighting method that integrates normalized information entropy (NIE) and the coefficient of variation (CV) into a Pearson correlation coefficient (PCC)-driven approach, thereby improving the objectivity and sensitivity of weight determination. Comparative experiments demonstrate that this hybrid method captures the relative influence of natural factors more accurately than traditional PCC-based techniques. Results reveal a pronounced scale effect: as the spatial analysis scale decreases, disparities in factor weights become more evident. The spatial distribution of suitability exhibits a distinct east-high, west-low gradient, reflecting strong spatial heterogeneity across the region. Among all factors, terrain relief emerges as the dominant driver of suitability variations. Based on the calculated suitability index, the study delineates five functional zones and formulates corresponding development strategies tailored to local conditions. These findings offer a scientific basis for optimizing rural spatial planning and promoting sustainable development in central Hunan and similar regions. Beyond the case region, the framework provides a transferable approach for evaluating natural suitability in other mountainous rural areas. It also offers practical guidance for policymakers seeking to balance ecological protection with sustainable land-use development.}, }
@article {pmid41628277, year = {2026}, author = {Marrec, L and Lehtinen, S}, title = {Cluster dispersal shapes microbial diversity during community assembly.}, journal = {PLoS computational biology}, volume = {22}, number = {2}, pages = {e1013918}, pmid = {41628277}, issn = {1553-7358}, mesh = {*Microbiota/physiology ; *Biodiversity ; *Models, Biological ; Computational Biology ; Cluster Analysis ; }, abstract = {Identifying the drivers of diversity remains a central challenge in microbial ecology. In microbiota, within-community diversity is often linked to host health, which makes it all the more important to understand. Since many communities assemble de novo, microbial dispersal plays a critical role in shaping community structure during the early stages of assembly. While theoretical models typically assume microbes disperse individually, this overlooks cases where microbes disperse in clusters, such as, for example, during host feeding. Here, we investigate how cluster dispersal impacts species richness, between-community dissimilarity, and species abundance in the initial steps of microbial community assembly. We developed a model in which microbes disperse from a pool into communities as clusters and then replicate locally. Using both analytical and numerical approaches, we show that cluster dispersal promotes community homogenization by increasing within-community richness and reducing dissimilarity across communities, even at low dispersal rates. Moreover, it modulates the influence of local selection on microbial community assembly and, consequently, on species abundance. Our results demonstrate that cluster dispersal has distinct effects from simply increasing the dispersal rate. This work reveals new evidence for the role of cluster dispersal in the early dynamics of microbial community assembly.}, }
@article {pmid41623561, year = {2026}, author = {Xiao, S and Adams, JM and Li, S and Slik, F and Griffith, DM and Quaresma, A and Sultana, A and Rozak, AH and Muñoz, AA and Marshall, AR and Gabriel, A and Dar, AA and Mansor, A and Narayanan, A and Herault, B and Joly, CA and Piotto, D and Harris, DJ and Drake, DR and Sheil, D and Rocha, DSB and de Oliveira, EL and Nurtjahya, E and van den Berg, E and Webb, EL and Ibrahim, FH and Saiter, FZ and Wittmann, F and Ardila, FM and Durigan, G and Shukla, G and Ibarra-Manríquez, G and Nagamasu, H and Theilade, I and Zo-Bi, IC and Huamantupa-Chuquimaco, I and Rangel-Ch, JO and Grogan, J and Dar, JA and Schöngart, J and Herbohn, J and Poulsen, JR and Williams, JN and Lovett, J and De Alban, JD and Lozada, JR and Pinto, JRR and Guevara-Andino, JE and Cristóbal-Azkarate, J and Homeier, J and Böhning-Gaese, K and Hakeem, KR and Feeley, K and Tomlinson, KW and Rasingam, L and Demarchi, LO and Laumonier, Y and Alves, LF and Montenegro, LT and Satdichanh, M and Macía, MJ and Tabarelli, M and Suganuma, MS and Ríos Paredes, MA and Fernandez Piedade, MT and Schulze, M and van de Bult, M and Bastian, ML and Khan, ML and Hussain, MS and Kessler, M and Lawes, MJ and Munguía-Rosas, MA and Parthasarathy, N and Seuaturian, N and Kanda, NB and Jagadeesan, N and Pitman, N and Onrizal, O and Vetaas, OR and Munishi, P and Chhang, P and Bispo, PDC and Zakaria, R and Sukri, RS and Muthu, R and Prasad, RC and V S, R and Harrison, RD and Veridiano, RK and Steinmetz, R and Chazdon, RL and Tumaneng, R and Gonçalves Rolim, S and Garkoti, SC and Báez, S and Wich, S and Mukul, SA and Joseph, S and Vieira, SA and Muthuramkumar, S and Sundarapandian, S and Chakravarty, S and Kothandaraman, S and Wendt, T and Metzker, T and Whitfeld, T and Su, T and Van Andel, TR and Hans, V and Arroyo-Rodríguez, V and Chutipong, W and Laurance, WF and Carrero, YA and Zhou, Z}, title = {Analogous environments across the tropics have similar levels of tree species alpha diversity.}, journal = {National science review}, volume = {13}, number = {2}, pages = {nwaf465}, pmid = {41623561}, issn = {2053-714X}, abstract = {Different regions of the tropics vary in overall tree species diversity, with the tropical Americas exhibiting strikingly higher regional tree species richness than Africa and Southeast Asia. We investigated whether these differences also occur at the local scale and whether the environmental conditions associated with tree species richness are consistent across tropical regions despite highly dissimilar species pools. A spatial random forest model was trained by using a network of 429 1-hectare plots across the tropics, together with 24 environmental variables, to predict plot-level tree α diversity. A combination of climatic, soil and topographical variables explained ∼86% of the variation in richness. Despite differences in regional species pools and the potentially disruptive effects of different geological, climatic and evolutionary histories, the relationship between environmental variables and local-scale tree species richness is closely similar across different continents. Our findings imply a pervasive role of niche-based mechanisms in structuring local tree species richness, regardless of the regional species assemblages. This pantropical convergence in the richness-environment relationship poses a challenge for ecology to explain.}, }
@article {pmid41621727, year = {2026}, author = {De Luca, D}, title = {FastqOrienter: A Python utility for the automated orientation and quality diagnostics of paired-end Illumina metabarcoding reads.}, journal = {Journal of microbiological methods}, volume = {242}, number = {}, pages = {107413}, doi = {10.1016/j.mimet.2026.107413}, pmid = {41621727}, issn = {1872-8359}, mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Software ; *Sequence Analysis, DNA/methods ; *DNA Barcoding, Taxonomic/methods ; *Computational Biology/methods ; }, abstract = {FastqOrienter is a Python tool that corrects inconsistent read orientations in Illumina paired-end metabarcoding reads using a primer-aware logic and IUPAC-compliant matching. In addition, it provides detailed diagnostics and actionable insights for discarded reads. It ensures data integrity for downstream pipelines like DADA2 and QIIME 2.}, }
@article {pmid41619592, year = {2026}, author = {Nguyen, HT and Wijaya, J and Kim, J and Lee, JE and Yoon, JK and Oh, S}, title = {Predictive monitoring, identification, and control of Microcystis blooms in a drinking water source basin: An integrative artificial intelligence and bioinformatics approach.}, journal = {Journal of hazardous materials}, volume = {504}, number = {}, pages = {141288}, doi = {10.1016/j.jhazmat.2026.141288}, pmid = {41619592}, issn = {1873-3336}, mesh = {*Microcystis/genetics/isolation &amp; purification/growth &amp; development ; *Artificial Intelligence ; *Harmful Algal Bloom ; Computational Biology ; *Drinking Water/microbiology ; *Environmental Monitoring/methods ; Water Supply ; Water Purification ; }, abstract = {Harmful algal blooms (HABs) pose serious challenges for drinking water utilities; however, conventional monitoring in drinking water source basins remains largely reactive. To address this, we present an integrative framework that combines artificial intelligence (AI) forecasting with strain-resolved bioinformatic diagnostics to enable proactive monitoring of bloom-causing HAB in drinking water source. The AI model employed environmental input features and was optimized, which achieved high predictive accuracy (up to 0.9 R[2]) with early warning capabilities (1 week lead time). Explainable AI pinpointed organic and nitrogen compounds as top predictors for HAB events. Phylogenomic analysis using short- and long-read sequencing elucidated the population structure, toxicological traits, and ecological adaptation of the bloom-causing Microcystis population (NRERC-214). Field surveys with bioinformatic analysis at a full-scale drinking water treatment plant found complete removal of Microcystis. The relative strengths and weaknesses of the individual units in removing Microcystis in the plant was validated with the phenotypic/genotypic features of Microcystis bioinformatically determined in this study. Overall, this study suggested the integration of a predictive surveillance and diagnosis framework into a source water management scheme, supporting a paradigm shift from reactive post-event management to proactive, risk-based control for drinking water.}, }
@article {pmid41618863, year = {2026}, author = {Mehr, S and Castoe, T and Daly, M and Jungo, F and Kirchhoff, KN and Koludarov, I and Mackessy, SP and Macrander, J and Naidu, P and Modica, MV and Sanchez, EE and Zancolli, G and Holford, M}, title = {A Proposed Unified, Scalable Platform for Integrative Research on Venomous Species.}, journal = {GigaScience}, volume = {}, number = {}, pages = {}, doi = {10.1093/gigascience/giaf153}, pmid = {41618863}, issn = {2047-217X}, abstract = {Venomous animal research is hampered by fragmented, specialized, and non-interoperable databases (isolated genomic, proteomic, and ecological data). Despite the immense promise of venomous organisms to yield novel bioactive compounds for pharmacological and evolutionary applications, the informatics landscape for such taxa has remained patchy, lacking macro-scale integration across species. We present VenomsBase, an integrated, modular resource that synthesizes multi-omics data, ecological metadata, and functional annotations for venom-bearing organisms. Following the FAIR guidelines, VenomsBase combines an ontology-driven architecture with big-data cloud workflows for sequence integration, motif clustering, 3D display, and linking ecological metadata. Standardized tools and training modules facilitate worldwide access to resources for both researchers in developed countries and in resource-limited areas. Its plug-and-play design allows for integration of additional analytical modules and extension to other species. One can also examine evolutionary trends and connect venom chemistry to ecological niches. VenomsBase would (i) accelerate the pace of venom discovery, whether for therapeutic purposes or evolutionary significance, by providing validated, cross-referenced data sets and community-driven curation, and (ii) foster an open, just, and innovation-ready venom research ecosystem.}, }
@article {pmid41617863, year = {2026}, author = {Sharma, A and Singh, AP and Rallapalli, S}, title = {Adaptive Basin Management under Determinate and Indeterminate Sustainability Factors.}, journal = {Environmental management}, volume = {76}, number = {3}, pages = {69}, pmid = {41617863}, issn = {1432-1009}, mesh = {*Conservation of Natural Resources/methods ; *Rivers ; Climate Change ; Fuzzy Logic ; Decision Support Techniques ; }, abstract = {Adaptive river basin management is uncertain and complex, as it requires assessing the combined effects of climate change and human activities. Conventional strength-weakness-opportunities and threat (SWOT) decision analysis failed to quantify the indeterminacy concerning factors in adaptive management. To address these limitations, this study introduces a hybrid decision-support system that combines interval valued fuzzy hybrid SWOT (IVFH-SWOT) analysis with fuzzy evaluation of resilience metrics (FERM). To demonstrate its effectiveness, the study evaluated 11 strategic options across four aspects of adaptive sustainability: ecological balance, hydrological-geomorphological integrity, socio-economic and energy potential, and catastrophe resilience. The derived strategies were prioritized based on the multi-stakeholder analysis performed on the data gathered about these four aspects. The findings underscore dam operations regulations (score: 0.7561), treatment of wastewater infrastructure (0.7226), and development of hydropower (0.7122) as the most efficacious strategies. These findings illustrate the trade-offs between resilience performance and sustainability under indeterminate conditions. The proposed framework offers a robust, transferable tool for practitioners and policymakers for adaptive sustainable river basin management.}, }
@article {pmid41617738, year = {2026}, author = {Sentil, A and Miličić, M and Benrezkallah, J and Ačanski, J and Andrić, A and Aubert, M and Bartomeus, I and Biella, P and Boustani, M and Carstensen, LB and Bogusch, P and Bot, S and Brau, T and Budrys, E and Salazar, LC and Cappellari, A and Carion, F and Castro, S and Cavaillès, S and Cerretti, P and Dathe, HH and De Groot, M and De Tandt, B and Devalez, J and Devorsine, R and Díaz-Calafat, J and Đorđević, A and Dormal, A and Dufrêne, E and Dussaix, C and Fedorova Zaytseva, LA and Fiordaliso, W and Flaminio, S and Földesi, R and Forgeois, V and Gadoum, S and Garrin, M and Gaspar, H and Gazzea, E and Geppert, C and Gérard, M and Geslin, B and Ghisbain, G and Gibernau, M and Grković, A and Heimburg, H and Herinckx, A and Demeter, I and Janković Milosavljević, M and Janssen, K and Kasparek, M and Kierat, J and Kleijn, D and Kuhlmann, M and Lair, X and Lemaire, S and Lenzi, L and Likov, L and Litman, J and Lopes, SB and Loureiro, J and Maarten, J and Maestracci, PY and Marini, L and Maritano, U and Mei, M and Mignot, M and Stojnić, SM and Nedeljković, Z and Ockermueller, E and Ortiz-Sanchez, FJ and Patiny, S and Paukkunen, J and Pennards, G and Perrard, A and Petanidou, T and Popov, G and Popov, S and Potts, SG and Prokhorov, A and Pruner, S and Radchenko, V and Radenković, S and Rasmont, P and Reverté, S and Ricarte, A and Rojo, S and Romig, T and Rosa, P and Ruiz, C and Sagot, P and Santerre, R and Scheper, J and Selis, M and Sgolastra, F and Shparyk, V and Siopa, C and Skendžic, T and Smit, J and Sommaggio, D and Soon, V and Ssymank, A and Ståhls, G and Stavrinides, M and Steffan-Dewenter, I and Straka, J and Thulier, J and Tot, T and Tourbez, C and van Steenis, J and van Steenis, W and Varnava, A and Veselić, S and Vesnic, A and Vray, S and Williams, P and Wood, TJ and Zimmermann, D and Żmuda, A and Vujić, A and Michez, D and de Manincor, N}, title = {Synthesised database of wild bee and hoverfly records in Europe.}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {227}, pmid = {41617738}, issn = {2052-4463}, mesh = {Animals ; Bees ; Europe ; *Diptera ; Pollination ; Databases, Factual ; }, abstract = {Wild bees (Hymenoptera: Anthophila) and hoverflies (Diptera: Syrphidae), the two major groups of insect pollinators, are undergoing alarming declines worldwide, including Europe. The lack of accessible and verified spatial and temporal occurrence records currently challenges efforts to understand and mitigate this decline. Here, we compiled datasets from diverse sources, including taxonomists, national experts, public repositories, museum collections, published literature, verified open-access platforms, and aggregated datasets from previous European projects. The collected data were standardised, cleaned and validated by taxonomists and national experts. This collective effort resulted in two databases comprising more than 4.34 million and 1.04 million records for wild bees and hoverflies, respectively. The databases cover 97% of the European bee fauna (2,083 species out of 2,138 recorded in Europe) and 97% of the European hoverfly fauna (886 species out of 913 recorded in Europe). These standardised databases constitute essential resources for future assessments of status and trends, habitat associations, and other research and conservation initiatives to protect and understand wild pollinators on the European continent.}, }
@article {pmid41617719, year = {2026}, author = {Li, T and Zhang, J and Guo, J and Sun, B and Han, Y and Xu, H and Weng, Y and Cao, Q and Li, M and Zhao, G and Liu, L and Gao, X and Dai, L and Wang, D and Cao, Y}, title = {Engineered internal architecture of core-shell lipid nanoparticles promotes efficient mRNA endosomal release.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-69017-8}, pmid = {41617719}, issn = {2041-1723}, abstract = {Messenger RNA (mRNA) therapeutics rely on lipid nanoparticles (LNPs) for delivery, yet inefficient endosomal escape remains a major bottleneck, with only a small fraction of internalized cargo reaching the cytoplasm. Conventional LNPs encapsulate mRNA in amorphous lipid cores, where partial charge neutralization and lack of structural order limit protonation-driven membrane disruption. Here, we present an architectural strategy that engineers LNP internal structure using ionizable lipid-coated gold nanoparticles (IC-AuNPs) as rigid, pH-responsive cores. The Au cores template the formation of radially ordered core-shell architectures that stabilize particles at physiological pH while amplifying charge segregation and curvature stress under acidic endosomal conditions. As a result, Au-LNPs achieve a twofold increase in endosomal escape and ~100-fold greater cytoplasmic mRNA diffusion compared to conventional LNPs. Functionally, Au-LNPs enhance mRNA expression in vitro, increases in vivo protein production up to sevenfold, boost antibody responses to SARS-CoV-2 vaccines, and improve therapeutic efficacy in a triple-negative breast cancer model.}, }
@article {pmid41611716, year = {2026}, author = {Xue, M and Yang, X and Chen, X and Ciais, P and Zhou, L and Reich, PB and Xiao, J and Li, X and Xiao, X and Green, JK and Chen, JM and Liu, J and Shang, J and Luo, X and Tian, J and Liu, H and Zhu, P and Yan, K and Fu, X and Han, L and Yuan, W and Wu, C}, title = {Pantropical moist forests are converging towards a middle leaf longevity.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-68989-x}, pmid = {41611716}, issn = {2041-1723}, abstract = {Leaf longevity is a fundamental plant trait that largely explains ecosystem functional dynamics in global pantropical moist forests. However, the signs, magnitudes, and mechanisms of the spatiotemporal variations in leaf longevity with ongoing climate change are still lacking. Using both ground measurements and gridded leaf age-dependent leaf area index data, we map the continental-scale variability of annual mean leaf longevity across pantropical moist forests over 2001-2023. We find a biome-dependent and converging trend in leaf longevity under climate change. In Amazon and tropical Asia with long leaf longevity (> ~1.8 years), leaf longevity decreases due to rising temperature and intensified atmospheric dryness. In contrast, an increasing trend is observed in Congo and subtropical Asia where forests have short leaf longevity (<~1.8 years). These responses cause a convergence of pantropical short and long leaf longevity into a middle longevity range, with maximization of plant functional traits, photosynthesis, and species evenness, which are expected to better resist climate variability. Our study provides emerging evidence for large-scale structural and functional adaptions across pantropical moist forests and is helpful for predicting climate-driven risks to ecosystem stability.}, }
@article {pmid41610871, year = {2026}, author = {Weiskopf, SR and Morelli, TL and Mozelewski, TG and Shiklomanov, AN and Lerman, SB}, title = {Restoration based on cost-benefit optimization: A grasslands pilot study.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {36}, number = {1}, pages = {e70174}, pmid = {41610871}, issn = {1939-5582}, mesh = {*Grassland ; *Conservation of Natural Resources/economics/methods ; Animals ; Pilot Projects ; Cost-Benefit Analysis ; *Environmental Restoration and Remediation/economics/methods ; Kansas ; Biodiversity ; }, abstract = {Ecological restoration is essential to meeting global biodiversity conservation goals. Given limited conservation budgets, deciding where to restore habitat is a key challenge for the coming decade. We developed a spatially explicit framework to optimize ecological restoration site selection by integrating land use history, species distributions, and economic costs. The framework includes the following steps: identify potential restoration area based on relevant environmental measures like land use; identify species of interest; calculate restoration benefits by modeling habitat and climate suitability and estimating reduced extinction risk associated with restoring a particular land parcel based on a modified species-area relationship; aggregate benefits across species; and compare to parcel-level land acquisition costs. We applied linear programming to maximize conservation benefit/restoration cost ratios to identify optimized restoration sites. We illustrate this approach using a case study for highly threatened grassland ecosystems in the Great Plains region of Kansas, USA. We selected five grassland animal species (greater prairie chickens [Tympanuchus cupido], lesser prairie chickens [Tympanuchus pallidicinctus], swift fox [Vulpes velox], pronghorn [Antilocapra americana], and regal fritillary [Speyeria idalia]) as indicators of restoration benefit across taxa. For the indicator species that we chose, shortgrass and mixed-grass prairies had the highest conservation benefit to cost ratio. Setting a minimum restoration threshold for each habitat type allowed us to identify high-priority tallgrass prairie sites. Despite increasing interest in ecological restoration, optimizing restoration site selection is challenging because one must consider habitat features that do not currently exist. The modeling approach described here is flexible and can be updated for different ecosystems, species, and conservation priorities. We outline potential alterations that can be made in future analyses, depending on desired restoration goals.}, }
@article {pmid41610663, year = {2026}, author = {Lu, W and Du, Q and Shang, Y and Du, Y and Zhang, Z and Jin, H and Zhang, W and Li, L}, title = {Multi-omics insights into Alizarin red S-induced alterations in redox balance, immune function and metabolism in juvenile silver carp (Hypophthalmichthys molitrix).}, journal = {Journal of hazardous materials}, volume = {504}, number = {}, pages = {141270}, doi = {10.1016/j.jhazmat.2026.141270}, pmid = {41610663}, issn = {1873-3336}, mesh = {Animals ; *Anthraquinones/toxicity ; *Water Pollutants, Chemical/toxicity ; *Carps/metabolism/immunology/genetics ; Oxidation-Reduction ; Gills/drug effects/metabolism/pathology ; Transcriptome/drug effects ; Oxidative Stress/drug effects ; Metabolomics ; Metabolome/drug effects ; Multiomics ; }, abstract = {Alizarin red S (ARS), a widely used anthraquinone dye in industrial processes, has emerged as a potential environmental contaminant with poorly understood ecotoxicological impacts on aquatic organisms. In this study, juvenile silver carp (Hypophthalmichthys molitrix) were exposed to graded concentrations of ARS (0, 100, 125, and 150 mg/L) for 96 h, revealing clear dose-dependent toxicity characterized by reduced survival and progressive histopathological damage in pelvic fins, opercula, and otoliths. Integrated multi-omics analyses of gill tissues demonstrated that high-dose ARS exposure profoundly disrupts physiological homeostasis. Transcriptomic profiling revealed concentration-dependent dysregulation of genes involved in xenobiotic metabolism, oxidative stress, immune response, and metabolic pathways. Notably, exposure to 150 mg/L ARS significantly perturbed signaling pathways associated with immune dysregulation and cellular stress responses. Metabolomic analysis identified 478 differentially abundant metabolites, with pathway enrichment indicating disruption of lipid and amino acid metabolism, particularly glutathione and arginine metabolism. Integrated transcriptome-metabolome analysis further highlighted coordinated alterations in critical pathways including glutathione metabolism, antigen processing and presentation, phagosome, and cytochrome P450-mediated drug metabolism, suggesting a transition from antioxidant defense to systemic immune and metabolic dysfunction under high-dose exposure. Functionally, the activities of catalase (CAT), superoxide dismutase (SOD), and glutathione peroxidase (GSH-Px), along with glutathione (GSH) content, peaked at 100 mg/L ARS. Critically, malondialdehyde (MDA) content decreased significantly with increasing ARS concentration, attaining a minimum at 150 mg/L ARS. Collectively, these findings define a critical threshold for toxicological transition, provide crucial insights into the ecological hazards posed by anthraquinone dyes and underscore the necessity for stringent regulatory control of ARS emissions into aquatic ecosystems.}, }
@article {pmid41610512, year = {2026}, author = {Lopez-Rodriguez, D and Guerrero-Limón, G and Chèvre, N}, title = {A chemical space model for the exploration of eco-toxicological data.}, journal = {Environment international}, volume = {208}, number = {}, pages = {110096}, doi = {10.1016/j.envint.2026.110096}, pmid = {41610512}, issn = {1873-6750}, mesh = {Animals ; Daphnia/drug effects ; *Ecotoxicology/methods ; Risk Assessment ; *Models, Chemical ; Databases, Factual ; Hazardous Substances/toxicity ; }, abstract = {With over 350,000 chemicals and mixtures currently registered for production and use worldwide, around 83% of authorized chemicals lack adequate toxicity data, leaving the majority of chemicals poorly characterized. International agencies urge scientists to develop screening methods to explore, identify, and predict chemical hazards, supporting the prioritization of chemical risk assessment. Here, Tree Manifold Approximation and Projection (TMAP) were applied, with the aim of reducing the dimensionality of large toxicological dataset, providing the foundations to data imputation methods allowing to get an understanding of chemical modes of action. Specifically, TMAP was implemented using MHFP6 fingerprints and the NORMAN SusDat database, which contains over 100,000 compounds. To ensure that the TMAP layout preserves chemical structural similarity, a quantitative parameter optimization procedure was developed. The defined optimal parameter set allowed us to define the embeddings that preserves the most structural similarity among nearest connected neighbors, with similarity progressively decreasing as the distance between nodes increases. Leveraging this approach, a graph-based spatial imputation function was generated to obtain insights into the potential ecotoxicity mechanisms of data poor chemicals using physicochemical properties and CTD toxicogenomic data. The relevance and meaningfulness of TMAP chemical space was explored for Daphnia magna, Pimephales promelas and Algae. Chemical classes known to be structurally similar were found to be grouped together in the TMAP chemical space, while heterogeneous classes were found to be sparse. Data imputation allowed for the identification of known and potential chemical mechanisms of action. Indeed, acetylcholinesterase and transthyretin were confirmed as major mechanisms of action of organothiophosphate and brominated flame retardant toxicity in Daphnia magna and Pimephales promelas, respectively. Overall, transdisciplinary toxicological databases combined with TMAP, stand out as a computationally efficient and suitable method to explore and analyze large datasets, allowing for the inference of associations between chemical structures and chemical hazard identification and other potential applications of this hypotheses-generating tool.}, }
@article {pmid41610226, year = {2026}, author = {Schakowski, A and Deffner, D and Kortet, R and Niemelä, PT and Kavelaars, MM and Monk, CT and Pykälä, M and Kurvers, RHJM}, title = {High-precision tracking of human foragers reveals adaptive social information use in the wild.}, journal = {Science (New York, N.Y.)}, volume = {391}, number = {6784}, pages = {eady1055}, doi = {10.1126/science.ady1055}, pmid = {41610226}, issn = {1095-9203}, mesh = {Humans ; Geographic Information Systems ; *Social Behavior ; Cognition ; *Decision Making ; *Feeding Behavior ; Video Recording ; }, abstract = {Foraging complexity and competitive social challenges are considered key drivers of human cognition. Yet, the decision-making mechanisms that underlie social foraging in the real world remain unknown. Integrating high-precision Global Positioning System (GPS) tracking and video footage from large-scale foraging competitions with cognitive-computational modeling and agent-based simulations, we show how foragers integrate personal, social, and ecological information to guide spatial search and patch-leaving decisions. We show how the social context emerges as a key driver of foraging dynamics. Foragers adaptively rely on social information to locate resources when unsuccessful and extend giving-up times in the presence of others, which results in increased area-restricted search at high social densities. These findings demonstrate the importance of sociality for human foraging decisions and provide a template for harnessing high-resolution tracking data to study real-world cognition.}, }
@article {pmid41604932, year = {2026}, author = {Mei, X and Zhu, T and Zhong, B and Wu, WM and Li, N and Wang, Y and Liu, X and Liu, R and Abdul, R and Yi, S and He, Y}, title = {Artificial intelligence in microplastics domain: Current progress, challenges, and sustainable prospects.}, journal = {Journal of hazardous materials}, volume = {503}, number = {}, pages = {141233}, doi = {10.1016/j.jhazmat.2026.141233}, pmid = {41604932}, issn = {1873-3336}, abstract = {Microplastics (MPs) have emerged as pervasive and persistent global environmental contaminants. However, the current inability to robustly analyze these particles hinders a deeper mechanistic understanding of their environmental behavior and ecological consequences. Artificial Intelligence (AI), with its computational power and data processing capabilities, is revolutionizing the analysis of MPs and transforming methodological paradigms. This critical review summarizes key challenges in the field, including persistent methodological limitations in characterization techniques and the interpretation of environmental behavior. We also critically examine emerging applications of AI in MPs domain. We explore the reliability and generalizability of these AI-driven approaches, highlighting that while data accessibility and computational resources pose core operational challenges, the environmental costs and ethical dilemmas of AI also demand scrutiny. Finally, we envision a paradigm shift towards an eco-conscious AI that harmonizes ecological accountability with computational efficiency. Fostering this transition through interdisciplinary collaboration is crucial for guiding MPs research toward a future that is sustainable across environmental, economic, and social consideration.}, }
@article {pmid41600098, year = {2026}, author = {Tajti, K and Farkas, A and Farkas, M and Bíró, T and Ördög, V and Maróti, G}, title = {Synergistic Plant Biostimulatory Effects of an Inter-Kingdom Interaction: Chlorella sp. and Kocuria rhizophila Algal-Bacterial Co-Culture for Sustainable Crop Production.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, pmid = {41600098}, issn = {2223-7747}, abstract = {Plant biostimulatory effects of the green alga Chlorella sp. MACC-360, the Kocuria rhizophila FSP120 bacterial strain, and the combined inter-kingdom co-culture of the alga and bacterium were investigated using Solanum lycopersicum as a model plant grown under controlled greenhouse conditions. The application of algal-bacterial co-cultures using the soil drench method significantly improved plant growth parameters, vegetative biomass yield, fruit yield, and photosynthetic performance of the tomato plants. The combined treatment resulted in a 43.7% increase in mean fruit yield, while individual applications of K. rhizophila FSP120 and Chlorella sp. MACC-360 enhanced yields by 30.85% and 19.44%, respectively. Although total yield increases did not reach statistical significance due to high intra-group variability, the treatment's efficacy was statistically confirmed through key yield parameters including significantly higher fruit weight and fruit diameter (p < 0.05). The enhanced specific biostimulatory effects of the combined treatment could be at least partly attributed to the increased level of algal extracellular polymeric substances (EPS), which was a specific effect of algal co-cultivation with a Kocuria rhizophila bacterium. Detailed analysis of plant phenotypic alterations, biomass yield, fruit and flowering parameters, as well as microbial community analysis of the rhizosphere, were conducted and compared among the various treatments. Our results indicate that an appropriately chosen combination and application of biostimulatory microbes can significantly enhance crop production, which might contribute to more sustainable agriculture.}, }
@article {pmid41599943, year = {2026}, author = {Rocha, HR and Ribeiro, P and Rodrigues, PM and Gomes, AM and Pintado, M and Coelho, MC}, title = {Bioinformatic Insights into the Carotenoids' Role in Gut Microbiota Dynamics.}, journal = {Nutrients}, volume = {18}, number = {2}, pages = {}, pmid = {41599943}, issn = {2072-6643}, mesh = {*Gastrointestinal Microbiome/drug effects ; *Carotenoids/pharmacology/chemistry ; *Computational Biology ; Humans ; Fermentation ; Lycopene/pharmacology ; Lutein/pharmacology ; Bacteria/drug effects/genetics/classification ; beta Carotene/pharmacology ; }, abstract = {Background/Objectives: Carotenoids are bioactive pigments with well-established antioxidant and immunomodulatory properties, yet their impact on gut microbiota remains poorly understood from a chemical standpoint. This study explores how carotenoid structure and gastrointestinal stability shape microbial responses combining in vitro fermentation with bioinformatic analyses. Methods: Individual carotenoids (beta (β)-carotene, lutein, lycopene) and combined carotenoids, as well as algal-derived extracts were subjected to 48 h in vitro fermentation, and microbial composition and activity were assessed through sequencing and computational analysis. Results: β-carotene and lycopene promoted acid-tolerant taxa such as Escherichia-Shigella, whereas lutein, due to its higher polarity, supported more transient fluctuations. Mixtures and algal carotenoids exhibited synergistic effects, sustaining beneficial genera including Bifidobacterium and Bacteroides and promoting structured ecological trajectories. Conclusions: These findings provide a chemistry-driven perspective on how carotenoids act as modulators of microbial ecosystems, with direct implications for the formulation of carotenoid-enriched functional foods and dietary interventions.}, }
@article {pmid41597522, year = {2025}, author = {Tamahara, T and Kouketsu, A and Fukase, S and Sripodok, P and Saito, T and Ito, A and Li, B and Kumada, K and Shimada, M and Iikubo, M and Shimizu, R and Yamauchi, K and Sugiura, T}, title = {Ecological and Functional Landscape of the Oral Microbiome: A Multi-Site Analysis of Saliva, Dental Plaque and Tongue Coating.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, pmid = {41597522}, issn = {2076-2607}, support = {JP24K1310 and JP22K17150//JSPS KAKENHI/ ; }, abstract = {The oral cavity contains several microbial niches, including saliva, dental plaque and tongue coating, each shaped by distinct local environments and host factors. This study compared the ecological and functional characteristics of the microbiomes of these three oral sites within the same individuals and examined host conditions associated with their variation. Saliva, supragingival plaque and tongue coating samples were collected simultaneously from 31 adults without clinical oral lesions. The bacterial 16S rRNA gene (V3-V4 region) was sequenced using the Illumina MiSeq platform, and analyses included α and β diversity, Mantel correlations, differential abundance tests, network analysis and functional prediction. The three sites displayed a clear ecological gradient. Saliva and tongue coating were taxonomically similar but were influenced by different host factors, whereas plaque maintained a distinct, biofilm-like structure with limited systemic influence. Functional divergence was most pronounced on the tongue coating despite its taxonomic similarity to saliva, whereas functional differences between saliva and plaque were modest despite larger taxonomic separation. These findings indicate that microbial composition and function vary independently across oral niches and support the need for multi-site sampling to more accurately characterize oral microbial ecology.}, }
@article {pmid41597405, year = {2026}, author = {Sekulic, M and Stepovic, M and Sorak, M and Mijailovic, S and Rajkovic Pavlovic, Z and Vulovic, M and Radmanovic, O and Radmanovic, B and Vuckovic Filipovic, J and Gavrilovic, J and Jovanovic, B and Spasic, B and Folic, N and Rosic, V and Dragicevic, T and Markovic, V}, title = {Elevated Blood Pressure and Risk Factors in 19-Year-Olds in Serbia: A Cross-Sectional Study.}, journal = {Medicina (Kaunas, Lithuania)}, volume = {62}, number = {1}, pages = {}, pmid = {41597405}, issn = {1648-9144}, mesh = {Humans ; Male ; Serbia/epidemiology ; Cross-Sectional Studies ; Female ; *Hypertension/epidemiology ; Risk Factors ; Young Adult ; Logistic Models ; Surveys and Questionnaires ; Feeding Behavior ; Blood Pressure/physiology ; Adult ; Prevalence ; }, abstract = {Background and Objectives: Hypertension in young adulthood is increasingly recognized as a precursor to future cardiovascular disease. Early identification of modifiable risk factors, such as dietary habits, lifestyle behaviors, and psychological indicators, is critical for prevention. This study aimed to examine the elevated clinic blood pressure and associated factors in 19-year-old individuals in Serbia. Materials and Methods: A cross-sectional study was conducted using data from the 2019 Fourth National Health Survey. A total of 212 participants underwent blood pressure measurement, anthropometric assessment, and completed standardized questionnaires on diet, physical activity, depressive symptoms, and sociodemographic characteristics. Blood pressure was classified according to ESC/ESH guidelines. Associations with elevated blood pressure were assessed using chi-square tests and multivariate logistic regression. Results: Most participants had optimal or normal blood pressure, while 18.9% had elevated blood pressure, including high-normal and Grade I-II hypertension. Elevated blood pressure was more prevalent among males and was associated with depressive symptoms. Nutrition status was significantly associated with elevated blood pressure, and some dietary habits like consumption of pure fruit or vegetable juices and the intake of processed meat products. Other socioeconomic factors, eating habits and physical activity were not significantly correlated. In multivariate logistic regression, elevated arterial blood pressure was significantly associated with consuming pure fruit or vegetable juices less than once per week (OR = 3.239; 95% CI: 1.413-7.427) and with consuming processed meat products several times per week in comparison to the daily consumption (OR = 0.325; 95% CI: 0.130-0.812), while no other variables remained statistically significant. Conclusions: Clinically elevated arterial blood pressure is present in a substantial proportion of 19-year-olds. Early lifestyle interventions targeting nutrition and psychological health may prevent progression to hypertension and reduce long-term cardiovascular risk.}, }
@article {pmid41597231, year = {2026}, author = {Feng, Y and Geng, Y and Liu, S and Huang, X and Mou, C and Zhao, H and Zhou, J and Li, Q and Deng, Y}, title = {Overwinter Syndrome in Grass Carp (Ctenopharyngodon idellus) Links Enteric Viral Proliferation to Mucosal Disruption via Multiomics Investigation.}, journal = {Cells}, volume = {15}, number = {2}, pages = {}, pmid = {41597231}, issn = {2073-4409}, support = {2024YFD2401102//National Key R&amp;D ProgramNational Key R&amp;D Program/ ; 2025ZNSFSC1081//Sichuan Provincial Natural Science Foundation/ ; NKYRCZX2025031//Research Initiation Funding from the Sichuan Academy of Agricultural Sciences/ ; SCCXTD-2025-15//Sichuan Freshwater Fish Innovation Team of the National Modern Agricultural Industrial Technology System/ ; }, mesh = {Animals ; *Carps/virology/microbiology ; *Fish Diseases/virology/microbiology/genetics ; *Intestinal Mucosa/virology/pathology/microbiology ; Gastrointestinal Microbiome ; Metagenomics ; Transcriptome ; Multiomics ; }, abstract = {Overwinter Syndrome (OWS) affects grass carp (Ctenopharyngodon idellus) aquaculture in China, causing high mortality and economic losses under low temperatures. Failure of antibiotic therapies shows limits of the 'low-temperature-pathogen' model and shifts focus to mucosal barrier dysfunction and host-microbiome interactions in OWS. We compared healthy and diseased grass carp collected from the same pond using histopathology, transcriptomics, proteomics, and metagenomics. This integrated approach was used to characterize intestinal structure, microbial composition, and host molecular responses at both taxonomic and functional levels. Results revealed a three-layer barrier failure in OWS fish: the physical barrier was compromised, with structural damage and reduced mucosal index; microbial dysbiosis featured increased richness without changes in diversity or evenness, and expansion of the virobiota, notably uncultured Caudovirales phage; and mucosal immune dysregulation indicated loss of local immune balance. Multi-omics integration identified downregulation of lysosome-related and glycosphingolipid biosynthesis pathways at transcript and protein levels, with disrupted nucleotide metabolism. Overall gut microbial richness, rather than individual taxa abundance, correlated most strongly with host gene changes linked to immunity, metabolism, and epithelial integrity. Although biological replicates were limited by natural outbreak sampling, matched high-depth multi-omics datasets provide exploratory insights into OWS-associated intestinal dysfunction. In summary, OWS entails a cold-triggered breakdown of intestinal barrier integrity and immune homeostasis. This breakdown is driven by a global restructuring of the gut microbiome, which is marked by increased richness, viral expansion, and functional shifts, ultimately resulting in altered host-microbe crosstalk. This ecological perspective informs future mechanistic and applied studies for disease prevention.}, }
@article {pmid41596699, year = {2026}, author = {Wang, R and Gu, C and Li, H and Wang, L and Sun, R and Fu, K and Shi, W and Wan, X}, title = {Multi-Omics Profiling of the Hepatopancreas of Ridgetail White Prawn Exopalaemon carinicauda Under Sulfate Stress.}, journal = {International journal of molecular sciences}, volume = {27}, number = {2}, pages = {}, pmid = {41596699}, issn = {1422-0067}, support = {JC2023085//The Nantong City Natural Science Foundation Project/ ; }, mesh = {Animals ; *Palaemonidae/metabolism/genetics/drug effects ; *Hepatopancreas/metabolism/drug effects/ultrastructure ; *Sulfates/toxicity ; Proteomics/methods ; *Stress, Physiological ; Transcriptome ; Multiomics ; }, abstract = {With intensifying global climate change and human activities, and with regional topography interactions, soil and water salinization has intensified, posing major ecological and environmental challenges worldwide. Here, we integrated histology, transmission electron microscopy, RNA sequencing (RNA-seq) and data-independent acquisition (DIA)-based proteomics to profile hepatopancreas responses of Exopalaemon carinicauda during acute sulfate stress (≤48 h). Sulfate exposure disrupted tubular architecture and organelle integrity, consistent with early cellular injury. Multi-omics analyses revealed metabolic reprogramming marked by suppressed glycolysis (e.g., HK2, ENO) and enhanced oxidative phosphorylation (e.g., ATP5F1B), together with activation of calcium signaling (e.g., SLC8A1, ADCY9) and reinforcement of antioxidant/one-carbon and glucose-branch pathways (e.g., SHMT2, PGAM2). These coordinated transcript-protein changes indicate a shift from rapid cytosolic ATP supply to mitochondrial ATP production while buffering Ca[2+] overload and reactive oxygen species. Collectively, our results delineate the physiological and molecular adjustments that enable E. carinicauda to cope with sulfate conditions and provide mechanistic targets for selective breeding and water-quality management in saline-alkaline aquaculture.}, }
@article {pmid41595990, year = {2026}, author = {Ha, S and Lee, T and Seo, H and Yoon, S and Lee, H}, title = {A Selective RAG-Enhanced Hybrid ML-LLM Framework for Efficient and Explainable Fatigue Prediction Using Wearable Sensor Data.}, journal = {Bioengineering (Basel, Switzerland)}, volume = {13}, number = {1}, pages = {}, pmid = {41595990}, issn = {2306-5354}, support = {RS-2024-00457381//National Research Foundation of Korea/ ; RS-2024-00440371//National Research Foundation of Korea/ ; }, abstract = {Fatigue is a multifactorial phenomenon affecting both physical and psychological performance, particularly in high-stress occupations. Although wearable sensors enable continuous monitoring, conventional machine-learning (ML) models can produce unstable, weakly calibrated, and opaque predictions in real-world settings. To improve reliability and interpretability, we developed a selective Retrieval-Augmented Generation (RAG)-enhanced hybrid ML-LLM framework that integrates the efficiency of ML with the reasoning capability of large language models (LLMs). Using wearable and ecological momentary assessment data from 297 emergency responders (9543 seven-day windows), logistic regression, XGBoost, and LSTM models were trained to classify fatigue levels dichotomized by the median of daily tiredness scores. The LLM was selectively activated only for borderline ML outputs (0.45 ≤ p ≤ 0.55), using symbolic rules and retrieved analog examples. In the uncertainty region, performance improved from 0.556/0.684/0.635/0.659 to 0.617/0.703/0.748/0.725 (accuracy/precision/recall/F1). On the full test set, performance similarly improved from 0.707/0.739/0.918/0.819 to 0.718/0.741/0.937/0.827, with gains confirmed by McNemar's paired comparison test (p < 0.05). SHAP-based ML interpretation and LLM reasoning analyses independently identified short-term sleep duration and heart-rate variability as dominant predictors, providing transparent explanations for model behavior. This framework enhances classification robustness, interpretability, and efficiency, offering a scalable solution for real-world fatigue monitoring.}, }
@article {pmid41595397, year = {2026}, author = {Jean-Baptiste, CO}, title = {A Prevention-Focused Geospatial Epidemiology Framework for Identifying Multilevel Vulnerability Across Diverse Settings.}, journal = {Healthcare (Basel, Switzerland)}, volume = {14}, number = {2}, pages = {}, pmid = {41595397}, issn = {2227-9032}, abstract = {Background/Objectives: Geographic Information Systems (GIS) offer essential capabilities for identifying spatial concentrations of vulnerability and strengthening context-aware prevention strategies. This manuscript describes a geospatial architecture designed to generate anticipatory, place-based risk identification applicable across diverse community and institutional environments. Interpersonal Violence (IPV), one of several preventable harms that benefit from this spatially informed analysis, remains a critical public health challenge shaped by structural, ecological, and situational factors. Methods: The conceptual framework presented integrates de-identified surveillance data, ecological indicators, environmental and temporal dynamics into a unified spatial epidemiological model. Multilevel data layers are geocoded, spatially matched, and analyzed using clustering (e.g., Getis-Ord Gi*), spatial dependence metrics (e.g., Moran's I), and contextual modeling to support anticipatory identification of elevated vulnerability. Framework Outputs: The model is designed to identify spatial clustering, mobility-linked risk patterns, and emerging escalation zones using neighborhood disadvantage, built-environment factors, and situational markers. Outputs are intended to support both clinical decision-making (e.g., geocoded trauma screening, and context-aware discharge planning), and community-level prevention (e.g., targeted environmental interventions and cross-sector resource coordination). Conclusions: This framework synthesizes behavioral theory, spatial epidemiology, and prevention science into an integrative architecture for coordinated public health response. As a conceptual foundation for future empirical research, it advances the development of more dynamic, spatially informed, and equity-focused prevention systems.}, }
@article {pmid41593706, year = {2026}, author = {Gothe, S and Jagtap, S and Böhmer, P and Reuter, M and Frank, S and Sreenu, VB and Bell-Sakyi, L and Merits, A and Altinli, M and Schnettler, E}, title = {Characterization of Culex pipiens cell lines: virus infection and RNAi response.}, journal = {Parasites &amp; vectors}, volume = {19}, number = {1}, pages = {}, pmid = {41593706}, issn = {1756-3305}, support = {Culifo3//BMLE/ ; TTU 01.708//Deutsches Zentrum f&#xfc;r Infektionsforschung/ ; TTU 01.701 and TTU 01.708//Deutsches Zentrum f&#xfc;r Infektionsforschung/ ; 500072465//Deutsche Forschungsgemeinschaft/ ; 497659464//Deutsche Forschungsgemeinschaft/ ; GSO KT/24//Klaus Tschira Stiftung/ ; BB/P024270/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 223743/Z/21/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Culex/virology/cytology ; Cell Line/virology ; *RNA Interference ; *Mosquito Vectors/virology ; Virus Replication ; *Arboviruses/physiology/genetics ; }, abstract = {BACKGROUND: Arboviruses transmitted by mosquitoes pose a global health threat, causing diseases ranging from mild fevers to severe encephalitis and hemorrhagic fevers. Despite their growing impact, arbovirus research is hindered by biosafety constraints and the need of specialized BSL-3 insectariums. To circumvent these challenges, mosquito-derived cell lines have become indispensable tools for investigating virus-vector interactions. However, most available cell lines originate from Aedes and Anopheles spp., creating a critical research gap for other key vectors such as Culex spp. Although a few cell lines were previously established, they did not represent primary transmitters of West Nile virus (WNV) and other emerging arboviruses in Europe, such as Culex pipiens.<br><br>METHODS: To address this gap, the current study aimed to characterize two recently established Culex pipiens cell lines: CPE/LULS50 (Culex pipiens pipiens &amp; molestus) and CPL/LULS56 (Culex pipiens molestus) in more detail including testing their virus susceptibility, antiviral RNAi response, and possible presence of insect-specific viruses.<br><br>RESULTS: The replication of arboviruses from three clinically relevant families (Flaviviridae, Peribunyaviridae, and Togaviridae), as well as insect-specific viruses, was observed in both CPE/LULS50 and CPL/LULS56 cell lines. Furthermore, small RNA profiling revealed production of virus-specific small interfering RNA (siRNA) in both cell lines for all tested viruses. Interestingly, virus-specific PIWI-interacting RNA (piRNA) was only detected for the Peribunyaviridae.<br><br>CONCLUSIONS: The current study demonstrates that the CPE/LULS50 and CPL/LULS56 cell lines are suitable candidates to facilitate research into Culex-specific virus-vector interactions, ultimately contributing to mitigation of the impact of Culex-borne arboviruses on public health.}, }
@article {pmid41593685, year = {2026}, author = {Naserrudin, NA and Rahman, AB and Manah, AM and Donnie, EM and Jamaji, L and Lin, PYP and Miller, A and Krishnan, M and Hassan, MR}, title = {What does monkey malaria mean to you? A participatory photovoice study in rural Malaysian Borneo.}, journal = {Malaria journal}, volume = {25}, number = {1}, pages = {105}, pmid = {41593685}, issn = {1475-2875}, mesh = {Adult ; Middle Aged ; Humans ; *Malaria/psychology/epidemiology/prevention &amp; control ; *Rural Population/statistics &amp; numerical data ; Young Adult ; Male ; *Plasmodium knowlesi/physiology ; Animals ; Female ; Adolescent ; Photography ; Borneo/epidemiology ; *Zoonoses ; Malaysia ; Focus Groups ; }, abstract = {BACKGROUND: Zoonotic (monkey) malaria, caused by Plasmodium knowlesi, is an escalating concern in Sabah, Malaysia, where humans, macaques and mosquito vectors share overlapping ecosystems. Conventional research methods often overlook how affected communities perceive and respond to this risk within their cultural and environmental contexts. This study uses photovoice, a participatory visual method to explore the question 'What does monkey malaria mean to you? and to elevate community voices in guiding locally relevant disease prevention strategies.<br><br>METHODS: From January to May 2024, twenty participants aged 18 to 62 from three rural Sabah villages captured photographs over a 20-day period using their smartphones to document their experiences and perceptions on monkey malaria. Follow-up focus group discussions (FGDs) enabled participants to collectively reflect on and interpret their images. Reflexive thematic analysis was applied to the visual and verbal data and findings. Digital tools supported coordination and data management without replacing the participant-researcher engagement.<br><br>RESULTS: Five interrelated themes were generated: (1) monkey malaria as an embedded, everyday risk, (2) community resilience manifested through locally derived practices, (3) structural and socio-ecological challenges shaping exposure, (4) the interface of human, wildlife, and environmental health, (5) cultural knowledge and blended practices for coping with malaria risk. Participants articulated how landscape features, economic dependence on forested and plantation areas, and daily routines collectively structure risk, reflecting a dynamic 'landscape of risk'. They also expressed aspirations for collaborative and culturally appropriate strategies.<br><br>CONCLUSION: Using photovoice, participants described how malaria risk is part of their everyday lives, the coping strategies they use and the social and environmental conditions that influence their understanding. By prioritising community voices, the findings show that effective malaria control should go beyond strictly biomedical models to include local priorities, cultural practices and lived experience. Photovoice generated deep insights grounded in the community context and encouraged meaningful participation, providing useful guidance for designing intervention strategies that are culturally appropriate and more sustainable.}, }
@article {pmid41593363, year = {2026}, author = {Sorensen, PO and Karaoz, U and Beller, HR and Bill, M and Bouskill, NJ and Banfied, JF and Chu, RK and Hoyt, DW and Eder, E and Eloe-Fadrosh, E and Sharrar, A and Tfaily, MM and Toyoda, J and Tolic, N and Wang, S and Wong, AR and Williams, KH and Zhong, Y and Brodie, EL}, title = {Multi-omics reveals nitrogen dynamics associated with soil microbial blooms during snowmelt.}, journal = {Nature microbiology}, volume = {11}, number = {2}, pages = {359-374}, pmid = {41593363}, issn = {2058-5276}, support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC05-76RL01830//U.S. Department of Energy (DOE)/ ; DBI-1315705//National Science Foundation (NSF)/ ; }, mesh = {*Bacteria/metabolism ; Biomass ; Bradyrhizobium/metabolism ; Climate Change ; Metagenome ; Microbiota ; Nitrogen/metabolism ; *Nitrogen Compounds/metabolism ; *Nitrogen Cycle ; *Seasons ; *Snow ; *Soil Microbiology ; Ecosystem ; Multiomics ; }, abstract = {Snowmelt triggers a soil microbial bloom and crash that affects nitrogen (N) export in high-elevation watersheds. The mechanisms underlying these microbial dynamics are uncertain, making soil nitrogen processes difficult to predict as snowpack declines globally. Here, integration of genome-resolved metagenomics, metatranscriptomics and metabolomics in a high-elevation watershed revealed ecologically distinct soil microorganisms linked across the snowmelt time-period by their unique nitrogen cycling capacities. The molecular properties and transformations of dissolved organic N suggested that degradation or recycling of microbial biomass provided N for biosynthesis during the microbial bloom. Winter-adapted Bradyrhizobia spp. oxidized amino acids anaerobically and had the highest gene expression for denitrification during the microbial bloom. A pulse of nitrate was driven by spring-adapted Nitrososphaerales after snowmelt, but dissimilatory nitrate reduction to ammonia (DNRA) gene expression indicated significant nitrate retention potential. These findings inform our understanding of nitrogen cycling in environments sensitive to snowpack decline due to global change.}, }
@article {pmid41593110, year = {2026}, author = {Syverson, VJP and Goring, SJ and Cullen, N and Jarzyna, MA and Bellvé, AM and Martindale, A and Blois, JL}, title = {Updated chronologies for North American small mammal fossil localities in the Neotoma Paleoecology Database.}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {173}, pmid = {41593110}, issn = {2052-4463}, support = {EAR-2410961//National Science Foundation (NSF)/ ; EAR-2149419//National Science Foundation (NSF)/ ; EAR-2149416//National Science Foundation (NSF)/ ; EAR-1948579//National Science Foundation (NSF)/ ; EAR-2410965//National Science Foundation (NSF)/ ; }, mesh = {*Fossils ; Animals ; *Mammals ; Paleontology ; North America ; Radiometric Dating ; Databases, Factual ; }, abstract = {Community paleoecology is a powerful approach for analyzing ecological communities during long-term climate shifts like the Pleistocene-Holocene transition, but it depends on accurate estimates of species co-occurrences. The Neotoma Paleoecology Database is an open paleodata resource that stores assemblage-level taxonomic, spatial, and temporal information for Quaternary fossil localities. However, its age estimates for many vertebrate fossil localities are based on uncalibrated radiocarbon dates, hindering comparisons with other paleoenvironmental proxies. In order to provide consistent and updated age inferences suitable for broad-scale paleoecological studies, we have reassessed the radiocarbon chronologies for all 14C-dated North American small mammal collections in Neotoma. Here we present the resulting database update, including 2074 radiocarbon dates newly added to Neotoma and new calibrated radiocarbon chronologies for 1553 fossil collections. The new chronologies cover more sites and include more dates than the chronologies previously available in Neotoma. They also provide fossil assemblage age estimates in calendar years, facilitating integration with other data sources. We anticipate that these updates will be useful for various applications in community paleoecology.}, }
@article {pmid41592132, year = {2026}, author = {Rathod, DR and Silverman, JD}, title = {PCR bias impacts microbiome ecological analyses.}, journal = {PLoS computational biology}, volume = {22}, number = {1}, pages = {e1013908}, pmid = {41592132}, issn = {1553-7358}, support = {R01 GM148972/GM/NIGMS NIH HHS/United States ; }, mesh = {*Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Polymerase Chain Reaction/methods ; Computational Biology ; Bias ; Biodiversity ; }, abstract = {Polymerase Chain Reaction (PCR) is a critical step in amplicon-based microbial community profiling, allowing the selective amplification of marker genes such as 16S rRNA from environmental or host-associated samples. Despite its widespread use, PCR is known to introduce amplification bias, where some DNA sequences are preferentially amplified over others due to factors such as primer-template mismatches, sequence GC content, and secondary structures. Although these biases are known to affect transcript abundance, their implications for ecological metrics remain poorly understood. In this study, we conduct a comprehensive evaluation of how PCR-bias influences both within-samples (α-diversity) and between-sample (β-diversity) analyses. We show that perturbation-invariant diversity measures remain unaffected by PCR bias, but widely used metrics such as Shannon diversity and Weighted-Unifrac are sensitive. To address this, we provide theoretical and empirical insight into how PCR-induced bias varies across ecological analyses and community structures, and we offer practical guidance on when bias-correction methods should be applied. Our findings highlight the importance of selecting appropriate diversity metrics for PCR-based microbial ecology workflows and offer guidance for improving the reliability of diversity analyses.}, }
@article {pmid41591867, year = {2026}, author = {Petraro, S and Tarracchini, C and Mancabelli, L and Lugli, GA and Turroni, F and Ventura, M and Milani, C}, title = {Microbial BioRemediation Database: A Comprehensive Database of Genes Involved in Microbial Bioremediation Processes.}, journal = {MicrobiologyOpen}, volume = {15}, number = {1}, pages = {e70215}, doi = {10.1002/mbo3.70215}, pmid = {41591867}, issn = {2045-8827}, support = {//European Union, NextGeneration EU, PNRR-M4C2- I1.1, PRIN 2022 - Project Code 20229LEB99 - CUP Code D53D23014150006/ ; T5-AN-11//Piano di Sviluppo e Coesione of the Italian Ministry of Health 2014-2020/ ; }, mesh = {*Biodegradation, Environmental ; *Bacteria/genetics/metabolism/classification ; *Databases, Genetic ; Microbiota/genetics ; Environmental Pollutants/metabolism ; Metagenome ; Metagenomics ; }, abstract = {Environmental pollution from a wide range of compounds poses serious ecological and health risks. While bioremediation offers a promising solution, its application is limited by fragmented genomic resources and unsatisfactory understanding of microbial biodegradation pathways. Here, we developed the Microbial BioRemediation (MBR) database, freely accessible at https://probiogenomics.unipr.it/cmu, a comprehensive and manually curated repository comprising over 643,351 bacterial protein sequences associated with the degradation of 564 pollutant compounds across 25 chemical classes. Optimized for both genomic and metagenomic analyses, the Microbial BioRemediation database enables high-resolution functional and taxonomic profiling of microbial communities and individual bacterial strains. Validation using public genome and metagenome datasets from contaminated environments confirmed the database ability to detect both conserved and environment-specific biodegradation functions. Its application to host-associated microbiomes further confirmed the suitability of MBR for assessing how environmental exposures shape microbial catabolic potential across ecological contexts. The MBR database thus serves as a strategic tool for the early-stage identification and prioritization of microbial candidates for bioremediation. By enabling the in silico selection of key microbial taxa and enzymatic functions, it supports a rational pipeline that progresses toward targeted in vitro validation and experimental characterization. This integrative approach facilitates development of next-generation, tailored strategies for the remediation of complex polluted ecosystems.}, }
@article {pmid41591842, year = {2026}, author = {Islam, H and Sharma, A and Blair, J and Lopatkin, AJ}, title = {PlasAnn: a curated plasmid-specific database and annotation pipeline for standardized gene and function analysis.}, journal = {Nucleic acids research}, volume = {54}, number = {3}, pages = {}, pmid = {41591842}, issn = {1362-4962}, support = {1R35GM150871-01/NH/NIH HHS/United States ; //Pew Charitable Trusts Foundation/ ; 2440082//National Science Foundation/ ; //Edward Mallinckrodt Jr. Foundation/ ; }, mesh = {*Plasmids/genetics ; *Molecular Sequence Annotation/methods ; *Databases, Genetic ; Genome, Bacterial ; Software ; DNA Transposable Elements ; Genes, Bacterial ; Bacteria/genetics ; }, abstract = {Conjugative plasmids are key drivers of bacterial adaptation, enabling the horizontal transfer of accessory genes within and across diverse microbial populations, yet annotating them remains challenging due to their highly mosaic genetic architectures and inconsistent gene naming conventions that complicate functional predictions and comparative analyses. To address this, we developed PlasAnn, a database designed specifically for genes encoded on natural plasmids, paired with a dedicated annotation pipeline (available via Bioconda or through the URL https://plasann.rochester.edu/). The curated database provides highly accurate, plasmid-type-specific gene names with standardized functional annotations, enabling direct comparison across plasmids without manual curation or specialized expertise, while the integrated annotation tool incorporates other common plasmid features for a fast, one-stop solution that outperforms broad prokaryotic genome annotation pipelines in both accuracy and efficiency. We demonstrate PlasAnn's utility by showing that plasmid accessory genes from different groups often share conserved repertoires, suggesting dynamic, modular networks of interconnected genes, and by revealing that plasmid-encoded transposable elements frequently carry genes related to bacterial adaptation beyond antibiotic resistance, including metabolism, virulence, and stress responses, emphasizing their broader contributions to fitness and adaptability. These insights, not captured by current field-standard tools, highlight how PlasAnn improves plasmid annotation and advances our understanding of plasmid biology, microbial ecology, and evolution.}, }
@article {pmid41588693, year = {2026}, author = {Bhattacharya, D and Nandi, S and Chille, EE and Arroyo, M and Stephens, TG}, title = {The Host Coral Bleaching Response Viewed Through the Lens of Multi-Omics: Multi-Omics Provides the Tools to Understand the Complex Molecular Basis of Coral Bleaching, Which Can Aid Conservation Efforts.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {48}, number = {1}, pages = {e70110}, pmid = {41588693}, issn = {1521-1878}, support = {23-7825575//Catalyst Science Fund, Revive &amp; Restore, and the National Philanthropic Trust/ ; 2128073//National Science Foundation/ ; NJ01180//USDA National Institute of Food and Agriculture Hatch Formula/ ; }, mesh = {Animals ; *Anthozoa/genetics/physiology ; Symbiosis ; *Coral Bleaching ; Genomics/methods ; Coral Reefs ; Conservation of Natural Resources ; Climate Change ; Oxidative Stress ; Heat-Shock Response ; Multiomics ; }, abstract = {We review recent multi-omics analyses of the coral heat stress response to explore the generality of the Oxidative Theory of Coral Bleaching (OTCB), which posits that algal symbiont release is the final act of defense by the coral host to survive alga-derived oxidative stress. The OTCB is particularly relevant given that ocean warming, which is accelerating under climate change, has proven devastating for corals, leading to the bleaching phenotype and widespread reef loss. Multi-omics results, in combination with other data, such as genome-wide association studies, support the idea that coral bleaching is a multifactorial response that reflects a wide array of causes and effects and is population-specific under most conditions, with coral ploidy and genotype being critical to bleaching sensitivity. This perspective leverages the location, algal and prokaryotic microbiome, and host genotype-specific aspects of coral resilience to promote a new "personal genomics" approach to coral conservation, analogous to that used in human health.}, }
@article {pmid41588622, year = {2026}, author = {Hessl, AE and Richardson, AD and Filwett, R and Andreu-Hayles, L and Walker, M and Oelkers, R and Robison, AS and Leshyk, VO and Carbone, MS}, title = {Carbon uptake, storage, and allocation patterns contribute to blurring of annual [14]C signals in tree rings.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.70868}, pmid = {41588622}, issn = {1469-8137}, support = {2411569//NSF Solar Terrestrial/ ; 2411571//NSF Solar Terrestrial/ ; 2136524//NSF GRF/ ; 1832210//NSF LTER/ ; 2224545//NSF LTER/ ; PID2021-126411OB-I00//MICIU/AEI/10.13039/501100011033/ ; }, abstract = {Tree rings are considered the gold standard for observing variation in past atmospheric radiocarbon ([14]C), yet little attention has been paid to whether different trees record tropospheric [14]C evenly. The discovery of Miyake events, rapid increases in [14]C production occurring in past millennia, has led to repeated measurements of [14]C in tree rings across species and locations. These records demonstrate remarkable synchrony, yet significant variability between samples remains, limiting reliable use of tree rings as a precise indicator of the timing and scale of past [14]C production. Understanding how trees and species record tropospheric [14]C would improve reconstructions of past [14]C production events, refine geochronological control, and because of the pulse-like nature of past [14]C production events, shed light on a fundamental question in tree physiology and dendrochronology: what is the lag time between photosynthesis, storage, and allocation to wood and how might this lag blur isotopic signals in tree rings? Here, we evaluate the implicit assumption that all trees record tropospheric [14]C evenly by focusing on the path carbon takes within trees including: phenology of carbon uptake and wood formation, storage and use of nonstructural carbohydrates, and how these factors interact to affect the tropospheric [14]C signal in wood.}, }
@article {pmid41588471, year = {2026}, author = {Sulaiman, N and Sõukand, R and Ullah, I and Pieroni, A}, title = {Searching for a ghost?! The vain ethnobotany of foraging in three coastal Mediterranean areas.}, journal = {Journal of ethnobiology and ethnomedicine}, volume = {22}, number = {1}, pages = {15}, pmid = {41588471}, issn = {1746-4269}, support = {Horizon ID 101159928//ETHCSTWIN/ ; }, mesh = {*Ethnobotany ; Humans ; Knowledge ; France ; Mediterranean Region ; Vegetables ; Malta ; }, abstract = {This paper explores the erosion of foraging-related ethnobotanical knowledge in three coastal Mediterranean areas: Gozo Island (Malta), Kasos Island (Greece), and the Castagniccia region of Corsica Island (France). Based on recent ethnobotanical fieldwork between the summer of 2023 and the spring of 2025 in the three study areas, we document the few remaining wild vegetable uses in each region and contextualise the absence of robust LEK linked to plant foraging within broader socio-environmental changes. Our findings show that land abandonment, mass migration, desertification, and the rise of seasonal tourism have contributed to the disintegration of Local Ecological Knowledge (LEK). These forces have severed communities from everyday land-based practices, transforming vibrant ethnobotanical traditions into fragmented memories. We argue that LEK, particularly foraging knowledge, cannot survive in the absence of continuous interaction with the landscape, and that the revival of such practices requires more than nostalgic return, demanding a reconnection with local agro-ecological systems.}, }
@article {pmid41587566, year = {2026}, author = {Liu, Y and Zhang, Z and Chen, X and Liu, G and Li, D and Li, J and Song, Y and Duan, J and Sun, K and Feng, Y}, title = {Multi-objective decision model for wastewater treatment technology selection based on machine learning.}, journal = {Bioresource technology}, volume = {446}, number = {}, pages = {134087}, doi = {10.1016/j.biortech.2026.134087}, pmid = {41587566}, issn = {1873-2976}, mesh = {*Machine Learning ; *Wastewater/chemistry ; *Water Purification/methods ; Bioreactors ; Monte Carlo Method ; *Decision Support Techniques ; }, abstract = {This study integrated life cycle assessment (LCA), machine learning (ML), and analytic hierarchy process (AHP) to optimize wastewater treatment technology selection in the upper Yellow River Basin-a region constrained by limited carrying capacity and ecological fragility. LCA results from a representative city in Gansu Province identified anaerobic-anoxic-oxic combined with sequencing batch reactor (AAO + SBR) as the configuration with the lowest environmental footprint. Monte Carlo simulations were employed to augment the dataset, ensuring statistical reliability. In a comparative analysis, the XGBoost outperformed random forest (RF) and support vector machine (SVM), reducing mean squared error (MSE) by 1.4-3.1%. Ultimately, the integrated AHP-ML model confirmed AAO + SBR and AAO with membrane bioreactor (AAO + MBR) as the optimal technologies under current condition. The data-driven intelligent model constructed in this study, reconciling treatment efficiency with ecological sustainability, provided precise guidance for low-carbon wastewater governance in the Yellow River Basin and similar ecologically fragile regions.}, }
@article {pmid41578851, year = {2026}, author = {Peltier, DMP and Malone, SC and McIntire, CD and Thompson, RA and Pinzon-Navarro, S and Pereverzeva, KA and Richardson, AD and McDowell, NG and Adams, HD and Carbone, MS and Pockman, WT and Trowbridge, AM}, title = {Resin-based defenses in Pinus edulis are only reduced after long-term drought.}, journal = {Tree physiology}, volume = {46}, number = {2}, pages = {}, doi = {10.1093/treephys/tpag004}, pmid = {41578851}, issn = {1758-4469}, support = {1019284//US Department of Agriculture, National Institute of Food and Agriculture, McIntire Stennis/ ; 1-842493//NSF GRFP/ ; 1936205//NSF-IOS/ ; 1755345//NSF-IOS/ ; 1755346//NSF-IOS/ ; }, abstract = {Constrained carbon allocation toward secondary metabolites involved in chemical defense is a common explanation for widespread drought-related beetle-kill in conifers-we challenge the generality of this explanation. While monitoring drought stress (ψpd), we tracked both carbon reserves (non-structural carbohydrates) and chemical defenses (terpenes, phenolics, resin flow) in mature Pinus edulis Englem. trees experiencing either short-term (3-year) or a 'legacy' long-term (13-year) throughfall exclusion treatments, plus a control. We also quantified the Δ14C-age of resin to measure past allocation to current defense. While 72% of trees in short-term throughfall exclusion plots died (attacked by bark beetles, Ips confusus LeConte), mortality patterns were unrelated to throughfall exclusion intensity and all 'legacy' trees survived. We thus assessed trees in four survivorship categories: control, 'legacy', surviving, and dying trees. We found concentrations of certain defense compounds (leaf phenolics, twig monoterpenes) increased with drought stress, particularly in dying trees. In the main stem, dying trees exhibited similar terpene concentrations (94%) and phenolic concentrations (139%) relative to control trees. Compared with control trees, only 'legacy' trees had reduced stem terpenes (-49%, P < 0.05) after a decade of drought. Δ14C-age of resin could be up to 10.2 ± 0.5 years old, where the oldest resin was exuded from trees with low sugar concentrations and more negative Ψpd. Our results suggest that drought imposes a weak constraint on carbon allocation to resin-based defense. Instead, we primarily found evidence of increased concentrations of terpene and phenolic compounds under drought, even in dying trees, and only observed reductions in resin-based defenses after 10+ years of drought. Δ14C-ages demonstrate limited resin turnover and/or synthesis of resin from old reserves, suggesting that long-term drought is required to reduce resin-based defenses. Persistent allocation coupled with past investments appears to preserve or enhance concentrations of resin-based defenses even under lethal drought stress in P. edulis.}, }
@article {pmid41578325, year = {2026}, author = {Lim, KO and Kummerfeld, E and Anderson, LM and Wonderlich, SA and Engel, S and Crosby, RD and Peterson, CB}, title = {Personal causal modeling of affect and eating behaviors in bulimia nervosa: implications for personalized treatment.}, journal = {Journal of eating disorders}, volume = {14}, number = {1}, pages = {52}, pmid = {41578325}, issn = {2050-2974}, support = {K23MH123910/NH/NIH HHS/United States ; R01MH059674/NH/NIH HHS/United States ; R34MH099040/NH/NIH HHS/United States ; K23MH123910/NH/NIH HHS/United States ; R01MH059674/NH/NIH HHS/United States ; R34MH099040/NH/NIH HHS/United States ; }, abstract = {BACKGROUND: Affect regulation models suggest high negative and low positive affect may drive binge eating and purging in bulimia nervosa (BN). While ecological momentary assessment (EMA) studies often support these theories, inconsistent outcomes in affect-targeted interventions suggest causal relations vary across individuals. This study applied causal discovery analysis (CDA) to EMA data to characterize such heterogeneity in person-specific causal models for BN.<br><br>METHODS: EMA data from 118 adult women with BN, collected over 14 days, assessed momentary negative affect, positive affect, binge eating, and self-induced vomiting. Using the Greedy Fast Causal Inference algorithm, we derived individual causal models and estimated effect sizes via structural equation modeling. Heterogeneity was evaluated by the proportion of participants with affect as a causal factor for BN behaviors.<br><br>RESULTS: Causal patterns were highly heterogeneous. Elevated negative affect was causal for binge eating in 16.9% of participants, vomiting in 18.6%, and either behavior in 27.1%. Low positive affect was causal for binge eating in 8.5%, vomiting in 11.0%, and either behavior in 15.3%. Behavior-behavior causality was also common: vomiting caused binge eating in 26.3% of participants, and binge eating caused vomiting in 22.0%.<br><br>CONCLUSIONS: CDA revealed marked heterogeneity in causal factors underlying BN behaviors, with some models showing affect-driven behaviors and others indicating behavior-driven patterns. Ultimately, this work indicates that the link between momentary affect and BN behaviors is highly individualized, underscoring the need for precision-targeted interventions rather than one-size-fits-all treatments.}, }
@article {pmid41575653, year = {2026}, author = {Astill Wright, L and Bakstein, E and Saunders, K and Guo, B and Morriss, R}, title = {Performance of active and passive ambulatory assessment measures and mood monitoring in bipolar disorder: a systematic review.}, journal = {International journal of bipolar disorders}, volume = {14}, number = {1}, pages = {4}, pmid = {41575653}, issn = {2194-7511}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {BACKGROUND: Ambulatory assessment uses digital technology to capture real-time data on mood, mental state and behaviour. It has the potential to enhance traditional clinical outcome measures, but the practical application of these tools fundamentally depends on their performance.<br><br>AIMS: This systematic review aimed to assess the performance of active and passive ambulatory assessment and mood monitoring outcome measures in non-randomised and randomised studies in bipolar disorder over 3&#xa0;months or longer. We aimed to evaluate their performance against established clinical measures and through inter-ambulatory assessment comparisons.<br><br>METHODS: Systematic review (PROSPERO: CRD42023396473) of performance of mood monitoring and ambulatory assessment protocols in RCTs and non-randomised studies in bipolar disorder. Identified studies were assessed for risk of bias. Due to the very high heterogeneity in included studies and performance metrics we were not able to aggregate the data via meta-analysis.<br><br>RESULTS: The review included 42 studies with a combined sample of 7,813 participants. We included 28 distinct ambulatory assessment protocols which reported 487 different smartphone-based performance metrics. The considerable variability and inconsistency across these metrics limited our ability to make definitive comparisons of performance. Overall, some active ambulatory assessment approaches showed good performance when compared with established clinical measures. There was a paucity of data examining the performance of passive ambulatory assessment measures. Most studies were rated as having low to moderate risk of bias.<br><br>CONCLUSIONS: While ambulatory assessment holds significant promise, current evidence fails to establish the validity and reliability of passive ambulatory assessment to measure mood. The substantial methodological variation-particularly in how performance metrics are defined and reported-limits meaningful comparison and replication. Greater consistency in ambulatory assessment design and reporting standards is essential to support reliable evaluation and broader adoption of these behavioural assessment tools.}, }
@article {pmid41575069, year = {2026}, author = {Zupunski, L and Yaumenenka, A and Veyalkin, I and Minenko, V and Moiseyev, P and Schüz, J and Kukhta, T and Trofimik, S and Harbron, R and Drozdovitch, V and Ostroumova, E}, title = {Lymphoma, multiple myeloma and leukaemia incidence in regions of Belarus most heavily contaminated by the Chernobyl accident.}, journal = {International journal of cancer}, volume = {}, number = {}, pages = {}, doi = {10.1002/ijc.70346}, pmid = {41575069}, issn = {1097-0215}, support = {001/WHO_/World Health Organization/International ; }, abstract = {There is little information on non-thyroid cancer risks, including haematological malignancies (HM), among the residents of most contaminated regions after the Chernobyl (Chornobyl) nuclear power plant accident. We studied the incidence of lymphoma, multiple myeloma and leukaemia in relation to the raion-average age-specific cumulative absorbed red bone marrow (RBM) dose among the residents of Gomel and Mogilev oblasts in Belarus, which were highly contaminated. The follow-up period was 40 years (1978-2018). HM cases and population size data were received from the Belarusian national cancer registry and the state department of statistics. Our ecological study included 7328 lymphoma, 9476 leukaemia and 2003 multiple myeloma incident cases and 90.8 million person-years in people who were born before the accident and have attained age <80 years old. The mean (median) RBM dose accumulated by December 31, 2018 was 14.2 (6.4) mGy. We found no evidence of increased risks of Hodgkin and non-Hodgkin lymphoma, multiple myeloma or total leukaemia associated with two-year lagged raion-average cumulative RBM dose after adjustment for sex, attained age, urban/rural status and calendar period effects. There was a suggestion of an elevated relative risk of myeloid leukaemia per 100 mGy after exclusion of Gomel and Mogilev cities. Little evidence was found on interaction between selected factors, except sex, and RBM dose for each study outcome. Studies with individually reconstructed cumulative absorbed RBM doses are warranted to provide more insight on dose-effect relationships between HM risk, specifically leukaemia, and protracted environmental exposure at a low dose range.}, }
@article {pmid41573256, year = {2025}, author = {Manzano-Marín, A and Böhne, A and Monteiro, R and Marcussen, T and Struck, TH and Oomen, RA and ,  and ,  and ,  and Howard, C and Howe, K and Blaxter, M and McCarthy, S and Wood, JMD and Martin, F and Lazar, A and Haggerty, L and Bortoluzzi, C}, title = {ERGA-BGE reference genome of Hirudo verbana, a once neglected freshwater haematophagous European medicinal leech.}, journal = {Open research Europe}, volume = {5}, number = {}, pages = {395}, pmid = {41573256}, issn = {2732-5121}, abstract = {Hirudo verbana Carena, 1820, commonly known as the southern medicinal leech, is one of several European medicinal leeches, whose full diversity has just recently started to be uncovered. Historically, it has been widely used as a medicinal leech and for centuries it was treated erroneously under the specific name of Hirudo medicinalis L. 1758. Recent molecular and taxonomic analyses have revealed subspecific diversity within the morphospecies H. verbana. Hirudo verbana is a blood-feeding species sucking blood from amphibians, fish, and mammals. It occupies freshwater habitats, typically shallow ponds and lakes. Studies show that this leech species has a "naturally limited microbiome", suggesting it may serve as a powerful model system for the study of gut microbiota. We expect this chromosome-level assembly of H. verbana to serve as a high-quality genomic resource for this most famous leech genus and to serve as a foundation to the study of the diversification and biodiversity of European medicinal leeches, as well as their gut-associated symbionts. The genome of H. verbana was assembled into two haplotypes through a phased assembly approach; however, only the primary haplotype was designated as the reference genome for annotation and downstream analyses. The entirety of the primary haplotype was assembled into 14 contiguous chromosomal pseudomolecules, including the mitogenome. This chromosome-level assembly encompasses 0.18 Gb, composed of 277 contigs and 27 scaffolds, with contig and scaffold N50 values of 1.3 Mb and 13.4 Mb, respectively.}, }
@article {pmid41572218, year = {2026}, author = {Liang, Y and Ma, S and Chen, X and Su, Y and Zhong, D and Yan, H and Chen, Y and Wang, M and Leng, Z and Huang, X}, title = {Integrative multi-omics reveal a CD4[+] T cell-derived six-gene signature linking the immune-stromal ecosystem to prognosis and immunotherapy selection in pancreatic cancer.}, journal = {BMC cancer}, volume = {26}, number = {1}, pages = {262}, pmid = {41572218}, issn = {1471-2407}, support = {2024YFHZ0358//Research Project of Science and Technology Department of Sichuan Province/ ; 2024ZD0525500/2024ZD0525506//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; }, mesh = {Humans ; *CD4-Positive T-Lymphocytes/immunology/metabolism ; *Pancreatic Neoplasms/genetics/immunology/therapy/mortality/pathology ; *Tumor Microenvironment/immunology/genetics ; Prognosis ; *Immunotherapy/methods ; *Biomarkers, Tumor/genetics ; Cell Line, Tumor ; Gene Expression Regulation, Neoplastic ; Single-Cell Analysis ; Transcriptome ; Gene Expression Profiling ; Stromal Cells/immunology ; Male ; Multiomics ; }, abstract = {BACKGROUND: Pancreatic cancer (PC) exhibits dismal outcomes and an immune-excluded microenvironment that blunts immunotherapy. Robust, immune-anchored biomarkers are needed to stratify risk and inform treatment design.<br><br>METHODS: We integrated The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) dataset and validated findings in Gene Expression Omnibus (GEO) dataset (GSE57495). Immune infiltration, survival modeling, pathway activity, tumor microenvironment, and immunotherapy responses were analyzed. Single-cell RNA sequencing (GSE212966) informed CD4&#x207a; T-cell differentially expressed genes (DEGs), pseudotime, and intercellular communication (CellChat). Quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot in H6C7, CAPAN-1, and PANC-1 cell lines were performed.<br><br>RESULTS: Among 28 immune subsets, CD4&#x207a; T-cell populations most strongly associated with overall survival (OS). A six-gene signature (KLF3, EZR, SMDT1, JPT1, ISG15, MT1X) derived from 111 CD4&#x207a; T-cell DEGs successfully stratified OS with time-dependent AUCs ranging from 0.637 to 0.838 across the training and validation cohorts. The high-risk group showed significantly poorer OS, higher stromal scores, broad checkpoint upregulation, and greater immune exclusion (P&#x2009;<&#x2009;0.05), indicating an immune-stromal ecosystem favoring tolerance. Single-cell RNA sequencing localized model genes to fibroblasts, ductal cells, and CD4&#x207a; T cells subsets. CellChat revealed globally intensified crosstalk in PC and strengthened CD4&#x207a; T-cell interactions with myeloid and stromal compartments. Western blot and qRT-PCR results confirmed up-expression of all model gene except SMDT1 in PC cell lines.<br><br>CONCLUSIONS: CD4&#x207a; T-cell subsets serve as central determinant of the immune landscape and clinical outcome in PC. The CD4&#x207a; T cell-anchored six-gene signature enables risk stratification, links immune contexture to stromal ecology, and motivates biomarker-guided trials and rational combinations that alleviate immunosuppression while targeting metabolic-stress pathways.}, }
@article {pmid41566104, year = {2026}, author = {Sau, D and Tudu, GC and Hazra, T and Shiuly, A}, title = {Evaluation of microplastic pollution in urban lentic ecosystem using remote sensing, GIS, and Support Vector Machine (SVM): relevance for environmental and ecological risk.}, journal = {Environmental monitoring and assessment}, volume = {198}, number = {2}, pages = {160}, pmid = {41566104}, issn = {1573-2959}, mesh = {*Microplastics/analysis ; *Environmental Monitoring/methods ; *Water Pollutants, Chemical/analysis ; Remote Sensing Technology ; India ; Support Vector Machine ; Geographic Information Systems ; Ecosystem ; Lakes/chemistry ; Risk Assessment ; }, abstract = {Plastic waste is a major source of microplastic (MP) pollution, posing adverse environmental and public health risks. This study assessed MP abundance in 24 urban ponds and lakes within the Kolkata Municipal Corporation, India, during the post- and pre-monsoon seasons of 2022-2023. Results showed that MP concentrations were significantly higher in the post-monsoon season (20 ± 3.46 items L[-][1]; ANOVA, p < 0.05), with red, white, and black particles being the most prevalent. MPs prevalently ranged between 500 and 1000 µm with fibers constituting 58-59% of the total MPs. Fourier-transform infrared (FTIR) analysis identified polyethylene (PE) as the dominant polymer. MP abundance showed negative correlations with dissolved oxygen and turbidity, and positive associations with pH, TDS, BOD5, and total coliform counts. A Support Vector Machine (SVM) model was developed for morphology-based MP classification, achieving an accuracy of 89%. Additionally, remote sensing and GIS techniques were used to develop index-based models for water-body identification and MP quantification (items L[-][1]) using spectral data from Sentinel-2 imagery. These models demonstrated high validation accuracy of 98.01% and 92.60%, respectively. Metal analysis of sediment and MPs of water detected chromium, suggesting possible MP-metal interactions within sediments. Although the Pollution Load Index (PLI) indicated relatively low contamination levels, the Polymer Hazard Index (PHI) exceeded 1000, indicating substantial ecological risk. Future studies should focus on long-term monitoring, socio-economic and health impact assessments and development of effective mitigation strategies particularly addressing plastic-waste derived-MPS.}, }
@article {pmid41561390, year = {2026}, author = {Fehrenbach, A and Mitrofanov, A and Backofen, R and Baumdicker, F}, title = {The complexity of multiple CRISPR arrays in strains with (co-occurring) CRISPR systems.}, journal = {microLife}, volume = {7}, number = {}, pages = {uqaf042}, pmid = {41561390}, issn = {2633-6693}, abstract = {CRISPR and their associated Cas proteins provide adaptive immunity in prokaryotes, protecting against invading genetic elements. These systems are categorized into types and are highly diverse. Genomes often harbor multiple CRISPR arrays varying in length and distance from Cas loci. However, the ecological roles of multiple CRISPR arrays and their interactions with multiple Cas loci remain poorly understood. We present a comprehensive analysis of CRISPR systems that uncovers variation between diverse Cas types regarding the occurrence of multiple arrays, the distribution of their lengths and positions relative to Cas loci, and the diversity of their repeat sequences. Some types tend to occur as the sole Cas locus present in the genome, but typically have two or more associated arrays, especially for types I-E and I-F. Multiple Cas types are also common, with some systems showing a preference for specific co-occurrence. Distinct array distributions and orientations around Cas loci indicate substantial differences in functionality and transcriptional behavior among Cas types. Our analysis suggests that arrays with identical repeats in the same genome acquire new spacers at comparable rates, irrespective of their proximity to the Cas locus. Furthermore, repeat similarities indicate that arrays of systems that often co-occur with other systems tend to have more diverse repeats than those mostly appearing alongside solitary systems. Our results indicate that co-occurring Cas-type pairs might not only collaborate in spacer acquisition but also maintain independent and complementary functions and that CRISPR systems distribute their defensive spacer repertoire equally across multiple CRISPR arrays.}, }
@article {pmid41559958, year = {2026}, author = {Lin, Y and Liu, Y and Tan, Y and Wu, N and Wang, L and Chen, J and Sun, X and Dong, X and Chen, B and Pan, Z and Wang, W and Lin, C}, title = {Source apportionment and ecological risks of trace metals in multiple media in a typical Chinese industrialized bay on the basis of SOM, PMF and GIS methods.}, journal = {Marine pollution bulletin}, volume = {223}, number = {}, pages = {119039}, doi = {10.1016/j.marpolbul.2025.119039}, pmid = {41559958}, issn = {1879-3363}, mesh = {*Environmental Monitoring/methods ; *Water Pollutants, Chemical/analysis ; China ; Bays/chemistry ; Geologic Sediments/chemistry ; Geographic Information Systems ; Seawater/chemistry ; *Trace Elements/analysis ; Risk Assessment ; *Metals, Heavy/analysis ; }, abstract = {The concentrations and risks of trace metals (TMs) in different media of aquatic systems are gradually increasing, driven by increasingly frequent anthropogenic activities. This research aimed to examine the distribution and bioaccumulation patterns of TMs in various environmental media via the analysis of samples from a typical petrochemical industrial bay in southern China. In addition, the ecological risks and anthropogenic sources of these elements were assessed. The results indicated that the levels of Zn and Hg were highest and lowest, respectively, in surface seawater, sediment, and seafood, with other TMs varying in content between those of these two trace metals. The integrated pollution index (IPI) values for TMs in seawater ranged from 1.13 to 3.16, remaining at a minimal contamination level. After multiple pollution assessment methods, were comprehensively applied, Cd and Hg were highlighted as key contributors to significant pollutant buildup and elevated ecological risks in sediments. Based on the combined use of geographic information system (GIS), self-organizing map (SOM), and positive matrix factorization (PMF) methods, the sources and contributions of TMs were analysed. The results revealed that fossil fuel combustion (24.3 %), natural geological processes (48.0 %), and aquaculture practices (27.7 %) were the primary sources of TM accumulation in sediments. This study provides important data for reducing TM pollution in typical petrochemical industry bays, enhancing ecological safety, and assessing the risks of potentially toxic elements in seafood to human health.}, }
@article {pmid41559770, year = {2026}, author = {Novak, M and Foust, P and Hennessey, S and Tanis, BP and Coblentz, KE and Wolf, C and Segui, LM and Henderson, JS and Ingeman, KE and Falke, LP and Layden, TJ and Gradison, DJ and Randell, Z and Harris, CL and Lester, S and Naito, KA and Nakata, T and Nichols, G and Postma, BC and Alves, R and Jarman, CN and Kalytiak-Davis, AR and Martin, A and Pajiah, TJ and Pinos-Sánchez, A and Preston, DL}, title = {FracFeed: Global database of the fraction of feeding predators.}, journal = {Ecology}, volume = {107}, number = {1}, pages = {e70296}, doi = {10.1002/ecy.70296}, pmid = {41559770}, issn = {1939-9170}, support = {DEB-1353827//Division of Environmental Biology/ ; }, mesh = {Animals ; *Predatory Behavior/physiology ; *Databases, Factual ; *Feeding Behavior/physiology ; *Diet ; *Vertebrates/physiology ; *Food Chain ; *Invertebrates/physiology ; Gastrointestinal Contents ; }, abstract = {The proportion of individuals that are found to have empty stomachs during a survey of a predator population's diet has been used as an indicator of the average individual's state of energy balance and of the degree to which its feeding rate (i.e., its functional response) is saturated with respect to prey availability. As such, the proportion of empty stomachs provides insights into the effects of prey on predators and vice versa, although it is typically unreported in deference to descriptions of the contents of the non-empty stomachs. The FracFeed database is an ongoing compilation of the proportions of empty and non-empty stomachs (for gut content surveys) and of feeding and not feeding individuals (for direct observation surveys) reported in publications of predator diet surveys. FracFeed contains data from 4920 diet surveys on 1507 taxa (>4.3 million individuals) spanning cnidarians, ctenophores, chaetognaths, birds, annelids, amphibians, arthropods, mammals, mollusks, reptiles, echinoderms, and fishes that were surveyed in terrestrial, marine, and freshwater ecosystems across the globe over more than 135 years (1887-2023). For most surveys, covariate data include information on the spatial and temporal extent of the diet survey, its central geographical coordinates, the method by which the survey was performed (lethal gut contents, lavage, or direct observation), as well as each predator's standardized taxonomic name and identifier in the Open Tree of Life, its body mass (compiled mostly from independent compilations and additional publications), and its apparent diet's taxonomic richness and resolution. We appeal to more researchers who perform diet surveys to report on the number of empty stomachs they find and encourage additional contributions to the database-particularly from underrepresented geographic regions (e.g., North and Central Asia, North and Central Africa)-to help grow its scope and utility. The database is provided under a CC-BY-NC-S4 4.0 license. Users are requested to cite this data paper when using the data.}, }
@article {pmid41559348, year = {2026}, author = {Deng, Y and Li, J and Wang, P and Luo, X and Xu, H and Xiao, Y and Wang, Z and Lu, Y and Chen, Y and Ge, F}, title = {DNAJB6 as an immuno-oncogenic hub in liver hepatocellular carcinoma: multi-omic profiling reveals prognostic significance and therapeutic vulnerability.}, journal = {Journal of molecular histology}, volume = {57}, number = {1}, pages = {57}, pmid = {41559348}, issn = {1567-2387}, support = {31601036//National Natural Science Foundation of China/ ; 32261133523//National Natural Science Foundation of China/ ; B2023023//Scientific Research Plan Project of Hubei Provincial Department of Education/ ; }, mesh = {Humans ; *Liver Neoplasms/genetics/immunology/pathology/metabolism ; *Carcinoma, Hepatocellular/genetics/immunology/pathology/metabolism ; *HSP40 Heat-Shock Proteins/genetics/metabolism ; Prognosis ; *Molecular Chaperones/genetics/metabolism ; Hep G2 Cells ; *Nerve Tissue Proteins/genetics/metabolism ; Gene Expression Regulation, Neoplastic ; Male ; Female ; Apoptosis/genetics ; Cell Proliferation ; Biomarkers, Tumor ; Middle Aged ; Gene Expression Profiling ; Multiomics ; }, abstract = {The DnaJ/Hsp40 family member B6 (DNAJB6) is a protein aggregation inhibitor, and its dysregulation has been associated with various diseases. Although early studies implicated DNAJB6's role in tumor progression, its prognostic and immunotherapy predictive value across cancers remain undefined. Integrated multi-omics data analysis revealed significant upregulation of DNAJB6 in multiple tumors, particularly in liver hepatocellular carcinoma (LIHC), supported by immunohistochemistry of liver tumor tissues and Western blot assays in HepG2 cells, and poor prognosis in LIHC patients was linked to increased DNAJB6 expression. ROC and univariate Cox analyses established DNAJB6 as an independent prognostic factor in LIHC, with good predictive value. Enrichment, immune scoring and single-cell sequencing analyses indicated that DNAJB6 was linked to immune responses, especially with myeloid-derived suppressor cell (MDSC) and exhausted CD8[+] T cell (Tex). Cell experiments demonstrated that siRNA targeting DNAJB6 inhibited HepG2 cells from proliferating and migrating while inducing apoptosis. Furthermore, we predicted and experimentally confirmed that DNAJB6 silencing conferred gefitinib resistance in HepG2 cells. In conclusion, our findings highlighted the significance of DNAJB6 expression in determining LIHC prognosis and immunotherapy response, as well as its potential in developing novel anti-cancer drugs and enhancing immunotherapy.}, }
@article {pmid41557733, year = {2026}, author = {Smith, C and Kasoar, M and Perkins, O and Millington, JDA and Mistry, J}, title = {Small-scale livelihood and cultural fire: Global spatiotemporal characteristics, and gaps in data.}, journal = {PloS one}, volume = {21}, number = {1}, pages = {e0339561}, pmid = {41557733}, issn = {1932-6203}, mesh = {Humans ; *Fires ; Ecosystem ; Spatio-Temporal Analysis ; Databases, Factual ; *Conservation of Natural Resources ; Agriculture ; *Wildfires ; }, abstract = {Human fire use is a key activity and process in many landscapes and ecosystems around the world, varying spatiotemporally depending on social, economic, and ecological factors. Recently, initiatives have begun to synthesise data on global fire use from across multiple disciplines and disparate sources into coherent databases. Here, we draw on information from one of these databases, the Livelihood Fire Database, which collates data on fire use practices worldwide from case studies in the literature. We examine data from 345 case study locations spanning 69 countries regarding return interval, area burned, and seasonality of anthropogenic fires set to meet small-scale rural livelihood objectives and/or for cultural reasons. We distinguish patterns in the spatiotemporal nature of fires associated with different fire-use purposes, such as clearing vegetation for agriculture, maintaining pasture for livestock, promoting certain plant species for gathering, or driving game when hunting. For many fire uses, especially those related to hunting, gathering, human wellbeing, and social signalling, there are very limited quantitative data available, but it is possible to draw qualitative insights from case studies. Case studies demonstrate that environmental and social conditions drive variation in fire use for the same purpose, reiterating that assumptions of uniform drivers of anthropogenic fire may be misleading. Nonetheless where quantitative data are available, we find some correspondence between the spatiotemporal nature of fires and fire-use purpose, suggesting that distinguishing between different fire-use purposes may be useful to understand and to better model their likely timing, size, and frequency relative to climate and other drivers. We recommend examples where the diagnosis of these broad relationships between fire-use purpose and fire properties could enable improved representation of anthropogenic fire in global land surface models, and aid interpretation of remote sensing data. Many of the smaller fires now being revealed in global burned area data by new fine-scale remote sensing products are likely human-set; continued collection, collation, and analyses of case study data on human fire use globally will be essential to help interpret this improved detection of small fires, and to ensure appropriate representation of the underlying drivers of human activity when modelling fire regimes.}, }
@article {pmid41556837, year = {2026}, author = {McConnell, RD and Jarrett, C and Ferreira, DF and Powell, LL and Quiñones, ALS and Dominoni, DM and Welch, AJ}, title = {Dietary DNA Metabarcoding From Animal Fecal Samples.}, journal = {Current protocols}, volume = {6}, number = {1}, pages = {e70226}, pmid = {41556837}, issn = {2691-1299}, mesh = {*Feces/chemistry ; Animals ; *DNA Barcoding, Taxonomic/methods ; *DNA/genetics ; *Diet ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; }, abstract = {Fecal DNA metabarcoding is a powerful tool for examining animal diets with unprecedented resolution, offering insights into ecological patterns shaped by trophic interactions. As a result, dietary metabarcoding has become widely applied across ecology, evolution, behavior, and conservation. This article provides a practical guide to the key steps involved in metabarcoding animal fecal samples, from field collection and storage through to laboratory processes, such as DNA extraction, PCR amplification, and sequencing library preparation. It also outlines a bioinformatics workflow using the open-source QIIME2 platform to filter, error-correct, and assign taxonomy to dietary DNA sequences. We present key considerations for study design, highlighting potential caveats and limitations to enable researchers to make informed methodological choices. In addition, we offer guidance on the statistical analysis of diet data, including generalized linear models, multivariate analyses, and network analyses. © 2026 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Metabarcoding library preparation of animal fecal dietary DNA for Illumina MiSeq sequencing Support Protocol 1: Making a SpeedBeads solution Support Protocol 2: Calibrating the SpeedBeads solution Basic Protocol 2: QIIME2 bioinformatics workflow for metabarcoded dietary DNA.}, }
@article {pmid41551931, year = {2026}, author = {Mak, L and Tierney, B and Wei, W and Ronkowski, C and Toscan, RB and Turhan, B and Toomey, M and Andrade-Martínez, JS and Fu, C and Lucaci, AG and Solano, AHB and Setubal, JC and Henriksen, JR and Zimmerman, S and Kopbayeva, M and Noyvert, A and Iwan, Z and Kar, S and Nakazawa, N and Meleshko, D and Horyslavets, D and Kantsypa, V and Frolova, A and Kahles, A and Danko, D and Elhaik, E and Labaj, P and Mangul, S and ,  and Mason, CE and Hajirasouliha, I}, title = {CAMP: a modular metagenomics analysis system for integrated multistep data exploration.}, journal = {NAR genomics and bioinformatics}, volume = {8}, number = {1}, pages = {lqaf172}, pmid = {41551931}, issn = {2631-9268}, support = {R01 AI151059/AI/NIAID NIH HHS/United States ; R35 GM138152/GM/NIGMS NIH HHS/United States ; T32 GM083937/GM/NIGMS NIH HHS/United States ; U54 AG089334/AG/NIA NIH HHS/United States ; }, mesh = {*Metagenomics/methods ; *Software ; Workflow ; *Computational Biology/methods ; Microbiota ; }, abstract = {Computational analysis of large-scale metagenomics sequencing datasets provides valuable isolate-level taxonomic and functional insights from complex microbial communities. However, the ever-expanding ecosystem of metagenomics-specific methods and file formats makes designing scalable workflows and seamlessly exploring output data increasingly challenging. Although one-click bioinformatics pipelines can help organize these tools into workflows, they face compatibility and maintainability challenges that can prevent replication. To address the gap in easily extensible yet robustly distributable metagenomics workflows, we have developed the Core Analysis Modular Pipeline (CAMP), a module-based metagenomics analysis system written in Snakemake, with a standardized module and directory architecture. Each module can run independently or in sequence to produce target data formats (e.g. short-read preprocessing alone or followed by de novo assembly), and provides output summary statistics reports and Jupyter notebook-based visualizations. We applied CAMP to a set of 10 metagenomics samples, demonstrating how a modular analysis system with built-in data visualization facilitates rich seamless communication between outputs from different analytical purposes. The CAMP ecosystem (module template and analysis modules) can be found at https://github.com/Meta-CAMP.}, }
@article {pmid41550274, year = {2023}, author = {Boyes, D and Holland, PWH and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Barred Straw, Gandaritis pyraliata (Denis &amp; Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {435}, pmid = {41550274}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Gandaritis pyraliata (the Barred Straw; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 295.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.74 kilobases in length. Gene annotation of this assembly on Ensembl identified 15,805 protein coding genes.}, }
@article {pmid41550075, year = {2026}, author = {Patron-Rivero, C and Yañez-Arenas, C and Ruane, S and Chiappa-Carrara, X and Rojas-Soto, OR}, title = {A comprehensive morphological database of hognose Porthidium pitvipers (Viperidae: Crotalinae).}, journal = {Database : the journal of biological databases and curation}, volume = {2026}, number = {}, pages = {}, pmid = {41550075}, issn = {1758-0463}, support = {1010703//Secretar&#xed;a de Ciencia, Humanidades, Tecnolog&#xed;a e Innovaci&#xf3;n/ ; //Programa de Apoyo a los Estudios de Posgrado/ ; //Secretar&#xed;a de Investigaci&#xf3;n, Innovaci&#xf3;n y Educaci&#xf3;n Superior/ ; }, mesh = {Animals ; *Viperidae/anatomy &amp; histology/classification ; *Databases, Factual ; }, abstract = {Generating and sharing primary biological data is essential to support reproducible research, stimulate new hypotheses, and advance our understanding of biodiversity. Here, we present a comprehensive database of morphological traits for snakes of the genus Porthidium (Viperidae: Crotalinae). This database includes linear measurements, pholidosis (scale counts), and head shape data from preserved specimens across five different herpetological collections. These data comprise 13 morphological traits, 8 scale counts, and 55 landmarks collected from 484 individuals across 9 species. The specimens represent both juvenile and adult stages. All data were collected using standardized protocols to ensure comparability across individuals and species. The dataset is a valuable resource for studies in systematics, morphological evolution, ecological adaptation, and ontogeny, as well as facilitating reproducibility and reuse in the fields of evolutionary biology, herpetology, and comparative morphology.}, }
@article {pmid41548666, year = {2026}, author = {van Kessel, SAM and Schoffelen, AF and van Son, KHS and Notermans, DW and Severin, JA and Bakhshi-Raiez, F and Velthuis, F and Schipper, M and Dongelmans, D and Verbon, A and Wielders, CCH and ,  and , }, title = {Water-free care in Dutch intensive care unit patient rooms: impact on Gram-negative bacteria detections in routine patient care.}, journal = {The Journal of hospital infection}, volume = {170}, number = {}, pages = {9-16}, doi = {10.1016/j.jhin.2025.12.013}, pmid = {41548666}, issn = {1532-2939}, abstract = {BACKGROUND: Patients in intensive care units (ICUs) are at an increased risk of healthcare-associated infections with Gram-negative bacteria (GNB), for which sinks in patient rooms are known reservoirs. We investigated the association between water-free care practices and the incidence of GNB detections in Dutch ICUs in non-outbreak settings.<br><br>METHODS: We performed a retrospective ecological study (2018-2022) using data from the Infectious diseases Surveillance Information System-Antibiotic Resistance (ISIS-AR), the National Intensive Care Evaluation registry and a questionnaire on water-free care. Detections (colonisation and infections) of seven bacteria groups (Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter spp., all Enterobacterales, extended-spectrum beta-lactamase-producing Enterobacterales [ESBL-E] and carbapenemase-producing Enterobacterales) were analysed at ICU-year level. Incidence rate ratios (IRRs) were calculated for water-free vs. non-water-free ICUs, adjusted for ICU and patient characteristics.<br><br>FINDINGS: Data from 37 ICUs were analysed, 22 ICU-years in the water-free group and 131 in the non-water-free group. Water-free ICUs were larger, with more surgery admissions and mechanically ventilated patients. For all bacteria, adjusted IRRs were close to 1 with broad 95% confidence intervals (CIs), ranging from 0.82 (95% CI: 0.44-1.52) for ESBL-E to 1.39 (95% CI: 0.69-2.84) for Acinetobacter spp. Sensitivity analyses showed similar results.<br><br>CONCLUSION: Although positive effects of water-free care on GNB detection rates have been described in single ICUs, these findings were not reflected in this Dutch multi-centre study. Possible explanations are low infection prevalence, high prevention standards, widespread usage of selective decontamination and insufficient power to detect small differences. Evidence for benefits of water-free care in non-outbreak settings remains limited, highlighting the importance of future research in different ICU settings.}, }
@article {pmid41547987, year = {2026}, author = {Ding, S and Zhou, F and Yang, S and Li, Y and Ma, Y and Qiu, Y}, title = {Chromosome-level genome assembly of a Chinese evergreen sweetgum (Liquidambar gracilipes, Altingiaceae).}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {66}, pmid = {41547987}, issn = {2052-4463}, support = {32300202//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {China ; *Chromosomes, Plant ; *Genome, Plant ; Molecular Sequence Annotation ; Datasets as Topic ; }, abstract = {Liquidambar gracilipes, an evergreen species endemic to China and a member of the Altingiaceae family, is morphologically distinguished by its unlobed leaves and represents an ecologically and economically valuable resource. Prized for its ornamental beauty, valuable timber, and medicinal properties, this species is a key component of subtropical evergreen broad-leaved forests in East China. To improve our understanding of its evolutionary and functional genomics, we performed a de novo genome assembly of L. gracilipes by integrating PacBio HiFi long reads, Illumina short reads, and Hi-C data. A high-quality chromosome-level genome assembly was obtained with a genome size of approximately 715.54 Mb and contig N50 of 18.61 Mb, of which 96.87% was anchored to 16 pseudo-chromosomes with a scaffold N50 of 42.40 Mb. Genome annotation identified 24,809 protein-coding genes (97.02% functionally annotated) and revealed a repetitive sequence content of 59.72%. BUSCO analysis against the embryophyte dataset indicated a high level of completeness, with a score of 98.70%. The high-quality genome assembly of L. gracilipes provides a valuable genetic resource for molecular breeding of sweetgums and lays the foundation for future in-depth evolutionary and functional genomics studies of this species.}, }
@article {pmid41546619, year = {2026}, author = {Atighi, MR and Meijer, A and De Meyer, T and Vandepoele, K and Kyndt, T}, title = {Ready for battle: histone modifications shape rice intergenerational memory to protect against nematode attack.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/erag020}, pmid = {41546619}, issn = {1460-2431}, abstract = {Accumulating scientific insights reveal the ecological and evolutionary implications of phenotypic plant plasticity in response to biotic and abiotic stress factors. This study confirms that root-knot nematode infection leads to intergenerational acquired resistance (IAR) in rice offspring. Genome-wide and targeted gene expression analyses demonstrated that offspring of nematode-infected rice plants are better prepared to fight against such attack through 'spring loading' of hormone-related plant defense genes. These genes are suppressed under basal conditions in IAR plants but show a more dramatic induction upon nematode attack. Here, ChIP-sequencing was executed on the offspring of IAR versus naive plants to investigate if histone modifications could be involved in the spring-loaded expression pattern. This revealed enrichment of H3K4me3 on defence related genes and H3K27me3 on development-related genes in roots of IAR plants. Detailed bio-informatic analyses pointed towards significant epigenetic changes to the ABA, ET and MAPK signalling pathways in the offspring of nematode-infected plants. A rice line with reduced activity for OsMPK5 was found to be deficient in defense spring loading and the IAR phenotype. Transmitting a memory of encountered stress factors to one's offspring is arguably an important asset for the adaptation of sessile plant communities to hostile environments.}, }
@article {pmid41545385, year = {2026}, author = {Verbiest, WWM and Hicter, P and Beeckman, H and Wallenus, D and Ilondea, BA and Bastin, JF and Bauters, M and Chave, J and De Blaere, R and de Hauleville, T and De Mil, T and de Ridder, M and De Troyer, C and Ewango, CEN and Fayolle, A and Gorel, A and Fischer, FJ and Kaçamak, B and Kimbuluma, C and Luambua, NK and Laurent, F and Liévens, K and Makana, JR and Malaisse, F and Wasukundi, M and Monnoye, M and Ngomanda, A and Ambounda, FRO and Toirambe, B and Otepa, C and Van Acker, J and Van den Abbeele, B and Van den Bulcke, J and Van Houtte Alonso, B and Wankana, T and Djiofack, BY and Hubau, W}, title = {The Tervuren xylarium Wood Density Database (TWDD).}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {243}, pmid = {41545385}, issn = {2052-4463}, support = {EOS O.0026.22//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; EOS O.0026.22//Fonds De La Recherche Scientifique - FNRS (Belgian National Fund for Scientific Research)/ ; PilotMAB//Belgisch Ontwikkelingsagentschap (Belgian Development Agency)/ ; }, mesh = {*Wood ; Forests ; *Databases, Factual ; Biomass ; Africa ; Trees ; }, abstract = {Wood density is a key plant property, indispensable for estimating forest biomass. Yet, despite tropical regions' substantial contributions to global tree diversity and carbon cycling, they remain underrepresented in wood density datasets such as the CIRAD and Global Wood Density Database (GWDD). To address this gap, we present the 'Tervuren xylarium Wood Density Database' (TWDD), containing 13,332 samples from 2,994 species, 1,022 genera, and 156 plant families across six continents (72% from Africa). TWDD offers direct measurements of oven-dry (oven-dry mass/oven-dry volume, all samples), air-dry (air-dry mass/air-dry volume, 6,408 samples), green (green mass/green volume, 1,657 samples), and basic wood density (oven-dry mass/green volume, 1,686 samples). Basic density was estimated for the remaining 11,646 samples via conversion from oven-dry density. TWDD closes a substantial wood density data gap, especially in Africa, adding 1,164 new species, 160 new genera, and 8 new plant families not included in GWDD or CIRAD datasets. The TWDD provides a critical resource for advancing research on forest community dynamics, ecosystem functioning, carbon cycling, and trait-based ecology worldwide.}, }
@article {pmid41539810, year = {2026}, author = {Liu, Y and Guo, Y and Mu, H and Aaqil, M and Zhang, F and Zheng, J and Sheng, J and Tian, Y and Zhao, C}, title = {Microbial succession-potential influence mechanism on flavor modulation in spontaneously fermented Moringa oleifera leaves: An integrative multi-omics approach.}, journal = {Food research international (Ottawa, Ont.)}, volume = {226}, number = {}, pages = {118184}, doi = {10.1016/j.foodres.2025.118184}, pmid = {41539810}, issn = {1873-7145}, mesh = {*Fermentation ; *Moringa oleifera/microbiology/chemistry ; *Taste ; *Plant Leaves/microbiology/chemistry ; Gas Chromatography-Mass Spectrometry ; Volatile Organic Compounds/analysis ; Odorants/analysis ; Amino Acids/analysis ; *Food Microbiology ; Flavoring Agents ; *Fermented Foods/microbiology ; Bacteria/metabolism/classification/genetics ; Microbiota ; Metagenomics ; Multiomics ; }, abstract = {In this study, the relationship between flavor composition and microbial succession in Moringa oleifera pickles (MOPs) at different stages of spontaneous fermentation was systematically investigated. The results demonstrated a significant increase in the content of organic acids and amino acids during fermentation including malonic acid, citric acid, valine (Val), and asparagine (Asn). These compounds not only enhanced the overall flavor profile but also provided favorable nutritional conditions that supported microbial succession. Furthermore, an integrated aroma network was established through the combined application of gas chromatography-mass spectrometry (GC-MS) and gas chromatography-ion mobility spectrometry (GC-IMS). GC-MS identified key aroma-active compounds such as ethyl caproate (fruity note), 3-hexenal (green, grassy note), and 2-phenylethanol (floral, rosy note). Complementarily, GC-IMS confirmed that esters, alcohols, and terpenes were the major contributors to fruit-like, mushroom-like, and fresh herbal aromas, indicating their critical role as flavor-modulating compounds throughout fermentation. Metagenomic analysis revealed Corynebacterium, Escherichia, Pseudomonas, Xanthomonas, and Pantoea as the dominant microbial genera involved in fermentation. These microbes primarily participated in amino acid, carbohydrate, and nucleotide metabolism and exhibited a close association with the formation of key flavor compounds. The strong influence of microbial succession on flavor evolution is likely driven by the observed correlations between microbial taxa and volatile organic compounds (VOCs). These correlations may stem from a series of complex ecological and metabolic interactions, including substrate competition, niche adaptation, and upstream-downstream dependencies within microbial metabolic networks. This study provides a theoretical foundation for the quality control of MOPs and the mitigation of potential pathogenic microorganisms, thereby supporting its application in enhancing product quality and consumer sensory satisfaction in the pickle industry.}, }
@article {pmid41539503, year = {2026}, author = {Li, S and Liu, J and Li, J and Han, M and Zhang, X and Wu, Z and Hu, S and Jin, H and Hua, K and Tu, K}, title = {Eco-friendly chitosan-based hydrogel for coal dust suppression via salting-out effect.}, journal = {International journal of biological macromolecules}, volume = {341}, number = {Pt 1}, pages = {150171}, doi = {10.1016/j.ijbiomac.2026.150171}, pmid = {41539503}, issn = {1879-0003}, mesh = {*Chitosan/chemistry ; *Dust/prevention &amp; control ; *Coal ; *Hydrogels/chemistry ; Hydrogen-Ion Concentration ; Coal Mining ; Adsorption ; Green Chemistry Technology ; Sodium Citrate/chemistry ; }, abstract = {Coal mining-related dust pollution poses significant threats to ecological integrity, occupational health, and industrial sustainability. Conventional dust suppressants, however, suffer from inherent limitations such as inadequate capture efficiency, poor water retention, and a tendency to cause secondary pollution. To overcome these challenges, this study developed a novel bio-based chitosan hydrogel dust suppressant using highly deacetylated chitosan and sodium citrate via an innovative salting-out method. By acting as both a salting-out agent and a pH regulator, sodium citrate enhances the binding affinity with coal dust to improve suppression performance. Its dust suppression primarily occurs through synergistic mechanisms including electrostatic adsorption, moisture retention/locking, and physical coverage. After 72 h, the hydrogel dust suppressant maintained a water retention rate close to 75%. Its wind erosion resistance rate remained at approximately 99% within 3-7 days, and its degradation rate reached about 96% within 25 days. Notably, compared to conventional materials, this formulation exhibits excellent biodegradability, with its carbon-containing degradation products providing nutrients for plant growth. This green multifunctional system avoids complex preparation processes, integrating high-efficiency dust suppression, environmental safety, and ecological compatibility. It demonstrates significant application potential in sustainable mining practices.}, }
@article {pmid41538792, year = {2026}, author = {Kurilla, A and Čavojská, N and Ikegwuonu, T and Nemčíková, M and Schulte-Strathaus, JC and Uyttebroek, L and Beames, JR and Breznoščáková, D and Dančík, D and Hajdúk, M and Heretik, A and Izáková, &#x13d; and Katreniaková, Z and Myin-Germeys, I and Pečeňák, J and Reininghaus, U and Schick, A and Wolters, M}, title = {Preferences for an Experience Sampling Method-Based Tool as an Adjunct to Usual Treatment in Patients With Problem Substance Use: Qualitative Study.}, journal = {JMIR formative research}, volume = {10}, number = {}, pages = {e79510}, pmid = {41538792}, issn = {2561-326X}, mesh = {Humans ; Male ; Female ; Adult ; Qualitative Research ; *Substance-Related Disorders/therapy/psychology ; *Patient Preference/psychology ; Middle Aged ; Adolescent ; Young Adult ; Europe ; Telemedicine ; Mental Health Services ; }, abstract = {BACKGROUND: Mobile health tools that use the Experience Sampling Method (ESM) appear to be a promising tool to streamline and improve the treatment of substance use disorders. However, patient involvement in the development of these tools is uncommon, and research on the preferences of people being treated for substance use disorders has been scarce. In the scope of the European Union IMMERSE (Implementing Mobile Mental health Recording Strategy for Europe) consortium, an ESM-based tool for Digital Mobile Mental Health (DMMH) was first codeveloped and later tested in 4 European countries.<br><br>OBJECTIVE: This study aimed to achieve an understanding of preferences for features of DMMH among mental health service users with problem substance use.<br><br>METHODS: In 4 European countries, service users were recruited for a semistructured&#xa0;qualitative interview, which started with the presentation of a prototype of the DMMH. Data analysis was performed through directed qualitative content analysis.<br><br>RESULTS: The analytical sample consisted of 12 (5 female, 6 male, and 1 nonbinary person) participants with problem substance use aged 18-50 years. There were 4 participants from Slovakia, 3 from Belgium, 4 from Germany, and 1 from Scotland. Patient preferences were classified into 7 categories: notifications, questions, user interface, functionality changes, visualizations, sharing data with clinicians, and sharing data with others. The proposed intensive notification schedule was deemed acceptable by service users as long as the questionnaire is short. Participants expressed a preference for open-text response options, Ecological Momentary Interventions, and options for individual customization of several elements of the tool. Data visualization was considered an important aid for communication with clinicians, with whom all participants wanted to share data obtained with DMMH. The possibility of sharing data with other people depended on the quality of the relationship with them.<br><br>CONCLUSIONS: In the development of ESM-based mobile health tools for people with problem substance use, their preferences for content, functionality, and appearance of the tools should be considered so they match patients' treatment needs.}, }
@article {pmid41538474, year = {2026}, author = {Chami, AM and Zózimo, TRS and Matosinho, CGR and Silva-Filho, ALD and Carvalho, MRS and Braga, LDC}, title = {Characterization of a novel MSH2 variant in Lynch syndrome: clinical data and complementary bioinformatics assessment.}, journal = {Einstein (Sao Paulo, Brazil)}, volume = {24}, number = {}, pages = {eAO0757}, pmid = {41538474}, issn = {2317-6385}, mesh = {Humans ; *MutS Homolog 2 Protein/genetics ; *Colorectal Neoplasms, Hereditary Nonpolyposis/genetics/pathology ; Female ; Computational Biology ; Middle Aged ; Pedigree ; Germ-Line Mutation/genetics ; Immunohistochemistry ; Phenotype ; Male ; }, abstract = {OBJECTIVE: To describe the clinical characteristics and perform a multi-step bioinformatics evaluation of the pathogenicity of NM_000251.3(MSH2):c.1894_1898del (p.Ile633Lysfs*9), an MSH2 germline variant detected in a family with Lynch syndrome.<br><br>METHODS: Clinical evaluation included description of phenotype, family history, and immunohistochemical characterization of the proband's tumors. For pathogenicity classification according to the American College of Genetics and Genomics/Association for Molecular Pathology (ACMG/APA) criteria, bioinformatics analyses included: (i) literature and database screening, searching for the variant allele frequency, case reports, or functional studies, including ClinVar, VarSome, Ensembl, PubMed, EVA, and ABraOM; (ii) prediction of variant impacts using ExPASy Translate, Pfam, and Modeller 9.24; and, (iii) mechanisms that could mitigate the effects of the variant included alternative splicing and exon skipping (UniProt and GTex) and nonsense-mediated decay (NMD; MutationTaster2021).<br><br>RESULTS: The proband, a 55-year-old female, was diagnosed with two metachronous colorectal cancers. Immunohistochemical analysis showed loss of expression (MSH2 in one tumor, and MSH2 and MSH6 in the other). Seven deceased family members were diagnosed with cancer (four colorectal, one uterine, and two unspecified). This variant caused a stop codon in MSH2 exon 12 of 16. When translated, the protein loses 294 C-terminal residues, which may prompt protein degradation. If the mutated protein escapes degradation, dimerization and DNA-binding domains will be present. Therefore, negative dominance effects were possible. No isoforms ending in exon 12 have been identified in the literature or in RNA splicing databases. A stop codon before the last exon-exon boundary indicated the occurrence of NMD.<br><br>CONCLUSION: No evidence of protein-rescuing mechanisms was found, supporting the classification of this variant as likely pathogenic/pathogenic.}, }
@article {pmid41535740, year = {2026}, author = {Ualiyeva, D and Guo, X and Dujsebayeva, T and Chirikova, M and Ananjeva, NB and Kryukov, K and Zeng, X}, title = {Mitochondrial genomic variations shed light on the phylogeny and biogeography of the Phrynocephalus guttatus species group (Reptilia: Agamidae) in arid Central Asia.}, journal = {BMC genomics}, volume = {27}, number = {1}, pages = {176}, pmid = {41535740}, issn = {1471-2164}, support = {180GJHZ2024036MI//Central Asia Drug Discovery and Development Centre of Chinese Academy of Sciences/ ; 32470466//National Natural Science Foundation of China/ ; BR21882199//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; 125012800908-0//Zoological Institute RAS/ ; }, abstract = {BACKGROUND: The lizard genus Phrynocephalus is an emerging model for studying mitochondrial genome evolution. Within this genus, the P. guttatus species-group represents a taxonomically and ecologically diverse clade whose evolutionary relationships remain poorly resolved. Previous studies based on morphology and partial molecular data have been unable to fully clarify relationships within this rapidly radiated group. Complete mitochondrial genomes provide a solid basement to clarify phylogenetic relationships and assess the role of genomic structural variation in diversification.<br><br>RESULTS: We sequenced and assembled the complete mitochondrial genomes from multiple representatives of the&#xa0;P. guttatus&#xa0;complex across Central Asia and performed comprehensive analyses including annotation, phylogenetic reconstruction, molecular dating, and biogeography assessment. Mitogenomic data resolved phylogenetic relationships with strong support and revealed pronounced structural dynamism, including lineage-specific tRNA duplications and rearrangements. Eastern lineages (P. melanurus 1 and 2, P. kuschakewitschii) differed from western taxa (P. g. kalmykus, P. g. guttatus) in tRNA composition, control region numbers, and rearrangement patterns. Eastern species exhibited duplication of tRNA-Phe and up to three control regions. Novel rearrangement types (F-, G-, and H-types) expand existing mitogenomic classification schemes. Divergence time analyses placed the initial radiation in the Late Miocene &#x2012; Pliocene (~&#x2009;3.13 Mya), with a major eastern diversification between 2.72 and 0.31 Mya, correlating with intense aridification of Central Asia. Ancestral range reconstruction indicated an origin in the Dzungar Basin, followed by dispersal and vicariance events driven by climatic and orographic changes.<br><br>CONCLUSIONS: Our study establishes a robust mitogenome-based phylogenetic framework for the P. guttatus complex and demonstrates that its diversification was shaped by Neogene environmental dynamics and intrinsic mitochondrial genome rearrangements. The discovery of lineage-specific structural changes highlight the evolutionary significance plasticity in desert lizards adaptation.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-026-12529-w.}, }
@article {pmid41534287, year = {2026}, author = {Yang, X and Ji, XH and Li, C and Lai, JL and Luo, XG}, title = {Multi-omic analysis reveals the microecological mechanism of organic arsenic toxicity in a Japanese abandoned chemical weapons site and targeted bioremediation strategies.}, journal = {Journal of hazardous materials}, volume = {503}, number = {}, pages = {141101}, doi = {10.1016/j.jhazmat.2026.141101}, pmid = {41534287}, issn = {1873-3336}, mesh = {Biodegradation, Environmental ; *Arsenicals/metabolism ; *Water Pollutants, Chemical/toxicity/metabolism ; Japan ; Bacillus subtilis/metabolism ; Multiomics ; }, abstract = {Diphenylarsonic acid (DPAA) and phenylarsonic acid (PAA), persistent degradation products of Japanese abandoned chemical weapons (JACWs), threaten aquatic ecosystems. However, their microecological toxicity mechanisms and effective remediation strategies remain poorly understood. Here, we constructed 60-day freshwater microcosms to systematically reveal the toxic effects of DPAA and PAA using integrated multi-omics. We found that both pollutants exhibited extreme persistence (> 98 % residue) and triggered a microbial energy crisis by specifically disrupting the oxidative phosphorylation pathway, with up to 46 genes in the NADH dehydrogenase complex significantly downregulated. Multi-omics integration identified cysteine and methionine metabolism as the central hub of metabolic network disturbance, impairing sulfur cycling and methyl donor supply. Furthermore, pollutant stress activated the viral community and increased antibiotic resistance gene abundance, revealing latent ecological risks. Crucially, guided by these mechanistic insights, we successfully screened a Bacillus subtilis strain from the stressed environment and immobilized it on bamboo biochar to create a novel composite remediation agent. This agent achieved complete mineralization of DPAA and PAA within 5 days, a process associated with the significant upregulation of nine key dioxygenases. Our study not only deciphers the microecological toxicity mechanisms of JACW-related organic arsenicals but also demonstrates a mechanism-informed strategy for developing effective in situ bioremediation.}, }
@article {pmid41532084, year = {2026}, author = {Carvalho, PC and Voltolini, GB and Goedert, A and Chiaratti, VKC and Cantarelli, EH and Francisco, JC and Almeida, TB and Burigo, IP}, title = {Hospitalizations due to Alzheimer's disease in Brazil during the COVID-19 pandemic: an update on frequency, mortality, and costs.}, journal = {Dementia &amp; neuropsychologia}, volume = {20}, number = {}, pages = {e20250322}, pmid = {41532084}, issn = {1980-5764}, abstract = {UNLABELLED: Hospitalizations related to Alzheimer's disease (AD) impose a growing burden on health systems, but recent, nationally representative estimates for Brazil are limited.<br><br>OBJECTIVE: To describe the epidemiological profile of hospital admissions due to AD in Brazil from 2018 to 2024.<br><br>METHODS: Ecological time-series study using the Hospital Information System of the Brazilian Unified Health System (SIH/SUS), accessed via the Department of Informatics of the SUS (DATASUS). We included all regions and states from January 2018 to December 2024. Admissions were identified by the International Classification of Diseases, 10[th] Revision (ICD-10) codes G30.0-G30.9 and F00.0-F00.9. Variables comprised sex, age group, race/color, admission type (urgent/elective), in-hospital mortality, length of stay, and hospital costs. Temporal trends were evaluated with linear regression.<br><br>RESULTS: From 2018 to 2024, 11,212 AD-related hospitalizations were recorded; 79.4% were urgent. The Southeast had the highest absolute number (47.8%), followed by the South (25.1%), Northeast (17.2%), Midwest (6.5%), and North (3.4%). Females accounted for 65% of admissions and 64.7% of in-hospital deaths. Older adults, especially those &#x2265;80 years, represented most hospitalizations (59.3%) and deaths (69.7%). Total hospital expenditures exceeded R$ 14 million, with the Southeast concentrating >60% of national costs. No significant linear trend was detected in annual rates.<br><br>CONCLUSION: Urgent admissions comprised the majority of AD hospitalizations nationwide, with the Southeast presenting the highest numbers. The predominance of older female patients and high in-hospital mortality underscore the need for targeted clinical and public health strategies. Rising expenditures reinforce investment in health infrastructure and long-term dementia-care policies in Brazil.}, }
@article {pmid41531076, year = {2026}, author = {Liu, PD and Huang, L and Meng, F and Zhao, HH and Liu, JT}, title = {[Multi-scenario Prediction and Ecological Security Pattern Construction Based on InVEST-PLUS Model: A Case Study of Liaoning Province].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {47}, number = {1}, pages = {467-480}, doi = {10.13227/j.hjkx.202412160}, pmid = {41531076}, issn = {0250-3301}, abstract = {Taking policy factors into account in constructing an ecological security pattern is of great significance in helping to realize the ecological civilization strategy. Taking Liaoning Province as an example， the study adopts a research framework of "core-regional-strip-multi-point" based on five land use data sets from 2000 to 2020 and couples the InVEST-PLUS model to predict the land use and carbon storage in the SN， SW， CLD， and SE scenarios for the year 2030. The study then combines the MSPA and MCR models to construct an ecological security pattern and proposes new ideas for ecological construction. The results showed that： ① The land use prediction results indicated that land use was mainly composed of farmland and forests. The farmland area decreased slowly， and the forest area increased continuously from 2000 to 2030. ② The spatial distribution of carbon storage was mainly in the east， and the eastern region was a key protected forest area. The trend of carbon storage in the eastern region was relatively stable， while the carbon storage in the western region continued to increase. ③ The ecological security network structure in the SE scenario was complex and highly connected， identifying 30 ecological source areas， 97 discontinuities， 56 ecological corridors with a total length of 211 km， and a northeastern-southeastern strip-shaped extension pattern with dense networks in the middle and western regions and sparse networks in the eastern coastal areas. ④ Comparing the structure and connectivity of the ecological security network in different scenarios， the study selected the SE scenario and proposed the "one core， three regions， three belts， and multiple points" ecological security pattern construction strategy. It also proposed ecological management policy recommendations to promote sustainable development in Liaoning Province.}, }
@article {pmid41529120, year = {2026}, author = {Li, J and Chen, S and Wu, Z and Wang, H and Xia, R and Meng, J and Zhang, Y}, title = {CircRM: profiling circular RNA modifications from nanopore direct RNA sequencing.}, journal = {Briefings in bioinformatics}, volume = {27}, number = {1}, pages = {}, pmid = {41529120}, issn = {1477-4054}, mesh = {*RNA, Circular/genetics/metabolism ; Humans ; *Sequence Analysis, RNA/methods ; *Nanopore Sequencing ; *RNA Processing, Post-Transcriptional ; Computational Biology/methods ; }, abstract = {Circular RNA (circRNA) represents a critical class of regulatory RNAs with distinctive structural and functional features. The functions of circRNAs are modulated by various RNA modifications. Here, we present CircRM, a nanopore direct RNA sequencing-based computational method for profiling RNA modifications in circRNAs at single-base and single-molecule resolution. By integrating circRNA detection, read-level modification detection, and quantitative assessment of methylation rates, CircRM identified 427 high-confidence circRNAs and enables systematic characterization of three major modifications, m5C (AUC = 0.855), m6A (AUC = 0.817) and m1A (AUC = 0.769). It revealed distinct modification patterns compared with linear RNAs, highlighting RNA-type-specific regulations. We also identified the key features of circRNA-specific modifications, such as the enrichment near the back-splice junctions. Cross-cell line analyses further demonstrated conserved and cell-type-specific modification patterns. Together, these findings reveal, at the computational level, a unique epitranscriptomic landscape associated with circRNAs and establish CircRM as a powerful tool for advancing the study of RNA modifications in circular RNA biology. CircRM is free accessible at: https://github.com/jiayiAnnie17/CircRM.}, }
@article {pmid41529073, year = {2026}, author = {Vessman, B and Guridi-Fernández, P and Arias-Sánchez, FI and Mitri, S}, title = {Novel artificial selection method improves function of simulated microbial communities.}, journal = {PLoS computational biology}, volume = {22}, number = {1}, pages = {e1013863}, pmid = {41529073}, issn = {1553-7358}, mesh = {Computer Simulation ; *Microbiota/physiology/genetics ; Computational Biology ; *Models, Biological ; *Selection, Genetic ; }, abstract = {There is increasing interest in artificially selecting or breeding microbial communities, but experiments have reported modest success. Here, we develop computational models to simulate two previously known selection methods and compare them to a new "disassembly" method. We evaluate all three methods in their ability to find a community that could efficiently degrade toxins, whereby investment into degradation results in slower growth. Our disassembly method relies on repeatedly competing different communities of known species combinations against one another, while regularly shuffling around their species combinations. This approach allows many species combinations to be explored, thereby maintaining enough between-community diversity for selection to act on, and resulting in communities with high performance. Nevertheless, selection at the community level in our simulations did not counteract selection at the individual level, nor the communities' ecological dynamics. Species in our model evolved to invest less into community function and more into growth, but increased growth compensated for reduced investment, such that overall community performance was barely affected by within-species evolution. Within-community ecological dynamics were more of a challenge, as we could control them during the selection process, but community composition and function dropped in the longer term. Our work shows that the strength of disassembly lies mainly in its ability to explore different species combinations, and helps to propose alternative designs for community selection experiments.}, }
@article {pmid41525703, year = {2026}, author = {Astill Wright, L and Roe, J and Guo, B and Morriss, R}, title = {Dropout, Attrition, Adherence, and Compliance in Mood Monitoring and Ambulatory Assessment Studies for Depression and Bipolar Disorder: Systematic Review and Meta-Analysis.}, journal = {JMIR mental health}, volume = {13}, number = {}, pages = {e83765}, pmid = {41525703}, issn = {2368-7959}, mesh = {Humans ; Affect ; *Bipolar Disorder/diagnosis ; *Depressive Disorder/diagnosis ; *Monitoring, Ambulatory/statistics &amp; numerical data ; *Patient Compliance/statistics &amp; numerical data ; *Patient Dropouts/statistics &amp; numerical data ; }, abstract = {BACKGROUND: Ambulatory assessment and mood monitoring are different methods that can use novel technology to deliver a more efficient, flexible, and usable method of clinical outcome assessment compared with established measures of behavior and mood. Concerns have been raised around attrition in and adherence to these new protocols, particularly over the medium to long term by people with mood disorders.<br><br>OBJECTIVE: This systematic review and meta-analysis assessed attrition from and adherence to active and passive ambulatory assessment and mood monitoring protocols by people with bipolar disorder and depression over the medium and long term.<br><br>METHODS: Randomized controlled trials and nonrandomized studies were identified and rated for risk of bias. Adherence and attrition data were pooled to calculate effect sizes. We analyzed specific factors that we hypothesized a priori could affect the prevalences of attrition and adherence by means of subgroup meta-analysis or metaregression modeling.<br><br>RESULTS: We evaluated 77 mood tracking or ambulatory assessment studies including 17,123 participants. Pooled adherence was 0.64% (95% CI 0.59%-0.70%; P<.001), and pooled attrition was 0.28% (95% CI 0.22%-0.34%; P<.001). Three factors had a statistically significant subgroup difference for adherence: The presence of financial incentives increased adherence, and the presence of mood monitoring reminders and a higher study risk of bias decreased adherence. Four factors had a statistically significant subgroup difference for attrition: Digital mood monitoring decreased attrition versus analogue studies, but mood monitoring reminders, mood monitoring versus other protocols, and a high risk of study bias increased attrition. These analyses, however, were vulnerable to confounding by study design and protocol design. Attrition rates were not reported by 17 studies (17/77, 22%), and 20 studies (20/77, 26%) did not report adherence rates. Most studies had a low-to-moderate risk of bias, but heterogeneity was very high. Only 16 studies reported adherence systematically.<br><br>CONCLUSIONS: Reporting of attrition and adherence to ambulatory assessments was not systematic nor universal, and until it is, analyses are unlikely to demonstrate clear conclusions. We found very high heterogeneity and evidence of publication bias, and this limited the certainty of our conclusions. Financial incentives may increase adherence, and attrition may be lower in digital than analogue studies of mood monitoring. There was no statistically significant difference in adherence and attrition between studies of passive and active ambulatory assessments. Reminders of mood monitoring increased attrition and decreased adherence, but the results may be confounded by longer length of follow-up versus other studies.}, }
@article {pmid41525285, year = {2026}, author = {Ramirez-Gil, JG and López-Hernández, F and Conejo-Rodriguez, DF and Henao-Rojas, JC and Quiroga-Benavides, KE and Cortés, AJ and Chacón-Sánchez, MI}, title = {GermVersity: A free and user-friendly interface to enhance the visualization and analysis of genebank data.}, journal = {PloS one}, volume = {21}, number = {1}, pages = {e0340826}, pmid = {41525285}, issn = {1932-6203}, mesh = {Genetic Variation ; Polymorphism, Single Nucleotide ; *User-Computer Interface ; *Databases, Genetic ; Phenotype ; *Seed Bank ; }, abstract = {Genebanks are crucial for food security and industrial applications. However, their heterogeneous nature hinders effective utilization. To address this, the GermVersity platform was developed to integrate conventional, artificial intelligence, and data science approaches to the transversal analysis of data associated with genebank accessions. GermVersity aids in the classification and prioritization of germplasm diversity, facilitating the conservation and utilization of valuable genetic resources in agriculture. The GermVersity proposal is focused on developing a user-friendly application to visualize, analyze and interpret analysis-ready data from genebanks. The application's case study uses data from the bean genebank at Bioversity International - CIAT but can be adapted for other genebanks and broader collections. GermVersity is divided into three modules. The first module analyzes genetic diversity using phenotypic and SNP data. In this module users can prioritize morphological descriptors for efficient classification of accessions, define genetic clusters or populations, calculate basic diversity statistics per locus and per population, and estimate genetic divergence among clusters or populations. The second module implements spatial distribution modeling, allowing users to understand ecological diversity across the geographical distribution range of a set of accessions. The third module characterizes the genomic architecture of phenotypic trait variation and adaptation to ecological niches using genome-wide association implemented in prediction integrated tools (GAPIT) and Latent Factor Mixed Model (LFMM) analysis. The GermVersity platform was built using Shiny-Golem and is hosted on GitHub for free use. To access it, users can install the library and run the application through specific commands in R. Responsible use of algorithms is recommended, along with the inspection of results for biological coherence. Ultimately, GermVersity offers an integrated analytical pipeline to leverage genebank diversity as part of pre-breeding efforts.}, }
@article {pmid41525251, year = {2026}, author = {Palenova, E and Veraverbeke, S and Drobyshev, I and Kontos, T and Ebert, K}, title = {Prioritizing areas for post-fire restoration in Greece using mixed-methods spatial analysis.}, journal = {PloS one}, volume = {21}, number = {1}, pages = {e0339998}, pmid = {41525251}, issn = {1932-6203}, mesh = {Greece ; *Conservation of Natural Resources/methods ; *Spatial Analysis ; *Wildfires ; Geographic Information Systems ; Humans ; Climate Change ; *Fires ; }, abstract = {The Mediterranean region will likely face an increase in the frequency and intensity of wildfires due to climate change. Despite being fire-prone, Greece lacks a developed standardized system for identifying and prioritizing burned areas in relation to their restoration needs. Prioritization of areas for post-fire restoration efforts using Geographic Information System and Remote Sensing is a powerful decision-making tool, which, however, can be insufficient in effectively integrating socio-ecological criteria and perspectives from multiple stakeholders. Combining qualitative methods such as interviews with remotely sensed data can enhance the understanding of nuances in a local context. We designed an approach to identify high-priority areas for post-fire vegetation restoration. The identification was based on stakeholder interviews and the subsequent integration of their responses with subsequent multi-criteria overlay analysis. We selected criteria to rank the areas by interviewing 15 stakeholders working on post-fire issues. The expert interviews revealed the key characteristics respondents consider essential for prioritizing burned areas for restoration. Areas covering 77.25 km[2] were selected for restoration depending on the fire history, slope, and designation as part of the protected areas. Outcomes of the analysis helped to highlight three locations that potentially need special attention, with the total area of 31 km[2]. We propose a prioritization system that is flexible, scalable, and can help government agencies, local foresters, private consultancies, and NGOs plan restoration actions and optimize the effectiveness of restoration programs in various ecosystems.}, }
@article {pmid41523158, year = {2025}, author = {Boyes, D and Boyes, C and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Light Arches, Apamea lithoxylaea (Denis &amp; Schiffermüller), 1775 (Lepidoptera: Noctuidae).}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {508}, pmid = {41523158}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Apamea lithoxylaea (Light Arches; Arthropoda; Insecta; Lepidoptera; Noctuidae). The assembly contains two haplotypes with total lengths of 577.73 megabases and 521.26 megabases. Most of haplotype 1 (98.15%) is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 16.43 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.}, }
@article {pmid41520592, year = {2026}, author = {Chen, H and Liu, Y and Wang, G and Fan, W and Rong, G and Wang, H}, title = {Multi-omics and stable isotopic reveal coordinated carbon-nitrogen metabolic reprogramming sustaining diatom cellular homeostasis under CO2 limitation.}, journal = {Marine environmental research}, volume = {215}, number = {}, pages = {107843}, doi = {10.1016/j.marenvres.2026.107843}, pmid = {41520592}, issn = {1879-0291}, mesh = {*Diatoms/physiology/metabolism ; *Carbon Dioxide/metabolism ; *Nitrogen/metabolism ; *Carbon/metabolism ; Homeostasis ; Eutrophication ; Metabolomics ; Transcriptome ; Nitrogen Isotopes ; Metabolic Reprogramming ; Multiomics ; }, abstract = {Algal blooms frequently trigger CO2 limitation, under which diatoms not only survive but dominate. However, the cellular metabolic adaptations underlying this ecological phenomenon remain poorly understood. This study systematically investigated the coordinated carbon-nitrogen metabolic response of the typical diatom Skeletonema costatum (S. costatum) to CO2 limitation (300 ppm, 100 ppm) via stable isotope and multi-omics analysis. CO2 limitation triggered the carbon concentrating mechanism (CCM) and attenuated nitrogen isotope fractionation, redirecting carbon flux towards amino acid biosynthesis rather than fatty acid biopathway. Integrated transcriptomic and metabolomic profiling revealed that carbon fixation and the tricarboxylic acid (TCA) cycle were activated, while fatty acid synthesis was inhibited. This redirected carbon skeletons from acetyl-CoA into the TCA cycle to support amino acid production. Concurrent upregulation of nitrogen assimilation genes, particularly those involved in glutamine/glutamate synthesis, facilitated ammonium incorporation. The alanine-aspartate-glutamate pathway served as a central hub, integrating carbon skeletons and amino groups to drive amino acid synthesis and maintain cellular homeostasis. These findings systematically delineate the metabolic reprogramming that enables diatoms to adapt to CO2 limitation, providing key insights into their dominance during algal blooms.}, }
@article {pmid41518802, year = {2026}, author = {Yang, X and Ji, XH and Li, C and Lai, JL and Luo, XG}, title = {Multi-omics assessment of synthetic microbiome-mediated remediation of cyclotetramethylene tetranitroamine (HMX) contaminated water.}, journal = {Journal of hazardous materials}, volume = {503}, number = {}, pages = {141026}, doi = {10.1016/j.jhazmat.2026.141026}, pmid = {41518802}, issn = {1873-3336}, mesh = {*Water Pollutants, Chemical/metabolism ; *Microbiota ; Biodegradation, Environmental ; *Nitrosamines/metabolism ; Bacteria/metabolism/genetics ; Multiomics ; Triazines ; }, abstract = {Cyclotetramethylene tetranitroamine (HMX) is a typical high-energy nitramine pollutant with an environmental persistence and toxic effects that pose serious ecological risks. In this study, a synthetic microbiome with complementary functions is built that enables the integration of multigroup technology to conduct a systematic analysis of the mechanism of remediation of HMX-contaminated water bodies. Four core bacterial strains (Bacillus altitudinis, B. cereus, B. subtilis, and Pseudomonas stutzeri) were directionally domesticated and screened from HMX-contaminated water. Through functional verification, they were confirmed to express key enzymes NfsA, YdhA, FdhA, and NirS, respectively, to form a complete HMX deep degradation-level connection path. The synthetic microbiome achieved 100 % removal of HMX and its intermediates within 60 days, and isotope tracing (δ[15]N enrichment +2.7 ‰) confirmed its complete mineralization ability. Multiomic analysis showed that the restoration process is accompanied by a systematic reshaping of the water microecology and chemical environment, so that the microbial community structure is optimized and the synthetic microbiome is successfully colonized and becomes the core node. Meanwhile, the energy metabolic network (glycolysis, TCA cycle, oxidative phosphorylation) is significantly enhanced; metagenomic data also revealed reduced viral abundance. Ionomics revealed that key nutrient elements, such as P and S, are efficiently assimilated and utilized. These findings identify an efficient HMX bioremediation strategy that utilizes the multiple dimensions of "community structure-metabolic function-environmental effects" through a multigroup integration framework. More importantly, this study provides a theoretical basis and practical paradigm for the rational design of functional microbial communities.}, }
@article {pmid41516498, year = {2025}, author = {Výbošťok, J and Chudá, J and Tomčík, D and Gretsch, D and Tomaštík, J and Pełka, M and Bedkowski, J and Skladan, M and Mokroš, M}, title = {An Open and Novel Low-Cost Terrestrial Laser Scanner Prototype for Forest Monitoring.}, journal = {Sensors (Basel, Switzerland)}, volume = {26}, number = {1}, pages = {}, pmid = {41516498}, issn = {1424-8220}, support = {09I03-03-V04-00341.//Recovery and Resilience Plan for Slovakia/ ; VEGA 1/0604/24//Ministry of Education of Slovak Republic/ ; VV-MVP-24-0412//Slovak Research and Development Agency/ ; }, abstract = {Accurate and efficient forest inventory methods are crucial for monitoring forest ecosystems, assessing carbon stocks, and supporting sustainable forest management. Traditional field-based techniques, which rely on manual measurements such as diameter at breast height (DBH) and tree height (TH), remain labour-intensive and time-consuming. In this study, we introduce and validate a fully open-source, low-cost terrestrial laser scanning system (LCA-TLS) built from commercially available components and based on the Livox Avia sensor. With a total cost of €2050, the system responds to recent technological developments that have significantly reduced hardware expenses while retaining high data quality. This trend has created new opportunities for broadening access to high-resolution 3D data in ecological research. The performance of the LCA-TLS was assessed under controlled and field conditions and benchmarked against three reference devices: the RIEGL VZ-1000 terrestrial laser scanner, the Stonex X120GO handheld mobile laser scanner, and the iPhone 15 Pro Max structured-light device. The LCA-TLS achieved high accuracy for estimating DBH (RMSE: 1.50 cm) and TH (RMSE: 0.99 m), outperforming the iPhone and yielding results statistically comparable to the Stonex X120GO (DBH RMSE: 1.32 cm; p > 0.05), despite the latter being roughly ten times more expensive. While the RIEGL system produced the most accurate measurements, its cost exceeded that of the LCA-TLS by a factor of about 30. The hardware design, control software, and processing workflow of the LCA-TLS are fully open-source, allowing users worldwide to build, modify, and apply the system with minimal resources. The proposed solution thus represents a practical, cost-effective, and accessible alternative for 3D forest inventory and LiDAR-based ecosystem monitoring.}, }
@article {pmid41515900, year = {2025}, author = {Wu, J and Zhou, L and Qiu, D and Wei, T and Xie, C and Chen, E and Lin, M and Fan, Y}, title = {Integrating Bioinformatics and Experimental Validation Identifies SCD as a Ferroptosis-Related Immune Regulator and Therapeutic Target in Crohn's Disease.}, journal = {International journal of molecular sciences}, volume = {27}, number = {1}, pages = {}, pmid = {41515900}, issn = {1422-0067}, support = {2025J011410//the Natural Science Foundation of Fujian Province/ ; 2025J08298//the Natural Science Foundation of Fujian Province/ ; }, mesh = {*Ferroptosis/genetics/immunology ; *Crohn Disease/genetics/immunology/metabolism/pathology/drug therapy ; *Computational Biology/methods ; Humans ; Animals ; Mice ; Disease Models, Animal ; Gene Expression Profiling ; Colitis/genetics/chemically induced/immunology ; }, abstract = {This study investigates the role of ferroptosis-related genes (FRGs) in the intestinal inflammation of Crohn's disease (CD). Through integrated bioinformatics and experimental validation, we identified differentially expressed genes from RNA-seq data and intersected them with known FRGs to obtain ferroptosis-related differentially expressed genes (FEDGs). Functional enrichment and immune infiltration analyses were performed, and seven hub FEDGs were selected using machine learning. A diagnostic model based on these genes showed strong predictive ability. Immune analysis revealed significant associations with macrophages, neutrophils, dendritic cells, and CD4+ T cells. Protein expression of key hub genes was validated in clinical CD samples and a DSS-induced colitis model. Importantly, localized inhibition of SCD alleviated disease severity in experimental colitis. These findings highlight the involvement of ferroptosis in CD immune dysregulation and propose SCD as a potential therapeutic target.}, }
@article {pmid41514910, year = {2025}, author = {Abdullah, NI and Elias, N' and Ohte, N and Vincenot, CE}, title = {Bat Community Response to Insect Abundance in Relation to Rice Phenology in Peninsular Malaysia.}, journal = {Biology}, volume = {15}, number = {1}, pages = {}, pmid = {41514910}, issn = {2079-7737}, support = {SS2011//Bat Conservation International/ ; ABDUMALA1220-00//Idea Wild/ ; RG-07012020/02//The Habitat Foundation/ ; }, abstract = {Bats provide essential ecosystem services, particularly in regulating insect populations within agricultural landscapes. However, research on bat-insect interactions in Malaysian rice fields remains limited. This study examined bat diversity and insect abundance in the rice field area of Gunung Keriang, Kedah, using two harp traps, two mist nets and a light trap at three selected sites. A total of 2499 bats representing 27 species were captured, alongside 161,539 insects from 11 orders. Rhinolophus pusillus was the dominant bat species across all seasons. During the dry season, Chilo polychrysus (stem borer) was the dominant insect pest, whereas Nilaparvata lugens (brown planthopper) prevailed during the wet season. Insects from the order Coleoptera, dominant in the dry season, are likely consumed by larger bat species with stronger bite forces. Bat foraging activity peaked concurrently with insect emergence, corresponding to periods of high food availability. Statistical analysis revealed significant associations between bat activity, temperature, and rainfall, but not insect abundance. These findings underscore the ecological importance of bats as natural pest regulators in rice field ecosystems and highlight their potential role in promoting sustainable, ecosystem-based agricultural management.}, }
@article {pmid41513661, year = {2026}, author = {Meyer, AR and Tan, JP and Mihaila, MP and Neugebauer, M and Nyström, L and Bokulich, NA}, title = {Shipped and shifted: modeling collection-induced bias in microbiome multi-omics using a tractable fermentation system.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {43}, pmid = {41513661}, issn = {2055-5008}, support = {101060247//HORIZON EUROPE European Research Council/ ; 22.00210//Swiss State Secretariat for Education, Research and Innovation (SERI)/ ; }, mesh = {Fermentation ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Temperature ; *Fungi/classification/genetics/metabolism/isolation &amp; purification ; Metabolome ; Metabolomics/methods ; Machine Learning ; *Specimen Handling/methods ; Bread/microbiology ; Multiomics ; }, abstract = {Large-scale, decentralized microbiome sampling surveys and citizen science initiatives often require periods of storage at ambient temperature, potentially altering sample composition during collection and transport. We developed a generalizable framework to quantify and model these biases using sourdough as a tractable fermentation system, with samples subjected to controlled storage conditions (4 °C, 17 °C, 30 °C, regularly sampled up to 28 days). Machine-learning models paired with multi-omics profiling-including microbiome, targeted and untargeted metabolome profiling, and cultivation-revealed temperature-dependent shifts in bacterial community structure and metabolic profiles, while fungal communities remained stable. Storage induced ecological restructuring, marked by reduced network modularity and increased centrality of dominant taxa at higher temperatures. Notably, storage duration and temperature were strongly encoded in the multi-omics data, with temperature exerting a more pronounced influence than time. 24 of the top 25 predictors of storage condition were metabolites, underscoring functional layers as both sensitive to and informative of environmental exposure. These findings demonstrate that even short-term ambient storage (<2 days) can substantially reshape microbiome, metabolome, and biochemical profiles, posing risks to data comparability in decentralized studies and emphasizing the need to recognize and address such biases. Critically, the high predictability of storage history offers a path toward bias detection and correction- particularly when standardized collection protocols are infeasible, as is common in decentralized sampling contexts. Our approach enables robust quantification and modeling of such storage effects across multi-omics datasets, unlocking more accurate interpretation of large-scale microbiome surveys.}, }
@article {pmid41513569, year = {2026}, author = {Narita, M and Matsugaki, R and Muramatsu, K and Fushimi, K and Matsuda, S}, title = {Corrigendum to "Obesity and risk of post-operative pneumonia among older adult patients with hip fracture: An obesity paradox" [Clin Nutr ESPEN 68 (2025) 342-347].}, journal = {Clinical nutrition ESPEN}, volume = {}, number = {}, pages = {102904}, doi = {10.1016/j.clnesp.2025.102904}, pmid = {41513569}, issn = {2405-4577}, }
@article {pmid41512299, year = {2026}, author = {Beavan, AJS and Domingo-Sananes, MR and McInerney, JO}, title = {PanForest: predicting genes in genomes using random forests.}, journal = {Bioinformatics (Oxford, England)}, volume = {42}, number = {1}, pages = {}, pmid = {41512299}, issn = {1367-4811}, support = {108290//Leverhulme Trust Research Fellowship/ ; }, mesh = {*Software ; *Genome, Bacterial ; Escherichia coli/genetics ; *Genomics/methods ; Algorithms ; *Computational Biology/methods ; Random Forest ; }, abstract = {MOTIVATION: The presence or absence of some genes in a genome can influence whether other genes are likely to be present or absent. Understanding these gene co-occurrence and avoidance patterns reveals fundamental principles of genome organization, with applications ranging from evolutionary reconstruction to rational design of synthetic genomes.<br><br>RESULTS: PanForest, presented here, uses random forest classifiers to predict the presence and absence of genes in genomes from the set of other genes present. Performance statistics output by PanForest reveal how predictable each gene's presence or absence is, based on the presence or absence of other genes in the genome. Further, PanForest produces statistics indicating the importance of each gene in predicting the presence or absence of each other gene. The PanForest software can run serially or in parallel, thereby facilitating the analysis of pangenomes at Network of Life scale.A pangenome of 12&#xa0;741 accessory genes in 1000 Escherichia coli genomes was analysed in around 5&#x2009;h using eight processors. To demonstrate PanForest's utility, we present a case study and show that certain genes associated with resistance to antimicrobial drugs reliably predict the presence or absence of other genes associated with resistance to the same drug. Further, we highlight several associations between those genes and others not known to be associated with antimicrobial resistance (AMR), or associated with resistance to other drugs. We envisage PanForest's use in studies from multiple disciplines concerning the dynamics of gene distributions in pangenomes ranging from biomedical science and synthetic biology to molecular ecology.<br><br>The software if freely available with a full manual and can be found with at www.github.com/alanbeavan/PanForest DOI: https://doi.org/10.5281/zenodo.17865482.}, }
@article {pmid41512284, year = {2026}, author = {Nemoto, Y and Okawara, M and Nishizawa, N and Mori, M and Takenaka, M and Kuroda, K and Fujino, Y and Matsuda, S and Fushimi, K and Tanaka, F}, title = {Robotic Versus Video-Assisted Thoracoscopic Lobectomy/Segmentectomy: Multilevel Analysis in Japan.}, journal = {Interdisciplinary cardiovascular and thoracic surgery}, volume = {41}, number = {1}, pages = {}, pmid = {41512284}, issn = {2753-670X}, mesh = {Humans ; *Thoracic Surgery, Video-Assisted/adverse effects/mortality ; Male ; Female ; Retrospective Studies ; *Lung Neoplasms/surgery/mortality/pathology ; Japan/epidemiology ; Aged ; *Robotic Surgical Procedures/adverse effects/mortality ; *Pneumonectomy/adverse effects/mortality/methods ; Middle Aged ; Postoperative Complications/epidemiology ; Risk Factors ; Treatment Outcome ; Databases, Factual ; }, abstract = {OBJECTIVES: Large-scale comparative data on the perioperative safety of robotic-assisted thoracoscopic surgery and video-assisted thoracoscopic surgery in Asia are limited. We compared the perioperative outcomes of these 2 approaches for lung cancer.<br><br>METHODS: This retrospective study used data from the Diagnostic Procedure Combination database in Japan. We included 47&#xa0;541 patients who underwent lobectomy or segmentectomy for lung cancer from 2018 to 2021 and performed multivariable analyses.<br><br>RESULTS: Among 47&#xa0;541 patients, 2835 underwent robotic-assisted thoracoscopic surgery. Perioperative mortality did not differ significantly between groups (incidence rate ratio, 1.71; 95% CI, 0.88-3.33). Robotic-assisted surgery was associated with longer anaesthesia time and a higher incidence of mechanical ventilation postoperatively (incidence rate ratio, 1.96; 95% CI, 1.36-2.81), although the absolute difference was small (Marginal risk difference, +0.52 percentage points; 95% CI, +0.14 to +0.91). No significant differences were observed in other major complications, reoperation, or hospital stay.<br><br>CONCLUSIONS: In this large, real-world Japanese cohort including the early experience with robotic surgery, overall perioperative safety was comparable between robotic-assisted and video-assisted thoracoscopic surgery, although a statistically significant but small absolute increase in postoperative ventilation was observed with the robotic approach. This association remained robust across a series of sensitivity analyses. However, it is likely influenced by unmeasured confounding. Future prospective studies should investigate specific procedural factors, including anaesthetic management and patient selection, to optimize outcomes.}, }
@article {pmid41512112, year = {2026}, author = {Shimmura, T and Kurachi, T and Matsuda, Y and Rafati, N and Shimura, K and Goto, T and Kawakami, SI and Maeda, R and Yamada, Y and Pettersson, ME and Nakamura, Y and Higashiura, Y and Shimura, NN and Bendesky, A and Tsudzuki, M and Andersson, L}, title = {Genomic and neurobiological bases of variation in fighting strategies in gamecocks.}, journal = {Molecular biology and evolution}, volume = {43}, number = {1}, pages = {}, pmid = {41512112}, issn = {1537-1719}, support = {18K19266//JSPS KAKENHI/ ; 19H03102//JSPS KAKENHI/ ; 21H00339//JSPS KAKENHI/ ; 21K19185//JSPS KAKENHI/ ; 24H00541//JSPS KAKENHI/ ; //MEXT/ ; JPMJFR211D//JST FOREST Program/ ; //TUAT TAMAGO/ ; //Kieikai Research Foundation/ ; }, mesh = {Animals ; *Chickens/genetics/physiology ; *Aggression/physiology ; Male ; Behavior, Animal ; Forkhead Transcription Factors/genetics ; }, abstract = {Aggression is an essential animal behavior for survival, particularly in situations where fighting cannot be avoided. In such situations, the choice of fighting strategy (eg biting, charging, or defending) is critical. Although the molecular bases of fighting and aggressiveness have been previously studied, how genetic, transcriptional, and neurobiological mechanisms contribute to the choice of fighting strategy remains largely unknown. Here, we use two subpopulations of chickens bred for cockfighting that show markedly different fighting strategies: offensive and defensive attack. A genome-wide screen comparing individuals from the two subpopulations indicated a polygenic background and we identified 15 candidate genes, five of which are implicated in neuronal development. Among these, the transcription factor gene FOXP1 was notable. FOXP1 is essential for neuronal development in the brain and has been implicated in the regulation of motor circuits. Transcriptomic analysis of the diencephalon also revealed differential expressions of genes involved in neurodevelopment, as well as in the synthesis and release of neurotransmitters. RNA-sequencing and immunohistochemistry suggested that activation of the indirect pathway of the brain motor circuit promotes the defensive fighting strategy. This was further supported by behavioral pharmacological experiments targeting dopaminergic signaling. Taken together, our results indicate that genomic variation and altered expression of neurodevelopment-related genes underlie differences in fighting strategies, and that the neuroendocrine changes in brain circuits further modulate these behavioral outcomes.}, }
@article {pmid41507331, year = {2026}, author = {Zhang, K and Zhang, LY and Qin, X and Zhang, YW and Xie, WJ and Wan, RD and Fang, YG and Yang, QE}, title = {Integrated multiomics analysis reveals the molecular features and crucial regulators of hair follicles in yak (Bos grunniens).}, journal = {Communications biology}, volume = {9}, number = {1}, pages = {190}, pmid = {41507331}, issn = {2399-3642}, support = {U22A20447//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; *Hair Follicle/metabolism/cytology ; Cattle/genetics ; Wnt Signaling Pathway ; Gene Expression Regulation ; Multiomics ; }, abstract = {Yak is a unique bovine species that adapts to the extreme climate of the Qinghai-Tibet Plateau in part owing to its dense skin coat. Despite its essential role in cold adaptation, the genetic basis of hair follicle structure and growth has not been extensively studied in this iconic animal. In the present study, we construct a single-cell atlas of hair follicle (HF) cells from yak and taurine cattle and examine differences in their cellular composition and gene expression. Among the 14 cell types identified in HFs, the dermal papilla (DP) displays the most dramatic differences between cattle and yak. Detailed analysis reveals that the genes in the WNT signaling pathway are differentially expressed in the dermal papilla (DP) cells of yak. Using primary cultures of DP cells, we reveal that the inhibition or activation of WNT/β-Catenin dramatically alters cell cycle progression and autophagy. In complimentary with the ATAC-seq data, we show that SOX4 is directly associated with the promoters of WNT1 and WNT3A. Interestingly, increased autophagy regulates the expression of SOX4/WNT/β-Catenin to promote the proliferation of DP cells in yak. Together, these results reveal the molecular signature of coat adaptation at the single-cell transcription level and provide a new understanding of animal adaptation to extreme environments.}, }
@article {pmid41506577, year = {2026}, author = {Sagar, K and Priti, K and Chandra, H}, title = {Artificial intelligence in metagenome-assembled genome reconstruction: Tools, pipelines, and future directions.}, journal = {Journal of microbiological methods}, volume = {241}, number = {}, pages = {107390}, doi = {10.1016/j.mimet.2026.107390}, pmid = {41506577}, issn = {1872-8359}, mesh = {*Artificial Intelligence ; *Metagenome/genetics ; *Metagenomics/methods ; Microbiota/genetics ; Computational Biology/methods ; Machine Learning ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Metagenomic sequencing has revolutionised the field of microbial ecology, as it has led to cultivation-independent exploration of complicated microbial communities. The assembly of metagenome-assembled genomes has provided genome-scale information about uncultivated microorganisms, but issues such as sequencing errors, fragmented assemblies, residual redundancy, uneven coverage, recovery of low-abundance taxa, and highly diversified taxa continue to impair the quality of these genomes. The latest achievements in artificial intelligence, particularly in machine learning and deep learning, have played a significant role in overcoming these limitations by enhancing quality control, error correction, assembly, binning, refinement, and annotation procedures. It is demonstrated that representation learning and graph-based binning methods have high strain-level resolution and can reduce contamination in complex microbial communities, whereas artificial intelligence-based assemblers and polishing tools improve base-level precision and assembly contiguity. This review synthesises traditional and artificial intelligence-based workflows involved in the reconstruction of metagenome-assembled genomes, encompassing quality control, assembly, binning, refinement, and annotation, as well as quantitative benchmarking of significant artificial intelligence-based pipelines. As future directions, the focus on emerging trends, such as explainable artificial intelligence, federated learning, cloud-native scalable pipelines, multimodal and multi-omics integration, and large language model-based annotation, is covered. In general, the incorporation of artificial intelligence represents a paradigm shift in the reconstruction of metagenome-assembled genomes, allowing for a more relevant, scalable, and biologically informative search of the microbial dark matter in various ecosystems.}, }
@article {pmid41506426, year = {2026}, author = {Geng, Y and Guo, W and Li, Q and Zhang, F and Zhong, A and Hu, Z}, title = {Driving mechanisms of vegetation carbon sink distribution based on explainable machine learning and evaluation of carbon sequestration in open-pit mines.}, journal = {Environmental research}, volume = {293}, number = {}, pages = {123715}, doi = {10.1016/j.envres.2026.123715}, pmid = {41506426}, issn = {1096-0953}, mesh = {*Carbon Sequestration ; *Mining ; China ; *Machine Learning ; Ecosystem ; *Environmental Monitoring ; Plants ; Bayes Theorem ; Soil/chemistry ; }, abstract = {Vegetation carbon sequestration plays a crucial role in mitigating global warming and maintaining regional carbon balance. The Yellow River Basin (YRB) is a key region for energy development and ecological conservation in China, yet the driving mechanisms underlying the spatial distribution of vegetation carbon sequestration and the carbon sequestration capacity of open-pit mines have not been systematically evaluated. Based on multi-source datasets, this study first employs the Sen's slope estimator combined with the Mann-Kendall trend test model to identify the temporal trends of vegetation carbon sequestration. It then applies a Bayesian-optimized Bayesian-optimized Extreme Gradient Boosting model integrated with Shapley Additive Explanations model to uncover the driving mechanisms of climate, soil, and human activities on its spatial distribution. Finally, a buffer zone comparison method is used to quantify the carbon sequestration potential of open-pit mines. The main conclusions are as follows: (1) Over the 24-year period, Net Ecosystem Productivity (NEP) in the YRB has shown a continuous increase, reaching 159.69 gC·m[-2] in 2024, which is five times the level in 2001. The most significant growth occurred in the middle and upper reaches, while the endorheic region exhibited limited improvement, with some areas even functioning as carbon sources. (2) Among the driving factors of NEP distribution in the YRB, precipitation, solar radiation, and soil organic carbon are the dominant contributors, accounting for more than 58 % in total. (3) The NEP of different types of open-pit mines varies substantially. Active mines function overall as carbon sources (-17.93 Gg), whereas stable and revegetated mines act as carbon sinks. The total carbon sequestration potential of all open-pit mines is 93.57 Gg, representing approximately 89 % of the current carbon sequestration level. This study provides a quantitative foundation for enhancing carbon sequestration, evaluating ecological restoration, and supporting the implementation of the "dual-carbon" strategy in the YRB.}, }
@article {pmid41503483, year = {2026}, author = {Castillo-Neyra, R and Ortiz-Cam, L and Díaz, EW and Cañari-Casaño, JL and Recuenco, SE and Paz-Soldán, VA}, title = {The return of human rabies: A foretold case in Latin America Through the Lens of One Health.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {41503483}, abstract = {BACKGROUND: Despite ongoing rabies control efforts in Arequipa, Peru-including mass dog vaccination campaigns and reactive ring interventions-the region has failed to reduce the number of rabid dogs, leading to the first reported human dog-mediated rabies case after 8 years. The gaps in the rabies control program and the complex dynamics among stakeholders are unknown.<br><br>OBJECTIVE: To integrate epidemiologic, socio-ecological, and policy data to identify the factors contributing to the 2023 human rabies case and propose strategies to make this a 'never event'.<br><br>METHODS: We used stakeholder mapping and field quantitative and qualitative data to identify the roles and connections of key actors in rabies control, identifying gaps in their functions. We then applied the Swiss Cheese model to characterize the defense layers against dog-mediated rabies, highlighting critical vulnerabilities across these protective barriers.<br><br>CONCLUSIONS: We identified multiple breaches in the defense against dog-mediated human rabies. Weak surveillance, insufficient dog vaccination, and inadequate management of free-roaming and feral dogs, coupled with bureaucratic inefficiencies, were key gaps. Outbreak responses were delayed and insufficient, and access to post-exposure prophylaxis (PEP) remained limited. Communication breakdowns exacerbated the problem. Systemic issues, such as outdated public health policies, insufficient training of health professionals, and fragmented efforts, further hindered timely exposure response. Dog ecology and demographic factors also contributed to dog rabies spread. These failures in policy, response, capacity, and external factors led to the 2023 human rabies case. Despite awareness of these challenges, the contributing conditions remain unchanged. Eliminating dog-mediated human rabies by 2030 will require targeted interventions, including enhanced surveillance, context-specific policy reforms, stronger community and institutional collaboration, and better management of free-roaming dogs.}, }
@article {pmid41502546, year = {2025}, author = {Boyes, D and Hutchinson, F and Crowley, LM and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Red-barred Tortrix moth, Ditula angustiorana (Haworth, 1811).}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {202}, pmid = {41502546}, issn = {2398-502X}, abstract = {We present a genome assembly from a female specimen of Ditula angustiorana (Red-barred Tortrix; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence has a total length of 468.36 megabases. Most of the assembly (99.83%) is scaffolded into 31 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled, with a length of 16.19 kilobases.}, }
@article {pmid41502542, year = {2025}, author = {Crowley, LM and Hutchinson, F and Boyes, D and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Barred Hook-tip, Watsonalla cultraria (Fabricius, 1775) (Lepidoptera: Drepanidae).}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {618}, pmid = {41502542}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from a male specimen of Watsonalla cultraria (Barred Hook-tip; Arthropoda; Insecta; Lepidoptera; Drepanidae). The genome sequence has a total length of 319.38 megabases. Most of the assembly (99.94%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. Gene annotation of this assembly on Ensembl identified 16 011 protein-coding genes. The mitochondrial genome has also been assembled, with a length of 15.21 kilobases.}, }
@article {pmid41502538, year = {2025}, author = {Boyes, D and Boyes, C and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Drinker, Euthrix potatoria (Linnaeus, 1758) (Lepidoptera: Lasiocampidae).}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {534}, pmid = {41502538}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Euthrix potatoria (Drinker; Arthropoda; Insecta; Lepidoptera; Lasiocampidae). The assembly contains two haplotypes with total lengths of 487.86 megabases and 466.06 megabases. Most of haplotype 1 (99.97%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 15.43 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.}, }
@article {pmid41501044, year = {2026}, author = {von Borries, K and Beckwith, KV and Goodman, JM and Chiu, WA and Jolliet, O and Fantke, P}, title = {Uncertainty-aware machine learning to predict non-cancer human toxicity for the global chemicals market.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {647}, pmid = {41501044}, issn = {2041-1723}, support = {P30 ES029067/ES/NIEHS NIH HHS/United States ; P42 ES027704/ES/NIEHS NIH HHS/United States ; DIA 2018/11//Stiftelsen f&#xf6;r Milj&#xf6;strategisk Forskning (Swedish Foundation for Strategic Environmental Research)/ ; EP/S024220/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; }, mesh = {*Machine Learning ; Humans ; Uncertainty ; }, abstract = {Humans are exposed to thousands of chemicals, yet limited toxicity data hinder effective management of their impacts on human health. High-performing machine learning models hold potential for addressing this gap, but their uncharacterized prediction performance across the wider range of chemicals undermines confidence in their results. We develop uncertainty-aware models to predict reproductive/developmental and general non-cancer human toxicity effect doses. Our well-calibrated models provide uncertainty estimates aligned with observed prediction errors and chemical familiarity. We predict toxicity with 95% confidence intervals for >100,000 globally marketed chemicals and identify toxicity and uncertainty hotspots. These results can be applied to inform decisions aimed at reducing potential human health impacts and guide targeted data generation and modeling efforts to reduce prediction uncertainty. Here, we show that enhancing transparency in prediction uncertainty provides key insights for building confidence in toxicity predictions, supporting the sound integration of machine learning-based predictions in chemical assessments.}, }
@article {pmid41499681, year = {2026}, author = {Astill Wright, L and Shajan, G and Purewal, D and Stone, J and Majid, M and Guo, B and Morriss, R}, title = {Mood Monitoring, Mood Tracking, and Ambulatory Assessment Interventions in Depression and Bipolar Disorder: Systematic Review and Meta-Analysis of Randomized Controlled Trials.}, journal = {JMIR mental health}, volume = {13}, number = {}, pages = {e84020}, pmid = {41499681}, issn = {2368-7959}, mesh = {Humans ; *Bipolar Disorder/therapy/diagnosis/psychology ; Randomized Controlled Trials as Topic ; *Affect ; *Monitoring, Ambulatory/methods ; *Depressive Disorder/therapy/diagnosis ; *Depression/diagnosis/therapy ; }, abstract = {BACKGROUND: Mood monitoring is widely used by people with depression and bipolar disorder (BD) to prevent relapse and improve insight into their condition, but it is unclear if these interventions have an impact on symptoms and for whom. As the capacity for passive mood monitoring increases, it is vital to improve our understanding of frequent mood assessment.<br><br>OBJECTIVE: This systematic review and meta-analysis assessed the effect of mood monitoring interventions in people with depression and BD to decrease relapse risk and symptoms of depression and mania.<br><br>METHODS: We conducted a systematic review and meta-analysis (PROSPERO, International Prospective Register of Systematic Reviews: CRD42023396473) and reported results according to PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analysis) guidelines. Randomized controlled trials with clinically important follow-up periods were identified via multiple database searches and rated for risk of bias using the Cochrane Risk of Bias tool. The primary outcomes were symptoms of depression and mania. Available data were pooled to calculate standardized mean differences (SMDs) for the primary outcomes: severity of depression, bipolar depression, and mania/hypomania.<br><br>RESULTS: We included 8 trials of 1230 participants and 6 different mood monitoring protocols. In BD, meta-analysis found a small but not statistically significant effect of mood monitoring interventions on decreasing mania symptoms (6 comparisons, n=873; SMD 0.16, 95% CI-0.34 to 0.01; P=.06) and no effect on bipolar depression (6 comparisons, n=873; SMD -0.08, 95% CI -0.31 to 0.15; P=.02). In depression, we found a small effect in decreasing symptoms of depression of borderline statistical significance at 12 months (2 comparisons, n=262; SMD -0.25, 95% CI -0.49 to 0.00; P=.05) but not at 6 months (2 comparisons, n=268; SMD -0.21, 95% CI -0.54 to 0.12; P=.21). There was an absence of evidence on the effect of mood monitoring on decreased relapse rates or readmission rates. Studies had a low risk of bias. There was no evidence on mood monitoring through ecological momentary assessment.<br><br>CONCLUSIONS: Overall mood monitoring interventions do not increase or decrease mood symptoms in people with BD, nor is there robust evidence of such effects in people with unipolar depression. Further research is merited on different forms of mood monitoring and to determine under what circumstances mood monitoring might have beneficial or adverse effects. These results initially suggest that ambulatory assessment does not induce large placebo effects or significantly negatively or positively affect mood, and thus that mood monitoring may be an appropriate outcome measure for research or for clinical practice.}, }
@article {pmid41497383, year = {2025}, author = {Hostens, M and Franceschini, S and van Leerdam, M and Yang, H and Pokharel, S and Liu, E and Niu, P and Zhang, H and Noor, S and Hermans, K and Salamone, M and Sharma, S}, title = {The future of big data and artificial intelligence on dairy farms: A proposed dairy data ecosystem.}, journal = {JDS communications}, volume = {6}, number = {Suppl 1}, pages = {S9-S14}, pmid = {41497383}, issn = {2666-9102}, abstract = {The dairy sector should overcome challenges in productivity, sustainability, and data management by adopting intelligent, scalable, and privacy-preserving technological solutions. Adopting data and artificial intelligence (AI) technologies is essential to ensure efficient operations and informed decision making and to keep a competitive market advantage. This paper proposes an integrated, multimodal AI framework to support data-intensive dairy farm operations by leveraging big data principles and advancing them through AI technologies. The proposed architecture incorporates edge computing, autonomous AI agents, and federated learning to enable real-time, privacy-preserving analytics at the farm level and promote knowledge sharing and refinement through research farms and cloud collaboration. Farms collect heterogeneous data, which can be transformed into embeddings for both local inference and cloud analysis. These embeddings form the input of AI agents that support health monitoring, risk prediction, operational optimization, and decision making. Privacy is preserved by sharing only model weights or anonymized data externally. The edge layer handles time-sensitive tasks and communicates with a centralized enterprise cloud hosting global models and distributing updates. A research and development cloud linked to research farms ensures model testing and validation. The entire system is orchestrated by autonomous AI agents that manage data, choose models, and interact with stakeholders, and human oversight ensures safe decisions, as illustrated in the practical use case of mastitis management. This architecture could support data integrity, scalability, and real-time personalization, along with opening up space for partnerships between farms, research institutions, and regulatory bodies to promote secure, cross-sector innovation.}, }
@article {pmid41495641, year = {2026}, author = {Khan, N and Das, A and Kumar, R and Jonnalagadda, M}, title = {Comparative evolutionary and structural bioinformatic analysis of the human N-Acetyltransferase-2 (NAT2) gene with different mammalian and avian taxa.}, journal = {BMC genomics}, volume = {27}, number = {1}, pages = {143}, pmid = {41495641}, issn = {1471-2164}, mesh = {*Arylamine N-Acetyltransferase/genetics/chemistry/metabolism ; Humans ; Animals ; *Evolution, Molecular ; Phylogeny ; *Computational Biology/methods ; *Birds/genetics/classification ; *Mammals/genetics/classification ; Molecular Docking Simulation ; Folic Acid/metabolism ; CpG Islands ; }, abstract = {Effective metabolization of exogenous compounds in humans is a key for health and drug efficacy albeit a complex process determined by one's genetic background. The enzyme, N-Acetyltransferase-2 (NAT2), which metabolizes different xenobiotic compounds (including folate) and various therapeutic drugs, is encoded by the NAT2 gene. Based on acetylation capacity, an individual is either a fast or slow acetylator. Although the apportionment of NAT2 gene and its acetylator types are widely documented in human populations, the evolutionary genetic affinities and functional background of NAT2 variations with closely-related taxa are not well understood. Herein, we have analyzed 60 NAT2 gene coding sequences (873 bp) representing 59 different taxa belonging to mammalian and avian taxa and two most prevalent human NAT2 alleles ((NAT2*4 and NAT2*6A) to document the phylogenetics relationship among taxa; to characterize DNA methylation patterns in this gene and to evaluate species specific binding efficiency to folate using molecular docking approach. Phylogenetic analysis showed 3 broad clades representing where humans and other primates were found to be closely related. The CpG analysis revealed a one conserved region of same length (total 200 bp) across taxa as well as variable short regions of differing lengths (ranging from minimum 50 to maximum 100 bp length sequences) in some taxa. Molecular docking showed variable binding affinities of NAT2 protein models with human slow acetylator allele (NAT2*6A) showing highest binding affinity to folate, indicative of adaptive response to folate bioavailability. Through our analysis we highlight the evolutionary conservation and functional divergence in NAT2 gene across Mammals and Aves likely to be driven by ecological and dietary factors. Our findings provide new insights into evolutionary adaptations to processing folate across various taxa, which may be significant in studies focusing on evolutionary genetics of drug metabolism.}, }
@article {pmid41495476, year = {2026}, author = {Green, A and Ontiveros-Palacios, N and Jandalala, I and Panni, S and Wood, V and Antonazzo, G and Attrill, H and Bateman, A and Sweeney, B}, title = {GOFlowLLM-curating miRNA literature with large language models and flowcharts.}, journal = {Bioinformatics (Oxford, England)}, volume = {42}, number = {1}, pages = {}, pmid = {41495476}, issn = {1367-4811}, support = {UKRI746:24BBR//United Kingdom Research and Innovation (UKRI) Biotechnology and Biological Sciences Research Council/ ; //European Union's Horizon 2020 Marie Sk&#x142;odowska-Curie Actions/ ; 310300/Z/24/Z &amp; 218236/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; MR/W024233/1/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; //European Molecular Biology Laboratory/ ; }, mesh = {*MicroRNAs/genetics ; *Software ; Gene Ontology ; *Data Curation/methods ; Humans ; *Computational Biology/methods ; Molecular Sequence Annotation/methods ; Large Language Models ; }, abstract = {MOTIVATION: The exponential growth of non-coding RNA research-with over 230 000 papers published since 2000-has created an urgent knowledge management crisis in molecular biology. Despite their crucial regulatory roles, microRNAs (miRNAs) face a significant curation bottleneck, with only 1400 articles manually curated to the Gene Ontology (GO) knowledgebase over a decade. This highlights the critical need for automated systems that can accelerate biocuration while maintaining high-quality standards.<br><br>RESULTS: We present GOFlowLLM, an automated curation pipeline powered by reasoning-enabled Large Language Models (LLMs) that follows established GO curation flowcharts to extract and structure miRNA-mediated gene silencing data at scale. When evaluated on existing curation, GOFlowLLM selects the correct GO term in 90% of cases, with curators agreeing with 95% of the system's reasoning steps and 90% of the evidence selected. Applied to 6996 previously uncurated articles using the Qwen QwQ-32B model, our system identified 2538 new candidate GO annotations on 1785 articles in just 58&#x2009;hours-potentially doubling the available miRNA GO curation. Manual review shows curators agreed with the selected term in 87% of cases, the model's reasoning in 92% of cases, and the extracted evidence in 93%. The integration of reasoning traces provides transparent justification for annotations that can be reviewed by human curators, addressing a key challenge in adopting AI for scientific curation.<br><br>GOFlowLLM is implemented as an automated pipeline that follows expert-designed reasoning frameworks to maintain curation quality. The system is available on GitHub: https://github.com/RNAcentral/GO_Flow_LLM.}, }
@article {pmid41494263, year = {2026}, author = {Mummidivarapu, SK and Rehana, S}, title = {Spatiotemporal risk assessment of river water quality for tropical river systems using hydrological dynamics, anthropogenic influences, and ecological health index.}, journal = {The Science of the total environment}, volume = {1013}, number = {}, pages = {181329}, doi = {10.1016/j.scitotenv.2025.181329}, pmid = {41494263}, issn = {1879-1026}, mesh = {*Rivers/chemistry ; Risk Assessment ; *Environmental Monitoring/methods ; *Water Quality ; Hydrology ; Anthropogenic Effects ; Tropical Climate ; Water Pollutants, Chemical/analysis ; Monte Carlo Method ; }, abstract = {Sustainable management of River Water Quality (RWQ) in tropical river systems requires an approach that addresses both spatial and temporal risks associated with hydrological dynamics, anthropogenic influences, and ecological health. This study develops an uncertainty-aware spatiotemporal risk assessment approach integrating upstream hydrological dynamics (SWAT), operational variability with Environmental Flow (Eflow), water quality simulations (QUAL2K), and probabilistic Water Quality Index (WQI) calculations. Block-Bootstrap ensembles and Monte Carlo techniques are used to quantify uncertainty propagation and construct confidence intervals within the model chain. The monthly WQI estimates under the different Eflow and pollution control scenarios are used to assess the spatial risk variability of the river system. Temporal risk was assessed with WQI using various probabilistic measures, including mean, variance, loss probability, entropy, mean excess loss, and value at risk. A unified risk ranking was developed by using Borda and Copeland aggregation techniques. Categorised spatial risk maps were created using GIS by integrating Eflows and ecological index. The results revealed significant seasonal variations in water quality, with April, March, and May identified as high-risk months due to increased pollution levels. The monthly WQI-mean in the Monte Carlo analysis (1000 iterations), as per the severity of the risk, April, March, and May months are identified as the riskiest months. Spatial risk mapping revealed distinct high-risk zones and highlighted the necessity of pollution treatment level of 25-50 % to reduce ecological risk under optimal Eflow regimes. This comprehensive framework underscores the need for both flow regulation and pollution management to protect river ecosystems, providing actionable insights for effective river health protection.}, }
@article {pmid41492055, year = {2026}, author = {Marinucci, M and Schaefer, CD and Dupont, PL and Manley, D and Taylor, LK and McKeown, S}, title = {Desegregating spaces: The interplay between ecological intergroup contact and GPS-traced spatial segregation among youth in two UK cities.}, journal = {The British journal of social psychology}, volume = {65}, number = {1}, pages = {e70043}, pmid = {41492055}, issn = {2044-8309}, support = {//Economic and Social Research Council/ ; }, mesh = {Humans ; Adolescent ; Male ; Female ; Geographic Information Systems ; United Kingdom ; *Social Segregation/psychology ; Cities ; Ecological Momentary Assessment ; Ethnicity/psychology ; *Group Processes ; *Interpersonal Relations ; }, abstract = {Recent advances in intergroup contact research have drawn on methods from human geography to investigate how segregation shapes, and is shaped by, everyday intergroup experiences. Emerging findings suggest that the phenomena might be reciprocally intertwined, but empirical evidence is limited and mixed. This research tested the reciprocal relationship between everyday intergroup contact and segregation using ecological momentary assessment and GPS-GIS tracking in two segregated UK cities with youths aged 15-17. Study 1 (Belfast; nparticipants = 15; ninteractions = 115; nGPS-point = 633) focused on Catholics-Protestants divisions, and Study 2 (Bradford; nparticipants = 30; ninteractions = 334; nGPS-point = 2868) addressed ethnic segregation among Asian, White, and Black communities. In both studies, youths reported on social interactions throughout 6 days, while their urban mobility in outgroup spaces was tracked. In Belfast, more mixed districts predicted higher anxiety during intergroup interactions, yet, positive intergroup contact was followed by increased visits to outgroup spaces. In Bradford, mixed districts increased the likelihood (but not the quality) of intergroup contact, while the link between positive contact and subsequent outgroup space use was replicated. The findings highlight a virtuous cycle depending on contextual norms by which positive contact and desegregation practices might reinforce each other, arguably demonstrating the potential of intergroup contact for levelling urban divisions.}, }
@article {pmid41491638, year = {2026}, author = {Wang, Y and Zhao, J and He, X and Yang, D and Jin, Y and Wu, R}, title = {A Computational Ecological Genetic Model of Phenotypic Plasticity in Species Interactions.}, journal = {Molecular ecology resources}, volume = {26}, number = {1}, pages = {e70095}, pmid = {41491638}, issn = {1755-0998}, support = {SIMIS-ID-2024-WN//Interdisciplinary Project at Shanghai Institute for Mathematics and Interdisciplinary Sciences/ ; 31971398//National Natural Science Foundation of China/ ; }, mesh = {Phenotype ; *Escherichia coli/genetics/physiology/growth &amp; development ; *Staphylococcus aureus/genetics/physiology/growth &amp; development ; *Models, Genetic ; *Computational Biology/methods ; Genotype ; *Microbial Interactions ; Epistasis, Genetic ; }, abstract = {Multiple species respond to each other in their co-existing communities. Such reciprocal phenotypic plasticity can shape the behaviour and evolution of ecological communities, but its genetic architecture remains elusive. We address this issue by developing a computational mapping model that combines community ecology and quantitative genetics into a unifying context. Culturing a pair of genotypes from two species in a socially isolated environment (monoculture) and a socialised environment (co-culture) allows for the quantitative estimation of reciprocal phenotypic plasticity, that is, the difference between trait values of one (defensive) species expressed in the monoculture and the co-culture with the other (offensive) species. Classic quantitative genetic theory is implemented to map genetic variants for reciprocal phenotypic plasticity, including defensive loci derived from the defensive species and offensive loci from the offensive species, and estimate the direct effects of the defensive loci, the indirect effects of the offensive loci and horizontal epistasis due to interactions between the two genomes. We design an ecological genetic experiment of monocultures and co-cultures using 100 pairs of genotyped Escherichia coli and Staphylococcus aureus strains, from which the model identifies the existence of defensive and offensive loci, despite a remarkable asymmetry between the two bacterial species. We find that horizontal epistasis between defensive and offensive loci plays a sizable role in mediating reciprocal phenotypic plasticity. The biological functions of these identified loci are annotated via GO analysis. Our model could produce unique results that shed light on the genetic mechanisms of interspecies interactions and their adaptation in ecological communities.}, }
@article {pmid41491008, year = {2026}, author = {Ajene, IJ and Tanga, CM and Akutse, KS and Karanu, SW and Khamis, FM}, title = {Multi-omics comparison of two emerging storage pests (Necrobia rufipes and Tribolium castaneum) of dried black soldier fly larvae product.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {4747}, pmid = {41491008}, issn = {2045-2322}, support = {ProteinAfrica: LS/2020/154//Australian Centre for International Agricultural Research/ ; WAVE-IN: 2021 FOD 030//Rockefeller Foundation/ ; G-2204-02144//IKEA Foundation/ ; NESTLER Project: 101060762 and INNOECOFOOD project: 101136739//European Commission/ ; }, mesh = {Animals ; Larva/microbiology/genetics ; Gastrointestinal Microbiome ; *Tribolium/microbiology/genetics ; Genome, Mitochondrial ; Bacteria/genetics/classification ; Multiomics ; }, abstract = {The black soldier fly (BSF) larvae is a rich and promising source of alternative protein that continues to increasingly gain global traction as a functional ingredient for sustainable livestock and fish production. The key setback to postharvest processing of stored BSF larvae (BSFL) products is the significant damage caused by two notable storage pests (Tribolium castaneum and Necrobia rufipes). Here, we present a comparative analysis of the complete mitochondrial genomes and gut microbiome profiles of T. castaneum and N. rufipes. The study mitogenomes were similar in size and structure to other coleopteran mitogenomes. The gut microbiome profiles of the two pests showed a high abundance of bacteria in the Proteobacteria and Firmicutes phyla. However, T. castaneum had 78% more phyla represented within its microbiome than N. rufipes. The most abundant genera in T. castaneum were Staphylococcus and Streptococcus, while in N. rufipes, the dominant genera were Klebsiella and Synechococcus. We also identified the presence of potentially clinically harmful microbial genera (Stenotrophomonas maltophilia) in the gut of T. castaneum and N. rufipes in relatively high abundance. These results provide insight into potential harmful associations in the gut of the storage pest, picked from contaminated, poorly processed BSFL products.}, }
@article {pmid41488783, year = {2026}, author = {Luongo, G and Dell'Anno, A and Tangherlini, M and Corinaldesi, C and A Ruhl, H and Danovaro, R}, title = {Major changes in micro-eukaryotic biodiversity of the abyssal ecosystem of the NE Atlantic: A comparison between 1996 and 2018.}, journal = {iScience}, volume = {29}, number = {1}, pages = {114266}, pmid = {41488783}, issn = {2589-0042}, abstract = {Time-separated snapshots of deep-sea regions can provide crucial insights into how fluctuations in environmental changes and food supply shape microbial communities. Here, we compared molecular and environmental data collected in 1996 and 2018 at 4,800-m depth in the northeast (NE) Atlantic Ocean. We report lower values of primary production (-66%) associated with lower concentrations of sedimentary labile organic matter (-12%). Metabarcoding analyses revealed a significant decrease in the Chlorophyta taxa, only partly compensated by the increase in Dinoflagellate taxa, consistent with patterns observed in NE Atlantic Ocean phytoplankton. Benthic prokaryotic assemblages showed a limited response to such changes, whilst micro-eukaryotic assemblages changed significantly even at subdivision level. Overall, data reported here suggest that the Porcupine abyssal plain may undergo significant variations in terms of quantity and quality of biopolymeric carbon and that such changes caused a shift in micro-eukaryotic biodiversity, with potentially relevant effects also on the deep-sea ecosystem functioning.}, }
@article {pmid41488433, year = {2025}, author = {LE, HA and Potter, V and Choube, A and Lakshminarayanan, R and Mishra, V and Intille, S}, title = {A Context-Assisted, Semi-Automated Activity Recall Interface Allowing Uncertainty.}, journal = {Proceedings of the ACM on interactive, mobile, wearable and ubiquitous technologies}, volume = {9}, number = {4}, pages = {}, pmid = {41488433}, issn = {2474-9567}, support = {P30 DA029926/DA/NIDA NIH HHS/United States ; R01 CA252966/CA/NCI NIH HHS/United States ; }, abstract = {Measuring activities and postures is an important area of research in ubiquitous computing, human-computer interaction, and personal health informatics. One approach that researchers use to collect large amounts of labeled data to develop models for activity recognition and measurement is asking participants to self-report their daily activities. Although participants can typically recall their sequence of daily activities, remembering the precise start and end times of each activity is significantly more challenging. ACAI is a novel, context-assisted ACtivity Annotation Interface that enables participants to efficiently label their activities by accepting or adjusting system-generated activity suggestions while explicitly expressing uncertainty about temporal boundaries. We evaluated ACAI using two complementary studies: a usability study with 11 participants and a two-week, free-living study with 14 participants. We compared our activity annotation system with the current gold-standard methods for activity recall in health sciences research: 24PAR and its computerized version, ACT24. Our system reduced annotation time and perceived effort while significantly improving data validity and fidelity compared to both standard human-supervised and unsupervised activity recall approaches. We discuss the limitations of our design and implications for developing adaptive, human-in-the-loop activity recognition systems used to collect self-report data on activity.}, }
@article {pmid41488255, year = {2025}, author = {Li, R and Li, J and ,  and ,  and ,  and ,  and Blaxter, ML}, title = {The genome sequence of the Atlantic Strawberry Cockle, Americardia media (Linnaeus, 1758) (Cardiida: Cardiidae).}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {630}, pmid = {41488255}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual Americardia media (Atlantic Strawberry Cockle; Mollusca; Bivalvia; Cardiida; Cardiidae). The assembly contains two haplotypes with total lengths of 1 299.87 megabases and 1 284.99 megabases. Most of haplotype 1 (99.42%) is scaffolded into 19 chromosomal pseudomolecules. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 47.2 kilobases.}, }
@article {pmid41484280, year = {2026}, author = {Lancaster, T and Tut, G and Sylla, P and Bone, D and Bentley, C and Spalkova, E and Jadir, A and Bruton, R and Spencer, K and Mallick, S and Elzaidi, A and Plass, S and Kaur, N and Butler, M and Hulme, S and Dowell, AC and Krutikov, M and Stirrup, O and Azmi, B and Hayward, A and Copas, A and Shallcross, L and Moss, P}, title = {Endemic penetrance of SARS-CoV-2 has impacted marginally on immunity to spike protein of human coronaviruses.}, journal = {Communications biology}, volume = {9}, number = {1}, pages = {196}, pmid = {41484280}, issn = {2399-3642}, support = {1400035//RCUK | Medical Research Council (MRC)/ ; National Core Study 1644507//RCUK | MRC | Medical Research Foundation/ ; }, mesh = {Humans ; *Spike Glycoprotein, Coronavirus/immunology ; *SARS-CoV-2/immunology ; *COVID-19/immunology/epidemiology ; Antibodies, Viral/immunology/blood ; Cross Reactions ; Pandemics ; Adaptive Immunity ; Coronavirus OC43, Human/immunology ; Coronavirus 229E, Human/immunology ; Antibodies, Neutralizing/immunology ; *Coronavirus Infections/immunology/virology/prevention &amp; control/epidemiology ; Female ; T-Lymphocytes/immunology ; COVID-19 Vaccines/immunology ; Adult ; Male ; }, abstract = {SARS-CoV-2 has emerged as the 5th endemic coronavirus and immunological cross protection between coronaviruses will influence their infectivity and clinical impact. We determined adaptive immunity against the spike protein of each human coronavirus during the course of the COVID-19 pandemic. A characteristic pattern of HCoV immunodominance, dominated by OC43 and 229E, was apparent prior to SARS-CoV-2 and was largely unaffected by SARS-CoV-2 infection, which itself elicited moderate antibody titre. Vaccination or hybrid immunity elicited supraphysiological levels of coronavirus-specific antibodies, only a proportion of which was cross-reactive with SARS-CoV-2 spike indicating substantial backboosting of HCoV-specific responses. SARS-CoV-2 vaccination focused antibody responses against the S1 domain of SARS-CoV-2 spike whilst T cell responses recognised peptides equivalently across S1 and S2. Coronavirus-specific T cells exhibited strong production of IFN-γ, IL-2 and CXCL8. In summary, the entry of SARS-CoV-2 into its ecological niche has impacted marginally on relative immunity against other human coronaviruses although vaccination provides a modest antibody increment which is unlikely to be maintained. Further, although SARS-CoV-2 vaccination elicits spike-specific adaptive immune responses that are focused against the S1 domain, thereby favouring neutralising antibodies, the natural history of HCoV immunity indicates that adaptive responses may transition towards S2 recognition across the life course.}, }
@article {pmid41483326, year = {2026}, author = {Liu, Z and Liu, W and Wang, S and Wang, X and Zhu, J and Wang, D and Dong, C and Cheng, G and Mei, Y and Qi, X}, title = {Divergent occupational heat stress strategies required for Northern and Southern China under climate change.}, journal = {International journal of biometeorology}, volume = {70}, number = {1}, pages = {6}, pmid = {41483326}, issn = {1432-1254}, support = {2025A04J5097//Guangzhou Basic and Applied Basic Research Foundation/ ; 42301021//National Natural Science Foundation of China/ ; }, mesh = {*Climate Change ; China/epidemiology ; *Heat Stress Disorders/epidemiology/economics/prevention &amp; control ; Humans ; Hot Temperature ; Climate Models ; *Occupational Exposure ; }, abstract = {Observable climate change has led to an increase in compound heat events, thereby amplifying the economic impacts of labor heat stress and necessitating intervention strategies. Current research lacks high-resolution precision in projecting future heat stress and quantifying adaptation strategies, which is particularly critical for China given its spatial disparities in climate, workforce distribution, and economic development. This study integrates high-resolution CMIP6 climate models, a Wet-bulb Globe Temperature (WBGT) algorithm, and localized Exposure-response Functions (ERFs) to project heat-induced labor productivity loss across China under the SSP5-8.5 scenario. It systematically analyzes and quantitatively compares the effectiveness of two adaptation strategies (shading and work schedule adjustments) while estimating direct economic losses in outdoor heavy labor industries. This study precisely identifies the thermal stress hotspots categorized as primary (South China: loss rate > 11%, increment 5-7%), secondary (middle-lower Yangtze River: 7-11% loss, 3-5% increment), and tertiary hotspots (Yangtze River Delta &amp; North China Plain: 6-9% loss, 2-4% increment) based on productivity loss magnitudes. Our findings also reveal that optimal strategies diverge north-south along the 33°N: shading dominates in the south and schedule adjustments in the north due to distinct heat patterns, though future climate trends may reduce the efficacy of time shift adjustments nationwide. Additionally, economic loss estimation reveals surging heat-induced losses in agriculture and construction over two decades (annual growth rates of 11.16% and 20.69%, respectively), with combined strategies potentially reducing direct losses by 65-70% in hotspot provinces. These findings enable province- and industry-specific intervention designs considering regional climate variations and strategy effectiveness.}, }
@article {pmid41482560, year = {2026}, author = {Chakaroun, RM and Pradhan, M and Björnson, E and Arvidsson, D and Fridolfsson, J and Gummesson, A and Schoeler, M and Mitteregger, M and Smith, GJ and Larsson, I and Börjesson, M and Blüher, M and Uhlén, M and Stumvoll, M and Bergström, G and Tremaroli, V and Bäckhed, F}, title = {Multi-omic definition of metabolic obesity through adipose tissue-microbiome interactions.}, journal = {Nature medicine}, volume = {32}, number = {1}, pages = {113-125}, pmid = {41482560}, issn = {1546-170X}, support = {2017.0026//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; 2017.0026//Diabetesfonden (Stiftelsen Svenska Diabetesf&#xf6;rbundets Forskningsfond)/ ; 20210366//Hj&#xe4;rt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 20240882//Hj&#xe4;rt-Lungfonden (Swedish Heart-Lung Foundation)/ ; NNF15OC0016798//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF21OC0070298//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF24OC0092455//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 17CVD01//Fondation Leducq/ ; ERC-2022-ADG 101096705//Fondation Leducq/ ; 2019-01599//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; EXC3105/1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {Humans ; *Obesity/metabolism/microbiology ; *Adipose Tissue/metabolism/microbiology ; Male ; Body Mass Index ; Female ; Middle Aged ; *Microbiota/physiology ; Adult ; Metabolome ; Insulin Resistance ; Metabolomics/methods ; Adiposity ; Multiomics ; }, abstract = {Obesity's metabolic heterogeneity is not fully captured by body mass index (BMI). Here we show that deep multi-omics phenotyping of 1,408 individuals defines a metabolome-informed obesity metric (metBMI) that captures adipose tissue-related dysfunction across organ systems. In an external cohort (n = 466), metBMI explained 52% of BMI variance and more accurately reflected adiposity than other omics models. Individuals with higher-than-expected metBMI had 2-5-fold higher odds of fatty liver disease, diabetes, severe visceral fat accumulation and attenuation, insulin resistance, hyperinsulinemia and inflammation and, in bariatric surgery (n = 75), achieved 30% less weight loss. This obesogenic signature aligned with reduced microbiome richness, altered ecology and functional potential. A 66-metabolite panel retained 38.6% explanatory power, with 90% covarying with the microbiome. Mediation analysis revealed a bidirectional, metabolite-centered host-microbiome axis, mediated by lipids, amino acids and diet-derived metabolites. These findings define an adipose-linked, microbiome-connected metabolic signature that outperforms BMI in stratifying cardiometabolic risk and guiding precision interventions.}, }
@article {pmid41480951, year = {2026}, author = {Zhang, S and Jiao, Z and Liu, Z and Peng, Z and Cui, L and Hu, Z and Jiao, Z and Yuan, Q and Qiu, Z and Yan, C}, title = {Multiomics Analysis Revealed the Role of LsBBX22-LsHY5a/b Module in Promoting UV-B-Mediated Anthocyanin Accumulation in Lettuce.}, journal = {Journal of agricultural and food chemistry}, volume = {74}, number = {1}, pages = {1788-1803}, doi = {10.1021/acs.jafc.5c08530}, pmid = {41480951}, issn = {1520-5118}, mesh = {*Anthocyanins/biosynthesis/metabolism ; *Lactuca/metabolism/genetics/radiation effects ; Ultraviolet Rays ; *Plant Proteins/genetics/metabolism ; Gene Expression Regulation, Plant/radiation effects ; *Transcription Factors/metabolism/genetics ; Multiomics ; }, abstract = {Ultraviolet-B (UV-B) radiation profoundly affects plant photomorphogenesis and secondary metabolism, yet its regulatory role in lettuce (Lactuca sativa) remains poorly understood. We conducted metabolome and transcriptome analyses to reveal the molecular basis of UV-B adaptation in highland-grown lettuce. Flavonoid accumulation was enhanced as a key adaptive strategy for UV-B acclimation. The key UV-B signaling components LsHY5a/b showed positive correlations with ten LsBBXs and flavonoid/anthocyanin-related genes. UV-B treatment rapidly induced the transcription of LsHY5a/b and LsBBX22-1. LsBBX22-1 physically interacted with LsHY5a/b. While LsBBX22-1 activated the expression of anthocyanin-related genes, it could not bind directly to their promoters. By contrast, LsHY5a/b directly bound to the promoters of LsCHS1, LsCHI3, and LsF3H. Thus, LsBBX22 and LsHY5a/b acted synergistically to regulate UV-B-induced anthocyanin biosynthesis. This study clarified the molecular mechanism of the LsBBX22-1-LsHY5a/b module in promoting UV-B-induced anthocyanin accumulation in lettuce, providing a theoretical basis for cultivating high-quality vegetables in highland regions.}, }
@article {pmid41480146, year = {2025}, author = {Formenti, G and Jain, N and Medico, JA and Sollitto, M and Antipov, D and Barcellos, S and Biegler, M and Borges, I and Chang, JK and Chen, Y and Cheng, H and Conceição, H and Davenport, M and De Oliveira, L and Duarte, E and Durham, G and Fenn, J and Forde, N and Galante, PA and Gerhardt, K and Giani, AM and Giunta, S and Kim, J and Komissarov, A and Koo, B and Koren, S and Larkin, D and Lee, C and Li, H and Makova, K and Masterson, P and Murphy, T and McCaffrey, K and Mercuri, RLV and Na, Y and O'Connell, MJ and Ou, S and Phillippy, A and Popova, M and Rhie, A and Ruiz-Ruano, FJ and Secomandi, S and Smeds, L and Suh, A and Tilley, T and Vontzou, N and Waters, PD and Balacco, J and Jarvis, ED}, title = {The complete genome of a songbird.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41480146}, issn = {2692-8205}, abstract = {Bird genomes are the smallest among amniotes, but remain challenging to assemble due to their structural complexity. This study presents the first fully phased, diploid, telomere-to-telomere (T2T) reference genome for the zebra finch (Taeniopygia guttata), a model organism for neuroscience and evolutionary genomics. Combining multiple sequencing strategies resulted in closing nearly all gaps, adding ~90 Mbp of previously missing sequence (7.8%). This includes T2T assemblies for all microchromosomes, including dot chromosomes, and the previously almost entirely missing chr16. The T2T genome is comprehensively annotated for genes, repeats, structural variants, and long-read methylation calls. Complete centromeric structures were assembled and annotated along with kinetochore binding sites. Relative to the previous high-quality reference of the Vertebrate Genomes Project, 2,778 (8.51%) previously unassembled or unannotated genes were identified, of which 9% overlap with segmental duplications. This first complete genome of a songbird, now the new public reference, illuminates avian genome architecture and function.}, }
@article {pmid41476124, year = {2025}, author = {Abdou, ANA and Hamed, M and Hassan, AMM and Khaled, MA}, title = {Assessment of industrial pollution and water quality in the Nile River using GIS-based indices at Aswan, Egypt.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {3731}, pmid = {41476124}, issn = {2045-2322}, mesh = {Egypt ; *Rivers/chemistry ; *Water Quality ; *Geographic Information Systems ; *Environmental Monitoring/methods ; *Water Pollutants, Chemical/analysis ; *Water Pollution/analysis ; Ecosystem ; *Industrial Waste/analysis ; }, abstract = {Industrial pollution represents a critical threat to freshwater ecosystems, particularly in regions where rivers serve multiple socio-economic functions. The Nile River in Aswan Governorate, southern Egypt, is a vital source of drinking water, irrigation, fisheries, and tourism, yet it is increasingly exposed to untreated industrial effluents. This study assessed the spatial extent and intensity of such pollution using geographic information system (GIS)-based spatial interpolation alongside two comprehensive indices: the weighted arithmetic water quality index (WAWQI) and the canadian water quality index (CWQI). Findings revealed distinct pollution hotspots near major industrial discharge areas, where water quality was classified as poor to very poor (WAWQI: 52.6-127.4; CWQI: 74.2-68.3). In contrast, upstream and downstream zones more distant from effluent sources exhibited good water quality (WAWQI: 24.5-38.1; CWQI: 93.69-85.52). The most degraded sites were characterized by elevated concentrations of chemical oxygen demand (13.1-59.6 mg/L), biochemical oxygen demand (7.67-36.5 mg/L), total suspended solids (4.67-13.1 mg/L), turbidity (6.01-17.1 NTU), total nitrogen (1.13-3.35 mg/L), and phenol (8.01-10.10 µg/L). These results highlight the ecological vulnerability of the Nile River in Aswan to industrial activities, with direct implications for ecosystem health and resource sustainability. They also underscore the limitations of relying solely on traditional water quality monitoring without spatial analysis, as GIS-based interpolation proved critical in detecting pollution gradients beyond sampling sites. The study supports the enforcement of Egypt's Law 48/1982 on water protection and contributes to global sustainable development goals, particularly SDG 6 (Clean Water and Sanitation), SDG 12 (Responsible Consumption and Production), and SDG 14 (Life Below Water).}, }
@article {pmid41475601, year = {2026}, author = {Tang, J and Liu, Y and Zhang, Q and Zhang, H and Ni, BJ and Lv, W}, title = {Multi-omics dissection of yeast-centric fungal-bacterial synergies in food-processing wastewater: insights from four full-scale treatment plants.}, journal = {Bioresource technology}, volume = {443}, number = {}, pages = {133911}, doi = {10.1016/j.biortech.2025.133911}, pmid = {41475601}, issn = {1873-2976}, mesh = {*Wastewater/microbiology ; *Bacteria/genetics/metabolism ; *Food Handling ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Fungi/genetics/metabolism ; *Yeasts/genetics/metabolism ; *Food-Processing Industry ; Multiomics ; }, abstract = {Fungal presence and ecological roles in activated sludge at municipal wastewater treatment plants are increasingly recognized, yet their diversity and functional contributions-especially of yeasts-in treating food-processing wastewater remain underexplored. High-throughput ITS and 16S rRNA sequencing and shotgun metagenomics, together with FUNGuild, were used to analyze microbial community structure, functional microorganisms, co-occurrence patterns, interkingdom interactions, functional pathways, and the distributions of degradation enzymes and functional genes for characteristic pollutants among four full-scale food-processing plants (seafood, pastry, orange-canning, and vegetable-oil refining). Community diversity and structural differences shaped by wastewater types, associated with metabolic traits and enzyme-secretion. Saccharomycetes emerged as the dominant fungal class; bacteria displayed more even class-level and genus-level distributions than fungi across plants, combining LEfSe (LDA > 4, p < 0.05) to reveal plant-specific environmental-driven taxa, mainly included members of Saccharomycetales among fungi. Module-based co-occurrence networks indicated symbiotic interactions among yeasts; predominant cooperation of fungal-bacterial interaction network, in which yeasts exhibited the highest degree among fungi; strong correlations between Saccharomycetales and functional genes. Metabolism was the most abundant functional pathway. "Undefined Saprotroph" was the most widespread fungal functional guild. We annotated 86 degradation enzymes and 150 functional genes targeting eight pollutant categories (proteins, lipids, starch, pectin, lignin, cellulose, hemicellulose, chitosan), elucidating plant-specific distributions and enzymatic synergies. These multi-plant comparisons disentangle conserved from plant-specific features of catabolism. Overall, this study elucidates microbial diversity, interactions, and functional potential in food-processing wastewater treatment, reveals yeasts as keystone microbes for pollutant degradation, and provides actionable insights for treatment strategies and process optimization.}, }
@article {pmid41475540, year = {2026}, author = {Han, M and Sang, R and Mao, R and Pan, M and Guo, Y and Chen, Z and Yan, X}, title = {Integrated multi-omics reveals the interactive mechanisms of antioxidant defense, energy metabolism, and programmed cell death in cadmium tolerance of Elymus nutans Griseb.}, journal = {Plant science : an international journal of experimental plant biology}, volume = {364}, number = {}, pages = {112969}, doi = {10.1016/j.plantsci.2025.112969}, pmid = {41475540}, issn = {1873-2259}, mesh = {*Cadmium/toxicity/metabolism ; *Antioxidants/metabolism ; *Energy Metabolism/drug effects ; *Apoptosis/drug effects ; *Soil Pollutants/toxicity ; Photosynthesis/drug effects ; Biodegradation, Environmental ; Transcriptome ; Metabolomics ; Gene Expression Regulation, Plant ; Multiomics ; }, abstract = {Cadmium (Cd), a non-essential toxic heavy metal, presents severe threats to agricultural productivity, plant development, and human health through food chain contamination. Although Elymus nutans Griseb. (E. nutans) exhibits substantial potential for phytoremediation of Cd-contaminated soils, its molecular Cd-tolerance mechanisms remain poorly characterized. This study employed integrated morphological, physiological, ultrastructural, transcriptomic, and metabolomic analyses to systematically investigate Cd stress responses in E. nutans. Results demonstrated that Cd stress significantly inhibited growth and photosynthesis, activated antioxidant system, and induced lipid peroxidation in E. nutans seedlings. Notably, cellular ultrastructural damage coincided with disrupted energy metabolism and substantial accumulation of reactive oxygen species (ROS), which ultimately triggered programmed cell death (PCD). Transcriptomic analysis revealed differentially expressed genes (DEGs) enriched in Plant hormone signal transduction and Carbon metabolism pathways. Metabolomic profiling identified 128 differentially expressed metabolites (DEMs) associated with ABC transporters and Isoquinoline alkaloid biosynthesis. Integrated multi-omics analysis demonstrated that glutathione metabolism and photosynthetic carbon fixation pathways regulate E. nutans response to Cd by modulating photosynthesis, antioxidant defense, and energy metabolism. This study reveals phytoremediation mechanisms of E. nutans under Cd stress, offering a scientific foundation for restoring soil health and ecological functions in high-altitude contaminated areas through sustainable soil management strategies.}, }
@article {pmid41474484, year = {2025}, author = {Kinkpe, L and Solomon, AI and Niu, Y and Goswami, N and Ikele, CM and Hu, D and Abdessan, R and Zhigang, H and Xia, W}, title = {A guide to network analysis, multi-omics integration, and applications in livestock microbiome research.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {1}, pages = {17}, pmid = {41474484}, issn = {1573-0972}, support = {2023YFD1300300//National Key Research and Development Program of China/ ; (CARS-42-2)//China Agriculture Research System of MOF and MARA/ ; }, mesh = {Animals ; *Livestock/microbiology ; *Gastrointestinal Microbiome ; *Genomics/methods ; *Microbiota ; Computational Biology/methods ; Machine Learning ; Multiomics ; }, abstract = {The function of the livestock gut microbiome in driving animal growth, health, and methane emissions is controlled by networks of interactions among microbes. A major challenge is to move beyond simply listing microbial members to understanding these interaction networks, which determine how the community functions as a whole. This review synthesizes how network analysis, combined with multi-omics data, can meet this challenge. We focus on the critical task of identifying keystone species, the disproportionately influential microbes that direct processes like fiber digestion and immune function, yet are often missed by standard surveys. We evaluate a progression of methods, from identifying correlated species to building models that integrate genomic, metabolic, and host data. This integration is key to separating true ecological relationships from statistical noise and to linking microbial presence to function. We highlight how computational techniques like metabolic modeling and machine learning are turning networks into predictive tools. Finally, we outline the path forward: field-ready studies that track microbiomes over time, the development of livestock-specific metabolic models, and analytical standards that will allow research to translate into practical strategies. The goal is to provide a framework for using network science to actively manage the microbiome, enhancing sustainable livestock production.}, }
@article {pmid41474351, year = {2026}, author = {Beumer, LT and Hertel, AG and Royauté, R and Tucker, MA and Albrecht, J and Beltran, RS and Cagnacci, F and Davidson, SC and Dejid, N and Kays, R and Kölzsch, A and Lohr, A and Neuschulz, EL and Safi, K and Scharf, AK and Schleuning, M and Wikelski, M and Mueller, T}, title = {MoveTraits-A Database for Integrating Animal Behaviour Into Trait-Based Ecology.}, journal = {Ecology letters}, volume = {29}, number = {1}, pages = {e70297}, pmid = {41474351}, issn = {1461-0248}, support = {//Hessian Ministry of Science and Research, Arts and Culture, Germany/ ; 80NSSC21K1182//NASA's Ecological Forecasting Program/ ; 101086640//HORIZON EUROPE Research and Innovation Programme/ ; 01LC2320A//German Federal Ministry for Research, Technology and Aeronautics/ ; HE 8857/1-1//Deutsche Forschungsgemeinschaft/ ; NE1863/2-2//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Animals ; *Databases, Factual ; *Birds/physiology ; *Behavior, Animal ; *Ecology/methods ; *Mammals/physiology ; Ecosystem ; Biodiversity ; }, abstract = {Trait-based approaches are key to understanding eco-evolutionary processes but rarely account for animal behaviour despite its central role in ecosystem dynamics. We propose integrating behaviour into trait-based ecology through movement traits-standardised and comparable measures of animal movement derived from biologging data, such as daily displacements or range sizes. Accounting for animal behaviour will advance trait-based research on species interactions, community structure and ecosystem functioning. Importantly, movement traits allow for quantification of behavioural reaction norms, offering insights into species' acclimation and adaptive capacity to environmental change. We outline a vision for a 'living' global movement trait database that enhances trait data curation by (1) continuously growing alongside shared biologging data, (2) calculating traits directly from individual-level data using standardised, consistent methodology and (3) providing information on multi-level (species, individual, within-individual) trait variation. We present a proof-of-concept 'MoveTraits' database with 52 mammal and 97 bird species, demonstrating calculation workflows for 5 traits across multiple timescales. Movement traits have significant potential to improve trait-based global change predictions and contribute to global biodiversity assessments as Essential Biodiversity Variables. By making animal movement data more accessible and interpretable, this database could bridge the gap between movement ecology and biodiversity policy, facilitating evidence-based conservation.}, }
@article {pmid41472845, year = {2025}, author = {Zhu, Z and Zhang, L and Yao, X and Zeng, M and Wang, Y and Luo, H and Zhou, Y and Zhang, T and Xun, J and Bai, D and Yang, H and Xu, S and Zhou, Y and Gao, Y and Xu, J and Han, W and Shen, Z and Zhang, B and Ma, T and Wan, XL and Ma, C and Hui, F and Bai, H and Bai, L and Bai, Q and Bao, Q and Cao, G and Cao, P and Cao, Q and Chen, H and Chen, J and Chen, J and Chen, L and Chen, T and Chen, Y and Cui, H and Dai, S and Dai, XJ and Dai, X and Dang, Y and Deng, L and Deng, Y and Ding, X and Dong, B and Dong, L and Dou, S and Du, H and Fang, Z and Feng, X and Fu, M and Gao, Y and Gong, W and Guo, X and Han, W and Hao, Z and He, ZG and Hu, H and Hu, H and Hu, X and Huang, L and Huang, X and Huang, X and Hui, H and Jia, D and Jiang, A and Jiang, D and Jiang, K and Jiang, D and Jin, Y and Lai, K and Li, C and Li, F and Li, F and Li, J and Li, J and Li, J and Li, K and Li, L and Li, M and Li, P and Li, P and Li, R and Li, S and Li, S and Li, W and Li, W and Li, X and Li, X and Li, X and Liang, Q and Liao, X and Liu, B and Liu, C and Liu, C and Liu, D and Liu, F and Liu, J and Liu, J and Liu, S and Liu, T and Liu, W and Liu, Y and Liu, Y and Liu, Y and Liu, Y and Liu, Y and Liu, Z and Liu, Z and Lu, X and Luo, X and Ma, G and Meng, J and Meng, Y and Miao, R and Miao, L and Ni, Y and Niu, D and Niu, T and Pan, H and Qin, G and Qiu, T and Qiu, Y and Qu, H and Qu, L and Ren, N and Sun, Q and Shang, R and She, P and Shen, X and Shi, B and Shu, Y and Song, J and Song, W and Su, Q and Sun, Q and Sun, Y and Sun, Z and Tang, B and Tang, D and Tang, H and Tao, Y and Teng, T and Tu, Y and Wang, C and Wang, H and Wang, Y and Wang, C and Wang, D and Wang, G and Wang, J and Wang, K and Wang, M and Wang, S and Wang, S and Wang, X and Wang, XC and Wang, Y and Wang, J and Wang, Z and Wang, W and Wei, Y and Xu, W and Wu, F and Wu, J and Wu, S and Xiao, J and Xiao, W and Xiao, Y and Xiong, X and Xiong, X and Xu, F and Xu, J and Xu, W and Xu, J and Xu, Y and Yan, J and Yao, L and Yang, J and Yang, L and Yang, X and Yin, N and You, H and You, M and Yu, T and Yu, Y and Yu, R and Yuan, S and Yue, C and Zeng, X and Zha, A and Zhai, L and Zhang, C and Zhang, D and Zhang, H and Zhang, H and Zhang, H and Zhang, J and Zhang, J and Zhang, L and Zhang, Q and Zhang, X and Zhang, X and Zhang, X and Zhang, Y and Zhang, Y and Zhang, Z and Zhao, J and Zhao, J and Zhao, K and Zhao, M and Zhao, Y and Zhao, Y and Zhong, J and Zhong, L and Zhong, X and Zhou, D and Zhou, W and Zhou, W and Zhou, Y and Zhou, Z and Zhu, S and Liu, SJ and Feng, S and Jin, S and Xiao, C and Wang, Z and Luo, P and Chen, T and Chen, G and Liu, YX}, title = {iMeta Conference 2025: Creating high-impact international journals.}, journal = {iMeta}, volume = {4}, number = {6}, pages = {e70086}, pmid = {41472845}, issn = {2770-596X}, abstract = {The iMeta Conference 2025, part of the iMeta Conference series, themed "Creating High-Impact International Journals," held at the Huangjiahu Campus of Hubei University of Chinese Medicine from August 23rd to 25th, 2025, and focused on frontier topics such as microbiology, medicine, traditional Chinese medicine, botany, and research career development. The event aimed to support the development of researchers and strengthen the impact of academic journals. Through invited reports, thematic seminars, and poster presentations, the conference highlighted hot topics including multi-omics technologies, microbe-host interactions, AI-assisted research, live biotherapeutic products, and the modernization of traditional Chinese medicine. The event demonstrated the innovative momentum of interdisciplinary integration and technological convergence, providing an international platform for academic exchange and laying a foundation for building an innovative scientific research ecosystem and enhancing the global influence of Chinese academic journals.}, }
@article {pmid41472087, year = {2025}, author = {Schalli, M and Inwinkl, SM and Platzer, S and Baumert, R and Reinthaler, FF and Ofner-Kopeinig, P and Haas, D}, title = {Correction: Schalli et al. Cefsulodin and Vancomycin: A Supplement for Chromogenic Coliform Agar for Detection of Escherichia coli and Coliform Bacteria from Different Water Sources. Microorganisms 2022, 10, 2499.}, journal = {Microorganisms}, volume = {13}, number = {12}, pages = {}, pmid = {41472087}, issn = {2076-2607}, abstract = {In the original publication [...].}, }
@article {pmid41468864, year = {2025}, author = {Cho, YJ and Kim, KH and Suh, DW and Baek, IS and Phee, JH and Yu, JY and Kim, KM and Park, YR}, title = {Shadow-Induced Forgetting in a Game-Based Paradigm on Nonclinical Adults and Its Effects on Consciousness, Emotional Valence, and Temporal Dynamics: Crossover Study.}, journal = {JMIR serious games}, volume = {13}, number = {}, pages = {e76946}, pmid = {41468864}, issn = {2291-9279}, abstract = {BACKGROUND: Memory suppression transiently disrupts hippocampal activity, leading to suppression-induced forgetting, especially for negative stimuli. However, traditional paradigms such as Think/No-Think rely on explicit control and lack ecological validity. This study introduces a game-based task that implicitly elicits suppression through reversed motor mappings, providing a naturalistic approach to studying memory inhibition.<br><br>OBJECTIVE: This study aims to examine how shadow-induced forgetting (ShIF) varies across short-term and long-term intervals (0 hours, 24 hours, and 72 hours), under conscious versus unconscious exposure, and between positive and negative emotional stimuli.<br><br>METHODS: This single-center, within-subjects experimental study involved 56 university students (mean age 23.37, SD 1.84 years) and was conducted between December 1, 2023, and March 1, 2024. Participants learned 36 cue-target image pairs varying in emotional valence (positive and negative). They underwent a game-based paradigm where habitual motor responses were disrupted through reversed key mappings to induce an amnesic shadow. During gameplay, selected cues were presented either consciously or unconsciously, while others served as controls. Memory performance was assessed using Metric for Evaluation of Translation with Explicit Ordering scores (semantic similarity) immediately after intervention (0 hour) and again at 24 hours and 72 hours. Electroencephalography was recorded in a subset of 40 participants to examine neural correlates of memory suppression.<br><br>RESULTS: ShIF effects were short-term, conscious-dependent, and selective for negative memories. A significant interaction between exposure condition and time (F&#x2083;.&#x2086;&#x2082;,&#x2081;&#x2089;&#x2089;.&#x2083;&#x2083;=2.7, P=.04, &#x3b7;&#xb2;p=0.05, 95% CI 0.00-1.00) indicated that the effect varied across time points. Specifically, a significant ShIF effect emerged immediately after the intervention (0 hour) in the conscious condition (t&#x2085;&#x2085;=-2.86, P=.02, d=0.38) but was absent in the unconscious condition and dissipated by 72 hours. Robust main effects of time (F&#x2082;,&#x2081;&#x2080;&#x2089;.&#x2089;&#x2089;=102.91, P<.001, &#x3b7;&#xb2;p=0.65, 95% CI 0.57-1.00) and emotional valence (F&#x2081;,&#x2085;&#x2085;=42.43, P<.001, &#x3b7;&#xb2;p=0.44, 95% CI 0.27-1.00) showed that overall recall declined over time and was consistently lower for negative images. Electroencephalography analyses revealed enhanced right frontal beta (FC6, F4, and F8: P<.001) and posterior gamma (O1: P<.001, O2: P<.001, and P8: P=.002) activity during suppression of negative cues, reflecting neural inhibition processes underlying ShIF.<br><br>CONCLUSIONS: ShIF occurs primarily for consciously processed negative memories and diminishes over several days, highlighting the temporal and emotional boundaries of intentional forgetting. This study introduces a game-based approach that extends traditional suppression paradigms and offers an ecologically valid framework for investigating memory control. Importantly, we demonstrate that suppression can be induced through a game-based paradigm. By examining emotional valence, exposure condition, and temporal dynamics, we extend previous work focused only on transient effects and clarify the potential for practical implementation in digital therapeutic applications such as posttraumatic stress disorder treatment.}, }
@article {pmid41468766, year = {2026}, author = {Zheng, J and Sun, Z and Guo, R and Wang, R and Jin, D and Hu, J and Xing, X and Tong, M and Wang, P}, title = {High-throughput and rapid classification on harmful algal bloom species based on mega image database and artificial intelligence.}, journal = {Marine pollution bulletin}, volume = {224}, number = {}, pages = {119170}, doi = {10.1016/j.marpolbul.2025.119170}, pmid = {41468766}, issn = {1879-3363}, mesh = {*Microalgae/classification ; *Harmful Algal Bloom ; *Artificial Intelligence ; *Environmental Monitoring/methods ; Databases, Factual ; Ecosystem ; }, abstract = {Microalgae are essential components of marine ecosystems and have significant industrial applications. However, their rapid identification, especially HAB species, poses a challenge. This study constructed a comprehensive microalgae image database and developed AI-based classification algorithms to improve identification accuracy. Using DenseNet, EfficientNet, and ViT models, we achieved high classification performance, with ViT showing the best results. The study highlighted the importance of dataset size and diversity in enhancing model performance. Additionally, the trained model was applied to analyze field-collected samples, and the results were compared with those obtained from microscopic examination and metabarcoding analyses. The application of AI technology in microalgae classification provides a reliable basis for early warning and rapid response to HABs, reducing ecological and economic losses. Our findings demonstrate the potential of AI in enhancing the speed and accuracy of microalgae identification, contributing to better management and protection of marine ecosystems.}, }
@article {pmid41467398, year = {2026}, author = {Sugimoto, N and Matsugaki, R and Cooray, U and Kuhara, S and Onoue, T and Saeki, S and Muramatsu, K and Fushimi, K and Matsuda, S and Murakami, M and Ikeda, T}, title = {Safety of Early Rehabilitation for Acute Heart Failure Using Japanese Medical Claims.}, journal = {Journal of the American Heart Association}, volume = {15}, number = {1}, pages = {e045953}, pmid = {41467398}, issn = {2047-9980}, mesh = {Humans ; *Heart Failure/rehabilitation/mortality/physiopathology ; Japan/epidemiology ; Male ; Female ; Aged ; Middle Aged ; Acute Disease ; Time Factors ; Aged, 80 and over ; Incidence ; *Cardiac Rehabilitation/methods/adverse effects ; Retrospective Studies ; Treatment Outcome ; East Asian People ; }, abstract = {BACKGROUND: The safety of initiating early physical rehabilitation therapy and its optimal load in patients with acute decompensated heart failure (ADHF) remain unclear. This study evaluated the safe timing and load of early rehabilitation therapy for patients with ADHF.<br><br>METHODS: In this cohort study using nationwide medical claims data from Japan, we included patients aged &#x2265;18&#x2009;years who were admitted for ADHF and received in-hospital rehabilitation therapy for at least 2&#x2009;days within the first 4&#x2009;days of admission between 2016 and 2020. Nine hypothetical treatment regimens within the first 7&#x2009;days of admission, varying in timing, duration, and load were used as exposures. The outcome was the cumulative incidence of adverse events (eg, death) within 30&#x2009;days after admission. A per-protocol analysis was conducted using a target trial emulation framework with a sequential doubly robust estimator.<br><br>RESULTS: Altogether, 10&#x2009;179 patients with ADHF were enrolled, with 752 developing adverse events (incidence 7.39%). The lowest incidence rate (4.13%) was observed in the regimen where therapy was initiated on the first day of admission with 20&#x2009;minutes of therapy, continuing for up to 7&#x2009;days (95% CI, 3.30-4.95). Conversely, the highest incidence rate was observed in the regimen where therapy was initiated on the third day of admission with 40&#x2009;minutes of therapy, continuing for up to 7&#x2009;days (8.67% [95% CI, 8.22-9.13]).<br><br>CONCLUSIONS: Very early, low-load rehabilitation therapy for patients with ADHF may reduce the risk of adverse events. These findings suggest important implications in the implementation of early rehabilitation.}, }
@article {pmid41464893, year = {2025}, author = {Yan, R and Chen, Z and Zhou, S and Niu, G and Li, Y and Liu, Z and Wang, J and Wu, X and Luo, Q and Zhou, Y and Jin, Y and Liu, K and Yuan, W and Xu, J and Xu, F}, title = {ForestFoodKG: A Structured Dataset and Knowledge Graph for Forest Food Taxonomy and Nutrition.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {24}, pages = {}, pmid = {41464893}, issn = {2304-8158}, abstract = {Forest foods play a vital role in enhancing dietary diversity, human health, and the sustainable use of forest ecosystems. However, structured and machine-readable resources that systematically describe their taxonomic and nutritional attributes remain scarce. To fill this gap, we introduce ForestFoodKG, a comprehensive resource that integrates taxonomic hierarchy and nutritional composition of 1191 forest food items. The resource consists of two components-(i) the ForestFoodKG dataset, containing standardized taxonomic and nutritional records across seven biological levels, and (ii) the ForestFoodKG Knowledge Graph (ForestFoodKG-KG), which semantically links forest food entities using named entity recognition and relation extraction. The constructed graph comprises 4492 entities and 14,130 semantic relations, providing a structured foundation for intelligent querying, nutrition analytics, and ecological informatics. All data were manually verified and made publicly available in CSV format on GitHub. ForestFoodKG serves as the first structured knowledge base for forest foods, promoting data-driven research in nutrition science, sustainable forestry, and knowledge-based decision-making.}, }
@article {pmid41464285, year = {2025}, author = {Alkattan, A and Norful, AA and Pan, CX and August, P and Crupi, RS and Schwartz, JE and Miele, A and Brondolo, E}, title = {Monitoring Redeployment-Associated Burnout in Healthcare Workers: A Real-Time Approach Using Ecological Momentary Assessment.}, journal = {Healthcare (Basel, Switzerland)}, volume = {13}, number = {24}, pages = {}, pmid = {41464285}, issn = {2227-9032}, support = {1K08MH130652-01/NH/NIH HHS/United States ; }, abstract = {Background/Objectives: Ecological momentary assessment (EMA) is a methodology that offers a real-time approach to monitoring clinician well-being, but its utility during high-intensity operational periods remains underexplored. This study examines the feasibility and performance of an EMA-based system for tracking clinical responsibilities and burnout among healthcare workers during the first year of the COVID-19 pandemic. Methods: Utilizing an intensive longitudinal design, 398 healthcare workers, including physicians, physician assistants, nurses, and trainees, completed brief EMA surveys every five days from April 2020 to March 2021. Burnout was assessed with a validated single-item measure and analyzed in relation to redeployment status and hospital caseloads. Results: The EMA approach successfully captured meaningful temporal fluctuations in burnout. Redeployment was associated with higher burnout levels (b = 0.125; p = 0.01), and rising caseloads amplified this effect (interaction b = 0.169; p = 0.001). Nurses showed the strongest caseload-related increases in burnout (b = 0.359; p < 0.001). These patterns persisted even after individuals returned to their usual roles. Conclusions: This study demonstrates that EMA is a scalable and sensitive approach for continuous burnout surveillance, capable of detecting role-specific and context-dependent stress responses in real time. EMA-based monitoring can support early identification of at-risk groups, guide staffing and redeployment decisions, and inform timely organizational interventions during crises and other periods of operational strain.}, }
@article {pmid41461568, year = {2026}, author = {Liu, Y and Luo, Z and Xiao, Y and Li, Y and Liu, M and Shi, Y and Li, Z and Lei, W and Li, C and Jin, LN and Yan, W}, title = {Microplastics in Motion: How Earthworm Guts Become Microbial Gateways through Plastic Surface Dynamics.}, journal = {Environmental science &amp; technology}, volume = {60}, number = {1}, pages = {338-349}, doi = {10.1021/acs.est.5c15257}, pmid = {41461568}, issn = {1520-5851}, mesh = {Animals ; *Oligochaeta ; *Microplastics ; Plastics ; Polystyrenes ; }, abstract = {Microplastics (MPs) pollution in terrestrial ecosystems poses significant ecological risks, particularly as carriers of microbial communities and potential pathogens. However, the mechanisms by which MPs interact with microbes during transit through soil animal digestive systems remain poorly understood. This study investigated the interactions between poly(ethylene terephthalate) (PET) and polystyrene (PS) MPs and gut-derived microbes using a biomimetic earthworm gut model. PET and PS MPs exhibited distinct microbial colonization patterns, driven by their physicochemical properties. PET MPs, with rougher surfaces, preferentially adsorbed cocci such as Paraclostridium, fostering high-density but low-activity bacterial populations. Conversely, PS MPs, with smoother surfaces, enriched bacilli such as Raoultella, supporting low-density but high-activity bacterial communities. PET MPs facilitated rapid bacterial proliferation but lacked long-term stability, whereas PS MPs created persistent microenvironments that increased the ecological risk of pathogen retention and spread. The oxidative degradation of MPs during gut transit enhanced bacterial adhesion by forming reactive surface functionalities. MPs significantly altered microbial diversity and served as selective vectors for microbial dissemination into soil ecosystems, disrupting the microbial dynamics. These findings underscore the dual role of MPs as microbial scaffolds and ecological disruptors, providing critical insights into their ecological impacts and guiding strategies to mitigate MP contamination and pathogenic risks.}, }
@article {pmid41460880, year = {2025}, author = {Langmüller, AM and Chandrasekher, KA and Haller, BC and Champer, SE and Murdock, CC and Messer, PW}, title = {Gaussian process emulation for exploring complex infectious disease models.}, journal = {PLoS computational biology}, volume = {21}, number = {12}, pages = {e1013849}, pmid = {41460880}, issn = {1553-7358}, support = {R35 GM152242/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Normal Distribution ; Dengue/epidemiology ; *Communicable Diseases/epidemiology ; *Epidemiological Models ; Computational Biology ; Disease Outbreaks/statistics &amp; numerical data ; Colombia/epidemiology ; Computer Simulation ; Epidemics/statistics &amp; numerical data ; Seasons ; Models, Statistical ; }, abstract = {Epidemiological models that aim for a high degree of biological realism by simulating every individual in a population are unavoidably complex, with many free parameters, which makes systematic explorations of their dynamics computationally challenging. In this study, we demonstrate how Gaussian Process emulation can overcome this challenge. To simulate disease dynamics, we developed an abstract individual-based model that is loosely inspired by dengue, incorporating some key features shaping dengue epidemics such as social structure, human movement, and seasonality. We focused on three epidemiological metrics derived from the individual-based model outcomes - outbreak probability, maximum incidence, and epidemic duration - and trained three Gaussian Process surrogate models to approximate these metrics. The GP surrogate models enabled the rapid prediction of these epidemiological metrics at any point in the eight-dimensional parameter space of the original model. Our analysis revealed that average infectivity and average human mobility are key drivers of these epidemiological metrics, while the seasonal timing of the first infection can influence the course of the epidemic outbreak. We used a dataset comprising more than 1,000 dengue epidemics observed over 12 years in Colombia to calibrate our Gaussian Process model and evaluated its predictive power. The calibrated Gaussian Process model identified a subset of municipalities with consistently higher average infectivity estimates; the notable overlap between these municipalities and previously reported dengue disease clusters suggests that statistical emulation can facilitate empirical data analysis. Overall, this work underscores the potential of Gaussian Process emulation to enable the use of more complex individual-based models in epidemiology, allowing a higher degree of realism and accuracy that should increase our ability to control diseases of public health concern.}, }
@article {pmid41459590, year = {2025}, author = {Holmqvist, S and Shou, H and Halberstadter, K and Kaplan, M and Chaturvedi, R and Rhodes, E and Giovannetti, T}, title = {Bidirectional associations of daily mood and subjective cognition in older adults using Ecological Momentary Assessment.}, journal = {Aging &amp; mental health}, volume = {}, number = {}, pages = {1-10}, doi = {10.1080/13607863.2025.2606875}, pmid = {41459590}, issn = {1364-6915}, abstract = {OBJECTIVES: Depressive symptoms and subjective cognition are linked in older adults, but traditional measures have numerous limitations that may be addressed by ecological momentary assessment (EMA). This study examined whether baseline depressive and cognitive measures correspond to daily EMA ratings and evaluated concurrent and lagged relations between mood and subjective cognition.<br><br>METHOD: Fifty-five community-dwelling older adults (31% Black/African American; 44 cognitively healthy, 11 mild cognitive impairment) completed a four-week daily EMA survey assessing mood and subjective cognition. Baseline measures included a global cognitive composite and self-reported depressive symptoms, functional independence, and cognitive decline. Cumulative link mixed models examined associations between baseline and EMA measures and concurrent and lagged EMA relations.<br><br>RESULTS: EMA mood correlated with baseline depressive symptoms, while EMA subjective cognition was most strongly associated with functional independence rather than objective cognition or self-reported cognitive decline. EMA mood and cognition were reciprocally associated concurrently. In lagged models, worse EMA subjective cognition predicted worse next-day mood, whereas the reverse association was not statistically significant. Lagged effects were attenuated after accounting for temporal trends and prior-day EMA values.<br><br>CONCLUSION: EMA provides low-burden insights into mood and subjective cognition, supporting its utility for naturalistic assessment in older adults.}, }
@article {pmid41458448, year = {2025}, author = {Lin, S and Zhang, M and Feng, L and Lu, M and Liu, X}, title = {Spatio-temporal evolution and influencing factors of cultural heritage embedded cultural tourism efficiency.}, journal = {Frontiers in public health}, volume = {13}, number = {}, pages = {1690535}, pmid = {41458448}, issn = {2296-2565}, mesh = {Humans ; China ; *Tourism ; *Spatio-Temporal Analysis ; }, abstract = {Enhancing the efficiency of cultural tourism serves as a critical catalyst for the synergistic development of culture and the economy. However, existing research has primarily focused on the content of the cultural tourism industry and its coupling coordination relationships, while comparatively little attention has been given to incorporating key resources-such as cultural heritage-into analytical frameworks access efficiency and underlying impact mechanisms. This study introduces an innovative perspective that embeds cultural heritage within the evaluation process. To address the issue of intertemporal and regional comparability, the Super SBM-DEA model is employed to measure the efficiency of cultural heritage embedded cultural tourism (CHECTE) across 30 Chinese provinces from 2012 to 2022 and identifies its driving factors through Tobit regression. The findings demonstrate that average efficiency exhibits a "declining-rising-declining" pattern over the observed period. Specifically, efficiency decreased to 0.5829 in 2015, reached a peak of 0.8511 in 2019, and then experienced a subsequently decline. During periods of decline, efficient areas contract toward the central and western regions, whereas during periods of improvements, these areas expand into the southwest and southeast. This spatial dynamic reveals a notable departure from traditional regional economic gradients. The central region attained a higher average efficiency of 0.7499 compared to the eastern region of 0.5746, suggesting that the central region derives greater benefits from cultural heritage resources than its eastern counterpart. Tobit regression results reveal that transportation conditions, informatization level, policy environment, higher education, and technological innovation are the key driving factors, with significant regional differences. The eastern region is primarily driven by technological innovation and consumption demand, the central region by the policy environment and informatization, and the western region by transportation conditions and higher education. This study offers theoretical and practical guidance for resource allocation and region-specific cultural tourism policies.}, }
@article {pmid41458310, year = {2025}, author = {Feiner, N and Uller, T and Abalos, J and Slimani, T and S'Khifa, A and Meier, J and ,  and ,  and ,  and , }, title = {The genome sequence of the Andalusian wall lizard, Podarcis vaucheri (Boulenger, 1905).}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {265}, pmid = {41458310}, issn = {2398-502X}, abstract = {We present a genome assembly from a female specimen of Podarcis vaucheri (Andalusian wall lizard; Chordata; Lepidosauria; Squamata; Lacertidae). The assembly contains two haplotypes with total lengths of 1,614.91 megabases and 1,510.74 megabases. Most of haplotype 1 (98.26%) is scaffolded into 20 chromosomal pseudomolecules, including the W and Z sex chromosomes. Most of haplotype 2 (98.63%) is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 17.24 kilobases.}, }
@article {pmid41456016, year = {2025}, author = {Guo, W and Chen, Y and Fan, H and Huang, X and Chen, X and Xiao, Y and Zhang, C and Zhou, W and Wei, F}, title = {Pygmy sperm whale multi-omics data reveal hypoxia adaptations in deep-diving cetaceans.}, journal = {BMC biology}, volume = {24}, number = {1}, pages = {20}, pmid = {41456016}, issn = {1741-7007}, mesh = {Animals ; *Adaptation, Physiological/genetics ; *Hypoxia/genetics ; Genome ; *Whales/physiology/genetics ; Multiomics ; }, abstract = {BACKGROUND: Deep-diving cetaceans tolerate acute hypoxia better than their terrestrial ancestors and shallow-diving counterparts. However, our poor understanding of how genetic factors, cellular functions, and physiological characteristics combine to drive hypoxia adaptation in deep-diving cetaceans remains a critical gap.<br><br>RESULTS: Here, we studied the genetic basis for this ability by creating a de&#xa0;novo genome assembly for the pygmy sperm whale (Kogia breviceps) and comparatively analyzing genomes from 12 cetacean species, including 2 other deep-diving cetaceans. We also sequenced and compared single-nucleus RNA data from the muscle and heart of the pygmy sperm whale and its terrestrial relative Bos taurus. We found that genetic and cellular changes in the HIF-1 pathway, electron transport chain, glucose and fatty acid catabolism, and heart rate may contribute to hypoxia tolerance in deep-diving cetaceans. Key adaptations include rapid evolution of glycolysis-related genes (PYGM and ENO3), differential expression of HIF-1 pathway genes like ARNT, and accelerated conserved noncoding elements in genes such as ATP5F1E (ATP synthase) and DMD (dystrophin). We found an increase in myocytes and type II cardiomyocytes in the pygmy sperm whale's muscle and heart tissues, which may support energy metabolism and homeostasis during deep dives.<br><br>CONCLUSIONS: These findings suggest deep-diving cetaceans have unique genetic and cellular adaptations to cope with hypoxia, offering insights into how mammals handle low oxygen levels at the cellular level.}, }
@article {pmid41455740, year = {2025}, author = {Deb, N and Rahman, T and Moniruzzaman, M and Bin Obadi, AS and Jizat, NM and Al-Bawri, SS and Rahman, AAM}, title = {Integrating feature selection and explainable CNN for identification and classification of pests and beneficial insects.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {2721}, pmid = {41455740}, issn = {2045-2322}, mesh = {Animals ; *Neural Networks, Computer ; *Insecta/classification ; Crops, Agricultural/parasitology ; Aphids/classification ; Coleoptera/classification ; }, abstract = {Reliable identification of agricultural pests and beneficial insects is crucial for sustainable crop protection and ecological balance, yet most vision-based models remain black boxes and require high-dimensional features. This paper proposes an explainable hybrid insect-classification framework that combines convolutional neural network (CNN) feature extraction with a dual-XAI feature selection strategy. SHapley Additive exPlanations (SHAP) and Permutation Feature Importance (PFI) are applied in parallel to rank handcrafted and CNN-derived features, and their intersection yields a compact, biologically meaningful subset for final classification. The selected features are evaluated using lightweight classifiers and a hybrid ensemble, enabling accurate inference under field variability. Experiments on a curated, balanced dataset of four classes (Colorado potato beetle, green peach aphid, seven-spot ladybird, and healthy leaves) collected under diverse lighting and background conditions achieve 96.7% overall accuracy, with precision, recall, and F1-scores all above 96%. Importantly, performance remains stable when reducing dimensionality, retaining ≥90% accuracy using only the top 11 hybrid-selected features. These results demonstrate that integrating SHAP and PFI improves both robustness and interpretability, supporting practical deployment for automated pest monitoring and precision agriculture.}, }
@article {pmid41455448, year = {2026}, author = {Nosair, AM and Samra, RE and Hassan, R and Gemail, K}, title = {Groundwater sustainability challenges in urban deltas: A DRASTIC-GIS and hydrogeophysical approach for assessing the Nile Delta aquifer for sustainable management.}, journal = {Journal of contaminant hydrology}, volume = {277}, number = {}, pages = {104823}, doi = {10.1016/j.jconhyd.2025.104823}, pmid = {41455448}, issn = {1873-6009}, mesh = {*Groundwater/chemistry/analysis ; Geographic Information Systems ; *Environmental Monitoring/methods ; Egypt ; Water Pollutants, Chemical/analysis ; *Conservation of Water Resources ; Cities ; *Conservation of Natural Resources ; Models, Theoretical ; Rivers ; Hydrology ; }, abstract = {Groundwater sustainability in densely populated deltas, such as Egypt's Nile Delta, faces growing threats from wastewater contamination, climate change, and unregulated urban development. This study employs a multidisciplinary approach, combining hydrochemical analysis, GIS-based DRASTIC modeling, and 1D/2D hydrogeophysical resistivity surveys to evaluate aquifer vulnerability in the southeastern Nile Delta. A significant innovation in this research is the integration of DC resistivity measurements with the DRASTIC index, which improves the identification of high-risk zones. Furthermore, anthropogenic impacts were incorporated as an additional layer in the vulnerability modeling, guided by a sensitivity analysis of the controlling parameters. The results indicate two major threats to the Quaternary aquifer. First, the southern and eastern regions are highly vulnerable due to the lack of protective clay layers and detrimental land-use practices, such as wastewater irrigation and urban growth. Second, hydraulic connectivity between the freshwater Quaternary and brackish Miocene aquifer exacerbates salinization and pollutant migration from intensive pumping. Validation using hydrogeophysical data reveals a strong correlation with the DRASTIC model, highlighting areas with significant groundwater degradation, including high total dissolved solids (TDS) levels (>6470 ppm) and nitrate concentrations (>102 mg/L). In contrast, northwestern areas with thick clay caps (exceeding 9 m) exhibit greater resilience. These findings highlight the critical role of land-use practices and aquifer connectivity in urban groundwater management. The study recommends strategies such as optimal extraction zone mapping, IoT monitoring, and drainage lining to minimize contamination, offering a scalable model for sustainable groundwater management in water-stressed deltaic regions.}, }
@article {pmid41452932, year = {2025}, author = {Giral Martínez, J and Barbier, M and De Monte, S}, title = {Interplay of structured and random interactions in complex ecosystems dynamics.}, journal = {PLoS computational biology}, volume = {21}, number = {12}, pages = {e1013786}, pmid = {41452932}, issn = {1553-7358}, mesh = {*Ecosystem ; *Models, Biological ; Computational Biology ; Population Dynamics ; Computer Simulation ; Animals ; }, abstract = {Minimal models for complex ecosystems often assume random interactions, whose statistics suffice to predict dynamical and macroecological patterns. However, ecological networks commonly possess a variety of properties, such as hierarchies or functional groups, that structure species interactions. Here, we ask how conclusions from random interaction models are altered by the presence of such community-level network structures. We consider a Lotka-Volterra model where pairwise species interactions combine structure and randomness, and study macroscopic community-level observables, abundance distributions and dynamical regimes. Randomness and structure combine in a surprisingly yet deceptively straightforward way: contributions from each component to community patterns are largely independent. Yet, their interplay has non-trivial consequences, notably out of equilibrium. We conclude that whether interaction structure matters depends on the pattern: when breaking species equivalence, static patterns of species presence and abundance predicted from random interaction models are less robust than the qualitative nature of dynamical regimes.}, }
@article {pmid41450553, year = {2025}, author = {Hao, W and Shan, YF and Kimura, T and Ukawa, S and Ohira, H and Okabayashi, S and Wakai, K and Ando, M and Tamakoshi, A}, title = {Effect modification by dietary patterns in the relationship between slow gait and incident depressive symptoms: a 6-year cohort study of older Japanese adults (NISSIN Project).}, journal = {Frontiers in nutrition}, volume = {12}, number = {}, pages = {1698581}, pmid = {41450553}, issn = {2296-861X}, abstract = {INTRODUCTION: Slower gait speed is a well-established predictor of late-life depressive symptoms. Previous research suggests that diet can influence biological processes implicated in both gait decline and depression and may therefore serve as an effect modifier in their association. This study aimed to examine whether adherence to healthy dietary patterns modifies the relationship between gait speed and incident depressive symptoms in older adults.<br><br>METHODS: In this longitudinal observational cohort study, we analyzed data from 1,887 depression-free, community-dwelling adults aged 64-65 years, obtained from the New Integrated Suburban Seniority Investigation (NISSIN) Project in Japan. Gait speed was self-rated at baseline as fast, normal, or slow. Dietary intake was assessed using a validated food frequency questionnaire (FFQ), and principal component analysis was performed to identify three dietary patterns: vegetables, Fat and Meat, and Bread and Egg. Incident depressive symptoms were defined as having a 15-item Geriatric Depression Scale (GDS-15) score of &#x2265;6 after a 6-year follow-up. Modified Poisson regression was used to estimate relative risks (RRs), and interactions were assessed on multiplicative and additive scales.<br><br>RESULTS: After 6 years, 12.5% of the participants developed depressive symptoms. Slow gait speed was significantly associated with a higher risk of depression (RR: 2.7; 95% CI: 1.6-4.6), while no dietary pattern was independently associated with depressive symptoms. This risk tended to be lower among slow walkers with higher adherence to a vegetable or Bread and Egg dietary pattern, although the interactions were not statistically significant. A significant negative interaction was found between slow gait and low adherence to a Fat and Meat diet on both additive (RERI = -2.5; 95% CI: -4.1 to -0.8) and multiplicative scales (Ratio of RRs: 0.3; 95% CI: 0.2-0.3).<br><br>DISCUSSION: Dietary patterns may influence the link between slow gait and depression in older adults. Notably, reduced adherence to Fat and Meat diets was associated with a lower overall risk. These findings support dietary improvement as a scalable mental health strategy for physically vulnerable older adults.}, }
@article {pmid41446515, year = {2025}, author = {Mehrotra, S and Duggal, C and Rustagi, N and Ransing, RS and Indu, PS and Chakraborty, S and Mene, T and Sharma, P and Prasad, D and Prinja, S and Verma, P and Dhamija, RK and Kataria, K and Munivenkatappa, M and Suthar, N and Anilkumar, TV and Dahiya, N and Grover, A}, title = {Multistate study on suicide risk reduction and improving mental well-being among school and college students in India - an implementation research study protocol.}, journal = {Frontiers in public health}, volume = {13}, number = {}, pages = {1708246}, pmid = {41446515}, issn = {2296-2565}, mesh = {Adolescent ; Female ; Humans ; Male ; Young Adult ; India ; *Mental Health ; Research Design ; *Risk Reduction Behavior ; Schools ; *Students/psychology/statistics &amp; numerical data ; Suicide/psychology ; *Suicide Prevention ; Universities ; }, abstract = {UNLABELLED: Suicide remains a crucial public health concern in India, especially among students and young adults. The growing academic pressure, social stigma, and lack of accessible mental health services contribute to the growing crisis and suicide rates in India. The study aims to develop an implementation model for educational institutions for reducing risk of suicide behavior (perceived stress and depressive symptoms) and enhance help-seeking behavior. This multi-sectoral implementation model is grounded in the WHO's recommendation for youth suicide prevention and UMMEED guidelines. The study will adopt a concurrent mixed methods design, incorporating both quantitative and qualitative aspects that would be captured simultaneously. A formative research phase will be initially conducted before taking on the main study and it will be guided by the Updated Consolidated Framework for Implementation Research (CFIR). Additionally, the evaluation of the implementation process will be structured using the RE-AIM framework. The study participants will be school and pre-university students, and college students The expected outcome will be achieving reduction of suicide risk behaviors among school and college students in selected districts. The key barriers and facilitators identified through this implementation research will inform recommendations for the potential nation-wide scale up of strategies aimed suicide prevention strategies at educational institutes.<br><br>CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov, CTRI/2024/08/072027.}, }
@article {pmid41443831, year = {2025}, author = {Okuda, N and Nakamura, K and Watanabe, M and Kamide, K and Yoshita, K and Torii, S and Miura, K and Higashiyama, A and Tanno, K and Yonekura, Y and Nagahata, T and Kuribayashi, T and Okayama, A}, title = {Factors Affecting Body Weight/Waist Circumference Changes after Specific Health Guidance for Obese People with CVD Risk Factors in Japan.}, journal = {Journal of atherosclerosis and thrombosis}, volume = {}, number = {}, pages = {}, doi = {10.5551/jat.65943}, pmid = {41443831}, issn = {1880-3873}, abstract = {AIM: Specific Health Checkups (SHCs) and Specific Health Guidance (SHG) were launched in 2008, but the factors related to their effectiveness have not been clarified. We examined the mean reduction in body weight (BW) and waist circumference (WC) of participants eligible for active support under SHG. Body size was considered, as well as the number of support points given during SHG, which indicates the amount of support they received.<br><br>METHODS: A dataset of participants (aged 40-64) who were eligible for SHG and had SHC results collected between 2011 and 2012 was analyzed (n = 76,565). The mean changes in BW and WC between 2011 and 2012 were compared among participants based on their participation status (did not participate, dropped out, finished) and the number of support points for those who finished. Participants were also stratified by sex and BMI (kg/m[2]): normal weight, overweight, and obese.<br><br>RESULTS: The mean BW change (95% CI) for those who did not participate and finished SHG was -0.45 kg (-0.47, -0.43) and -1.32 kg (-1.39, -1.25) in men, and -0.66 kg (-0.72, -0.60) and -1.68 kg (-1.87, -1.49) in women, respectively. Higher support points and larger body sizes correlated with greater reductions in BW in men (P&#xff1c;0.001), but the associations were not significant in women. The reduction in WC was greater in women with normal weight than in obese women.<br><br>CONCLUSION: Sex differences were observed in the association between BW/WC reduction and body size or the amount of support given during SHG.}, }
@article {pmid41443507, year = {2026}, author = {Zhou, M and Tian, H and Ma, M}, title = {Multi-omics analysis of gibberellin-induced internode elongation in Apocynum pictum Schrenk and preliminary investigation into the potential role of WRKY40.}, journal = {Plant science : an international journal of experimental plant biology}, volume = {364}, number = {}, pages = {112957}, doi = {10.1016/j.plantsci.2025.112957}, pmid = {41443507}, issn = {1873-2259}, mesh = {*Gibberellins/metabolism/pharmacology ; *Plant Growth Regulators/metabolism ; Gene Expression Regulation, Plant ; *Transcription Factors/metabolism/genetics ; *Plant Proteins/metabolism/genetics ; Indoleacetic Acids/metabolism ; Gene Expression Profiling ; Transcriptome ; Cell Wall/metabolism ; Cytokinins/metabolism ; Gene Regulatory Networks ; Signal Transduction ; Multiomics ; }, abstract = {This study aimed to elucidate the molecular mechanisms underlying gibberellin (GA3)-induced internode elongation in Apocynum pictum Schrenk. Through exogenous GA3 application, transcriptome sequencing, phytohormone profiling, and weighted gene co-expression network analysis (WGCNA), we proposed an innovative three-tier regulatory framework encompassing "signal perception, network transduction, and coordinated response." The results demonstrated that exogenous GA3 significantly promoted plant height and internode elongation by enhancing cell length rather than increasing cell number. Transcriptomic analysis identified 4321 differentially expressed genes, with KEGG and GO enrichment analyses revealing their significant involvement in plant metabolism, signal transduction, and cell wall organization processes. Hormonal profiling indicated that GA3 dynamically regulated the metabolism and signaling pathways of multiple phytohormones, including auxin and cytokinin, by suppressing cytokinin biosynthesis and delaying auxin activation, thereby reprogramming hormonal homeostasis to drive cell elongation. WGCNA further identified a WRKY40-centered transcriptional regulatory network, which is postulated to mediate GA3 responses, potentially by coordinating the expression of genes involved in auxin biosynthesis and cell wall remodeling genes while coordinating cross-talk among multiple hormone pathways. Concurrently, GA3 optimized cell wall composition by upregulating lignin biosynthesis genes and repressing cellulose hydrolase genes. Additionally, it modulated the stability of key proteins through genes associated with protein turnover, collectively facilitating internode elongation. This study unveils a systematic regulatory mechanism governing GA3-induced internode elongation in A. pictum, providing theoretical insights into phytohormone-mediated growth regulation and potential targets for crop architecture improvement.}, }
@article {pmid41442946, year = {2026}, author = {Huang, XL and Xiong, YX and Yu, S and Chen, XW and Li, DW and Ou, LJ}, title = {Construction of a coccolithophore database platform for ecological and molecular applications.}, journal = {Water research}, volume = {291}, number = {}, pages = {125107}, doi = {10.1016/j.watres.2025.125107}, pmid = {41442946}, issn = {1879-2448}, mesh = {*Haptophyta/genetics ; *Databases, Factual ; China ; Microalgae ; }, abstract = {Coccolithophores play a critical role in marine carbon cycling and biogeochemical processes, yet their ecological distribution and in situ abundance remain understood. This study introduces an open-access coccolithophore database, integrating global occurrence records of Gephyrocapsa huxleyi and Chrysotila spp. from multiple microalgal datasets. The platform integrates taxonomic, distributional, and ecological information of coccolithophores, offering BLAST-based sequence analysis and user data submission features to enhance ecological monitoring and functional studies. To evaluate the database's utility and quantify field abundance, we developed and validated species-specific qPCR primers, demonstrating high specificity and efficiency. Application in Daya Bay, China, revealed G. huxleyi as dominant in offshore and central regions, while C. dentata showed lower abundance, confined to nearshore areas. QPCR-based estimates aligned closely with microscopy-based counts (R[2] > 0.89), affirming method reliability. This study provides a robust digital framework and molecular tools, advancing systematic monitoring of coccolithophore communities and their contributions to oceanic carbon cycling.}, }
@article {pmid41438403, year = {2025}, author = {Khaleghi, P and Cakir, D and Hamidoğlu, A and Gul, OM and Kadry, S}, title = {Interpretable deep learning for depression detection in neurological patients using EEG signals.}, journal = {MethodsX}, volume = {15}, number = {}, pages = {103736}, pmid = {41438403}, issn = {2215-0161}, abstract = {Depression affects over 280 million people worldwide, with neurological patients particularly prone to medication-induced episodes. Conventional diagnostic approaches rely on subjective evaluations, limiting reproducibility and consistency in clinical settings. This study proposes an interpretable deep learning framework for objective depression detection using EEG signals. We hypothesize that combining EEG-based features with explainable artificial intelligence can provide both high accuracy and transparency in diagnosis. The model was trained on EEG data from 232 neurological patients, achieving 98 % classification accuracy. Interpretability was enhanced through SHAP (SHapley Additive exPlanations) analysis, which identified clinically meaningful EEG biomarkers such as the delta/alpha ratio and theta band power. This paper highlights the following contributions: Integration of EEG features with a lightweight deep learning model for depression detection High diagnostic accuracy achieved while maintaining interpretability for clinicians An objective tool that is compatible with existing EEG infrastructure, supporting clinical adoption These results show that our framework bridges predictive performance with interpretability, offering a transparent and scalable EEG-based diagnostic tool. We conclude that this approach can complement clinical decision-making, reducing dependence on subjective evaluation and enabling more consistent, data-driven mental health care.}, }
@article {pmid41436485, year = {2025}, author = {Sardeshpande, M and Bangira, T and Azong Cho, M and Matongera, TN and Mabhaudhi, T}, title = {Exploring the social-ecological potential for indigenous agroforestry in peri-urban areas: a participatory mapping approach.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {44344}, pmid = {41436485}, issn = {2045-2322}, support = {/WT_/Wellcome Trust/United Kingdom ; 205200/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Forestry/methods ; Humans ; South Africa ; Geographic Information Systems ; *Agriculture/methods ; Conservation of Natural Resources ; Socioeconomic Factors ; }, abstract = {Peri-urban agroforestry can provide affordable, fresh, and nutritious food and a departure from conventional forms of cropping. Indigenous foods are well-adapted to local conditions, and may hold cultural and economic value for peri-urban residents. Social, ecological, and economic variables influence the feasibility of indigenous agroforestry in peri-urban areas. This study uses participatory mapping and geographic information systems (GIS) to assess these variables and to map suitable spaces and species for peri-urban indigenous agroforestry at three peri-urban sites in Durban, South Africa. We find that: land tenure, livelihood opportunities, and indigenous food perceptions factor into socioeconomic preferences; topography and soil quality influence ecological feasibility; access to water and roads influences perceived economic viability. Although GIS techniques can identify land suitability, participatory mapping adds local fine-scale context to enhance decision-making. Based on the social-ecological conditions at the three sites, we suggest specific configurations of locally adapted foods and farm designs for peri-urban agroforestry. Our study demonstrates how agroforestry is more feasible in places where basic living conditions are fulfilled, and how co-design can improve recognition of local needs, accessibility to services, and balancing urban green equity.}, }
@article {pmid41435586, year = {2025}, author = {Zeng, T and Du, H and Wu, R}, title = {The chemical structures, and biological activities of marine terpenoids: a review and perspective from cheminformatics.}, journal = {Chinese journal of natural medicines}, volume = {23}, number = {12}, pages = {100006}, doi = {10.1016/j.cjnm.2025.100006}, pmid = {41435586}, issn = {1875-5364}, mesh = {*Terpenes/chemistry/pharmacology ; *Aquatic Organisms/chemistry ; *Biological Products/chemistry/pharmacology ; *Cheminformatics ; Humans ; Animals ; Molecular Structure ; Anti-Inflammatory Agents/chemistry/pharmacology ; Antineoplastic Agents/chemistry/pharmacology ; }, abstract = {Marine terpenoids are a structurally diverse class of natural products produced by marine organisms, characterized by unique molecular architectures and notable biological activities. They play essential roles in ecological interactions and chemical defense, while also exhibiting promising therapeutic properties, including anti-inflammatory and anti-tumor effects. In this review, we compile 13 132 reported marine terpenoids, of which 2066 have documented biological activities, and provide a concise summary of their organismal origins, molecular scaffolds, and associated activities. Cheminformatics approaches are further applied to compare the chemical space of marine versus terrestrial terpenoids, highlighting their structural distinctiveness. Finally, we discuss promising directions for the discovery, utilization, and synthesis of marine terpenoids, with the goal of promoting comprehensive and sustainable exploration of these valuable marine resources.}, }
@article {pmid41432923, year = {2025}, author = {Pu, SY and Lu, JS and Tao, XL and Li, ZF and Wang, YN and Zhang, HM and Lu, X}, title = {The Odonata of China: a data-driven, open-access resource for biodiversity research and conservation.}, journal = {Database : the journal of biological databases and curation}, volume = {2025}, number = {}, pages = {}, pmid = {41432923}, issn = {1758-0463}, support = {202401BC070017//Yunnan Fundamental Research Projects/ ; //Yunnan Revitalization Talent Support Program Yunling Scholar Project (Xuemei Lu)/ ; XDA0460405//Chinese Academy of Sciences/ ; 202505AT350003//Chinese Academy of Sciences/ ; 202405AS350022//Chinese Academy of Sciences/ ; 202305AD160021//Yunnan Technology Innovation Talent Program/ ; }, mesh = {China ; *Biodiversity ; Animals ; *Conservation of Natural Resources ; *Odonata/genetics/classification ; *Databases, Factual ; Phylogeny ; }, abstract = {Odonata (dragonflies and damselflies) are among the most ancient winged insects, with over 900 species recorded in China, representing the highest global diversity. However, the lack of a centralized database integrating morphological, ecological, and multiomics data has hindered large-scale research and conservation efforts. We present Odonata of China (http://dragonflies.kiz.ac.cn), a comprehensive database compiling taxonomic, biogeographic, phenotypic, and multiomics data for 820 species across 3 suborders, 22 families, and 172 genera. The database features advanced search modules (direct, phylogenetic, and map-based), genomic and transcriptomic data for 20 representative families, and high-resolution images. The platform is constructed based on mainstream open-source technologies, ensuring scalability and reproducibility. Odonata of China provides a critical resource for evolutionary biology, conservation, and ecological studies. By integrating heterogeneous data types and leveraging modern technologies, this database bridges a significant gap in invertebrate biodiversity informatics and supports global initiatives to monitor insect declines.}, }
@article {pmid41432418, year = {2026}, author = {Weiss, AS and Santos-Santiago, JA and Keenan, O and Smith, AB and Knight, M and Zackular, JP and Tamayo, R}, title = {Enterococcus faecalis modulates phase variation in Clostridioides difficile.}, journal = {Journal of bacteriology}, volume = {208}, number = {1}, pages = {e0037425}, pmid = {41432418}, issn = {1098-5530}, support = {R01 AI187174/AI/NIAID NIH HHS/United States ; R01 AI143638/AI/NIAID NIH HHS/United States ; R01-AI188648/NH/NIH HHS/United States ; K22-AI7220/NH/NIH HHS/United States ; R01-AI143638/NH/NIH HHS/United States ; R01 AI188648/AI/NIAID NIH HHS/United States ; R35 GM138369/GM/NIGMS NIH HHS/United States ; U19 AI174998/AI/NIAID NIH HHS/United States ; U19-AI174998/NH/NIH HHS/United States ; R01-AI187174/NH/NIH HHS/United States ; R35-GM138369/NH/NIH HHS/United States ; }, mesh = {*Enterococcus faecalis/physiology/genetics ; *Clostridioides difficile/genetics/growth &amp; development/physiology ; Bacterial Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Phenotype ; *Microbial Interactions ; Gastrointestinal Microbiome ; Signal Transduction ; }, abstract = {To adapt and persist in the gastrointestinal tract, many enteric pathogens, including Clostridioides difficile, employ strategies such as phase variation to generate phenotypically heterogeneous populations. Notably, the role of the gut microbiota and polymicrobial interactions in shaping population heterogeneity of invading pathogens has not been explored. Here, we show that Enterococcus faecalis, an opportunistic pathogen that thrives in the inflamed gut during C. difficile infection, can impact the phase-variable CmrRST signal transduction system in C. difficile. The CmrRST system controls multiple phenotypes, including colony morphology, cell elongation, and cell chaining in C. difficile. Here, we describe how interactions between E. faecalis and C. difficile on solid media lead to a marked shift in C. difficile phenotypes associated with phase variation of CmrRST. Specifically, E. faecalis drives a switch of the C. difficile population to the cmr-ON state, leading to chaining and a rough colony morphology. This phenomenon is most pronounced with E. faecalis, as other enterococcal species and select Gram-negative enteric bacteria do not show a similar effect. These results suggest that the composition of the polymicrobial environment in the gut is critical to influencing C. difficile population heterogeneity. Our findings shed light on the complex role that microbial ecology and polymicrobial interactions can have in the phenotypic heterogeneity of invading pathogens.IMPORTANCEClostridioides difficile is an enteric pathogen with critical implications for public health. The microbial ecosystem in which C. difficile resides shapes the behavior and fitness of C. difficile; however, the mechanisms underlying these interactions are not well defined. Here, we demonstrate that Enterococcus faecalis, an opportunistic pathogen known to co-colonize the gut with C. difficile, influences phase variation and downstream growth phenotypes in C. difficile. This phenomenon represents a new paradigm by which co-residing bacteria can modulate phase variation dynamics in C. difficile or other enteric pathogens. Understanding factors that influence C. difficile behavior may elucidate new therapeutic strategies, especially in complex polymicrobial infections.}, }
@article {pmid41432067, year = {2025}, author = {Banse, SA and Sedore, CA and Coleman-Hulbert, A and Johnson, E and Onken, B and Hall, D and Segerdell, E and Jackson, EG and Song, Y and Osman, HC and Xue, J and Basttistoni, E and Guo, S and Foulger, A and Achanta, M and Sheikh, M and Fitzgibbon, T and Willis, JH and Woodruff, GC and Driscoll, M and Lithgow, G and Phillips, PC}, title = {Computer prediction and genetic analysis identifies retinoic acid modulation as a driver of conserved longevity pathways in genetically diverse Caenorhabditis nematodes.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {41432067}, issn = {2050-084X}, support = {AG045844/NH/NIH HHS/United States ; AG045864/NH/NIH HHS/United States ; U01 AG045829/AG/NIA NIH HHS/United States ; U01 AG045864/AG/NIA NIH HHS/United States ; U24 AG056052/AG/NIA NIH HHS/United States ; AG045829/NH/NIH HHS/United States ; AG056052/NH/NIH HHS/United States ; U01 AG045844/AG/NIA NIH HHS/United States ; P40 OD010440/OD/NIH HHS/United States ; }, mesh = {Animals ; *Longevity/drug effects/genetics ; *Tretinoin/metabolism/pharmacology ; *Caenorhabditis elegans/genetics/drug effects/physiology ; Signal Transduction/drug effects ; Caenorhabditis elegans Proteins/metabolism/genetics ; Computational Biology ; }, abstract = {Discovery of new compounds that ameliorate the negative health impacts of aging promises to be of tremendous benefit across a number of age-based comorbidities. One method to prioritize a testable subset of the nearly infinite universe of potential compounds is to use computational prediction of their likely anti-aging capacity. Here, we present a survey of longevity effects for 16 compounds suggested by a previously published computational prediction set, capitalizing upon the comprehensive, multi-species approach utilized by the Caenorhabditis Intervention Testing Program. While 11 compounds (aldosterone, arecoline, bortezomib, dasatinib, decitabine, dexamethasone, erlotinib, everolimus, gefitinib, temsirolimus, and thalidomide) either had no effect on median lifespan or were toxic, 5 compounds (all-trans retinoic acid, berberine, fisetin, propranolol, and ritonavir) extended lifespan in Caenorhabditis elegans. These computer predictions yield a remarkable positive hit rate of 30%. Deeper genetic characterization of the longevity effects of one of the most efficacious compounds, the endogenous signaling ligand all-trans retinoic acid (atRA, designated tretinoin in medical products), demonstrated a requirement for the regulatory kinases AKT-1 and AKT-2. While the canonical Akt-target FOXO/DAF-16 was largely dispensable, other conserved Akt-targets (Nrf2/SKN-1 and HSF1/HSF-1), as well as the conserved catalytic subunit of AMPK AAK-2, were all necessary for longevity extension by atRA. Our results highlight the potential of combining computational prediction of longevity interventions with the power of nematode functional genetics and underscore that the manipulation of a conserved metabolic regulatory circuit by co-opting endogenous signaling molecules is a powerful approach for discovering aging interventions.}, }
@article {pmid41429884, year = {2025}, author = {Song, W and Hu, Q and Liu, S and Hou, Y}, title = {Decadal spatiotemporal dynamics of surface water bodies in Zhengzhou, China: remote sensing monitoring and analysis of driving factors.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {45089}, pmid = {41429884}, issn = {2045-2322}, abstract = {Water is essential for life, human activities, and ecological balance. Understanding the spatiotemporal dynamics of urban water bodies is critical for sustainable water management, especially in fast-growing cities like Zhengzhou. This study investigates the evolution of water bodies in Zhengzhou from 2014 to 2023, using multi-seasonal Landsat 8 imagery and GIS analysis. Three water extraction methods-thresholding, random forest (RF), and a hybrid RF model incorporating spectral indices (NDWI, MNDWI, EWI) and GLCM-based texture features-were evaluated. The hybrid RF approach demonstrated the highest classification accuracy and was applied to generate seasonal water body maps for the target years. The results show a general increase in surface water area, with seasonal peaks in July–September, and spatial expansion mainly in the northern and northeastern regions. These changes are driven by both natural (e.g., precipitation) and anthropogenic (e.g., urban development, artificial lake construction) factors. Compared to previous studies, this research offers three key innovations: (1) a decade-long, seasonal-scale analysis of water dynamics; (2) a robust multi-feature classification framework for complex urban settings; and (3) an integrated interpretation of natural and human influences. The findings provide valuable references for water resource planning and urban ecological restoration, and the methods used may be transferable to similar inland cities under monsoon climates.}, }
@article {pmid41427890, year = {2026}, author = {Martin, SLF and La Torre, R and Danneels, B and Tooming-Klunderud, A and Skage, M and Kollias, S and Tørresen, OK and Anbaran, MF and Stur, E and Jakobsen, KS and Martin, MD and Ekrem, T}, title = {Haplotype-resolved chromosome-level genome assemblies of four Diamesa species reveal the genetic basis of cold tolerance and high-altitude adaptations in arctic chironomids.}, journal = {GigaScience}, volume = {15}, number = {}, pages = {}, pmid = {41427890}, issn = {2047-217X}, support = {326819//Research Council of Norway/ ; 270068//Research Council of Norway/ ; //University of Bergen/ ; //University of Oslo/ ; //Norwegian University of Life Sciences/ ; }, mesh = {Animals ; *Chironomidae/genetics/physiology/classification ; Altitude ; Phylogeny ; Cold Temperature ; *Haplotypes ; *Adaptation, Physiological/genetics ; *Genome, Insect ; Arctic Regions ; *Acclimatization/genetics ; Genomics/methods ; }, abstract = {BACKGROUND: Arctic and alpine insects experience extreme environmental stressors, yet the genomic basis of their adaptation is poorly understood. Diamesa midges (Diptera: Chironomidae) are cold-adapted insects inhabiting glacial and high-altitude freshwater ecosystems, but no chromosome-level genomes have been available to date.<br><br>FINDINGS: We present the first haplotype-resolved, chromosome-level genomes for four Diamesa species (Diamesa hyperborea, Diamesa lindrothi, Diamesa serratosioi, and Diamesa tonsa), assembled using PacBio HiFi sequencing and Hi-C scaffolding. The assemblies show high completeness and k-mer representation. Phylogenomic analyses place Diamesinae as sister to other Chironomidae except Podonominae, and comparisons suggest introgression between the distinct species D. hyperborea and D. tonsa. Comparative genomic analyses across 20 Diptera species identified significant gene family contractions in Diamesa related to oxygen transport and metabolism, consistent with adaptation to high-altitude, low-oxygen environments. Expansions were observed in histone-related and Toll-like receptor gene families, suggesting roles in chromatin remodeling and immune regulation under cold stress. A glucose dehydrogenase gene family was significantly expanded across all cold-adapted species studied, implicating it in cryoprotectant synthesis and oxidative stress mitigation. Diamesa exhibited the largest gene family contraction at any phylogenetic node, with limited overlap in expansions with other cold-adapted Diptera, indicating lineage-specific adaptation.<br><br>CONCLUSIONS: Our findings support the hypothesis that genome size condensation and selective gene family changes underpin survival in cold environments. These new genome assemblies provide a valuable resource for studying adaptation, speciation, and conservation in cold-specialist insects. Future integration of gene expression and population genomics will further clarify the evolutionary resilience of Diamesa in a warming world.}, }
@article {pmid41427113, year = {2025}, author = {Garai, S and Vo, S and Blank, L and Xu, F and Chen, J and Duong-Tran, D and Zhao, Y and Brown, BC and Shen, L}, title = {H-VIP: quantifying regional topological contributions of the brain network to cognition.}, journal = {Frontiers in radiology}, volume = {5}, number = {}, pages = {1686780}, pmid = {41427113}, issn = {2673-8740}, abstract = {INTRODUCTION: Understanding the role of various brain regions of interest (ROIs) in various cognitive functions or tasks, across healthy or neurodegenerative conditions and multiple degrees of separation, remains a key challenge in neuroscience. Conventional network measures can only capture localized or quasi-localized features of brain ROIs. Topological data analysis (TDA), particularly persistent homology, provides a threshold-free, mathematically rigorous framework for identifying topologically salient features in complex networks. In this paper, we introduce a new metric, the Homological Vertex Importance Profile (H-VIP), designed to assess the relevance of vertices that participate in persistent topological structures (e.g., connected components, cycles or cavities) in brain networks. The H-VIP quantifies the topological features of the network at the ROI (node) level by compressing its higher-order connectivity profile using homological constructs.<br><br>METHODS: Leveraging homological constructs of brain connectomes, we extend two of our previously defined network-level measures-average persistence and persistence entropy-to an ROI-level measure, i.e., the H-VIP. We then applied the H-VIP to two independent datasets: structural connectomes from the Human Connectome Project and functional connectomes from the Alzheimer's Disease Neuroimaging Initiative. Persistent homology was computed for each network, and H-VIP scores were derived to evaluate vertex-level contributions. Finally, H-VIP scores were used for the prediction of multiple cognitive measures.<br><br>RESULTS: In both anatomical and functional brain networks, H-VIP values demonstrate predictive power for various cognitive measures. Notably, the connectivity of the frontal lobe exhibited stronger correlations with cognitive performance than the whole-brain network.<br><br>DISCUSSION: H-VIP offers a robust and interpretable means to locate, quantify, and visualize region-specific contributions to network's topological, higher-order landscape. Its ability to detect potentially impaired connectivity at the individual level suggests possible applications in personalized medicine for neurological diseases and disorders. Beyond brain connectomics, the H-VIP can be used for other types of complex networks where topological features are of importance, such as financial, social, or ecological networks.}, }
@article {pmid41425965, year = {2025}, author = {Lin, Y and Chen, S and Che, J and Sun, M and Wang, Y}, title = {Multi-omics approaches for image classification in disease diagnosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1616189}, pmid = {41425965}, issn = {2235-2988}, mesh = {Humans ; *Genomics/methods ; *Computational Biology/methods ; *Proteomics/methods ; *Metabolomics/methods ; Multiomics ; }, abstract = {INTRODUCTION: The integration of multi-omics data for disease diagnosis holds transformative potential in the field of computational biology, especially when applied to the intricate and dynamic interactions between microbial communities and their human hosts.<br><br>METHODS: This integrative approach enables to capture diverse biological signals across genomic, transcriptomic, proteomic, and metabolomic layers, providing a more comprehensive understanding of disease mechanisms. In alignment with emerging priorities in disease microbiology, our study addresses a critical and timely need for interpretable, scalable, and biologically robust computational models that can extract clinically meaningful diagnostic insights from inherently high-dimensional, heterogeneous, and often incomplete biological datasets.<br><br>RESULTS AND DISCUSSION: Traditional image classification approaches in disease contexts-such as those relying solely on histopathological features or genomic imaging-tend to overlook the broader ecological and systemic dimensions that are essential for decoding the mechanisms of microbial pathogenesis. These single-modal methods often suffer from significant limitations, including reduced scalability to diverse clinical settings, poor generalizability across patient populations, and an inability to handle partially observed or biologically variable data. Such constraints diminish their effectiveness in precision diagnostics, disease subtyping, and therapeutic decision-making. By contrast, our approach emphasizes multi-modal integration and model interpretability, aiming to overcome these limitations and advance the development of next-generation diagnostic tools that are both clinically actionable and biologically grounded.}, }
@article {pmid41425596, year = {2025}, author = {Yu, R and Hasan, A and Ibrahim, M and Alonazi, WB and Bin, L}, title = {An integrated immunoinformatic approach to design a novel multiepitope chimeric vaccine against Mycoplasma phocimorsus as a causal agent of bloodstream infections.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1719398}, pmid = {41425596}, issn = {1664-3224}, mesh = {*Bacterial Vaccines/immunology/genetics ; *Mycoplasma Infections/immunology/prevention &amp; control/microbiology ; Humans ; *Mycoplasma/immunology ; Computational Biology/methods ; Epitopes, B-Lymphocyte/immunology ; Animals ; Epitopes/immunology ; Proteomics/methods ; Vaccine Development ; *Sepsis/immunology/prevention &amp; control/microbiology ; }, abstract = {INTRODUCTION: Mycoplasma phocimorsus is increasingly recognized as an emerging human pathogen, despite its primary association with marine mammals. It has recently been identified as a causative agent of bloodstream infections and sepsis, a major cause of mortality among hospitalized patients. To date, no approved vaccine is available against M. phocimorsus, underscoring the urgent need for preventive strategies.<br><br>METHODS: The current study was aimed at employing immunoinformatic approaches to design a vaccine based on multiple epitopes derived from the six core proteomic datasets of representative M. phocimorsus strains.<br><br>RESULTS: By subtractive genomics, we retrieved 3,576 nonredundant proteins from M. phocimorsus proteomes following only one putative immunoglobulin-blocking virulence outer membrane protein conserved in six strains. The epitopes derived from the putative immunoglobulin-blocking virulence protein exhibited promising features such as strong binding affinity, lack of allergenicity, nontoxic properties, high antigenicity scores, and excellent solubility. Moreover, these epitopes include nine linear B cell epitopes, eight MHC class I epitopes, and five MHC class II epitopes. In addition, adjuvants and linker molecules were successfully merged into a chimeric vaccine with significant immunogenicity and stimulation of both adaptive and innate immune responses. The promising potential of the selected vaccine candidates was further validated through their favorable physico-chemical characteristics, strong interaction with TLR-4, and stable performance in molecular dynamics simulations.<br><br>DISCUSSION: These results suggest that the putative immunoglobulin-blocking outer membrane virulence protein could effectively participate in activating the primary innate immune response, thereby serving as a strong foundation for subsequent adaptive immune activation. The proposed vaccine provides substantial basis for developing effective preventive and therapeutic measures against the zoonotic M. phocimorsus, whose association with sepsis, soft tissue, and respiratory infections, particularly in immunocompromised individuals emphasizes the crucial need for vaccine development.}, }
@article {pmid41423362, year = {2025}, author = {Yang, B and Molton, I and Humbert, A and Gregg, E and Iribarren, S and Hurvitz, P and Lee, D}, title = {Is doing more always better? A mixed methods study examining the relationship between subjective and objective aspects of community participation among people with multiple sclerosis.}, journal = {Disability and health journal}, volume = {}, number = {}, pages = {102020}, pmid = {41423362}, issn = {1876-7583}, support = {R01 NR016942/NR/NINR NIH HHS/United States ; }, abstract = {BACKGROUND: Community participation is an important health outcome among people with multiple sclerosis (PwMS) and includes subjective (e.g., satisfaction) and objective aspects (e.g., frequency). Conceptual literature emphasizes the need for measuring both types of aspects to fully understand participation, yet empirical evidence remains limited.<br><br>OBJECTIVE: To examine the relationship between subjective and objective aspects of community participation and their associations with person-related and environmental factors.<br><br>METHODS: A mixed methods design was used. Correlation analyses of previously collected self-reported and GPS-based data from 100 PwMS assessed statistical associations between subjective and objective participation. Four focus groups were conducted with 24 PwMS discussing the relationship between participation satisfaction and performance. Qualitative data were analyzed using content analysis.<br><br>RESULTS: Moderate to strong correlations (.4-.78, p&#xa0;<&#xa0;0.001) were found within objective (trip frequency, distance, duration, and activity space) and subjective participation measures (perceived ability and satisfaction). However, associations between subjective and objective aspects were mostly weak (.2-.32, p&#xa0;<&#xa0;0.05). Person-related and environmental factors showed varying correlations, with generally stronger associations for subjective participation measures (.17 to -.57, p&#xa0;<&#xa0;0.01) than objective measures (.16-.36, p&#xa0;<&#xa0;0.05). Aligned with quantitative results, qualitative themes revealed that greater participation quantity may facilitate satisfaction, but frequent and extensive participation is not necessary to reach satisfaction.<br><br>CONCLUSIONS: This study provides integrated quantitative and qualitative evidence that subjective and objective aspects of participation are related but distinct. Attention must be paid to the divergence between these aspects to address real-world barriers.}, }
@article {pmid41422551, year = {2025}, author = {Almeida-Filho, N and Ayres, JRCM}, title = {[Intersubjectivity and modes of care in health: eco-ethno-social sensitivity and critical technological competence for quality-equity in digital health].}, journal = {Salud colectiva}, volume = {21}, number = {}, pages = {e5763}, pmid = {41422551}, issn = {1851-8265}, mesh = {Humans ; *Delivery of Health Care/organization &amp; administration ; *Digital Technology ; *Quality of Health Care ; Digital Health ; }, abstract = {In this essay, we propose that Mendes Gonçalves' theory of the labor process in health can contribute to a critical theory of digital health capable of deconstructing technological alienation within digital transformation processes in the health sector. First, we identify modes of care and models of technological organization of healthcare delivery. Second, we analyze the collective-informational mode of care oriented toward sociotechnical health networks, highlighting collaborative practices rooted in territories and local realities. Third, we propose a theoretical platform for understanding digital transformation in health, based on the articulation of the following concepts: sociotechnical appropriation, metapresence, critical technological competence, quality-equity, and eco-ethno-social sensitivity. Finally, we outline the epistemological and theoretical foundations necessary for a "digital epistemodiversity," understood as an ecology of knowledges in which technical objects, sociotechnical systems, human agents, and transhuman beings may coexist, interact, and produce systemic changes in the health field, with the protagonism of healthcare workers and broad popular participation.}, }
@article {pmid41421202, year = {2026}, author = {Webster, AB and Bennett, NC and Clauss, M and Ganswindt, A and Abraham, AJ}, title = {Soil ingestion: An important contamination pathway for toxic element exposure in wild herbivores.}, journal = {The Science of the total environment}, volume = {1012}, number = {}, pages = {181193}, doi = {10.1016/j.scitotenv.2025.181193}, pmid = {41421202}, issn = {1879-1026}, mesh = {Animals ; *Soil Pollutants/analysis/metabolism ; *Herbivory ; *Environmental Monitoring ; Soil/chemistry ; Animals, Wild ; }, abstract = {Human activities have increased pollution and toxic element concentrations in soils across the Earth's surface. These activities could have profound implications for wildlife that directly or incidentally ingest soil during foraging, and for humans that consume animals as a primary source of protein. To date, levels of soil ingestion in large herbivores and species-specific vulnerability to toxic element exposure via this pathway have not yet been assessed. Here, we tested the hypothesis that animals feeding closer to the ground ingest more soil than their browsing counterparts. Across a community of 16 African herbivore species, we found that soil ingestion was highest in grazing (blue wildebeest, white rhino and buffalo) and fossorial (warthog and porcupine) animals. This translated to 20-60 % higher total element intake for chromium, cobalt, tin, lead, vanadium and arsenic in these groups. Faecal and fur concentrations were similarly elevated in these species, highlighting that the toxic elements ingested from soil are assimilated into body tissues with potential repercussions for animal and human health. In ungulates, soil ingestion rates align with species-level hypsodonty (height of the tooth crown). We propose that hypsodonty can be used as a proxy for identifying species-specific vulnerability to toxic-element exposure at broad scales. The non-invasive framework developed here, may be applied to monitoring wild herbivore exposure to toxic elements and may be particularly relevant for ongoing conservation and rewilding efforts in areas with high levels of anthropogenic pollution.}, }
@article {pmid41420859, year = {2026}, author = {Beghini, F and Brito, IL and Gerstein, M and Christakis, NA}, title = {Characterization of gut microbiomes in rural Honduras reveals uncharacterized species and associations with human genetic variation.}, journal = {Cell reports}, volume = {45}, number = {1}, pages = {116724}, doi = {10.1016/j.celrep.2025.116724}, pmid = {41420859}, issn = {2211-1247}, mesh = {Humans ; Honduras ; *Gastrointestinal Microbiome/genetics ; *Genetic Variation ; Rural Population ; Male ; Female ; COVID-19/virology/microbiology ; Adult ; Metagenomics ; Middle Aged ; SARS-CoV-2 ; Metagenome ; }, abstract = {The gut microbiome is integral to human health, yet research data to date have emphasized industrialized populations. Here, we performed large-scale shotgun metagenomic sequencing on 1,893 individuals from rural Honduras, providing the most comprehensive microbiome dataset from Central America. We identify a distinct microbial composition enriched in Prevotella species. Longitudinal analysis in 301 individuals reveals microbiome instability, with shifts in taxonomic diversity and metabolic potential, including changes associated with severe acute respiratory syndrome coronavirus 2 infection. Additionally, we characterize the gut virome and eukaryotic microbiome, identifying uncharacterized viral taxa and a high prevalence of Blastocystis species in individuals with greater microbial diversity. Finally, by integrating host genomic data, we uncover significant host-microbiome associations, highlighting the influence of human genetic variation on microbial composition. These findings expand our understanding of microbiome diversity in non-industrialized populations, underscoring the need for global microbiome research.}, }
@article {pmid41419039, year = {2026}, author = {Rozen-Rechels, D and Lemesle, P and Jouanneau, W and Sebastiano, M and Harris, SM and Blévin, P and Angelier, F and Gernigon, J and Lemesle, JC and Robin, F and Budzinski, H and Labadie, P and Bustamante, P and Chastel, O}, title = {How does habitat use influence PFAS contamination in wildlife? Combining stable isotopes and GPS tracking in three gull species.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {391}, number = {}, pages = {127556}, doi = {10.1016/j.envpol.2025.127556}, pmid = {41419039}, issn = {1873-6424}, mesh = {Animals ; *Charadriiformes/metabolism ; *Fluorocarbons/metabolism/blood ; *Ecosystem ; *Environmental Monitoring/methods ; France ; Geographic Information Systems ; Male ; *Environmental Pollutants/metabolism/blood ; Female ; Carbon Isotopes/analysis ; Nitrogen Isotopes/analysis ; Food Chain ; }, abstract = {Per- and polyfluoroalkyl substances (PFAS) are toxic and persistent compounds widely distributed in the environment and accumulate in top predators, including seabirds. Because of the biomagnification potentials of some PFAS, diet is thought to be a key exposure route for PFAS. However, other factors such as habitat use, may mask interspecific differences in PFAS exposure expected from trophic structure. Among seabirds, gulls are generalists that forage in both terrestrial and marine habitats, making them relevant models to concurrently investigate the influence of foraging habitats and trophic position on PFAS exposure. We combined plasma PFAS concentrations with GPS tracking and stable isotopes to define foraging habitats (δ[13]C; δ[34]S; GPS) and trophic positions (δ[15]N) in three sympatric gull species breeding in France (Isle of Ré). In herring gulls (Larus argentatus), long-chain perfluoroalkyl carboxylic acids (PFCAs) were positively correlated with high trophic resources from marine habitats. We found compound- and sex-dependent relationships between PFAS concentrations and stable isotope values in lesser black-backed gulls (Larus fuscus), while no association was found with habitat use. No association was found between PFAS levels and stable isotopes in great black-backed gulls (Larus marinus). Our study suggests that coastal habitat could be a source of PFCA contamination and highlights that the influence of habitat use on gull exposure to PFAS varied depending on species, sex, and compounds.}, }
@article {pmid41415319, year = {2025}, author = {Agboli, E and Zahouli, JZB and Sauer, FG and Sombie, A and Biré, YN and Adjobi, CN and Cadar, D and Horváth, B and Tomazatos, A and Schmidt-Chanasit, J and Lühken, R and Tóth, GE and Badolo, A and Jöst, H}, title = {Morphological and Genetic Heterogeneity in Aedes aegypti (Diptera: Culicidae) Populations Across Diverse Landscapes in West Africa.}, journal = {Ecology and evolution}, volume = {15}, number = {12}, pages = {e72748}, pmid = {41415319}, issn = {2045-7758}, abstract = {Native to sub-Saharan Africa, Aedes aegypti (Linnaeus, 1762) has spread across the globe and is now one of the most significant vectors of arboviruses worldwide. However, data on the ranges of its populations remain sparse, and the genetic variability and ecological adaptability in West Africa are still poorly understood. In this study, we characterized the morphological and genetic diversity of Ae. aegypti across four landscape types (urban, peri-urban, rural, and sylvatic sites) in three West African countries (Burkina Faso, Côte d'Ivoire, and Ghana). The population exhibited significant variation in abdominal scaling patterns across countries and landscape types, with the sylvatic and urban populations in Burkina Faso displaying the highest proportions of white scales (> 50% white scales), while black scales predominated among those from Côte d'Ivoire and Ghana (> 80% black scales). Wing shape displayed limited differentiation between the countries, landscape types, and genetic clusters. Bayesian analysis indicated high gene flow among populations, with notable outliers observed in sylvatic sites from Burkina Faso and admixture patterns suggesting possible human-mediated dispersal. Additionally, two major mitochondrial lineages, clades A and B, were identified. Most samples were categorized under clade B, showing no evidence of clustering by country or landscape type. In contrast, clade A comprised primarily sylvatic specimens from Burkina Faso and a single urban individual from Côte d'Ivoire. These findings highlight the complex interplay of genetic, environmental, and ecological factors shaping the variations in Ae. aegypti populations in West Africa. They provide insights into the phenotypic and genetic diversity of Ae. aegypti, offering valuable implications for understanding arbovirus transmission dynamics and formulating targeted interventions against arboviral diseases.}, }
@article {pmid41413899, year = {2025}, author = {Peng, M and Li, J and Xu, L and Chroumpi, T and Garrigues, S and Kun, RS and Meng, J and Aguilar-Pontes, MV and Lipzen, A and Ng, V and Clendinen, CS and Tolic, N and Baker, SE and Grigoriev, IV and de Vries, RP}, title = {Multi-Omics Analyses Reveal Divergent Molecular Mechanisms Underlying Plant Biomass Conversion by Five Fungi.}, journal = {MicrobiologyOpen}, volume = {14}, number = {6}, pages = {e70201}, pmid = {41413899}, issn = {2045-8827}, support = {OCENW.XS23.2.218//NWO ENW-XS program/ ; OCENW.XS24.2.218//NWO ENW-XS program/ ; NGF.1609.241.001//NWO NGF-AiNedXS program/ ; NGF.1609.23.006//NWO NGF-AiNedXS program/ ; 202107720100//China Scholarship Council Scholarship/ ; 201907720027//Chinese Scholarship Council (CSC)/ ; //Dutch Research Council (NWO)/ ; //Ministry of Infrastructure and Water Management/ ; //Facilities Integrating Collaborations for User Science (FICUS)/ ; }, mesh = {*Biomass ; Lignin/metabolism ; *Ascomycota/metabolism/genetics/growth &amp; development ; Zea mays/metabolism/microbiology ; *Basidiomycota/metabolism/genetics/growth &amp; development ; Proteome/analysis ; Transcriptome ; Metabolome ; Gene Expression Profiling ; *Plants/metabolism/microbiology ; Multiomics ; }, abstract = {Fungal plant biomass conversion (FPBC) is of great importance to the global carbon cycle and has been increasingly applied for the production of biofuel and biochemicals from lignocellulose. However, the comprehensive understanding of relevant molecular mechanisms in different fungi remains challenging. Here, we comparatively analyzed the transcriptome, proteome and metabolome profile of four ascomycetes and one basidiomycete fungi during their growth on two common agricultural feedstocks (soybean hulls and corn stover). We revealed strong time-, substrate- and species-specific responses at multi-omics levels for the tested fungi, highlighting species-specific carbon utilization approaches and evolutionary adaptation to environmental niches. Notably, a remarkable expressional diversity of lignocellulose degrading enzymes, sugar transporter and metabolic genes, as well as industrially relevant metabolites were identified across different fungi and cultivation conditions. The findings improves our understanding of complex molecular networks underlying FPBC and fungal ecological roles, offering novel insights that can guide future genetic engineering of fungi for valorization of agriculture waste into value-added bioproducts.}, }
@article {pmid41411944, year = {2026}, author = {Nour, HE and Garoub, MM}, title = {Heavy metal bioaccumulation and risk assessment in intertidal molluscan shells and sediments of Suez Bay.}, journal = {Marine pollution bulletin}, volume = {224}, number = {}, pages = {119141}, doi = {10.1016/j.marpolbul.2025.119141}, pmid = {41411944}, issn = {1879-3363}, mesh = {*Water Pollutants, Chemical/analysis/metabolism ; *Geologic Sediments/chemistry ; Animals ; *Metals, Heavy/analysis/metabolism ; Risk Assessment ; *Environmental Monitoring ; Bays/chemistry ; *Mollusca/metabolism/chemistry ; Bioaccumulation ; *Animal Shells/chemistry ; }, abstract = {This study investigated heavy metal (HM) concentrations in molluscan shells and associated sediments along the Suez Bay coast to assess bioaccumulation patterns, ecological and human health risks, and potential pollution sources. Bioaccumulation studies in this region remain scarce, making the present work a valuable contribution to addressing a critical knowledge gap. Three molluscan species (Cerithium ruppelli, Septifer bilocularis, and Modiolus auriculatus) were analyzed across five coastal sites. C. ruppelli accumulated higher levels of Pb, Co, and Cr, whereas S. bilocularis was more indicative of Cu and Cd enrichment. Bioaccumulation factors exhibited clear interspecific differences, with the shell-to-sediment ratios reflecting both localized metal exposure and the varying bioaccumulation capacities of each species. Sediment quality indices (Igeo, Cf, mCdeg, PLI, TRI) indicated a generally uncontaminated status; however, localized enrichment of Cd and Co was identified, requiring continuous monitoring. Human health risk assessment confirmed no immediate carcinogenic or non-carcinogenic risks, although potential hazards may arise from future increases in Ni and Cr. Overall, molluscan shells particularly S. bilocularis and C. ruppelli proved to be effective bioindicators, highlighting the need for continued biomonitoring and stricter regulation of industrial and urban discharges into Suez Bay.}, }
@article {pmid41411345, year = {2025}, author = {Fairbanks, EL and Baylis, M and Daly, JM and Tildesley, MJ}, title = {Quantifying vector diversion effects in zoonotic systems: A modelling framework for arbovirus transmission between reservoir and dead-end hosts.}, journal = {PLoS computational biology}, volume = {21}, number = {12}, pages = {e1013359}, pmid = {41411345}, issn = {1553-7358}, mesh = {Animals ; Humans ; *Mosquito Vectors/virology ; Culex/virology ; *Disease Reservoirs/virology ; *Models, Biological ; West Nile Fever/transmission ; *Zoonoses/transmission/virology ; West Nile virus ; Computational Biology ; Vector Borne Diseases/transmission ; *Arbovirus Infections/transmission ; }, abstract = {Vector-borne disease transmission involves complex interactions between vectors, reservoir hosts and dead-end hosts. We present a mathematical model for the vectorial capacity that incorporates multiple host types and their interactions, focusing specifically on West Nile virus transmission by Culex pipiens mosquitoes. Our model integrates climate-dependent parameters affecting vector biology with vector control interventions to predict transmission potential under various scenarios. We demonstrate how vector control interventions targeting one host type can significantly impact transmission dynamics across all host populations. By examining the effects of different vector control tool modes of action (repellency, preprandial killing, disarming and postprandial killing), we develop target product profiles that minimise unintended consequences of vector control. Notably, we identify the optimal intervention characteristics needed to prevent repellency on dead-end hosts from inadvertently increasing transmission among reservoir hosts. This research provides valuable insights for public health officials designing targeted vector control strategies and offers a flexible modelling framework that can be adapted to other vector-borne diseases with complex host dynamics.}, }
@article {pmid41408553, year = {2025}, author = {Wyatt, S and Hobro, G and Seamer, P and Mohammed, MA and Spilsbury, P}, title = {Decomposing the effects of changes of population size, age-sex profile, health status and residual factors on growth in hospital activity in English hospitals: an ecological database study from 2011-2019.}, journal = {BMC health services research}, volume = {25}, number = {1}, pages = {1601}, pmid = {41408553}, issn = {1472-6963}, mesh = {Humans ; England ; Female ; Male ; Retrospective Studies ; *Health Status ; Adult ; Middle Aged ; *Population Density ; Aged ; State Medicine ; Databases, Factual ; Age Factors ; Sex Factors ; Adolescent ; Young Adult ; *Hospitalization/statistics &amp; numerical data/trends ; *Hospitals/statistics &amp; numerical data ; *Population Growth ; Infant ; }, abstract = {BACKGROUND: Hospitals are central to healthcare systems and understanding the drivers of hospital activity is critical for effective capacity planning, especially amid demographic shifts and fiscal pressure. In the English National Health Service (NHS), there are plans to construct 40 new hospitals. There is limited evidence on factors driving hospital activity. This study provides retrospective estimates of the effects of population growth (P), changes in the age-sex structure (S), shifts in age-specific health status (H), and residual factors (R) on hospital activity in England.<br><br>METHODS: Total annual growth is modelled as G&#x2009;=&#x2009;(1&#x2009;+&#x2009;P)(1&#x2009;+&#x2009;S)(1&#x2009;+&#x2009;H)(1&#x2009;+&#x2009;R)&#x2009;-&#x2009;1. Negative binomial regression models using hospital episode statistics from 2011 to 2019 were used to decompose total annual growth rates (G) into P,S,H and R by five points of delivery (listed below).<br><br>RESULTS: The annual growth rate for elective admissions was 2.29% (95% CI: 1.06% to 3.54%) which was made up of p&#x2009;=&#x2009;0.88% (-0.96% to 2.67%), S&#x2009;=&#x2009;0.69% (-0.62% to 2.18%), H&#x2009;=&#x2009;-0.03% (-0.23% to 0.17%) and R&#x2009;=&#x2009;0.73% (0.58% to 0.88%). The annual growth rate for non-elective admission was 2.69% (1.55% to 3.83%) which was made up of p&#x2009;=&#x2009;0.59% (-1.08% to 2.50%), S&#x2009;=&#x2009;0.25% (-1.17% to 1.61%), H&#x2009;=&#x2009;0.18% (-0.43% to 0.81%) and R&#x2009;=&#x2009;1.65% (1.13% to 2.17%). The annual growth rate for maternity admissions was -0.70% (-5.65% to 4.51%) which was made up of p&#x2009;=&#x2009;0.41% (-6.25% to 8.36%), S&#x2009;=&#x2009;-0.08% (-4.93% to 5.23%), H&#x2009;=&#x2009;0.00% (NA) and R&#x2009;=&#x2009;-1.02% (-1.61% to -0.43%). The annual growth rate for outpatient attendance was 4.51% (3.62% to 5.40%) which was made up of p&#x2009;=&#x2009;0.61% (-0.71% to 1.96%), S&#x2009;=&#x2009;0.46% (-0.63% to 1.56%), H&#x2009;=&#x2009;-0.02% (-0.43% to 0.38%) and R&#x2009;=&#x2009;3.41% (3.11% to 3.71%). The annual growth rate for emergency department attendance was 1.29% (0.71% to 1.88%) which was made up of p&#x2009;=&#x2009;0.27% (-0.56% to 1.09%), S&#x2009;=&#x2009;0.09% (-0.55% to 0.70%), H&#x2009;=&#x2009;0.09% (-0.21% to 0.39%) and R&#x2009;=&#x2009;0.84% (0.58% to 1.10%).<br><br>CONCLUSIONS: In general, growth in hospital activity was mostly driven by residual (R) factors, followed by population growth (P). Age-specific health status (H) had the lowest impact. These data may provide useful context for planning future hospital activity in England.}, }
@article {pmid41408523, year = {2025}, author = {Wirth, M and Bischoff, S and Hering, R and Schulz, M and Mackowiak, M and Piedboeuf-Potyka, K and Brinks, R and Hoyer, A and Tönnies, T}, title = {Prevalence of type 2 diabetes from 2011 to 2023 by regional socioeconomic deprivation in Germany: an ecological study.}, journal = {BMC public health}, volume = {26}, number = {1}, pages = {258}, pmid = {41408523}, issn = {1471-2458}, abstract = {BACKGROUND: Type 2 diabetes prevalence is increasing globally and is unequally distributed across socioeconomic groups. In Germany, little is known about how these socioeconomic inequalities have developed over time. Therefore, we aimed to estimate the age- and sex-specific prevalence of type 2 diabetes in Germany from 2011 to 2023 and assess related temporal trends in socioeconomic inequality.<br><br>METHODS: We used nationwide claims data (N&#x2009;~&#x2009;70&#xa0;million persons per year) from the German statutory health insurance, aggregated at the county level and linked them to the German Index of Socioeconomic Deprivation (GISD), an area-based measure of deprivation based on education, occupation, and income. We identified prevalent type 2 diabetes cases using ICD-10 codes E11, E12, E13, and E14. Log-binomial regression was used to estimate prevalence ratios for the association between GISD quintiles and type 2 diabetes prevalence, with temporal trends assessed through the four-way interaction between age, sex, GISD, and calendar year.<br><br>RESULTS: Crude type 2 diabetes prevalence increased from 9.00% (95% confidence interval: 8.99&#x2013;9.01) in 2011 to 9.60% (9.59&#x2013;9.61) in 2023, while age-standardised prevalence showed a smaller increase, from 9.00 (8.99-9.00) in 2011 to 9.35% (9.34&#x2013;9.35) in 2023. A clear socioeconomic gradient emerged, with the highest prevalence of 11.80% (11.78&#x2013;11.82) in 2023 in the most deprived regions (quintile 5), compared to 8.00% (7.99&#x2013;8.01) in the least deprived regions (quintile 1). Prevalence was consistently higher in men than women, but the socioeconomic gradient was more pronounced among women (prevalence ratio 2023 women 1.29 (1.23&#x2013;1.35), men 1.22 (1.17&#x2013;1.26)).<br><br>CONCLUSIONS: Our findings highlight persistent socioeconomic disparities in type 2 diabetes prevalence, especially among women. Further research is needed to explore the mechanisms underlying these disparities and to evaluate targeted interventions for high-risk populations.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12889-025-25908-x.}, }
@article {pmid41407116, year = {2026}, author = {Dey, D and Lateef, HA and Leroux, A and Zipunnikov, V and Merikangas, K}, title = {Associations between daily outdoor temperature and subjective real-time ratings of emotional states and sleep in mood disorder subtypes.}, journal = {Journal of affective disorders}, volume = {397}, number = {}, pages = {120918}, doi = {10.1016/j.jad.2025.120918}, pmid = {41407116}, issn = {1573-2517}, mesh = {Humans ; Male ; Female ; Middle Aged ; Adult ; Aged ; Adolescent ; Aged, 80 and over ; *Temperature ; Child ; Ecological Momentary Assessment ; Young Adult ; *Mood Disorders/psychology ; *Sleep/physiology ; *Affect ; Seasons ; Sleep Quality ; *Emotions ; Bipolar Disorder/psychology ; }, abstract = {There is growing evidence for the influence of weather on mental health at both the aggregate level indices of mental health statistics of hospitalizations, morbidity, and mortality, and individual level dynamics of mood states. Most research on this topic has focused on light exposure and depressed mood as the sole indicators of seasonal fluctuations of mood disorders. This paper evaluates the association between daily maximum outdoor temperature (DMOT) and contemporaneously reported mood, energy, anxiousness, and sleep quality assessed with Ecological Momentary Assessment (EMA) in a community-based sample of 452 people, aged 11 to 85 years, comprising people with or without a history of mood disorders. After controlling for demographics, daily activity levels, and daytime cloud coverage as an index of light exposure, we found that higher DMOT was associated with better mood, increased energy, and better sleep quality among those with a history of mood disorders, particularly in the spring. These findings suggest that the dynamics of mood, energy, and sleep may underlie the aggregate population-level influences of temperature and correlated environmental influences on negative mental health outcomes, particularly among those with BD. Therefore, the conceptualization of risk and intervention for mood disorders should consider both the aggregate influences of temperature and light and associated environmental conditions, as well as individual-level sleep quality and energy as potential mechanisms for seasonal patterns of emotional states.}, }
@article {pmid41406850, year = {2026}, author = {Suzuki, J and Kobayashi, Y and Fujino, Y and Tabuchi, T and Katori, Y}, title = {Prevalence and associated factors of self-reported olfactory dysfunction in Japan: Findings from a nationwide web-based cross-sectional survey.}, journal = {Auris, nasus, larynx}, volume = {53}, number = {1}, pages = {61-69}, doi = {10.1016/j.anl.2025.12.008}, pmid = {41406850}, issn = {1879-1476}, mesh = {Humans ; Male ; Female ; Japan/epidemiology ; Middle Aged ; Cross-Sectional Studies ; Prevalence ; Adult ; *Olfaction Disorders/epidemiology ; Aged ; Self Report ; *COVID-19/epidemiology ; Asthma/epidemiology ; Severity of Illness Index ; Risk Factors ; SARS-CoV-2 ; Chronic Disease ; Hypertension/epidemiology ; }, abstract = {OBJECTIVE: Olfactory dysfunction (OD) compromises safety and well-being in humans; however, large-scale Japanese data are lacking. We quantified the prevalence of subjective chronic OD (self-reported olfactory impairment persisting ≥3 months), identified associated health and occupational factors, and evaluated determinants for severity using data from a nationwide web-based survey in Japan.<br><br>METHODS: We analyzed data from the Japan coronavirus disease 2019 and Society Internet Survey 2023, a stratified, nationwide, cross-sectional survey of community-dwelling residents in Japan. From the initial 33,000 participants, we used the data of 25,569 participants (12,323 men, 13,246 women), after excluding those with implausible responses and missing data, to calculate prevalence. Inverse probability weighting was used to align the sample with the 2019 National Living Conditions Survey. Group differences concerning the presence and severity of OD were tested with &#x3c7;&#xb2; or Wilcoxon tests after excluding participants with additional missing data; independent associations were examined using weighted multivariable logistic regression analyses.<br><br>RESULTS: The weighted prevalence for chronic subjective OD was 1.3 % (95 % confidence interval [CI] 1.1-1.4); age-specific rates ranged from 0.6 % (40-49 years) to 2.1 % (60-69 years). Independent OD correlates included the factors current smoking (odds ratio [OR] 2.09, p = 0.016), homeworking (OR 2.75, p = 0.004), somatic symptoms (Somatic Symptom Scale-8 score &#x2265; 12; OR 2.66, p = 0.009), dysgeusia (OR 193.2, p < 0.001), current hypertension (OR 3.69, p = 0.005), current bronchial asthma (OR 6.09, p < 0.001), current allergic rhinitis (OR 1.97, p = 0.012), and moderate-severe presenteeism (Work Functioning Impairment Scale score &#x2265; 21; OR 3.04, p < 0.020). Being a woman was associated with lower OD severity (OR 0.34, p = 0.035, for moderate-severe vs mild), whereas having &#x2265; 1 day of sick absences in the previous month was associated with higher OD severity (OR 3.17, p = 0.044).<br><br>CONCLUSION: Subjective OD prevalence in Japan was 1.3 %. Presenteeism was associated with OD and absenteeism was associated with moderate-severe OD. Further studies on the relationship between OD and work productivity are warranted.}, }
@article {pmid41406178, year = {2025}, author = {Somsen, ED and Septer, KM and Field, CJ and Patel, DR and Lowen, AC and Sutton, TC and Koelle, K}, title = {Quantifying viral pandemic potential from experimental transmission studies.}, journal = {PLoS computational biology}, volume = {21}, number = {12}, pages = {e1013808}, pmid = {41406178}, issn = {1553-7358}, support = {75N93021C00017/AI/NIAID NIH HHS/United States ; F31 AI186550/AI/NIAID NIH HHS/United States ; T32 AI138952/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Ferrets/virology ; Humans ; *Pandemics/statistics &amp; numerical data ; *Influenza, Human/transmission/epidemiology/virology ; Computational Biology ; Influenza A virus ; Risk Assessment ; Models, Biological ; *Orthomyxoviridae Infections/transmission/epidemiology/virology ; }, abstract = {In an effort to avert future pandemics, surveillance studies aim to identify animal viruses at high risk of spilling over into humans. These studies have revealed substantial diversity in identified viruses. However, the number of tools currently available to assess pandemic risk is limited. Methods currently in use include the characterization of candidate viruses using in vitro laboratory assays and experimental transmission studies in animal models. However, transmission experiments yield relatively low-resolution outcomes that are not immediately translatable to projections of viral dynamics at the level of a host population. To address this gap, we present an analytical framework to extend the use of measurements from experimental transmission studies to generate more quantitative risk assessments. Specifically, we use within-host viral titer data from index and contact animals to estimate parameters relevant to transmission between pairs of individuals. We then extend this model to estimate epidemiological parameters, such as reproduction numbers and generation intervals. We present our analytical framework in the context of two influenza A virus (IAV) ferret transmission experiments: one using influenza A/California/07/2009 (Cal/2009) and one using influenza A/Hong Kong/1/1968 (Hong Kong/1968). In a head-to-head comparison, we find that Cal/2009 has higher pandemic potential than Hong Kong/1968. Our results depend on several assumptions, including that within-host viral dynamics in humans and those in the model animal used (here, ferrets) share quantitative similarities and that viral transmissibility between model animals reflects viral transmissibility between humans. The methods we present to assess pandemic risk of viral isolates can be used to improve relative risk assessment of other emerging viruses of pandemic concern.}, }
@article {pmid41405388, year = {2026}, author = {Lahey, Z and Jones, T-KL and Simmons, AM and Andreason, SA}, title = {In silico detection and characterization of novel Picornavirales mined from publicly available insect RNA-seq data sets.}, journal = {Microbiology spectrum}, volume = {14}, number = {2}, pages = {e0170125}, pmid = {41405388}, issn = {2165-0497}, support = {//U.S. Department of Agriculture/ ; }, mesh = {Animals ; Genome, Viral ; Phylogeny ; *Picornaviridae/genetics/classification/isolation &amp; purification ; *Insecta/virology/genetics ; Computational Biology/methods ; RNA-Seq ; RNA, Viral/genetics ; Computer Simulation ; }, abstract = {Picornavirales is a hyperdiverse order of viruses that infect assorted hosts, including arthropods. Members of this group contain a positive-sense, single-stranded RNA genome with a polyadenylated tail. As such, they are often sequenced as "bycatch" in RNA-seq experiments targeting other organisms. We developed a simple-to-follow bioinformatic pipeline to assemble and annotate genomes of the order Picornavirales using publicly available insect metatranscriptome data sets. Using our pipeline, 40 novel viruses were discovered, including putative new members of the families Dicistroviridae, Iflaviridae, and Polycipiviridae. The hosts of the new picornaviruses include beetles (two families), crickets, parasitic wasps, sap-sucking hemipterans (members of all suborders), and thrips. We validated each virus as new in silico by performing a sequence similarity (BLAST) search of each virus against the NCBI non-redundant database and by phylogenetic reconstruction of the RNA-dependent RNA polymerase amino acid sequence from each novel virus and other members of the order Picornavirales. Three taxa classified as iflaviruses by the International Committee on Taxonomy of Viruses that infect Lepidoptera (butterflies and moths) render Iflaviridae paraphyletic, and their taxonomic status should be reevaluated. Two of the newly identified iflaviruses are dicistronic, the first genomes with this phenotype in the family Iflaviridae. A newly characterized psyllid iflavirus displays an inverted genome architecture and forms a clade with other psyllid-infecting iflaviruses that share this feature. We also detected and sequenced two of the novel iflaviruses, GnV2 and DcV1, in wild-captured Graminella nigrifrons and purchased Delphastus catalinae, demonstrating their presence in populations beyond those previously sequenced. Our pipeline provides an additional method by which novel viruses can be discovered, assembled, annotated, and submitted to nucleotide sequence archives.IMPORTANCEInsects are the most abundant group of animals on Earth and serve as reservoirs for myriad microscopic organisms, including viruses. Just a fraction of this viral diversity has been characterized despite some having considerable consequences to human and animal health, agricultural production, and overall ecological stability. In this study, we illustrate a bioinformatic viral discovery pipeline using single-stranded, positive-sense RNA viruses of the order Picornavirales as a case study. Picornaviruses are some of the 'dark taxa' of the virosphere that are ubiquitous in arthropods, including the vectors of serious plant diseases. Discoveries of these viruses have been accelerated by the advent of next-generation sequencing technologies, opening potential research avenues that could be exploited for pest control.}, }
@article {pmid41404704, year = {2026}, author = {Saghaei, S and Siemers, M and Ossetek, KL and Richter, S and Edwards, RA and Roux, S and Zielezinski, A and Dutilh, BE and Marz, M and Cassman, NA}, title = {VirJenDB: a FAIR (meta)data and bioinformatics platform for all viruses.}, journal = {Nucleic acids research}, volume = {54}, number = {D1}, pages = {D912-D924}, pmid = {41404704}, issn = {1362-4962}, support = {//NFDI4Microbiota/ ; 460129525//Deutsche Forschungemeinschaft/ ; ZMII2-2524FSB62C//German Federal Ministry of Health/ ; 390713860//Germany's Excellence Strategy EXC 2051/ ; 101046203//Horizon Europe programme/ ; //PHI/ ; //Alexander von Humboldt Foundation/ ; //Federal Ministry of Education and Research/ ; DP220102915//Australian Research Council/ ; DP250103825//Australian Research Council/ ; FL250100019//Australian Research Council/ ; //U.S. Department of Energy Joint Genome Institute/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; //Friedrich-Schiller-Universit&#xe4;t Jena/ ; 865694/ERC_/European Research Council/International ; }, mesh = {*Viruses/genetics/classification ; *Software ; *Computational Biology/methods ; Metadata ; Internet ; High-Throughput Nucleotide Sequencing ; *Databases, Genetic ; Data Curation ; Genome, Viral ; }, abstract = {High-throughput sequencing has generated an unprecedented volume of data. However, researcher-submitted data in repositories requires extensive curation and quality control for reuse. These tasks are hindered by the multiplicity of repositories, the sheer volume of the data, and the complexity of virus (meta)data curation. To address these challenges, VirJenDB offers a user-friendly platform to facilitate versioned, community-driven curation, and ontology development. Virus sequences were ingested from 16 sources, including ~200 fields of metadata or standards, covering taxonomy, sample, and host information. Up to 85 metadata fields have undergone at least one round of curation, and are linked to 15.4 million virus sequences, with 88 % from those infecting eukaryotes and the remaining infecting prokaryotes. Subsets were created, including a novel collection of 0.91 million viral operational taxonomic unit (vOTU) sequences across all viruses, while keeping the original sequences from each vOTU to facilitate downstream analyses, e.g. sequence variation. The VirJenDB web portal (https://www.virjendb.org) provides HTTPS and Application Programming Interface (API) access to the sequence datasets and metadata, offering a search engine, filtering, download, visualizations, and documentation. VirJenDB aims to connect the phage and eukaryotic virus research communities by supporting webtool integration, meta-analyses, and metadata schema extensions.}, }
@article {pmid41403705, year = {2025}, author = {Paccagnella, D and Bağcı, C and Gavriilidou, A and Ziemert, N}, title = {PanBGC: a pangenome-inspired framework for comparative analysis of biosynthetic gene clusters.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf225}, pmid = {41403705}, issn = {2730-6151}, abstract = {Bacterial secondary metabolites are a major source of therapeutics and play key roles in microbial ecology. These compounds are encoded by biosynthetic gene clusters (BGCs), which show extensive genetic diversity across microbial genomes. While recent advances have enabled clustering of BGCs into gene cluster families (GCFs), there is still a lack of frameworks for systematically analysing their internal diversity at a population scale. Here, we introduce "PanBGC", a pangenome-inspired framework that treats each GCF as a population of related BGCs. This enables classification of biosynthetic genes into core, accessory, and unique categories and provides openness metrics to quantify compositional diversity. Applied to over 250 000 BGCs from more than 35 000 genomes, PanBGC maps biosynthetic diversity of more than 80 000 GCFs. Our analysis reveals that gene composition reshuffling, rather than acquisition of new genes, is the dominant driver of diversity within GCFs, with most families exhibiting closed gene repertoires but high compositional variability. Additionally, transporter-related domains were commonly identified among core genes, reflecting the fundamental importance of compound export in BGC function. To facilitate exploration, we present PanBGC-DB (https://panbgc-db.cs.uni-tuebingen.de), an interactive web platform for comparative BGC analysis. PanBGC-DB offers gene- and domain-level visualizations, phylogenetic tools, openness metrics, and custom query integration. Together, PanBGC and PanBGC-DB provide a scalable framework for exploring BGCs at population resolution and for contextualizing newly discovered BGCs within the global landscape of secondary metabolism.}, }
@article {pmid41399480, year = {2025}, author = {Bhat, R and Narayanan, P and Chanda, MM and Walsh, M}, title = {Parasitiformes (ticks) and Acariformes (mites) vectors and their vertebrate host diversity: A global scoping review.}, journal = {One health (Amsterdam, Netherlands)}, volume = {21}, number = {}, pages = {101278}, pmid = {41399480}, issn = {2352-7714}, abstract = {BACKGROUND: While the infection ecology and epidemiology of some vector-borne pathogens have received extensive research focus, many tick- and mite-borne zoonoses, particularly in the global South, have been largely neglected. The current scoping review aims to understand the global state of knowledge for the infection ecology and epidemiology of tick- and mite-borne pathogens, contextualised by their maintenance community composition, in the landscapes in which these pathogens circulate.<br><br>METHODS: Online databases were searched with keyword combinations to gather evidence on the relationship between vertebrate host species diversity and the occurrence of tick- and mite-borne diseases. Information related to pathogen, vector species involved in transmission, geographic location, and ecological and epidemiological relationships between host species diversity and tick- and mite-borne disease was recorded.<br><br>RESULTS: A total of 5510 papers were initially selected for screening based on this search with a final total of 36 papers included in the review. The review found that the literature is highly skewed toward Lyme disease (29 out of 36 studies) and focused on the global North regions (32 out of 36 studies). A general lack of studies on mite-borne diseases globally was evident. Additionally, 42&#xa0;% of all studies reported evidence for the dilution effect whereby greater species richness in the maintenance community appeared to diminish pathogen transmission, while 31&#xa0;% of the studies identified both dilution and amplification effects in the disease systems.<br><br>CONCLUSIONS: While there has been an increase in studies on tick-borne diseases other than Lyme disease in the past decade, the current scoping review has identified an urgent need to study tick- and mite-borne diseases in the global South. The state of knowledge on these unique vector-pathogen systems with respect to relevant maintenance communities is sparse and requires targeted investigation in regions of the global South experiencing rapid habitat loss and subsequent changes in vertebrate species diversity.}, }
@article {pmid41399279, year = {2026}, author = {Culina, A}, title = {Co-BreeD: A milestone resource for studies on cooperative breeding.}, journal = {The Journal of animal ecology}, volume = {95}, number = {1}, pages = {17-20}, doi = {10.1111/1365-2656.70205}, pmid = {41399279}, issn = {1365-2656}, support = {HRZZ-IP-2022-10-2872//Hrvatska Zaklada za Znanost/ ; }, mesh = {Animals ; *Cooperative Behavior ; *Breeding ; *Databases, Factual ; *Birds/physiology ; *Mammals/physiology ; *Reproduction ; }, abstract = {Research Highlight: Ben Mocha, Y., Woith, M., Scemama de Gialluly, S., Bruscagnin, L., Kestel, N., Markman, S., Drobniak, S. M., Baglione, V., Boersma, J., Cousseau, L., Covas, R., Braga de Miranda, G. H., Dey, C. J., Doutrelant, C., Gula, R., Heinsohn, R., Keynan, O., Kingma, S. A., Leitão, A. V., … Griesser, M. (2025). An integrative, peer-reviewed open-source cooperative-breeding database (Co-BreeD). Journal of Animal Ecology. https://doi.org/10.1111/1365-2656.70154. The Cooperative-Breeding Database (Co-BreeD) is an open, peer-reviewed resource that collects data on cooperative breeding across birds and mammals, including humans. As such, it serves as a valuable resource for studies on sociality and cooperation. Currently, Co-BreeD provides population-level data on nearly 40,000 breeding events from 316 species and is growing. The database allows for cooperative breeding to be treated as a continuous rather than binary trait, and at finer spatial and temporal scales, enabling detailed exploration of the ecological and evolutionary drivers of cooperation. This novel approach revealed that alloparental care, and hence cooperative breeding, is likely more widespread than previously recognised. The importance of curated, high-quality, and accessible data across ecology and evolution is becoming evident; Co-BreeD has great potential to contribute to such collaborative, reproducible, and robust research.}, }
@article {pmid41397974, year = {2025}, author = {Zheng, F and Yao, W and He, W and Zhang, W and Chen, Y and Chen, H and Zeng, Z and Liu, XL and Ding, S and Zheng, Y and Huang, L and Zhu, Y and Zhang, C}, title = {A comprehensive database for high-throughput identification of archaeal lipids using high-resolution mass spectrometry.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {588}, pmid = {41397974}, issn = {2041-1723}, support = {32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42372354//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Archaea/chemistry/metabolism ; *Lipids/chemistry/analysis ; *Mass Spectrometry/methods ; *Lipidomics/methods ; Tandem Mass Spectrometry/methods ; *Databases, Factual ; *Membrane Lipids/chemistry ; }, abstract = {Archaeal membrane lipids are markedly distinct from those in bacteria and eukaryotes, serving as biomarkers for unraveling their ecological and biogeochemical roles. Recent advancements in high-resolution mass spectrometry-based lipidomic research facilitate detailed cellular-level characterizations of lipid compounds. However, the lack of a comprehensive and dedicated database severely limits large-scale, high-throughput investigations of archaeal lipids. We present ArchLips, a comprehensive database containing 219,348 in silico molecular structures and tandem mass spectra of 199,248 corresponding archaeal lipid compounds. ArchLips enables the automatic and accurate annotation of archaeal lipid compounds characterized by high-resolution mass spectrometry from both pure cultures and environmental samples, serving as a transformative tool for enhancing our understanding of archaeal diversity and its ecological and evolutionary significance within global ecosystems.}, }
@article {pmid41396997, year = {2025}, author = {Li, M and Cao, Y and Wu, W and Mo, Y and Wang, J and Geng, X and Xu, J and Fei, Y and Su, G and Hu, H and Li, K and Ni, J and Xu, ZF}, title = {EucaMOD: a comprehensive multi-omics database for functional genomics research and molecular breeding of fast-growing eucalyptus trees.}, journal = {The Plant journal : for cell and molecular biology}, volume = {124}, number = {5}, pages = {e70603}, pmid = {41396997}, issn = {1365-313X}, support = {JB22035001//Guangxi Key Research and Development Program/ ; AA23062055-2//Guangxi Science and Technology Major Program/ ; AD23026337//Guangxi Specific Project for Science and Technology Bases and Talents/ ; //Guangxi 'Bagui Young Talents' Special Fund/ ; }, mesh = {*Eucalyptus/genetics/growth &amp; development ; *Genomics ; *Databases, Genetic ; *Plant Breeding ; Genome, Plant/genetics ; Transcriptome/genetics ; Trees/genetics/growth &amp; development ; Multiomics ; }, abstract = {Eucalyptus, one of the most widely planted plantation tree species globally, is primarily found in tropical and subtropical regions and contributes significantly to economic and social benefits. With advances in sequencing technologies, there is an increasing demand for the systematic analysis of multi-omics data among Eucalyptus species to enhance genetic breeding efforts. Although several early genomic databases have been established for eucalyptus, they have not been updated in a timely manner and lack recent multi-omics data, rendering them insufficient for current research needs. To address this gap, we developed the eucalyptus multi-omics database (EucaMOD, http://eucalyptusggd.net/eucamod), a comprehensive resource for cross-omics studies. In this study, we functionally annotated 45 eucalyptus genomes and structurally annotated 15, conducting comparative genomics and pan-proteomics analyses across all genomes. Additionally, we analyzed eucalyptus transcriptome, epigenome, and variome data through standardized workflows, enabling the in-depth mining and reanalysis of multi-omics datasets. EucaMOD is the most comprehensive multi-omics database for eucalyptus to date and includes data from 45 genomes (39 species), 870 mRNA-seq samples, 17 miRNA-seq samples, 52 epigenomic datasets (histone modifications and transcription factor binding), and genetic variation data from 1219 samples. To support functional genomics and molecular breeding research, the database is organized into the following 11 modules: Home, Species, Genomics, Comparative genomics, Pan-proteomics, Transcriptomics, Epigenetics, Variomics, Tools, Download, and Help. EucaMOD also offers online analysis tools for data mining, providing free public services to aid eucalyptus gene function and genetic engineering studies.}, }
@article {pmid41391105, year = {2026}, author = {Edwards, CJ and Smith, R and Lafit, G and Ward, T and Emsley, R and Rus-Calafell, M and Myin-Germeys, I and Peters, E and Bucci, S and Craig, TK and Haddock, G and Ball, H and Fornells-Ambrojo, M and Hardy, A and McLeod, H and Gumley, AI and McDonnell, J and Montague, A and Clancy, M and Huckvale, M and Garety, PA}, title = {The Impact of AVATAR Therapy on Voice Hearing in Everyday Life: ESM Outcomes of the AVATAR2 Trial.}, journal = {Schizophrenia bulletin}, volume = {52}, number = {1}, pages = {}, pmid = {41391105}, issn = {1745-1701}, support = {/WT_/Wellcome Trust/United Kingdom ; 215471/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; Female ; Male ; Single-Blind Method ; Adult ; Middle Aged ; *Hallucinations/therapy ; *Ecological Momentary Assessment ; *Outcome Assessment, Health Care ; Follow-Up Studies ; Young Adult ; *Psychotherapy/methods ; Avatar ; }, abstract = {AVATAR therapy involves facilitated dialogs between a voice hearer and a digital embodiment of their distressing voice ("the avatar"). We conducted a multi-site single-blind randomized controlled trial to evaluate the efficacy of brief (AV-BRF) and extended (AV-EXT) forms of AVATAR therapy, compared with treatment as usual (TAU) alone (AVATAR2). This study reports the data from experience sampling method (ESM) assessments conducted at baseline, end of therapy (16 weeks), and follow-up (28 weeks). The research questions focused on whether those in the AV-BRF or AV-EXT arms experienced less voice-related distress, anxiety, and beliefs as measured by ESM, compared to TAU. Separate mixed-effects models were fitted for each research question. The final sample (n = 200) completed approximately 40% of questionnaires across all timepoints. Participants who received AV-EXT therapy, but not AV-BRF, reported reduced momentary voice-related distress at 16 (P = .022) and 28 weeks (p = .029). Appraisals of voice control were also reduced in the AV-EXT arm at 16 weeks when the voice was present (P = .002) or not (P = .008). Voice power appraisals were reduced (P < .035) in both arms when the voice was "not present but on my mind" at all timepoints. There were no changes in the frequency of voice hearing, appraisals of voice intent, or assertive responding. These findings from everyday life, reported for the first time, provide evidence of the impact on the primary AVATAR therapy treatment targets, including appraisals of voice power and control. The weight of evidence favors the AV-EXT protocol in the further development and implementation of AVATAR therapy.}, }
@article {pmid41389554, year = {2026}, author = {Yang, T and Zhan, Y and Sha, J and Zhao, J and Wang, C and Peng, T and Zhang, L}, title = {Integrative multi-omics elucidates the impact of microalgae on growth, quality, phytohormones, and rhizosphere microbiome of Angelica sinensis.}, journal = {Microbiological research}, volume = {304}, number = {}, pages = {128418}, doi = {10.1016/j.micres.2025.128418}, pmid = {41389554}, issn = {1618-0623}, mesh = {*Rhizosphere ; *Angelica sinensis/microbiology/growth &amp; development/metabolism ; *Plant Growth Regulators/metabolism ; *Microbiota ; *Microalgae/metabolism/physiology ; Nitrogen/metabolism ; Soil Microbiology ; Coumaric Acids/metabolism ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Biomass ; Soil/chemistry ; Metagenomics ; Metabolomics ; Carbon/metabolism ; Chlorella vulgaris/metabolism ; Multiomics ; }, abstract = {Microalgae have recently been recognized as sustainable biofertilizers that improve soil fertility while enhancing crop performance. However, their roles in regulating medicinal plant growth and quality, as well as the underlying ecological mechanisms, remain poorly understood. In this study, we systematically assessed the effects of three representative microalgae-Anabaena cylindrica (AC), Phormidium tenue (PT), and Chlorella vulgaris (CV)-on the growth, quality, hormonal regulation, soil nutrient dynamics, and rhizosphere microbiome of Angelica sinensis. Field inoculation trials demonstrated that all three microalgae significantly promoted biomass accumulation and increased antioxidant capacity. AC and CV further enhanced the accumulation of ferulic acid and flavonoids, which are two key quality determinants. Microalgal inoculation significantly altered rhizosphere soil properties by increasing total organic carbon and alkali-hydrolyzable nitrogen, with AC uniquely elevating available phosphorus and iron. Metagenomic analysis revealed that AC and PT stimulated nitrification while suppressing denitrification, thereby reducing nitrogen loss and stabilizing the soil nitrogen pools. Distinct microbial taxa, including Rhodanobacter, Streptomyces, and Pseudomonas, were identified as the major contributors to carbon and nitrogen cycling. Hormone metabolomics showed that microalgal inoculation reprogrammed A. sinensis phytohormone profiles in a species-specific manner. Partial least squares path modeling suggested that AC and CV promote ferulic acid biosynthesis through distinct mechanisms, with AC associated with reduced investment in C-mineralization processes and CV associated with lower salicylic acid levels, whereas PT enhances biomass accumulation mainly by stimulating N-cycle processes. Collectively, this study provides integrated evidence linking microalgae-mediated nutrient cycling, rhizosphere microbiome shifts and hormonal regulation to enhanced quality formation in A. sinensis.}, }
@article {pmid41389419, year = {2026}, author = {Li, WC and Li, HM and Guo, ZW and Yan, P and Shen, Y and Chen, YP}, title = {A prior knowledge-enhanced Transformer model for data anomaly identification and processing in industrial park wastewater treatment plants.}, journal = {Water research}, volume = {290}, number = {}, pages = {125125}, doi = {10.1016/j.watres.2025.125125}, pmid = {41389419}, issn = {1879-2448}, mesh = {*Wastewater ; *Waste Disposal, Fluid ; China ; *Water Purification ; Industrial Waste ; Parks, Recreational ; }, abstract = {Accurate identification of anomalies and reconstruction of missing data are crucial for the intelligent operation of industrial park wastewater treatment plants (WWTPs). However, traditional statistical and model-based approaches often fall short in addressing anomalies characterized by complex spatio-temporal coupling within WWTP data. Accordingly, this study introduces a novel prior knowledge-enhanced Transformer (PK-T) model. The PK-T model leverages domain-specific knowledge from wastewater treatment within a deep learning architecture, which demonstrates superior performance in the high-precision identification and reconstruction of complex anomalies. The model was evaluated using one year of operational data from two industrial park WWTPs in China. Comparative analysis with conventional methods, including statistical, distance-based, and model-based approaches, reveals that PK-T significantly outperforms these approaches in both anomaly identification accuracy and data reconstruction precision. Remarkably, the model achieves reconstruction accuracies exceeding 90 % for critical water quality parameters. This research provides an innovative solution for robust data management and intelligent operation in industrial wastewater treatment, with considerable practical implications for enhancing the operational efficiency of WWTPs.}, }
@article {pmid41388108, year = {2026}, author = {Yuan, H and Mancuso, CA and Johnson, K and Braasch, I and Krishnan, A}, title = {Computational strategies for cross-species knowledge transfer.}, journal = {Nature methods}, volume = {23}, number = {2}, pages = {312-327}, pmid = {41388108}, issn = {1548-7105}, support = {R35 GM128765/GM/NIGMS NIH HHS/United States ; R01 OD011116/CD/ODCDC CDC HHS/United States ; 1017799//Simons Foundation/ ; R01OD011116//U.S. Department of Health &amp; Human Services | NIH | NIH Office of the Director (OD)/ ; R35 GM128765/GM/NIGMS NIH HHS/United States ; R01 OD011116/CD/ODCDC CDC HHS/United States ; }, mesh = {Humans ; *Computational Biology/methods ; Animals ; Transcriptome ; Species Specificity ; Molecular Sequence Annotation ; Gene Regulatory Networks ; }, abstract = {Research organisms provide invaluable insights into human biology and diseases, serving as essential tools for functional experiments, disease modeling and drug testing. However, evolutionary divergence between humans and research organisms hinders effective knowledge transfer across species. Here, we review state-of-the-art methods for computationally transferring knowledge across species, primarily focusing on methods that use transcriptome data and/or molecular networks. Our Perspective addresses four key areas: (1) transferring disease and gene annotation knowledge across species, (2) identifying functionally equivalent molecular components, (3) inferring equivalent perturbed genes or gene sets and (4) identifying equivalent cell types. We conclude with an outlook on future directions and several key challenges that remain in cross-species knowledge transfer, including introducing the concept of 'agnology' to describe functional equivalence of biological entities, regardless of their evolutionary origins. This concept is becoming pervasive in integrative data-driven models in which evolutionary origins of functions can remain unresolved.}, }
@article {pmid41385957, year = {2026}, author = {Zhang, C and Wang, X and Wang, L and Li, P and Bao, Y and Zhang, Z and Jiang, Z and Feng, C and Chen, L}, title = {Multi-omics reveals gut microbiota-mediated environmental adaptation in Mallards and domesticated Shaoxing ducks.}, journal = {Poultry science}, volume = {105}, number = {1}, pages = {106177}, pmid = {41385957}, issn = {1525-3171}, mesh = {Animals ; *Ducks/microbiology/physiology ; *Gastrointestinal Microbiome ; Domestication ; *Adaptation, Physiological ; Cecum/microbiology ; Ileum/microbiology ; *Metabolome ; Metabolomics ; Multiomics ; }, abstract = {Gut microbiota remodeling is a critical component of the domestication syndrome. However, the structural and functional consequences of domestication on gut microbiomes in ducks remain poorly understood. Understanding how domestication and associated ecological transitions influence gut microbial communities can shed light on host adaptation mechanisms. We performed integrated metagenomic and metabolomic analyses of the ileal and cecal microbiota from Mallards and Shaoxing ducks-two ecotypes of Anas platyrhynchos representing wild and domesticated lineages-to investigate microbial community structure, functional capacity, and host-microbe metabolic interactions. Principal coordinates analysis (PCoA) revealed distinct microbial stratification between intestinal compartments (ileum vs. cecum), with domestication-associated divergence observed primarily in the cecum. Metabolomic profiles were relatively stable across both segments and populations. Mallards harbored a more diverse and metabolically versatile gut microbiota, with significant enrichment in pathways related to carbohydrate, amino acid, and vitamin metabolism. The genus Gemmiger emerged as a key functional contributor, supporting branched-chain amino acid biosynthesis, coenzyme activation, and carbohydrate utilization, thus reflecting enhanced metabolic adaptability. In Shaoxing ducks, the gut microbiome was enriched in the glucagon signaling pathway and glucose-regulatory metabolites such as l-carnitine, myo-inositol, and quinate. Butyricicoccus sp017886875 was identified as a candidate taxon associated with glucose homeostasis. Additionally, immune-related pathways, including the NOD-like receptor signaling and antigen processing and presentation, were significantly enriched and linked to Anaerobiospirillum and Parabasalia, respectively. Co-enrichment of anti-inflammatory metabolites suggests the presence of a host-microbiota feedback mechanism that mitigates inflammation while maintaining immune readiness. These findings reveal that gut microbiota contribute to population-specific environmental adaptation in ducks, with distinct microbiome and functional traits associated with domestication history. The study highlights microbiota-mediated host adaptation as a key feature of domestication-related ecological transitions.}, }
@article {pmid41379974, year = {2025}, author = {Edwards, SV and Fang, B and Khost, D and Kolyfetis, GE and Cheek, RG and DeRaad, DA and Chen, N and Fitzpatrick, JW and McCormack, JE and Funk, WC and Ghalambor, CK and Garrison, E and Guarracino, A and Li, H and Sackton, TB}, title = {Multispecies pangenomes reveal a pervasive influence of population size on structural variation.}, journal = {Science (New York, N.Y.)}, volume = {390}, number = {6778}, pages = {eadw1931}, doi = {10.1126/science.adw1931}, pmid = {41379974}, issn = {1095-9203}, mesh = {*Population Density ; Animals ; *Genomic Structural Variation ; DNA Copy Number Variations ; *Evolution, Molecular ; Genome Size ; *Genome ; }, abstract = {Structural variants (SVs) are widespread in vertebrate genomes, yet their evolutionary dynamics remain poorly understood. Using 45 long-read de novo genome assemblies and pangenome tools, we analyze SVs among three closely related species of North American jays (Aphelocoma, scrub-jays) displaying a 55-fold range in effective population size. We find rapid evolution of genome architecture, including ~100-megabase decreases in genome size driven by shifts in complex satellite landscapes. SVs exhibit slightly deleterious dynamics modulated by variant length and population size, with consistent evidence of adaptive fixation only in the largest population. Gene copy number variants exhibit an inverse relationship with population size, indicating strongly deleterious dynamics, with consequences for gene expression. Our long-read dataset and pangenome analysis demonstrate how population size shapes genome complexity.}, }
@article {pmid41378881, year = {2025}, author = {Blin, K and Loureiro, C and Louwen, NLL and Navarro-Muñoz, JC and Gerstmans, H and Robinson, SL and Rutz, A and Reitz, ZL and Doering, DT and van der Hooft, JJJ and Weber, T and Medema, MH and Zdouc, MM}, title = {Strategies for community-sourced biocuration in bioinformatics: a case study on MIBiG 4.0.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {6}, pages = {}, pmid = {41378881}, issn = {1477-4054}, support = {1229222&#xa0;N//Research Foundation-Flanders/ ; PZPGP2_209124/SNSF_/Swiss National Science Foundation/Switzerland ; NNF20CC003558//Novo Nordisk Foundation/ ; DNRF137//Danish National Research Foundation CeMiSt/ ; KICH1.LWV04.21.013/NWO_/Dutch Research Council/Netherlands ; }, mesh = {*Computational Biology/methods ; *Databases, Genetic ; *Multigene Family ; Machine Learning ; *Data Curation/methods ; Genomics ; Biocuration ; }, abstract = {Biocuration is essential to transform molecular sequence data into standardized, machine-readable resources. Such curated datasets enable comparative analysis, predictive modeling, and data integration across bioinformatics platforms. While professional biocuration is resource-intensive and usually limited to institutional settings, community-driven approaches can mobilize large-scale annotation of specialized datasets and are more resilient to disruptions in scientific funding. Here, we present a model for community-powered curation applied to the Minimum Information about a Biosynthetic Gene Cluster (MIBiG) repository. Through a framework of workflows for metadata capture, annotation validation, and contributor coordination, the MIBiG 4.0 initiative recruited 267 scientists across 178 institutions from 33 countries, volunteering an estimated 4000 h of work. These efforts expanded the MIBiG repository by 22% and enhanced its usability in downstream molecular data analyses in comparative genomic analyses, natural product discovery, and machine learning applications. We provide strategies and actionable lessons for adopting this model, supporting the sustainability of curated bioinformatics resources central to nucleic acid research and related fields.}, }
@article {pmid41373816, year = {2025}, author = {Wang, F and Sun, X and Wang, K and Long, B and Li, F and Xie, D}, title = {Physiological and Multi-Omics Insights into Trichoderma harzianum Alleviating Aged Microplastic Stress in Nicotiana benthamiana.}, journal = {International journal of molecular sciences}, volume = {26}, number = {23}, pages = {}, pmid = {41373816}, issn = {1422-0067}, support = {2022GDASZH-2022010110//'GDAS' Project of Science and Technology Development/ ; 0525149001//Innovation Capacity Building Project for Provincial Scientific Research Institutions/ ; 2024A1515030175//Guangdong Basic and Applied Basic Research/ ; }, mesh = {*Nicotiana/microbiology/drug effects/metabolism/genetics/growth &amp; development ; *Stress, Physiological/drug effects ; *Microplastics/toxicity ; *Hypocreales/physiology ; Reactive Oxygen Species/metabolism ; Transcriptome ; Gene Expression Regulation, Plant/drug effects ; *Trichoderma ; Multiomics ; }, abstract = {Microplastics derived from biodegradable PBAT film, widely used in agriculture, pose ecological and biological hazards. This study explores how Trichoderma harzianum T4 mitigates this microplastic-induced stress in Nicotiana benthamiana. Using five experimental setup-control (CK), low/high-dose aged microplastics (MP80/MP320), and their co-treatments with T. harzianum T4 (MP80+T4/MP320+T4), multi-omics analyses reveal the microplastic stress-alleviating mechanisms of T. harzianum T4. Aged microplastics significantly inhibit plant growth, promote reactive oxygen species (ROS) and malondialdehyde (MDA) accumulation, and disrupt metabolic homeostasis. Conversely, T. harzianum T4 activates the plant antioxidant defense system, reducing ROS/MDA levels and upregulating superoxide dismutase (SOD)/peroxidase (POD) activities, and promotes biomass. Transcriptomic analysis shows T. harzianum T4 reverses gene expression patterns disrupted by microplastics, particularly in DNA replication and pentose-glucuronic acid pathways. Metagenomic sequencing indicates T. harzianum T4 restores soil microbial diversity, increases the abundance of Bacteroidota and Myxococcota, downregulates antibiotic resistance genes (e.g., tetA5, MDR), and upregulates carbohydrate-active enzymes (CAZys), thereby enhancing carbon metabolism. In conclusion, T. harzianum T4 alleviates microplastic stress through a tripartite mechanism: activating plant stress-response gene networks, reshaping soil microbial communities, and modulating functional gene expression, offering a promising bioremediation strategy.}, }
@article {pmid41370329, year = {2025}, author = {Damsma, A and Cannon, J and Fink, LK and Doelling, KB and Grahn, JA and Honing, H and Kaplan, T and Large, EW and Bouwer, FL}, title = {Computational modeling of rhythmic expectations: Perspectives, pitfalls, and prospects.}, journal = {PLoS computational biology}, volume = {21}, number = {12}, pages = {e1013798}, pmid = {41370329}, issn = {1553-7358}, mesh = {Humans ; *Computer Simulation ; Computational Biology ; Music ; Learning/physiology ; *Periodicity ; }, abstract = {Rhythmic structure enables precise temporal expectations that are essential to human communication, including speech and music. Computational models have been developed to account for how humans perceive, produce, and learn rhythmic sequences. However, it is unclear how different types of models relate to each other and how they can be evaluated. In this review and perspective, we discuss how three major classes of models-entrainment, probabilistic, and timekeeper models-have been used to study rhythmic expectations. We critically assess each model class in terms of its level of explanation, the rhythmic behaviors it captures, its ability to account for learning and enculturation, and its ability to integrate other features, such as pitch. We show that entrainment, probabilistic, and timekeeper models differ substantially in the aspects of rhythmic expectations they can capture. To move the field forward, we propose that model comparison and integration are crucial. We identify key challenges to this effort, such as the varying nature of the input and output signals and divergent modeling goals. To address these challenges, we arrive at several practical recommendations: to equate input and output signals when comparing models, to consider several model outcomes beyond goodness-of-fit measures in model evaluation, to use model-integration efforts to inform theory building, and to make code and data openly accessible. Ultimately, understanding how models of rhythmic expectations relate, and how features in these models account for behavioral, neural, and cognitive aspects of rhythmic expectations, will deepen our understanding of a core aspect of human behavior.}, }
@article {pmid41369995, year = {2025}, author = {Bouzemlal, H and Hentabli, M and Laidi, M and Laidani, Y and Kouider Amar, M and Ibrir, A and Zhang, J}, title = {Predicting adsorption capacities of pharmaceutical pollutants using chemoinformatics and machine learning techniques.}, journal = {Environmental geochemistry and health}, volume = {48}, number = {1}, pages = {39}, pmid = {41369995}, issn = {1573-2983}, mesh = {Adsorption ; *Machine Learning ; *Water Pollutants, Chemical/chemistry ; *Cheminformatics ; Pharmaceutical Preparations/chemistry ; Neural Networks, Computer ; Support Vector Machine ; }, abstract = {Pharmaceutical pollutants are increasingly recognized as emerging contaminants in aquatic environments. Their persistence, bioactivity, and resistance to conventional treatment processes raise ecological and human health concerns, including the spread of antimicrobial resistance. Adsorption has emerged as a promising polishing step for their removal, but adsorption capacity (Qe, mg/g) varies widely depending on molecular structure and operational conditions, making predictive modeling essential. In this work, we developed machine learning models to predict adsorption capacities for Aspirin, Caffeine, Carbamazepine, Ketoprofen, Sulfamethoxazole, Nimesulide, and Paracetamol using chemoinformatics descriptors derived from SMILES strings and experimental inputs, including equilibrium concentration (Ce), initial concentration (C0), temperature, and contact time. Feature reduction with LassoCV and multicollinearity analysis yielded a compact, chemically interpretable descriptor set. Support Vector Regression (SVR), Extreme Gradient Boosting (XGB), and Artificial Neural Networks (ANN) were optimized with Optuna and evaluated using cross-validation. XGB delivered the best predictive performance (R2 = 0.997, RMSE = 2.62 mg/g), outperforming SVR and ANN. SHAP analysis highlighted the influence of charge-partitioned surface areas and nitro functionalities on adsorption outcomes. The best-performing model was deployed in a Streamlit application, enabling predictions of Qe from SMILES and experimental conditions with built-in applicability-domain checks.}, }
@article {pmid41368505, year = {2025}, author = {Di Leo, D and Nilsson, E and Krinos, A and Pinhassi, J and Lundin, D}, title = {The Nextflow nf-core/metatdenovo pipeline for reproducible annotation of metatranscriptomes, and more.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e20328}, pmid = {41368505}, issn = {2167-8359}, mesh = {*Software ; Reproducibility of Results ; Workflow ; *Transcriptome ; *Computational Biology/methods ; *Molecular Sequence Annotation/methods ; *Metagenomics/methods ; }, abstract = {Metatranscriptomics-the sequencing of community RNA-has become a popular tool in microbial ecology, proving useful for both in situ surveys and experiments. However, annotating raw sequence data remains challenging for many research groups with limited computational experience. Standardized and reproducible analyses are important to enhance transparency, comparability across studies, and long-term reproducibility. To simplify metatranscriptome processing for biologists, and to promote reproducible analyses, we introduce nf-core/metatdenovo, a Nextflow-based workflow. Nextflow pipelines run on different computing platforms, from standalone systems to high-performance computing clusters and cloud platforms (e.g., AWS, Google Cloud, Azure) and use container technology such as Docker or Singularity to reproducibly provision software. Biologists can access the pipeline using either the command line or the Seqera platform, which provides a web browser-based interface to Nextflow pipelines. Collaborating with nf-core ensures high-quality, documented, reproducible workflows. Our nf-core/metatdenovo pipeline adheres to these established standards, enabling FAIR metatranscriptome de novo assembly, quantification, and annotation.}, }
@article {pmid41368214, year = {2025}, author = {Lima, R and Barradas, G and Bermúdez I Badia, S}, title = {Music-induced physiological markers for detecting Alzheimer's disease using machine learning.}, journal = {Frontiers in aging neuroscience}, volume = {17}, number = {}, pages = {1701970}, pmid = {41368214}, issn = {1663-4365}, abstract = {INTRODUCTION: Alzheimer's disease (AD) is characterized by progressive cognitive and emotional decline, highlighting the need for novel, non-invasive biomarkers to aid in early detection, monitoring, and stage-specific interventions. This study investigates music-evoked physiological responses as potential biomarkers of AD and evaluates their translational value using machine learning (ML).<br><br>MATERIALS AND METHODS: A total of 36 AD patients, spanning different severity levels, listened to emotionally evocative musical excerpts while electrodermal activity and facial electromyography (corrugator and zygomaticus muscles) were recorded. Machine learning models were then trained on these signals to classify the presence and severity of AD and to detect residual emotion-specific physiological responses elicited by music.<br><br>RESULTS: Physiological reactivity to music declined with disease progression, with positive emotions eliciting more distinct responses than negative ones. The Random Forest classifier distinguished AD patients from healthy controls with 70.5% accuracy, while the Na&#xef;ve Bayes model predicted severity with 65.6% accuracy, demonstrating that ML models can detect subtle music-evoked physiological differences even in individuals with AD.<br><br>DISCUSSION: Music-evoked physiological signals reflect the hierarchical disruption of emotion-related neural circuits in AD and hold promise as complementary biomarkers for disease presence and stage. When combined with machine learning (ML), these measures provide a non-invasive, ecologically valid approach to support early detection, monitoring, and the development of stage-specific interventions.}, }
@article {pmid41367904, year = {2025}, author = {Pélabon, C and Agudelo-Cantero, GA and Araya Ajoy, YG and Bolstad, GH and Cheng, C and Galis, F and Guillaume, F and Haaland, TR and Hallgrímsson, B and Hansen, TF and Holstad, A and Houle, D and Hunt, G and Isaksen, A and Milocco, L and Mubalegh, N and Nuño de la Rosa, L and Orzack, SH and Porto, A and Reid, JM and Sztepanacz, JL and Undheim, EAB and Villegas, C and Voje, KL and Walling, C and Wright, J}, title = {Evolvability: progress and key questions.}, journal = {Bioscience}, volume = {75}, number = {12}, pages = {1042-1057}, pmid = {41367904}, issn = {0006-3568}, abstract = {Since the 1990s, evolutionary biologists have recognized the importance of explaining the ability of biological systems to evolve and how this ability itself evolves. This recognition of the need to explain evolvability emerged from an awareness that the kind and the amount of heritable variation available for natural selection require explanation. The concept of evolvability is now the focus of many research programs in diverse subdisciplines within evolutionary biology. In the present article, we first review and synthesise progress made in evolvability research. We then present key questions to set an agenda for future research on evolvability, identify challenges to answer these questions, and discuss opportunities to apply results from the evolvability research to conservation biology.}, }
@article {pmid41367046, year = {2025}, author = {Saputra, YA and Armawan, LVA and Lisa, M and Muharramah, DH and Pratiwi, LD}, title = {The Role of Hydrometeorological Factors in Leptospirosis Transmission in Central Java, Indonesia.}, journal = {Journal of preventive medicine and public health = Yebang Uihakhoe chi}, volume = {58}, number = {6}, pages = {553-562}, pmid = {41367046}, issn = {2233-4521}, mesh = {Indonesia/epidemiology ; *Leptospirosis/epidemiology/transmission ; Humans ; Geographic Information Systems ; Humidity ; Temperature ; Linear Models ; Rain ; }, abstract = {OBJECTIVES: This study investigates the relationship between hydrometeorological factors and leptospirosis cases in Central Java to elucidate disease spread patterns.<br><br>METHODS: An ecological study design was utilized, incorporating spatial elements by integrating geographic information systems (GIS) with statistical techniques. The analysis included data on temperature, humidity, rainfall, solar radiation, flooding, and monthly leptospirosis cases recorded from 2018 to 2022. Data sources comprised the Ministry of Health of the Republic of Indonesia, the Meteorology, Climatology, and Geophysics Agency, and the Central Java Provincial Water Resources Management Center. The study employed correlation tests, multiple linear regression, and spatial data visualization.<br><br>RESULTS: Correlation analysis indicated that monthly leptospirosis cases were significantly and positively correlated with minimum temperature (r=0.423; p=0.001), humidity (r=0.589; p<0.001), and rainfall (r=0.413; p=0.001). In contrast, maximum temperature (r=-0.355; p=0.005) and solar radiation (r=-0.431; p=0.001) showed significant negative correlations. Subsequent multiple linear regression showed that higher monthly leptospirosis was associated with higher humidity.<br><br>CONCLUSIONS: The findings offer essential insights for developing a comprehensive, science-based leptospirosis management strategy. A recommended approach is to establish a spatial monitoring system aimed at identifying high-risk areas, especially those with increased humidity and frequent flooding.}, }
@article {pmid41366043, year = {2026}, author = {Abraham, AJ and Hempson, GP and le Roux, E and Maré, C and Taylor, LL and Webster, AB and Duvall, ES and Prys-Jones, T and Coppock, J and Ridenour, C and de Jager, P and Augustine, D and Chapman, CA and Fashing, PJ and Harfoot, MBJ and Holdo, RM and Hopcraft, JGC and Johnson, C and van Langevelde, F and Malhi, Y and Morel, A and Nguyen, N and Owen-Smith, N and Potter, AB and Prins, HHT and Rothman, JM and Swedell, L and Svenning, JC and Thomson, ER and van der Plas, F and Veldhuis, MP and Pringle, RM and Clauss, M and Doughty, CE}, title = {Sodium constraints on megaherbivore communities in Africa.}, journal = {Nature ecology &amp; evolution}, volume = {10}, number = {1}, pages = {105-116}, pmid = {41366043}, issn = {2397-334X}, support = {16-HW16_2-0025//National Aeronautics and Space Administration (NASA)/ ; 18-SLSCVC18-0032//National Aeronautics and Space Administration (NASA)/ ; 101062339//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; }, mesh = {*Herbivory ; Animals ; *Sodium/metabolism/analysis ; Africa South of the Sahara ; Feces/chemistry ; *Mammals/physiology ; *Plants/chemistry/metabolism ; Africa ; Population Density ; }, abstract = {Sodium (Na) is an essential nutrient for animals, but not for most plants. Consequently, herbivores may confront a mismatch between forage availability and metabolic requirement. Recent work suggests that larger-bodied mammals may be particularly susceptible to Na deficits, yet it is unknown whether Na availability constrains the density or distribution of large herbivores at broad scales. Here we show that plant-Na availability varies >1,000-fold across sub-Saharan Africa and helps explain continent-scale patterns of large-herbivore abundance. We combined field data with machine-learning approaches to generate high-resolution maps of plant Na, which revealed multi-scale gradients arising from sea-salt deposition, hydrology, soil chemistry and plant traits. Faecal Na concentration was positively correlated with modelled dietary Na, supporting the prediction that variation in plant Na is a major determinant of herbivore Na intake. Incorporating plant-Na availability improved model predictions of large-herbivore population density, especially for megaherbivore species, which are depressed in very-low-Na regions (<100 mg kg[-1]), consistent with Na limitation. Our study offers an explanation for the scarcity of megaherbivores in parts of Central and West Africa, which has major ecological ramifications given the strong influence of large herbivores on ecosystem functioning and the profound human-induced changes to Na availability in Africa and beyond.}, }
@article {pmid41365954, year = {2025}, author = {González, AL and Merder, J and Andraczek, K and Brose, U and Filipiak, M and Harpole, WS and Hillebrand, H and Jackson, MC and Jochum, M and Leroux, SJ and Nessel, MP and Onstein, RE and Paseka, R and Perry, GLW and Peace, A and Rugenski, A and Sitters, J and Sperfeld, E and Striebel, M and Zandona, E and Mozsár, A and Bluhm, S and Doi, H and Eisenhauer, N and Farjalla, VF and Hood, J and Kratina, P and Lovelock, C and Moody, EK and Pollierer, ME and Potapov, A and Romero, GQ and Roussel, JM and Scheu, S and Scheunemann, N and Seeber, J and Steinwandter, M and Susanti, WI and Tiunov, A and Dézerald, O}, title = {Nitrogen deposition reveals global patterns in plant and animal stoichiometry.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10977}, pmid = {41365954}, issn = {2041-1723}, mesh = {*Nitrogen/metabolism/analysis ; Phosphorus/metabolism/analysis ; *Plants/metabolism/chemistry ; Ecosystem ; Animals ; Temperature ; }, abstract = {The elemental content of organisms links cellular biochemistry to ecological processes, from physiology to nutrient dynamics. While plant stoichiometry is thought to vary with climate and nutrient availability across latitudes, the consistency of these patterns across trophic groups and realms remains unclear. Using the StoichLife database, which includes nitrogen and phosphorus content data for 5443 species across 1390 sites, we examine how solar energy (temperature, radiation) and nutrients (nitrogen and phosphorus) influence stoichiometric variation. We find that plant stoichiometry in terrestrial and freshwater ecosystems is more strongly associated with environmental gradients, particularly nitrogen deposition, than animal stoichiometry. Contrary to expectations, temperature, radiation, and labile P show limited global effects. Latitudinal patterns in stoichiometry are more closely associated with species turnover rather than intraspecific variation. Given the strong links between stoichiometry and organismal performance, these findings underscore the need to predict the ecological consequences of anthropogenic disruption to global biogeochemical cycles.}, }
@article {pmid41360908, year = {2025}, author = {Huang, Y and Han, X and Xia, C}, title = {Assessing the completeness and consistency of global-scale avian datasets.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {1201}, pmid = {41360908}, issn = {2045-2322}, support = {32170491//National Natural Science Foundation of China/ ; }, mesh = {*Birds/physiology/classification ; Animals ; Ecosystem ; *Databases, Factual ; Biodiversity ; Ecology ; }, abstract = {The advancement of ecological research has increasingly focused on comparative methods and global-scale analyses. Birds are frequently selected for such studies for their widespread distribution and sensitivity to environmental changes. Given the need to integrate fragmented avian data, we aim to collect global-scale avian datasets and evaluate the completeness and consistency of them. We reviewed literature published in Springer Nature and American Association for the Advancement of Science (AAAS) from 2020 to 2024 and identified 90 articles with large-scale coverage and broad taxonomic representation. From these, we compiled 123 datasets covering environmental factors, avian traits, and ecosystem-level data. These were categorized into species-level and spatial data for completeness assessment, while consistency was evaluated across three modalities: species lists, nominal variables, and continuous variables. The database encompassed 12 distinct data types, including morphological, physiological, behavioural, and life-history traits, niche characteristics, evolutionary data, and environmental factors. Our assessment revealed that species distribution and abundance data were most frequently utilized in avian research worldwide. Both the species-level and spatial data exhibited high completeness. Continuous variables showed high consistency, whereas nominal variables and species lists exhibited moderate consistency with notable variability. Therefore, the supplementation of low-integrity data such as reproductive and behavioural datasets remains imperative. Systematic reconciliation between legacy and revised avian taxonomic inventories are critical for ensuring the consistency of data. We hope that the work can advance understanding of macroecology and providing guidance for global avian research.}, }
@article {pmid41353493, year = {2025}, author = {Gautam, A and Verma, P and Kushwaha, S and Dubey, S and Bhatt, D and Singh, A and Kalle, R}, title = {Three decades of remote sensing applications in avian ecological studies in India: A review and future directions in avian monitoring.}, journal = {Environmental monitoring and assessment}, volume = {198}, number = {1}, pages = {19}, pmid = {41353493}, issn = {1573-2959}, support = {NTA Ref. No. 200510046214//University Grants Commission/ ; }, mesh = {Animals ; *Birds ; India ; *Remote Sensing Technology ; *Environmental Monitoring/methods ; Ecosystem ; Conservation of Natural Resources ; Geographic Information Systems ; }, abstract = {Remote sensing technology enables broad-scale ecological studies, with birds indicating global changes and validating its data. Despite its global relevance, the integration of remote sensing in ornithological research in India remains limited and fragmented. We conducted extensive literature review on the remote sensing applications in ornithological studies in India from 1992 to 2022 to reorient ornithological research primarily focusing on the existing satellite data, telemetry and GIS tools. The objectives of the review are: (1) to provide an overview of remote-sensing data applications in avian ecological studies, (2) to report the spatiotemporal trends and patterns in the characteristics of remote sensing data (scale, resolution, data source) applied in the studies, and identify the region-specific approaches and (3) to identify the research gaps, improve the methods and propose priority research themes by outlining the future scope of its applications in avian ecology and the conservation efforts as an opportunity to strengthen avian research using remote sensing technology in rapidly changing landscapes. We systematically reviewed literature (N = 108) that related remotely sensed data to bird distribution, abundance assessment, and migration. Our review covered 132 bird species across 19 orders and 5 feeding guilds. Forest birds were more frequently studied than wetland birds, with nearly 50% of the studies focused on single species. Galliformes were the most represented while Falconiformes, Columbiformes, and Ciconiiformes were the least. Studies largely focused on habitat suitability using avian occurrence data (51%) while avian disease outbreak, genetics, and nest site data (each 2%) had least contribution. Our review suggests the need to bridge ecological knowledge gaps using remote sensing and GIS tools through interdisciplinary collaboration among ornithologists, remote sensing experts, and scientists from other allied fields as this can improve data-sharing policies and develop innovative user-friendly products for applications in avian research. Additionally, community participation through citizen science can generate valuable crowd-sourced data for bird conservation and ecosystem management.}, }
@article {pmid41352621, year = {2026}, author = {Kissane, ZM and Warren, KS and Yeap, L and Shephard, JM}, title = {Hazard identification and ecological risk assessment of pesticide exposure in wildlife using GPS telemetry: Case study on endangered Carnaby's Cockatoos.}, journal = {Environmental toxicology and pharmacology}, volume = {121}, number = {}, pages = {104894}, doi = {10.1016/j.etap.2025.104894}, pmid = {41352621}, issn = {1872-7077}, mesh = {Animals ; Risk Assessment ; Endangered Species ; *Pesticides/toxicity/analysis ; Telemetry ; Environmental Monitoring/methods ; Geographic Information Systems ; *Environmental Exposure/analysis ; Animals, Wild ; *Environmental Pollutants/analysis/toxicity ; }, abstract = {Wildlife toxicology faces increasing threats from pesticide use, yet the impacts on biodiversity remain unclear, as current toxicity thresholds often rely on laboratory data that do not reflect environmental exposure. Here we present a two-step methodology integrating ecotoxicology and movement ecology to investigate pesticide exposure in endangered Carnaby's cockatoos (Zanda latirostris). Using GPS telemetry and satellite tracking, this study identified pesticide exposure sites and quantified the likelihood and consequences of exposure. A total of 26 pesticides were detected in forage sources (agricultural seed), with 80 % of seed samples having one or more pesticides detected. The Maximum Residue Limit (MRL) was exceeded for multiple pesticides including imidacloprid, thiamethoxam, clothianidin, difenoconazole and metalaxyl. Results have highlighted the risks that granivorous birds face being exposed to insecticides, herbicides, and fungicides in agroecosystems. This methodology is broad in scope and applicable across species, providing the ecological realism missing in laboratory-based studies.}, }
@article {pmid41350530, year = {2025}, author = {Mottl, O and Gaiser, F and Šímová, I and Flantua, SGA}, title = {VegVault dataset: linking global paleo-, and neo-vegetation data with functional traits and abiotic drivers.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1923}, pmid = {41350530}, issn = {2052-4463}, support = {GN23-06386I//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky (Grant Agency of the Czech Republic)/ ; UNCE/24/SCI/006//Univerzita Karlova v Praze (Charles University)/ ; TMS2022STG03//Universitetet i Bergen (University of Bergen)/ ; }, mesh = {*Climate Change ; *Biodiversity ; *Ecosystem ; *Plants ; *Databases, Factual ; }, abstract = {Understanding the dynamics and persistence of biodiversity patterns over short (contemporary) and long (thousands of years) time scales is crucial for predicting ecosystem changes under global climate and land-use changes. A key challenge is integrating currently scattered ecological data to assess complex vegetation dynamics over time. Here, we present VegVault, an interdisciplinary SQLite database that uniquely integrates paleo- and neo-ecological plot-based vegetation data on a global and millennial scale, directly linking them with functional traits, soil, and climate information. VegVault currently comprises data from BIEN, sPlotOpen, TRY, Neotoma, CHELSA, and WoSIS, providing a comprehensive and ready-to-use resource for researchers across various fields to address questions about past and contemporary biodiversity patterns and their abiotic drivers. To further support the usability of the data, VegVault is complemented by the {vaultkeepr} R package, enabling streamlined data access, extraction, and manipulation. This study introduces the structure, content, and diverse applications of VegVault, emphasizing its potential role in advancing ecological research to improve predictions of biodiversity responses to global climate change.}, }
@article {pmid41350118, year = {2025}, author = {Fukase, S and Kouketsu, A and Tamahara, T and Saito, T and Ito, A and Higashi, Y and Kajita, T and Kurobane, T and Miyakoshi, M and Iikubo, M and Shimizu, R and Takahashi, T and Yamauchi, K and Sugiura, T}, title = {Differences in the Oral Microbiome Between Patients With and Without Oral Squamous Cell Carcinoma.}, journal = {Journal of oral pathology &amp; medicine : official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jop.70099}, pmid = {41350118}, issn = {1600-0714}, abstract = {BACKGROUND: Although studies have demonstrated a relationship between pathogenic microorganisms and oral cancer, no study has demonstrated a relationship between changes in bacterial flora and oral squamous cell carcinoma (OSCC). Therefore, we investigated the association between oral microbiota and oral squamous cell carcinoma using metagenomic analysis.<br><br>METHODS: Saliva samples from 64 patients with OSCC and 50 healthy controls who visited the Department of Oral Surgery, Tohoku University Hospital, were collected, and bacterial genomic DNA was extracted using polymerase chain reaction amplification. Single-end sequencing was performed using the Illumina MiSeq platform, and sequence data were analyzed using the Quantitative Insights Into Microbial Ecology 2 platform. The Steel-Dwass test was used for between-group comparisons, and Analysis of Compositions of Microbiomes with Bias Correction was used to detect significant differences in microbiome composition.<br><br>RESULTS: Significant differences were observed in alpha-diversity indices of bacterial flora (richness, Faith- phylogenetic diversity, Shannon index) in the OSCC group compared to those in the control group. Among the OSCC group, patients with larger tumor diameters and lymph node metastases (T3/T4, N1 or greater) formed independent clusters in the beta diversity analysis of the bacterial flora. Bacteria of the Actinomycetia phylum, such as Actinomyces and Rothia, were significantly reduced in patients with higher stage and pathological grade. Conversely, bacteria of the phylum Spirochaetia and Proteobacteria, particularly those of the genus Treponema, were significantly elevated in advanced cancer cases.<br><br>CONCLUSIONS: Our results suggest that changes in the oral microbiota may play a role in OSCC development and progression.}, }
@article {pmid41348937, year = {2025}, author = {Xu, X and Cai, Z and Jia, W and Cao, Y and Hao, Y and Zhou, X and Liang, A and Lin, Z and Zhuang, S and Zhang, Z and Han, L and Zhao, J and White, JC and Ma, C and Xing, B}, title = {Multiomics Insights into Nanoscale Boron Nitride Mediated Antioxidant Defense and Metabolic Reprogramming in Cucumber in Response to Fusarium Infection.}, journal = {ACS nano}, volume = {19}, number = {50}, pages = {42349-42364}, doi = {10.1021/acsnano.5c14128}, pmid = {41348937}, issn = {1936-086X}, mesh = {*Fusarium/drug effects ; *Antioxidants/metabolism/pharmacology/chemistry ; *Plant Diseases/microbiology ; *Boron Compounds/pharmacology/chemistry ; *Cucumis sativus/metabolism/microbiology/drug effects ; *Nanoparticles/chemistry ; Oxidative Stress/drug effects ; Metabolic Reprogramming ; Multiomics ; }, abstract = {Fusarium poses a significant threat to the global crop productivity and food security. This study evaluated the mechanisms of nanoscale boron nitride (nano-BN, 0-500 mg/kg) against Fusarium oxysporum in cucumber. Fusarium infection severely impaired plant growth with biomass declining by 60%. However, 50 mg/kg nano-BN treatment significantly increased shoot biomass by 64.9% compared to disease controls, restoring photosynthetic parameters to near-healthy levels. Nano-BN inhibited Fusarium proliferation by disrupting hyphal and spore structures and reduced mycotoxin production (beauvericin and enniatin) by over 63%. Metabolomic analysis demonstrates that nano-BN mitigated oxidative stress by enhancing glutathione metabolism, with significant increases in glutathione and ascorbic acid content by 166.67% and 478.78%, respectively. Importantly, the protein-protein interaction network shows that nano-BN counteracted Fusarium-induced suppression of ribosomal proteins and endoplasmic reticulum stress-related proteins, promoting protein synthesis and folding. The coexpression network identified sucrose and geshoidin as key metabolites linked to ribosomal and mitochondrial proteins, bridging metabolic resilience with enhanced disease resistance. Multiomics analysis suggests that nano-BN alleviated the Fusarium stress by regulating the phenylpropanoid biosynthesis and restoring the expression levels of key enzymes in carbohydrate metabolism. Overall, nano-BN effectively mitigates Fusarium stress by enhancing plant growth and modulating metabolic processes, offering a promising strategy for plant protection.}, }
@article {pmid41348921, year = {2025}, author = {Ammar, M and Fogarty, L and Kandler, A}, title = {Memory, innovation and vertical learning.}, journal = {PLoS computational biology}, volume = {21}, number = {12}, pages = {e1013785}, pmid = {41348921}, issn = {1553-7358}, mesh = {Humans ; *Memory/physiology ; *Learning/physiology ; *Social Learning/physiology ; Computer Simulation ; Computational Biology ; Animals ; Cultural Evolution ; }, abstract = {One of the most controversial and actively debated questions about both human and non-human animal culture concerns its relationship with adaptation - under what circumstances might we expect culture, and the ability to learn socially from others, to be beneficial, and favored by natural selection? Existing theory posits that the benefit of social learning depends on the rate at which the environment changes, and recent work has shown that this relationship is mediated by how much information an individual can retain over time - by memory. Based on extensive ethnographic research, vertical learning-social learning from parent to offspring-appears to be an extremely salient and important type of social learning. Here we develop large-scale agent-based simulation models to investigate the evolutionary relationship between vertical social learning in particular and the memory and retention of cultural information. We show that the benefit of vertical learning depends on how quickly those information is forgotten and on the exact way in which individuals innovate. This work points to the importance of a complex interplay between the size of cultural repertoires, the benefits of cultural preservation, changing selective environments, and the mechanism of innovation - none of which can be fully understood in isolation.}, }
@article {pmid41348596, year = {2025}, author = {Hernández-Velázquez, R and Ziemski, M and Bokulich, NA}, title = {ViromeXplore: integrative workflows for complete and reproducible virome characterization.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {6}, pages = {}, pmid = {41348596}, issn = {1477-4054}, support = {22.00210//Swiss State Secretariat for Education, Research and Innovation/ ; //European Union nor European Research Executive Agency/ ; }, mesh = {*Virome ; *Workflow ; *Metagenomics/methods ; *Software ; High-Throughput Nucleotide Sequencing ; *Computational Biology/methods ; *Viruses/genetics/classification ; Metagenome ; Microbiota ; Genome, Viral ; Reproducibility of Results ; }, abstract = {Viruses play a crucial role in shaping microbial communities and global biogeochemical cycles, yet their vast genetic diversity remains underexplored. Next-generation sequencing technologies allow untargeted profiling of metagenomes from viral communities (viromes). However, existing workflows often lack modularity, flexibility, and seamless integration with other microbiome analysis platforms. Here, we introduce "ViromeXplore," a set of modular Nextflow workflows designed for efficient virome analysis. ViromeXplore incorporates state-of-the-art tools for contamination estimation, viral sequence identification, taxonomic assignment, functional annotation, and host prediction while optimizing computational resources. The workflows are containerized using Docker and Singularity, ensuring reproducibility and ease of deployment. Additionally, ViromeXplore offers optional integration with QIIME 2 and MOSHPIT, facilitating provenance tracking and interoperability with microbiome bioinformatics pipelines. By providing a scalable, user-friendly, and computationally efficient framework, ViromeXplore enhances viral metagenomic analysis and contributes to a deeper understanding of viral ecology. ViromeXplore is freely available at https://github.com/rhernandvel/ViromeXplore.}, }
@article {pmid41346809, year = {2025}, author = {Castillo-Neyra, R and Díaz, EW and Bellotti, BR and Morucci, K and De la Puente-León, M and Ortiz-Cam, L and Levy, MZ}, title = {Cave dogs around major urban areas of Arequipa, Peru, threaten rabies elimination program.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1649737}, pmid = {41346809}, issn = {2297-1769}, support = {D43 TW012741/TW/FIC NIH HHS/United States ; K01 AI139284/AI/NIAID NIH HHS/United States ; }, abstract = {BACKGROUND: In the city of Arequipa, Peru, the government has implemented control measures against dog rabies virus since the detection of its reintroduction in 2015. The city was previously considered free of animal reservoirs, except for free-roaming owned dogs, animals with identifiable owners but allowed to move unsupervised, and stray dogs, which include both abandoned and street-born dogs that roam freely while relying on human settlements for food, within its urban boundaries. However, multiple reports from peri-urban residents have suggested the presence of feral dogs, a population living independently of humans on the city's outskirts. We aim to document the presence and dietary patterns of feral dogs adjacent to the city margins.<br><br>METHODS: We conducted monthly field visits to four peri-urban localities in eastern Arequipa, an area where the presence of feral dogs had been previously reported. Dog caves were identified by tracking footprints and other field signs left by dogs, and their locations were georeferenced. Each cave was revisited monthly three times to record the presence of live and dead dogs, and puppies. Fecal samples collected around the caves were analyzed to assess dietary patterns.<br><br>RESULTS: We observed that feral dogs use caves for resting, hiding, and reproduction-some of which appear to be constructed by the dogs themselves. The high number of puppies and dead adult dogs indicates a high population turnover. Dietary analysis revealed that these dogs feed on local fauna, including birds, rodents, cats, sheep, and, notably, other dogs.<br><br>CONCLUSIONS: These unowned, cave-dwelling dogs are not reached by mass rabies vaccination or sterilization programs. Moreover, they exist outside the jurisdiction of health inspectors responsible for rabies surveillance, resulting in a lack of data on rabies infection in this subpopulation. Our findings highlight the need for integrated One Health strategies to address the potential challenges posed by feral dog populations in rabies elimination efforts.}, }
@article {pmid41346804, year = {2025}, author = {Morucci, K and Ortiz Cam, L and Diaz, EW and Porras-Cotrina, G and Bustos, J and Verastegui, M and Gavidia, CM and Castillo-Neyra, R}, title = {GPS tracking of free-roaming dogs and human spillover risk of Echinococcus granulosus in highly endemic Peru.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1647590}, pmid = {41346804}, issn = {2297-1769}, abstract = {INTRODUCTION: Cystic echinococcosis (CE), a neglected disease that results from infection with the larval stage of the Echinococcus granulosus sensu lato (s.l.) tapeworm, poses significant zoonotic risk to humans and is a persistent threat in developing agricultural communities around the world. While the prevalence of human CE in the central highlands of Peru has previously been estimated around 5-7%, true prevalence is likely higher given the protracted period of asymptomatic disease, reduced medical access of at-risk populations, increased contact between herders, livestock, and herding dogs, and poor understanding of local disease epidemiology. To beIer understand CE epidemiology in a highly endemic region of Peru, we studied the movement of free-roaming dogs in the community of Chanchayllo, Junin, Peru.<br><br>METHODS: We performed copro-ELISA to identify E. granulosus s.l. positive dogs, tracked the ranging behavior and calculated home ranges of 19 owned, free-roaming dogs to understand the movement of the definitive host of E. granulosus s.l. on the landscape. Specifically, we investigated the spatial association between E. granulosus-infected dog home ranges and proximity to their owners' houses and a local slaughterhouse.<br><br>RESULTS: Echinococcus granulosus s.l. infection prevalence was alarmingly high in our canine population, with 85% positivity (binomial exact 95% CI: 62.1-96.8%). All dog home ranges overlapped with their owners' households, and notably, even negative dog households overlapped with nearby positive dog home ranges.<br><br>DISCUSSION: These data suggest that widespread environmental contamination of E. granulosus s.l. egg-containing feces may be a significant driver of locally elevated disease prevalence in human populations. We use our findings to understand the local disease ecology of CE in free roaming dogs, assess pillover risk, and guide future intervention strategies aimed at reducing human cases. Our findings suggest that existing trategies delivering anthelmintic drugs to individual households have the potential to reduce spillover of E. granulosus s.l.}, }
@article {pmid41345722, year = {2025}, author = {Bridgen, JRE and Jewell, C and Lewis, JM and Todd, S and Semple, MG and Feasey, N and Read, JM}, title = {Model-based methods for hospital infection prevention and control: potential and challenges.}, journal = {BMC global and public health}, volume = {3}, number = {1}, pages = {111}, pmid = {41345722}, issn = {2731-913X}, }
@article {pmid41345546, year = {2025}, author = {Marko, &#x160; and Rusinko, A and Barka, M and Balogová, M and Rubáčová, L and Papežík, P}, title = {Snakes among citizens: distribution and ecology of the Aesculapian snake, Zamenis longissimus (Laurenti, 1768) in Bratislava revealed by citizen science.}, journal = {BMC ecology and evolution}, volume = {25}, number = {1}, pages = {136}, pmid = {41345546}, issn = {2730-7182}, mesh = {Animals ; *Animal Distribution ; Cities ; *Citizen Science ; *Colubridae ; Datasets as Topic ; *Ecosystem ; Slovakia ; *Social Media ; Humans ; }, abstract = {BACKGROUND: Urban environments are increasingly recognized as important habitats for wildlife, yet information on how reptiles use urban environments remains scarce. The Aesculapian snake (Zamenis longissimus), a non-venomous colubrid widespread in Central Europe, is considered a habitat generalist with a frequent association with human settlements. However, data on its occurrence and ecology in metropolitan areas are limited. To address this gap, we implemented a citizen science initiative in Bratislava, Slovakia, aiming to document the distribution and habitat use of the Aesculapian snake and to evaluate the potential and limitations of citizen science for reptile monitoring in urban environments.<br><br>RESULTS: Between April 2019 and October 2022, a citizen science initiative was implemented to monitor the distribution and ecology of the Aesculapian snake in Bratislava, Slovakia. The project relied primarily on social media, which proved to be the most effective channel for data collection, complemented by direct e-mail submissions. Altogether, volunteers provided 588 verified records of the focal species, alongside 184 misidentified observations of other native reptiles, most frequently Natrix spp. Spatial analyses showed that most observations of the Aesculapian snake in Bratislava were concentrated in natural and semi-natural areas at lower elevations below 300&#x2009;m a.s.l., with a few records above 500&#x2009;m. Within these areas, snakes were most often reported from built-up and forested land cover, while agricultural land yielded comparatively few sightings. Seasonal patterns indicated a pronounced peak in spring and early summer, while diurnal activity was dominated by midday and afternoon observations. Specifically, the number of reports declined with increasing urbanization intensity but was higher in more densely populated areas, reflecting both ecological patterns and the availability of observers.<br><br>CONCLUSION: This study delivers one of the most comprehensive datasets on the Aesculapian snake in an urban setting, highlighting its synanthropic behavior and frequent use of anthropogenic habitats. At the same time, the results underscore both the opportunities and inherent biases of citizen science, confirming its value as a complementary tool for monitoring reptile populations in metropolitan environments.}, }
@article {pmid41345410, year = {2025}, author = {Gómez-Suárez, M and Laeseke, P and Seebens, H}, title = {A global dataset of native and alien distributions of alien species.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1914}, pmid = {41345410}, issn = {2052-4463}, support = {521530235//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 521530235//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 521529463//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {*Introduced Species ; Animals ; }, abstract = {Biological invasions have been identified as a major threat to nature with far-reaching consequences also for human-wellbeing. Mitigating and preventing further impacts requires knowledge about the origins of alien species and their spread dynamics. While several new datasets have been published recently about alien species distributions, information about their native ranges is scarce and scattered. Here, we present a comprehensive dataset of the regions of origin and introduction of alien species worldwide. We accessed multiple global datasets of species distributions to compile, harmonize and integrate data of alien species distributions and their native ranges. Building on previous efforts, we advanced an existing workflow to allow full reproducibility and transparency in creating the dataset. The final dataset contains 427,956 records including alien distributions of 39,700 species and native distributions of 21,345 alien species in 289 regions worldwide. This dataset provides a solid foundation for analyses of alien species flows, the identification of new emerging alien species and the management of biological invasions through prioritizing major routes of spread.}, }
@article {pmid41345123, year = {2025}, author = {Tucker, SJ and Füssel, J and Freel, KC and Kiefl, E and Freel, EB and Ramfelt, O and Sullivan, CES and Gajigan, AP and Mochimaru, H and de Souza, MR and Quinn, M and Ratum, C and Tran, LL and Sobczyk, M and Miller, SE and Trigodet, F and Lolans, K and Morrison, HG and Fallon, B and Huettel, B and Pan, T and Rappé, MS and Eren, AM}, title = {A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA transcripts.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1913}, pmid = {41345123}, issn = {2052-4463}, support = {687269//Simons Foundation/ ; 989028//Simons Foundation/ ; 989028//Simons Foundation/ ; 2019589//NSF | GEO | Division of Ocean Sciences (OCE)/ ; }, mesh = {Ecosystem ; *Metagenome ; Microbiota ; Pacific Ocean ; *RNA, Transfer/genetics ; *Seawater/microbiology ; *Transcriptome ; Datasets as Topic ; }, abstract = {The roles of marine microbes in ecosystem processes are inherently linked to their ability to sense, respond, and ultimately adapt to environmental change. Capturing the nuances of this perpetual dialogue and its long-term implications requires insight into the subtle drivers of microbial responses to environmental change that are most accessible at the shortest scales of time. Here, we present a multi-omics dataset comprising surface ocean metagenomes, metatranscriptomes, tRNA transcripts, and biogeochemical measurements, collected every 1.5 hours for 48 hours at two stations within coastal and adjacent offshore waters of the tropical Pacific Ocean. We expect that this integrated dataset of multiple sequence types and environmental parameters will facilitate novel insights into microbial ecology, microbial physiology, and ocean biogeochemistry and help investigate the different mechanisms of adaptation that drive microbial responses to environmental change.}, }
@article {pmid41345120, year = {2025}, author = {Abad-Recio, IL and Rubel, V and Filker, S and Garate, L and Stoeck, T and Logares, R and Lanzén, A}, title = {The Basque Coast Estuarine Sediment Gene Catalogue.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1909}, pmid = {41345120}, issn = {2052-4463}, support = {Fi 2089/3-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; STO 414/19-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {Archaea/genetics ; Bacteria/genetics ; Biodiversity ; Ecosystem ; *Estuaries ; Eukaryota/genetics ; *Geologic Sediments/microbiology ; Metagenomics ; Viruses/genetics ; Datasets as Topic ; }, abstract = {Estuaries are critical transition zones that link marine, riverine, and terrestrial ecosystems, including habitats like intertidal mudflats and tidal marshes. These ecosystems are biodiversity hotspots providing essential ecological functions such as nutrient cycling and pollutant removal. Despite their importance, there is a significant knowledge gap regarding the ecological functioning of these habitats and how they are impacted by anthropogenic pressures. From intertidal estuarine benthos along the Basque Coast 92 microbial metagenomic assemblies were retrieved that allowed us to reconstruct 390 medium plus 81 high quality MAGs, along with 108 million putative genes from bacteria, archaea, eukaryotes, and viruses. This unique dataset will enhance our understanding of ecosystem functioning, biodiversity, and be useful to reveal biogeochemical processes and the role of unculturable biomass.}, }
@article {pmid41344766, year = {2026}, author = {Zhang, L and Zhang, Y and Huang, J and Zhou, R and Wu, C}, title = {A synthetic microbial community enhances flavor and safety in reduced-salt soy sauce fermentation: Multi-omics insights into microbial stabilization and metabolic regulation.}, journal = {Food microbiology}, volume = {135}, number = {}, pages = {104974}, doi = {10.1016/j.fm.2025.104974}, pmid = {41344766}, issn = {1095-9998}, mesh = {Fermentation ; *Soy Foods/microbiology/analysis ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; *Sodium Chloride/metabolism/analysis ; *Microbial Consortia ; Flavoring Agents/metabolism ; Taste ; Food Microbiology ; *Microbiota ; Multiomics ; }, abstract = {Reducing sodium in soy sauce fermentation while preserving flavor and safety presents significant technical challenges. To address this, we constructed a synthetic microbial community (SynMC) comprising Tetragenococcus halophilus T10, Zygosaccharomyces rouxii QH-25, and Wickerhamiella versatilis CGMCC 3790 for reduced-salt fermentation (13 %NaCl). Multi-omics analysis revealed three coordinated improvements: First, microbial community stabilization through suppression of spoilage taxa (e.g., Millerozyma) and enrichment of functional genera (e.g., Wickerhamiella), reducing negative ecological correlations from 5.3 % to 1.7 % compared to the low-salinity control group. Second, metabolic restructuring enhanced characteristic aromas while reducing biogenic amines (BAs) to 21.98 mg/L (76 % lower than L group). Third, metatranscriptomics identified upregulated amino acid metabolism (238 % more BA-degrading enzymes) and carbohydrate utilization pathways. These synergistic effects indicate that strategic microbial consortia design can overcome the salt reduction challenge through targeted ecological and metabolic regulation, enabling industrial-scale production of superior, safer low-salt soy sauce.}, }
@article {pmid41343702, year = {2025}, author = {Oba, T and Moriishi, C and Takano, K and Katahira, K and Kimura, K}, title = {Mobile-Based Ecological Momentary Intervention for Improving Physical Activity in Adults Without Regular Physical Activity: Pilot Randomized Controlled Trial.}, journal = {JMIR formative research}, volume = {9}, number = {}, pages = {e79360}, pmid = {41343702}, issn = {2561-326X}, mesh = {Humans ; Pilot Projects ; Female ; Male ; *Ecological Momentary Assessment ; *Exercise/psychology/physiology ; Adult ; Middle Aged ; Japan ; *Mobile Applications ; *Health Promotion/methods ; Fitness Trackers ; Health Behavior ; Heart Rate ; Feasibility Studies ; }, abstract = {BACKGROUND: The ecological momentary intervention (EMI) is one of the most promising digital-primarily mobile-interventions to enhance physical activity (PA) and other health behaviors. It is a combination of ecological momentary assessment (EMA), in which participants are prompted to indicate their momentary states and ongoing behaviors in daily life, and the just-in-time delivery of interventions tailored to the EMA responses. The EMI has typically been implemented in message-based interventions (eg, activity recommendations tailored to users' physical locations), but its efficacy and feasibility have not been sufficiently established because of the variability in design and implementation.<br><br>OBJECTIVE: This pilot, two-arm, parallel-group randomized controlled trial aimed to be an exemplar of EMI for improving PA and establishing efficacy and feasibility among adults without a habit of PA.<br><br>METHODS: A total of 40 participants (23 women; mean age 45.40, SD 10.50 years) were recruited from among community dwellers in northeast Japan and randomly allocated to the EMI or control group. Each participant wore an activity tracker to monitor their daily step count and heart rate (HR) for 4 weeks (fully automated). Simultaneously, they responded to EMA questions about the current weather, location, and social context 3 times during the daytime and an additional evening question about motivations for PA each day. Only the EMI group received messages tailored to their responses to EMA, recommending more active alternative behaviors suited to EMA-reported contexts.<br><br>RESULTS: Participants wore a Fitbit device for 90.3% (21.66/24 hours per day) of the study period (mean 90.3, SD 10.0), and no dropouts were observed. The EMI group showed no significant improvement in the self-reported amount of PA (P=.44), step count (P=.24), or motivation for PA (from P=.11 to P=.91) compared with the control group. However, the EMI group showed a significantly larger increase in the minutes of 40% HR reserve, a measure of moderate or high intensity of PA (mean 16.03, 95% CI 3.76-28.29; Cohen d=0.20-0.41; P=.02 for the follow-up weeks). The intervention was rated as marginally useful and satisfactory, and approximately half of the participants expressed a willingness to continue the intervention. The timing of the EMA prompting was considered inappropriate.<br><br>CONCLUSIONS: These findings suggest that the EMI with messages tailored to EMA-reported contexts was not effective in increasing the amount or motivation for PA but may increase the intensity as assessed by the HR. The intervention aimed to help individuals implement small but slightly more active behaviors in their daily routine, which may not accompany prominent body movements but may be reflected in the increased HR. Marginal feasibility indicates that the intervention has sufficient scope for improvement, particularly in terms of prompt timing.}, }
@article {pmid41343618, year = {2025}, author = {Athreya, GS and Gokhale, CS and Verma, P}, title = {Coexistence rules for small, antagonistically interacting microbial communities.}, journal = {PLoS computational biology}, volume = {21}, number = {12}, pages = {e1013763}, pmid = {41343618}, issn = {1553-7358}, mesh = {*Microbiota/physiology/drug effects ; Anti-Bacterial Agents/pharmacology/metabolism ; *Microbial Interactions/physiology ; *Microbial Consortia/physiology/drug effects ; Biodiversity ; Computational Biology ; *Models, Biological ; Computer Simulation ; }, abstract = {The coexistence of diverse microbial communities despite the common presence of antimicrobial weapons presents a fundamental puzzle in ecology. To address this issue, we investigate the role of antibiotic-mediated interactions in driving microbial diversity using methods from graph theory and theoretical ecology. Our exhaustive analysis of small interaction graphs involving antibiotic production, resistance, and degradation reveals that two factors together determine whether an interaction pattern can support coexistence or not: a certain producer-sensitive-degrader (PSD) motif is critical, and a form of cyclicity between the action of different antibiotics is necessary. Using individual-based simulations, we also explore the role of the PSD motif in spatially structured populations and demonstrate that community coexistence is robust over a wide range of antibiotic and degrader diffusivities. Our findings provide a deeper understanding of the interaction patterns that drive diversity in complex microbial communities. Specifically, we emphasize how antagonism does not preclude biodiversity. These results offer clear pathways for cultivating synthetic microbial consortia, enabling the design of more effective strategies for manipulating microbial communities.}, }
@article {pmid41340097, year = {2025}, author = {Wang, L and Zhou, N and Jaffe, NM and Pidvirny, K and Tierney, AO and Fisher, HB and Morfini, F and Forbes, EE and Pizzagalli, DA and Cai, T and Webb, CA}, title = {Multimodal prediction of future depressive symptoms in adolescents.}, journal = {BMC psychiatry}, volume = {26}, number = {1}, pages = {21}, pmid = {41340097}, issn = {1471-244X}, support = {K23 MH108752/MH/NIMH NIH HHS/United States ; P50 MH119467/MH/NIMH NIH HHS/United States ; P50MH119467/MH/NIMH NIH HHS/United States ; K23MH108752/MH/NIMH NIH HHS/United States ; }, abstract = {BACKGROUND: Depression rates surge during adolescence. Early identification of youth at increased risk for depression is crucial for timely intervention and, ideally, prevention. This study aims to improve the prediction of future depressive symptoms in adolescents by using a multimodal approach that integrates relevant clinical, demographic, behavioral, and neural characteristics.<br><br>METHODS: 103 adolescents (ages 12&#x2013;18; 72.8% female) underwent a baseline assessment including self-report questionnaires, ecological momentary assessment, a clinical interview, and behavioral and neural measures of reward responsiveness. We used nested cross-validation to compare machine learning approaches as well as conventional linear regression in predicting depressive symptoms (Center for Epidemiological Studies Depression Scale [CES-D] and the Mood and Feelings Questionnaire [MFQ]) at a 3-month follow-up.<br><br>RESULTS: For the prediction of CES-D depression scores, the best performing model was a multivariable linear regression using as predictors five principal component scores from a principal component analysis of baseline variables (RMSE&#x2009;=&#x2009;6.501, R[2]&#x2009;=&#x2009;0.688). For the MFQ, the best performing model was a univariable linear regression with baseline MFQ scores as the sole predictor (RMSE&#x2009;=&#x2009;8.054, R[2]&#x2009;=&#x2009;0.671). A factor analysis revealed that items assessing melancholic features were most predictive of future depressive symptoms.<br><br>CONCLUSION: More complex machine learning approaches did not outperform regression in predicting future depressive symptoms. The integration of relevant multimodal predictors reveals which adolescent characteristics (e.g., melancholic features and physical anxiety) have a larger contribution to predicting short-term future depressive symptoms. Future studies are needed with larger sample sizes and longer follow-up periods to provide a more comprehensive test of such models.<br><br>CLINICAL TRIAL NUMBER: Not applicable.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12888-025-07665-8.}, }
@article {pmid41339692, year = {2025}, author = {Hmidi, S and Cassir, N and Colson, P and Ruimy, R and Chaudet, H}, title = {Haemophilus influenzae and Staphylococcus aureus population shifts during social distancing as monitored by MALDI-TOF MS.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {920}, pmid = {41339692}, issn = {2045-2322}, mesh = {Humans ; *Staphylococcus aureus/isolation &amp; purification ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; *Haemophilus influenzae/isolation &amp; purification ; *COVID-19/epidemiology/virology/prevention &amp; control ; *Staphylococcal Infections/epidemiology/microbiology ; SARS-CoV-2/isolation &amp; purification ; *Haemophilus Infections/epidemiology/microbiology ; Physical Distancing ; }, abstract = {The COVID-19 pandemic prompted widespread public health interventions, including lockdowns and social distancing measures, which influenced microbial transmission dynamics. This study evaluates the evolution of the hospital incidence and spectral diversity of Haemophilus influenzae and Staphylococcus aureus associated with these measures using MALDI-TOF mass spectrometry-based epidemiological surveillance. MALDI-TOF MS spectra analyses of routine clinical bacterial identifications were used as proxies for strain typing. Spectra from lockdown and reference periods were compared using unsupervised classification methods. A total of 251 main spectrum profiles of H. influenzae, 2079 main spectrum profiles of S. aureus for respiratory tract and blood samples, and 414 main spectrum profiles for skin samples of S. aureus were examined. The data were analyzed using hierarchical clustering and binary discriminant analysis. Spectral diversity of H. influenzae showed a transient shift, reverting to pre-lockdown patterns by 2021, whereas S. aureus exhibited a spectral shift that persisted post-lockdown. Clustering analyses revealed statistically significant grouping of lockdown strains, suggesting selection pressures due to containment measures. Social distancing measures were associated with modifications in bacterial population structures, with distinct post-lockdown recovery patterns. MALDI-TOF MS fingerprints proved to be a valuable tool for real-time epidemiological surveillance. This full-size experiment of social distancing highlights the complex interactions involving human behavior, bacterial ecology, and population dynamics and suggests different effects for different bacterial species.}, }
@article {pmid41339657, year = {2025}, author = {Yao, G and Cai, X and Liu, J and Ding, S and Chen, X and Lin, C and Li, X and Yang, D}, title = {Chromosome-level genome assembly of Anastoechus asiaticus (Diptera: Bombyliidae).}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {10}, pmid = {41339657}, issn = {2052-4463}, support = {31970435//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32300372//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; *Chromosomes, Insect ; *Diptera/genetics ; *Genome, Insect ; Molecular Sequence Annotation ; Datasets as Topic ; }, abstract = {The genus Anastoechus plays a crucial role in ecosystems, functioning both as a pollinator and as a natural enemy, with its larvae parasitizing grasshopper egg masses and adults visiting flowers. Despite its ecological significance, research on Anastoechus remains limited. In this study, we present a chromosomal-level genome assembly of Anastoechus asiaticus, utilizing BGI sequencing, PacBio sequencing and High-throughput chromosome conformation capture (Hi-C) technology. This represents the first genomic data for the genus Anastoechus, with a final genome size of 512.14 Mb and a scaffold N50 of 82.71 Mb. Genome annotation identified 12,751 protein-coding genes, of which functional annotations are available for 11,305. Additionally, non-coding RNA annotation revealed 1,753 tRNAs, 56 miRNAs, 79 rRNAs, and 49 snRNAs. Repetitive elements account for 290.64 Mb, constituting 56.75% of the genome. This high-quality genome provides valuable data for future studies on population genetics, ecological adaptation, and the evolution of Bombyliidae and other related insect groups.}, }
@article {pmid41339386, year = {2025}, author = {Camilo Fagua, J and Jantz, P and Burns, P and Jantz, SM and Kilbride, JB and Goetz, SJ}, title = {Maps of forest vertical structure for Colombia, a megadiverse country.}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {1}, pmid = {41339386}, issn = {2052-4463}, mesh = {Colombia ; *Forests ; Ecosystem ; }, abstract = {Vegetation vertical structure refers to the 3D distribution of vegetation aboveground biomass. Vegetation vertical structure of tropical forests influences other ecological and environmental variables that are essential for the functioning of the ecosystems. Integrating over 5.9 million Globel Ecosystem Dynamics Investigation (GEDI) LiDAR (Light Detection and Ranging) footprints, multispectral, and synthetic aperture radar (SAR) imagery, we built five national maps at 25 m resolution of five forest structural metrics for Colombia, South America, for the year 2020. We mapped canopy height, the height of half the cumulative returned energy from GEDI (RH50), total canopy cover, foliage height diversity, and total plant area index. The resulting maps tended to have the highest errors in the Amazon and Andean regions. Total cover had the highest relative error. Interrelationship curves between forest structural metrics of GEDI footprints are maintained across mapped metrics, indicating that the predictive models preserve structural relationships observed in GEDI data. Due to the medium-high spatial resolution and national coverage of the forest structural maps presented in this work, these maps will be useful for evaluating and mapping other ecological variables and conservation priorities in Colombia.}, }
@article {pmid41337153, year = {2025}, author = {Mustri, MP and Duan, Q and Pawar, S}, title = {Accuracy of the Lotka-Volterra model fails in strongly coupled microbial consumer-resource systems.}, journal = {PLoS computational biology}, volume = {21}, number = {12}, pages = {e1013719}, pmid = {41337153}, issn = {1553-7358}, mesh = {*Models, Biological ; Computational Biology ; *Microbial Interactions/physiology ; Ecosystem ; *Microbiota/physiology ; Computer Simulation ; }, abstract = {The generalized Lotka-Volterra (GLV) model is a cornerstone of theoretical ecology for modeling the dynamics emerging from species interactions within complex ecological communities. The GLV is also increasingly being used to infer species interactions and predict dynamics from empirical data on microbial communities, in particular. However, despite its widespread use, the accuracy of the GLV's pairwise interaction structure in capturing the unseen dynamics of microbial consumer-resource interactions-arising from resource competition and metabolite exchanges-remains unclear. Here, we rigorously quantify how well the GLV can represent the dynamics of a general mathematical model that encapsulates key consumer-resource processes in microbial communities. We find that the GLV significantly misrepresents the feasibility, stability, and reactivity of microbial communities above a threshold biologically feasible level of consumer-resource coupling, because it omits higher-order nonlinear interactions. We show that the probability of the GLV making inaccurate predictions can be quantified by a simple, empirically accessible measure of timescale separation between consumers and resources. These insights advance our understanding of the temporal dynamics of resource-mediated microbial interactions and provide a method for gauging the GLV's reliability across various empirical and theoretical scenarios.}, }
@article {pmid41335619, year = {2025}, author = {Yoshimura, M and Suwabe, M and Tsuji, K and Baba, Y and Kakazu, H and Miyagi, T and Ogasawara, M and Uematsu, J and Economo, EP and Ono, K}, title = {Maximum effect with minimum impact: A new selective control strategy for the Browsing ant Lepisiota frauenfeldi (Formicidae: Formicinae) minimize the impact on non-target species.}, journal = {PloS one}, volume = {20}, number = {12}, pages = {e0337230}, pmid = {41335619}, issn = {1932-6203}, mesh = {Animals ; *Ants/physiology ; *Introduced Species ; Japan ; *Insect Control/methods ; Biodiversity ; Ecosystem ; }, abstract = {Early-stage control of invasive ants provides an opportunity to suppress establishment while conserving existing biodiversity. We developed and tested a selective control strategy targeting the Browsing ant Lepisiota frauenfeldi, an emerging omnivorous, polygynous, and polydomous invader, during its initial establishment in an urban area of Okinawa Island, Japan. Because the local ant community was still present when the invasion was detected, the trial aimed at reducing the competitive advantage of the target species while preserving biotic resistance from resident species. We hypothesized that weakening L. frauenfeldi through selective chemical treatment would allow existing species to occupy its vacant niches, thereby accelerating eradication. Species-specific baits were formulated using a growth regulator with protein- and carbohydrate-based substrates. Baits were placed near nest entrances identified through monthly surveys over an area of approximately 1.6 hectares. Ant community dynamics were monitored for 44 months using hand-collection and sticky-trap surveys. The invasive ant showed a strong negative response to treatment, with an estimated 92% reduction in occurrence probability, ultimately disappearing from the treated area. Several non-target ant species increased in frequency, consistent with expectation of the niche reoccupation, while most other species remained stable, indicating minimal impact on the broader community. Compared to conventional methods, this approach used drastically less chemical while achieving high efficacy. Implementation through cross-organizational collaboration enabled parallel treatment in adjacent restricted areas and contributed to the program's success. These results highlight the practical and ecological value of nest-targeted, community-collaborative selective baiting as a strategy for managing omnivorous invasive ants during early establishment.}, }
@article {pmid41331158, year = {2025}, author = {Castellano, S and Clarke, M and D'Acunto, L and Romañach, S and Cadaval, S}, title = {Restoring the Florida Everglades: Insights on Integrating Sea Level Rise into Decision-Support Tools.}, journal = {Environmental management}, volume = {76}, number = {1}, pages = {28}, pmid = {41331158}, issn = {1432-1009}, support = {G22AC00433-00//U.S. Geological Survey/ ; G22AC00433-00//U.S. Geological Survey/ ; G22AC00433-00//U.S. Geological Survey/ ; G22AC00433-00//U.S. Geological Survey/ ; G22AC00433-00//U.S. Geological Survey/ ; }, mesh = {Florida ; Climate Change ; *Conservation of Natural Resources/methods ; *Sea Level Rise ; *Decision Support Techniques ; Ecosystem ; Models, Theoretical ; *Wetlands ; }, abstract = {Although coastal ecosystems are impacted by climate change and sea-level rise, many ecological and hydrological models do not yet incorporate sea-level rise projections in their modeling outputs. Therefore, this research examined the various challenges that may prevent sea-level rise from being effectively incorporated in modeling and decision-support tools. We conducted semi-structured interviews with twenty-six professionals involved in Florida's Everglades restoration. We applied the Diffusions of Innovations Theory to better understand factors that can impact practitioners' adoption of newly designed decision-support tools that examine sea-level rise in the freshwater Everglades. The Diffusions of Innovations Theory provided insights into practitioners' perceptions of these tools. We found that these practitioners have a strong interest in using dynamic decision-support tools to plan for sea-level rise impacts on Everglades restoration, particularly when they receive information at appropriate geographic and temporal scales and are given hands-on tools and training. However, challenges that prevent developing these tools include outdated data, limited organizational capacity and funding, limited use of long-term indicators, uncertainty about climate change impacts on local ecosystems, and lack of integration between hydrological and ecological models. Our research also highlights that greater availability of different types of tools can help to meet the needs of the scientific and non-scientific audiences involved in Everglades restoration.}, }
@article {pmid41330243, year = {2026}, author = {Bénézech, M and Drouineau, H and Bornarel, V and Briand, C and Díaz, E and Mateo, M and Beaulaton, L}, title = {Shifts in the European eel recruitment distribution: the impact of changing environmental conditions?.}, journal = {Marine environmental research}, volume = {214}, number = {}, pages = {107723}, doi = {10.1016/j.marenvres.2025.107723}, pmid = {41330243}, issn = {1879-0291}, mesh = {Animals ; *Anguilla/physiology ; Europe ; *Animal Migration ; Population Dynamics ; *Environmental Monitoring ; *Environment ; Ecosystem ; }, abstract = {The European eel (Anguilla anguilla) is a facultative catadromous migratory species that spawns in the Sargasso Sea, and grows over a wide continental range from the Barents Sea (72°N) to the southern limit of Morocco (30°N). Recruitment refers to the arrival of glass eels on continental shelves after an oceanic larval drift from the spawning ground. Although recruitment trends used to be quite consistent across European regions, recent modelling exercises have highlighted regional variations. At the European scale, we examined the relative contributions of six regions to overall recruitment over time using trend analysis methods. Variations in these contributions may be related to changes in environmental conditions. We identified the ecological processes preceding recruitment and their associated spatial and temporal scopes (e.g., spawning in the Sargasso Sea from March to May) to propose hypotheses regarding the potential influence of environmental factors on these processes. Using short- and long-term correlation strategies, we examined the relationships between recruitment and selected environmental variables. Our findings support the existence of spatial heterogeneity in recruitment distribution across Europe, which may inform management decisions at both local and broader levels for this species.}, }
@article {pmid41330108, year = {2025}, author = {Casagrande, S and Pham, HV and Rufo, O and Critto, A}, title = {Unravelling the influence of projected land use/land cover on surface water ecological status in Italian watersheds.}, journal = {The Science of the total environment}, volume = {1009}, number = {}, pages = {181003}, doi = {10.1016/j.scitotenv.2025.181003}, pmid = {41330108}, issn = {1879-1026}, abstract = {This research examines the influence of land use and land cover (LULC) on water quality in Italian watersheds, with a focus on predicting the likelihood of achieving good surface water ecological status (SWES) under future scenarios (SSP2-RCP4.5 and SSP5-RCP8.5) for the years 2050 and 2100. The developed methodology includes remapping future LULC, conducting Principal Component Analysis to examine the interactions between land use classes and the impact of upstream LULC on downstream SWES, and regression analysis to predict future SWES. Future projections indicate a decline in SWES in human-influenced areas, but potential improvements in natural regions with conservation efforts. For both scenarios, over 60 % of Italian watersheds are expected to fail to achieve good SWES by 2050 and 2100, emphasizing the need for targeted land management strategies to mitigate these effects. This analysis represents valuable support for the development of adaptive strategies that safeguard water resources and ensure the long-term sustainability of freshwater ecosystems.}, }
@article {pmid41327808, year = {2026}, author = {Li, XD and Wu, QJ and Guo, YW and Chang, YJ and Chu, J}, title = {Treatment of acid coal gangue leaching wastewater with constructed wetland based on ceramsite substrate.}, journal = {Environmental technology}, volume = {47}, number = {5}, pages = {657-672}, doi = {10.1080/09593330.2025.2593569}, pmid = {41327808}, issn = {1479-487X}, mesh = {*Wetlands ; *Wastewater/chemistry ; *Water Pollutants, Chemical/analysis/chemistry ; *Waste Disposal, Fluid/methods ; *Coal ; Industrial Waste/analysis ; Biodegradation, Environmental ; }, abstract = {This study investigates the use of constructed wetlands (CWs) with ceramsite derived from surplus sludge pyrolysis ash for acid mine drainage (AMD) remediation. The system, incorporating ceramsite, limestone, and gravel, used soybean wastewater as a microbial carbon source. Results showed that the ceramsite-based system effectively raised pH from 3.5 to 8.0, achieving removal rates of 99.96% for Fe, 96.53% for Mn, 94.84% for Cu, 99.26% for Zn, and 96.02% for total phosphorus. Metal ion removal was primarily through ceramsite adsorption, with minor plant-mediated adsorption. Microbial analysis revealed that pH and metal concentrations influenced bacterial composition, with dominant genera including Trichococcus, Clostridium_Sensu_Stricto_1, and Citrobacter. Sulfate-reducing bacteria such as Desulfovibrio and Desulfobulbus played crucial roles in sulfate reduction. This study demonstrates a sustainable AMD treatment method that not only improves metal ion removal but also addresses sludge disposal challenges, highlighting the environmental benefits of using waste-derived materials for pollution control and resource recovery.}, }
@article {pmid41327539, year = {2026}, author = {Mabuchi, K and Mai, JZ and Yauseyenka, VV and Brenner, AV and Little, MP and Minenko, VF and Veyalkin, I and Kukhta, TS and Trofimik, S and Drobyshevskaya, V and Vij, V and Ostroumova, E and Hatch, M and Drozdovitch, V and Cahoon, EK and Rozhko, AV}, title = {Thyroid nodules after prenatal exposure to chernobyl radioactive fallout in Belarus.}, journal = {International journal of radiation biology}, volume = {102}, number = {1}, pages = {20-26}, doi = {10.1080/09553002.2025.2588398}, pmid = {41327539}, issn = {1362-3095}, mesh = {Humans ; *Chernobyl Nuclear Accident ; Republic of Belarus/epidemiology ; Female ; Pregnancy ; *Thyroid Nodule/epidemiology/etiology ; Adult ; *Prenatal Exposure Delayed Effects/epidemiology ; *Radioactive Fallout/adverse effects ; Male ; Iodine Radioisotopes/adverse effects ; *Radiation Exposure/adverse effects ; Young Adult ; Radiation Dosage ; Dose-Response Relationship, Radiation ; }, abstract = {PURPOSE: To assess the risk of thyroid nodules associated with prenatal radiation exposure.<br><br>MATERIALS AND METHODS: Thyroid screening was conducted among 1,439 Belarusians who were prenatally exposed to radioactive fallout from the Chernobyl nuclear plant accident. Estimated thyroid doses (mean, 0.14; median, 0.02 gray [Gy]) were predominately from intake of [131]I. Binary logistic regression models were used to estimate excess odds ratios (EORs) for thyroid nodules associated with radiation dose.<br><br>RESULTS: A total of 258 screening participants had one or more nonneoplastic thyroid nodules. Among all participants, there was a linear dose response with an EOR/Gy of 0.44 (95% CI: -0.01, 1.38) of borderline significance (p = .06). This was driven by a significant EOR/Gy of 0.84 (95% CI: 0.07, 2.45; p = .02) among participants who were in the third trimester at the time of the accident (ATA). No significant associations with radiation were found among those who were in the second or first trimester ATA, but there were considerable uncertainties. No significant differences in dose response were found by nodule size or multiplicity.<br><br>CONCLUSIONS: The significant risk of thyroid nodules associated with exposure in the third trimester indicates the presence of a vulnerable subgroup of pregnant women at the time of an accidental radioiodine release. Because of the strong correlation between gestational age and [131]I dose in the fetal thyroid, the extent to which this excess risk is attributable to elevated [131]I dose and/or radiosensitivity of the thyroid in later stage of fetal development remains unclear.}, }
@article {pmid41325472, year = {2025}, author = {Przybylska, MS and Violle, C and Vile, D and Scheepens, JF and Cornet, D and Beurier, G and Rouan, L and Estarague, A and Kazakou, E and Mahaut, L and Munoz, F and Weigel, D and Exposito-Alonso, M and Bossdorf, O and Chevin, LM and Vasseur, F}, title = {Divergent and stabilizing selection shape the phenotypic space of Arabidopsis thaliana.}, journal = {PLoS biology}, volume = {23}, number = {12}, pages = {e3003536}, pmid = {41325472}, issn = {1545-7885}, mesh = {*Arabidopsis/genetics/physiology ; Phenotype ; *Selection, Genetic ; Genetic Variation ; Arabidopsis Proteins/genetics ; Flowers/genetics ; Genome, Plant ; Transcription Factors/genetics ; }, abstract = {Why do we observe some plant phenotypes but not others? The multivariate phenotypic space occupied by individuals or species often reveals both limits and phenotypes strikingly deviating from main syndromes. These observations are usually thought to indicate, respectively, inviable trait combinations and unique phenotypes adapted to specific environments. However, the evolutionary drivers underlying trait covariations often remain unclear. Here, we characterized the phenotypic space of Arabidopsis thaliana by comparing 713 wild accessions collected across the globe with 2,544 artificially-created recombinant individuals. This, combined with the detection of adaptive processes operating within species, allowed us to elucidate the roles of natural selection as a driver of phenotypic (co)variations within A. thaliana. We found that the phenotypic space of this species is constrained and driven by varying levels of divergent and stabilizing selection across different traits. Moreover, at the margins of the European geographic range, strong directional selection favored outlier phenotypes characterized by very late flowering and variation in a WRKY transcription factor gene. Genome analyses revealed that these extreme phenotypes may be explained by hybridization between ancestral and modern lineages of A. thaliana. Our findings demonstrate how interplays between population history and natural selection shape phenotypic diversity in a plant species.}, }
@article {pmid41325459, year = {2025}, author = {Paredes-Vázquez, A and Balsa-Canto, E and Banga, JR}, title = {Identification of dynamic models of microbial communities: A workflow addressing identifiability and modeling pitfalls.}, journal = {PLoS computational biology}, volume = {21}, number = {12}, pages = {e1013204}, pmid = {41325459}, issn = {1553-7358}, mesh = {*Microbiota/physiology ; *Models, Biological ; Computational Biology/methods ; Workflow ; Humans ; Computer Simulation ; }, abstract = {Microbial communities, complex ecological networks crucial for human and planetary health, remain poorly understood in terms of the quantitative principles governing their composition, assembly, and function. Dynamic modeling using ordinary differential equations (ODEs) is a powerful framework for understanding and predicting microbiome behaviors. However, developing reliable ODE models is severely hampered by their nonlinear nature and the presence of significant challenges, particularly critical issues related to identifiability. Here, we address the identification problem in dynamic microbial community models by proposing an integrated methodology to tackle key challenges. Focusing on nonlinear ODE-based models, we examine four critical pitfalls: identifiability issues (structural and practical), unstable dynamics (potentially leading to numerical blow-up), underfitting (convergence to suboptimal solutions), and overfitting (fitting noise rather than signal). These pitfalls yield unreliable parameter estimates, unrealistic model behavior, and poor generalization. Our study presents a comprehensive workflow incorporating structural and practical identifiability analysis, robust global optimization for calibration, stability checks, and rigorous predictive power assessment. The methodology's effectiveness and versatility in mitigating these pitfalls are demonstrated through case studies of increasing complexity, paving the way for more reliable and mechanistically insightful models of microbial communities.}, }
@article {pmid41324682, year = {2025}, author = {Koç, &#x130;}, title = {Predicting the potential geographic distribution of Fagus orientalis Lipsky under climate change using an ensemble model approach in Türkiye.}, journal = {Die Naturwissenschaften}, volume = {112}, number = {6}, pages = {93}, pmid = {41324682}, issn = {1432-1904}, mesh = {*Climate Change ; *Fagus/physiology ; Ecosystem ; Models, Theoretical ; Models, Biological ; }, abstract = {Oriental beech (Fagus orientalis Lipsky) is an ecologically and economically significant species, covering 8.5% of Türkiye's total forest area. However, climate change threatens its distribution due to increasing temperatures and decreasing precipitation. This study integrates geospatial informatics and ensemble modeling (EM) to predict the potential geographic distribution (PGD) of F. orientalis under future climate scenarios using Biomod2 within the ShinyBIOMOD framework. An EM model has been developed from six models [Generalized Boosting Model (GBM), Generalized Linear Model (GLM), Multivariate Adaptive Regression Splines (MARS), Generalized Additive Model (GAM), Artificial Neural Networks (ANN), and Maximum Entropy (MaxEnt)] using 76 validated occurrence records and 19 environmental predictors. Model validation achieved high predictive accuracy (AUC = 0.96, TSS = 0.85). Spatial projections for SSP2-45 and SSP5-85 scenarios indicate significant shifts in PGD. Notably, high-suitability habitats will decline under SSP2-45 but expand under SSP5-85. Bio2 [Mean Diurnal Range (mean of monthly (maximum temperature - minimum temperature))] and Bio4 [Seasonal temperature fluctuation (temperature seasonality (standard deviation x 100))] emerged as the dominant drivers of distribution changes. Based on geospatial analyses, F. orientalis is expected to migrate to higher altitudes in the Black Sea region and expand into southern and inner Türkiye. This shift reflects a broader trend of temperate forest adaptation to climate change. This study underscores the power of ensemble modeling for ecological forecasting and conservation planning, demonstrating the value of computational tools in assessing climate-driven species distribution changes. The findings contribute to predictive modeling for biodiversity conservation and ecosystem management.}, }
@article {pmid41324251, year = {2025}, author = {Ruiz Cuenca, P and Souza, FN and Coutinho do Nascimento, R and Goncalves da Silva, A and Eyre, MT and Santana, JO and de Oliveira, D and Ribeiro de Souza, EV and Palma, FG and de Carvalho Santiago, DC and Dos Santos Ribeiro, P and Ferreira Dos Santos, PE and Khalil, H and Read, JM and Cremonese, C and Costa, F and Giorgi, E}, title = {Using step selection functions to analyse human mobility using telemetry data in infectious disease epidemiology: a case study of leptospirosis.}, journal = {eLife}, volume = {14}, number = {}, pages = {}, pmid = {41324251}, issn = {2050-084X}, support = {PhD studentship/MRC_/Medical Research Council/United Kingdom ; R01 AI160780/AI/NIAID NIH HHS/United States ; Fellowship//Reckitt Global Hygiene Institute/ ; 150142/2024-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 10.35802/218987/WT_/Wellcome Trust/United Kingdom ; 1R01AI160780-01//National Institute of Allergy and Infectious Diseases/ ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Leptospirosis/epidemiology/transmission ; Female ; Male ; Brazil/epidemiology ; *Telemetry/methods ; Adult ; Middle Aged ; Young Adult ; Adolescent ; Risk Factors ; Aged ; Geographic Information Systems ; Movement ; }, abstract = {BACKGROUND: Human movement plays a critical role in the transmission of infectious diseases, especially those with environmental drivers like leptospirosis-a zoonotic bacterial infection linked to mud and water contact. Using GPS loggers, we collected detailed telemetry data to understand how fine-scale movements can be analysed in the context of an infectious disease.<br><br>METHODS: We recruited individuals living in urban slums in Salvador, Brazil, to analyse how they interact with environmental risk factors such as domestic rubbish piles, open sewers, and a local stream. We aimed to identify differences in movement patterns inside the study areas by gender, age, and leptospirosis serological status. Step selection functions, a spatio-temporal model used in animal movement ecology, estimated selection coefficients to represent the likelihood of movement toward specific environmental factors.<br><br>RESULTS: With 128 participants wearing GPS devices for 24-48 hr, recording locations every 35 s during active daytime hours, we segmented movements into morning, midday, afternoon, and evening. Our results suggested women moved closer to the central stream and farther from open sewers compared to men, while serologically positive individuals avoided open sewers.<br><br>CONCLUSIONS: This study introduces a novel method for analysing human telemetry data in infectious disease research.<br><br>FUNDING: Funding provided by Wellcome Trust, UK Medical Research Council, Brazilian National Research Council, Reckitt Global Hygiene Institute, and National Institute of Allergy and Infectious Diseases.}, }
@article {pmid41319542, year = {2026}, author = {Chen, X and Tie, Y and Zhu, M and Wu, Z and Xu, W and Zhang, Z and Ju, F and Zhang, W}, title = {Unraveling microbial synergy in blended Daqu: A multi-omics approach to decoding the unique flavor profile of Jiuliangxiang baijiu.}, journal = {Food chemistry}, volume = {499}, number = {}, pages = {147314}, doi = {10.1016/j.foodchem.2025.147314}, pmid = {41319542}, issn = {1873-7072}, mesh = {*Flavoring Agents/metabolism/chemistry ; *Bacteria/genetics/metabolism/isolation &amp; purification/classification ; Gas Chromatography-Mass Spectrometry ; Taste ; *Alcoholic Beverages/analysis/microbiology ; Volatile Organic Compounds/chemistry/metabolism ; *Wine/analysis/microbiology ; Microbial Consortia ; Metabolomics ; Multiomics ; }, abstract = {This study deciphers the microbial-ecological basis of Jiuliangxiang Baijiu's (JLX) unique flavor through blended Daqu multi-omics. GC-MS comparative analysis of five market-representative Baijiu types identified 25 aroma-active compounds (OAV ≥ 1) in JLX, with ethyl palmitate (OAV = 2) established as a potential characteristic marker. Subsequent investigation of its blended Daqu revealed how microbial consortia govern flavor formation. Physicochemical and microbial analyses demonstrated that Daqu blending elevated enzymatic capacities, including saccharification (+227.5 % vs single Daqu), esterification (+27.4 %), and liquefaction (+15.4 %), while enhancing microbial diversity. Metabolomic profiling identified glycerophospholipid Gpgro (14:0/16:0) as the ethyl palmitate precursor. Metagenomic tracking revealed that the core ester-producing taxa-primarily Bacillus licheniformis (from high-temperature Daqu) and Kroppenstedtia eburnea (from bacterial Daqu)-harbor complementary genetic potential for both esterase and acyltransferase pathways. The results provide a microbial-ecological framework for rational Daqu blending, offering actionable strategies to engineer microbial consortia for flavor-directed liquor innovation.}, }
@article {pmid41318763, year = {2025}, author = {Turek, S and Skarzyńska-Łyżwa, A and Aparna, A and Pląder, W and Riewe, D and Junker, A and Altmann, T and Pawełkowicz, M}, title = {Multi-omics integration of transcriptome, miRNA, and metabolome uncovers molecular mechanisms of male flower development in cucumber line B10 (Cucumis sativus L.).}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {45734}, pmid = {41318763}, issn = {2045-2322}, support = {UMO-2020/37/B/NZ9/00586//Narodowe Centrum Nauki/ ; CUC_GC-MS//European Plant Phenotyping Network - EPPN/ ; }, mesh = {*Cucumis sativus/genetics/growth &amp; development/metabolism ; *Flowers/genetics/growth &amp; development/metabolism ; *MicroRNAs/genetics/metabolism ; Gene Expression Regulation, Plant ; *Transcriptome ; *Metabolome ; Gene Expression Profiling ; Metabolomics/methods ; Multiomics ; }, abstract = {Male flower development in cucumber (Cucumis sativus L.) is a highly coordinated and genetically regulated process, yet the full complexity of its molecular underpinnings remains incompletely understood. In this study, we present a comprehensive, multi-omics analysis of male flower development in the cucumber line B10, integrating transcriptomic (RNA-seq), small RNA (miRNA) profiling, and metabolomic data across key tissues, including leaves, shoot apex, and floral buds at distinct developmental stages. Our analyses reveal dynamic gene expression changes and novel regulatory miRNAs, several of which have not previously been linked to male bud formation in cucumber. Functional enrichment analyses using GO and KEGG highlight critical pathways, including starch and sucrose metabolism, carbohydrate utilization, sporopollenin biosynthesis, and lignin catabolism. An integrative analysis combining miRNA-target interactions, transcriptomic shifts, and differential metabolite accumulation revealed coherent regulatory cascades linking transcription factors, carbohydrate metabolism, and cell wall dynamics. This study provides novel insights into the intricate genetic and metabolic networks shaping male flower morphogenesis and provides a valuable resource for advancing cucumber reproductive biology and crop improvement strategies.}, }
@article {pmid41318529, year = {2025}, author = {Wang, Y and Zhou, K and Lin, Z and Shen, H and Liu, R and Su, Z and Womer, FY and Wang, Y and Wei, Y and Zhu, R and Zheng, J and Zhang, X and Wang, F}, title = {Evaluation of the efficacy of group cognitive behavioral therapy on anxiety in college students based on wearable devices and mobile applications: a randomized controlled trial.}, journal = {BMC psychiatry}, volume = {26}, number = {1}, pages = {6}, pmid = {41318529}, issn = {1471-244X}, mesh = {Humans ; Male ; Female ; *Cognitive Behavioral Therapy/methods ; *Students/psychology ; *Psychotherapy, Group/methods ; Young Adult ; Universities ; *Mobile Applications ; *Anxiety Disorders/therapy ; *Wearable Electronic Devices ; Adult ; Heart Rate/physiology ; Treatment Outcome ; Ecological Momentary Assessment ; Adolescent ; *Anxiety/therapy ; }, abstract = {BACKGROUND: Anxiety disorders are highly prevalent worldwide and have significant comorbidities including depression and substance use disorders. The global burden of anxiety disorders necessitates early intervention for high-risk populations, including college students facing stress during major life transitions. Objective measures and ecological momentary assessments may advance the development of early interventions.<br><br>OBJECTIVE: To test the efficacy of group cognitive-behavioral therapy (GCBT) intervention by implementing a randomized controlled trial and identifying potential objective measures.<br><br>METHODS: College students with a Generalized Anxiety Disorder Scale 7 scores &#x2265; 5 were randomized into GCBT (n&#x2009;=&#x2009;31) and wait-list control (WLC; n&#x2009;=&#x2009;28) groups. For both groups, self-reported symptom severity was assessed at baseline and follow-up in weeks 4, 8, and 28. Continuous heart rate and step counts measurements were captured by wearable sensors, along with ecological momentary assessments of mood and energy, which were obtained within 4&#x2009;weeks of treatment.<br><br>RESULTS: Compared to the WLC group, the GCBT group showed significant improvements in anxiety symptoms at week 28. Moreover, the GCBT group had significantly increased step counts and faster heart rates, more stable moods in the morning and evening, and better energy in the morning. Improvements in anxiety symptoms were closely associated with increases in step counts in the GCBT group.<br><br>CONCLUSION: Preliminary findings suggest that GCBT is associated with improvements in anxiety symptoms in college students over the long term. Changes in daily heart rates and step counts were correlated with mood and energy levels, suggesting that physiological markers may be useful in assessing treatment response.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov (NCT05913349), trial registration date: June 13, 2023 (retrospectively registered).}, }
@article {pmid41316784, year = {2025}, author = {Wu, ZQ and Yu, XC and Ning, YJ and Lin, F and Niu, JJ and Zhao, L and Luo, JY}, title = {[Multi-scale Ecosystem Services Trade-off/Synergy and Ecological Function Zoning in Taiyuan City].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {46}, number = {11}, pages = {7234-7245}, doi = {10.13227/j.hjkx.202410223}, pmid = {41316784}, issn = {0250-3301}, mesh = {*Ecosystem ; China ; *Conservation of Natural Resources/methods ; Cities ; Soil ; Forests ; Geographic Information Systems ; Agriculture ; Ecology ; Sustainable Development ; }, abstract = {A thorough understanding of the relationships between ecosystem services and ecological functional zoning is crucial for ecological restoration, land spatial planning, resource management, and sustainable economic development. We evaluated four types of ecosystem services-water yield, carbon storage, food production, and soil conservation-of Taiyuan City from 2000 to 2020 using the InVEST model. We also employed R language, GIS technology, and self-organizing maps to identify trade-offs and synergies between ecosystem services at three scales: whole regional, pixel and county, and ecological functional zoning. The results showed that: ① Between 2000 and 2020, significant changes occurred in land use and ecosystem services in Taiyuan City, including a decrease in cultivated land and grassland area and an increase in construction land and forest area. An enhancement in soil conservation, food production, and water yield value was observed, while carbon storage service value declined slightly. ② At the whole scale, trade-offs were predominant among ecosystem services, while weak synergistic effects were found at the pixel scale, and regional heterogeneity was observed at the county scale. ③ Three ecosystem service clusters were identified, which were divided into three ecological functional areas: ecological conservation, agricultural production, and ecologically vulnerable, with the largest proportion being the ecological conservation area. Based on these divisions, differentiated management recommendations were proposed. The findings may provide scientific guidance for the sustainable management of ecosystem services in Taiyuan City.}, }
@article {pmid41316726, year = {2026}, author = {Nishijima, S and Fullam, A and Schmidt, TSB and Kuhn, M and Bork, P}, title = {VIRE: a metagenome-derived, planetary-scale virome resource with environmental context.}, journal = {Nucleic acids research}, volume = {54}, number = {D1}, pages = {D902-D911}, pmid = {41316726}, issn = {1362-4962}, support = {12/RC/2273-P2//Uehara Memorial Foundation/ ; //EMBL/ ; }, mesh = {*Genome, Viral ; *Virome/genetics ; *Metagenome ; *Viruses/genetics/classification ; *Databases, Genetic ; Metagenomics/methods ; Open Reading Frames ; Microbiota/genetics ; Humans ; Software ; Molecular Sequence Annotation ; }, abstract = {Viruses are the most abundant biological entities on Earth, yet their global diversity remains largely unexplored. Here, we present VIRE, a comprehensive resource comprising over 1.7 million high- and medium-quality viral genomes recovered from >100 000 publicly available metagenomes derived from samples that cover diverse ecosystems, including host-associated, aquatic, terrestrial, and anthropogenic environments. Using a unified and scalable pipeline, we systematically assembled viral genomes and provided detailed information on genome completeness, taxonomic classification, predicted lifestyle, and host assignment based on CRISPR spacer matches. VIRE contains >89 million predicted viral open reading frames, as well as detailed functional annotations derived from multiple databases. Importantly, VIRE is seamlessly integrated with related microbiome resources such as SPIRE (https://spire.embl.de) and Metalog (https://metalog.embl.de), enabling users to jointly explore viral genomes, metagenome-assembled genomes, and associated environmental or clinical metadata. Accessible at https://vire.embl.de, VIRE provides an open-access, scalable platform for investigating viral diversity, evolution, and ecology on a planetary scale.}, }
@article {pmid41315930, year = {2025}, author = {Chaussard, A and Bonnet, A and Le Corff, S and Sokol, H}, title = {TaxaPLN: a taxonomy-aware augmentation strategy for microbiome-trait classification including metadata.}, journal = {BMC bioinformatics}, volume = {27}, number = {1}, pages = {1}, pmid = {41315930}, issn = {1471-2105}, mesh = {*Metadata ; Humans ; *Gastrointestinal Microbiome ; Machine Learning ; *Microbiota ; *Software ; *Computational Biology/methods ; Algorithms ; }, abstract = {BACKGROUND: The gut microbiome plays a crucial role in human health, making it a cornerstone of modern biomedical research. To study its structure and dynamics, machine learning models are increasingly used to identify key microbial patterns associated with disease and environmental factors, but their performance is often limited by the intrinsic complexity of microbiome data and the small size of available cohorts. In this context, data augmentation has emerged as a promising strategy to overcome these challenges by generating artificial microbiome profiles.<br><br>RESULTS: We introduce TaxaPLN, a data augmentation method based on PLN-Tree generative models, which leverages the taxonomy and a data-driven sampler to generate realistic synthetic microbiome compositions. Additionally, we propose a conditional extension based on feature-wise linear modulation, enabling covariate-aware generation. Experiments on diverse curated microbiome datasets show that TaxaPLN preserves ecological properties and generally improves or maintains predictive performances, outperforming state-of-the-art baselines on most tasks. Furthermore, the conditional variant of TaxaPLN establishes a new benchmark for metadata-aware microbiome augmentation.<br><br>CONCLUSION: TaxaPLN provides a model-based framework for augmenting microbiome datasets while preserving their ecological and clinical relevance. By integrating taxonomic structure and host metadata, it enhances predictive modeling across diverse real-world settings. To facilitate reproducible and scalable microbiome analysis using our method, TaxaPLN is released as an open-source Python package available on PyPI (plntree), with MIT-licensed source code hosted at https://github.com/AlexandreChaussard/PLNTree-package .}, }
@article {pmid41315389, year = {2025}, author = {Demetriou, J and Martinou, AF and Bowler, D and Peyton, J and Pescott, OL and Michailidis, N and Mountford, O and Onete, M and Stoumboudi, M and Rathod, B and van Breda, J and Roy, HE and Zenetos, A}, title = {The Cyprus Database of Alien Species (CyDAS).}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1881}, pmid = {41315389}, issn = {2052-4463}, mesh = {Cyprus ; *Introduced Species ; *Databases, Factual ; *Biodiversity ; Animals ; }, abstract = {Invasive alien species (IAS) are a direct driver of global biodiversity loss, and can also affect societies, economies and human health. Maintaining up-to-date alien species inventories is important for informing policy and management decisions. Here we present the Cyprus Database of Alien Species (CyDAS), an openly accessible, online dataset providing informational resources on alien species on the island of Cyprus. The dataset (up to end of December 2023) includes information on 1,293 terrestrial, freshwater and marine introduced taxa, with species profiles being constantly updated to keep track of new arrivals. The CyDAS aims to catalogue and supplement our knowledge on the alien species of Cyprus; to help develop and enhance early warning and rapid response systems; to raise public awareness of the risks posed by the IAS subset; to strengthen and enhance engagement and public participation in surveys in the field of biological invasions; and to inform IAS policy. CyDAS is a free, online database and we would like to encourage other researchers and decision-makers to provide information on IAS.}, }
@article {pmid41313826, year = {2026}, author = {Xu, QQ and Wang, QQ and Lv, QL and Liu, ZG and Guo, Z}, title = {Anchoring single-atom iron sites onto carbon spheres for boosting electrochemical sensing of bisphenol A.}, journal = {Talanta}, volume = {300}, number = {}, pages = {129158}, doi = {10.1016/j.talanta.2025.129158}, pmid = {41313826}, issn = {1873-3573}, abstract = {Bisphenol A (BPA), a common endocrine-disrupting chemical, poses serious threats to both ecological systems and human health even at trace concentrations. However, the accurate detection of BPA in complex matrices remains challenging due to the low sensitivity and poor selectivity of conventional electrochemical sensing platforms. The saturated N4-coordinated single-atom sites derived from metal phthalocyanines exhibit high catalytic specificity and atomic utilization efficiency, enabling selective recognition of BPA. These characteristics enhance adsorption and electron transfer processes, potentially overcoming the limitations of traditional sensing materials and offering a feasible route for the ultra-sensitive detection of trace BPA in complex environments. In this study, we have developed a highly efficient electrochemical sensor for BPA by anchoring saturated N4-coordinated single-atom sites of metal phthalocyanine onto carbon spheres (MPc/CSs, where M = Fe, Co, and Ni). The carbon spheres (CSs) serve as substrates to support the metal phthalocyanine molecules, improving the stability of the active sites and preventing aggregation. Among the materials tested, FePc/CSs exhibited the highest sensitivity (0.53 μA μM[-1]) and the lowest limit of detection (0.031 μM), exhibiting better performance than other modified electrodes, including CoPc/CSs, NiPc/CSs, and metal-free phthalocyanine-loaded CSs (H2Pc/CSs). Structural analysis revealed that the Fe-N4 single-atom sites possess higher charge density than the Co-N4 and Ni-N4 single-atom sites, resulting in their superior catalytic activity. Practical validation of the FePc/CSs modified glassy carbon electrode (GCE) in real samples, such as supermarket receipts and plastic products, yielded satisfactory recovery rates (97.5-103.4 %), confirming the sensor's reliability in complex matrices. These results demonstrate that electrodes based on CSs-supported single-atom iron sites can serve as highly sensitive, selective, and cost-effective electrochemical sensors for BPA. Overall, this work provides an efficient strategy for designing high-performance environmental sensors based on engineered electronic microenvironments and offers valuable insights for the sensitive analysis of environmental pollutants.}, }
@article {pmid41312645, year = {2026}, author = {Fiamenghi, MB and Camargo, AP and Chasapi, IN and Baltoumas, FA and Roux, S and Egorov, AA and Aplakidou, E and Ndela, EO and Vasquez, YM and Chen, IA and Palaniappan, K and Reddy, TBK and Mukherjee, S and Ivanova, NN and Schulz, F and Woyke, T and Eloe-Fadrosh, EA and Pavlopoulos, GA and Kyrpides, NC}, title = {Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes.}, journal = {Nucleic acids research}, volume = {54}, number = {D1}, pages = {D801-D812}, pmid = {41312645}, issn = {1362-4962}, support = {FWP 70880//BER's Genomic Sciences Program/ ; 1U01DE034196-01/GF/NIH HHS/United States ; //Royal Physiographic Society of Lund/ ; 45379//Natural Sciences, Medicine and Technology/ ; //Hellenic Foundation for Research and Innovation/ ; DE-AC02-05CH11231//US DOE/ ; U01 DE034196/DE/NIDCR NIH HHS/United States ; }, mesh = {*Genome, Viral ; *Viruses/genetics/classification ; *Databases, Genetic ; Metagenomics/methods ; Phylogeny ; Biodiversity ; Genetic Variation ; Metagenome ; Software ; }, abstract = {Viruses are ubiquitous in all environments and impact host metabolism, evolution, and ecology, although our knowledge of their biodiversity is still extremely limited. Viral diversity from genomic and metagenomic datasets has led to an explosion of uncultivated virus genomes (UViGs) and the development of specialized databases to catalog this viral diversity, though many lack comprehensive integration. Here, we introduce meta-virus resource (MetaVR), the successor of the IMG/VR database, designed to overcome previous limitations such as large-scale querying and programmatic access. Drawing on the increase of publicly available genomes and metagenomes, MetaVR significantly expands viral diversity, now comprising 24,435,662 UViGs, a 57.6% increase from its predecessor, organized into over 12 million viral operational taxonomic units. Key enhancements include the integration of curated eukaryotic host information, the integration of protein clusters and predicted structures for comparative studies, and an API for programmatic data access. Furthermore, MetaVR features an updated taxonomic framework based on ICTV release 39, assignment to Baltimore classes, and enhanced host assignment through novel computational tools like iPHoP. These advancements position MetaVR as a unique resource for exploring viral diversity, evolution, and host interactions across diverse environments. MetaVR can be freely accessed at https://www.meta-virome.org/.}, }
@article {pmid41312302, year = {2025}, author = {Steindler, L and Maldonado, M and Pita, L and Riesgo, A and Erpenbeck, D and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and ,  and ,  and ,  and ,  and , }, title = {The chromosomal genome sequence of the stone sponge Petrosia ficiformis (Poiret, 1789) and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {450}, pmid = {41312302}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual Petrosia ficiformis (stone sponge; Porifera; Demospongiae; Haplosclerida; Petrosiidae). The genome sequence is 191.3 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.89 kilobases in length. Gene annotation of the host organism assembly identified 18,339 protein coding genes. The metagenome of the specimen was also assembled, and 112 binned bacterial genomes were identified, including 57 high-quality MAGs. Besides MAGs characteristic of HMA sponge symbionts (i.e., Chloroflexota, Acidobacteriota), the P. ficiformis specific symbiont Candidatus Synechococcus feldmanni (formerly Aphanocapsa feldmanni (Cyanobacteriota) was recovered, as well as notably MAGs of several candidate phyla (Candidatus Latescibacteria, Poribacteria, Tectomicrobia, Dadabacteria, Kapabacteria and Binatia).}, }
@article {pmid41309085, year = {2025}, author = {Berrocal, A and Concepcion, W and Wac, K}, title = {A 6-Month Evaluation of the Peer-Ceived Momentary Assessment Method in a Small Sample of Liver Transplant Patients and Their Support Persons: Longitudinal Observational Study.}, journal = {JMIR formative research}, volume = {9}, number = {}, pages = {e55907}, pmid = {41309085}, issn = {2561-326X}, mesh = {Humans ; Longitudinal Studies ; Female ; Male ; Middle Aged ; *Liver Transplantation/psychology ; *Ecological Momentary Assessment ; Reproducibility of Results ; Adult ; *Patient Reported Outcome Measures ; Aged ; *Caregivers/psychology ; *Peer Group ; }, abstract = {BACKGROUND: Patient-reported outcomes, including ecological momentary assessments (EMAs), are acquired from patients via repeated self-reports of their perceived momentary physical and emotional states before and after medical procedures. Patient-reported outcomes are used to measure health outcomes and quality of care. However, certain observable states or behaviors (eg, moods such as fatigue, hope, or medication adherence), or behaviors suggestive of health decline (eg, depression, cognitive decline), are not easily measured via self-reports in certain situations (eg, patients undergoing certain medical procedures, patients with dementia, and others). The peer-ceived momentary assessment (PeerMA) method involves support persons or peers (eg, family members and friends) to report their perception of a patient's subjective physical and emotional states and has been validated in healthy populations.<br><br>OBJECTIVE: We examined the value of the PeerMA method in assessing the disease progression and recovery pathways of patients undergoing liver transplantation. Herein, the PeerMA method is operationalized via the patient's informal caregivers and the patient-based EMA, and wearable-based physical activity datasets from the patients. We report the feasibility results and human factors influencing the acceptance and reliability of the PeerMA method in a small study comprising 8 patients and support persons.<br><br>METHODS: We conducted a longitudinal observational study of 6 months (autumn 2019 to spring 2020), collecting EMA/self-reports from 8 patients (at the liver transplant clinic at Stanford University Hospital, California) about their perceived levels of hope, sleep, fatigue, depression, and pain in addition to PeerMA-based reports of the same aspects from 7 caregivers. We collected physical activity records from 5 patients using a Fitbit bracelet. Participants completed pre- and poststudy surveys, contributing qualitative data. We implemented the PeerMA method using a smartphone app, making it easy to use by both patients and support persons.<br><br>RESULTS: We collected 1142 patient-days and 976 support person-days. On average, each patient received 103 EMAs and responded to 64 (63%) of them, while support persons received 87 PeerMAs and responded to 64 (74%) of them. We report empirical evidence about the methodological feasibility of PeerMA, showing its dual and unique information streams unavailable by EMA alone. We show examples where support person assessments and physical activity data can inform health professionals about the actual state of a patient regarding outcomes such as hope, sleep quality, fatigue, pain, and depression. We discuss human factors influencing the acceptance of the method and make methodological recommendations.<br><br>CONCLUSIONS: It is possible to leverage data acquired via the PeerMA method and a wearable activity monitor to complement EMA. The PeerMA method incorporates frequent observations from support persons in patients' daily lives, which can be compared and analyzed next to the patient's self-reports. Such data may help to study and assist patients during disease recovery, which is beneficial for patients recovering from an organ transplant.}, }
@article {pmid41307499, year = {2025}, author = {Campbell, R and Mevers, E}, title = {Structural Characterization and Multiomics Analysis Reveal Extensive Diversity and Global Distribution of Kurstakin Lipopeptides.}, journal = {Journal of natural products}, volume = {88}, number = {12}, pages = {2960-2967}, pmid = {41307499}, issn = {1520-6025}, support = {R35 GM146740/GM/NIGMS NIH HHS/United States ; }, mesh = {*Lipopeptides/chemistry ; Molecular Structure ; *Bacillus cereus/chemistry ; Multiomics ; }, abstract = {Bacillus species, particularly those investigated as biocontrol agents, are known to produce a cocktail of bioactive lipopeptides that act synergistically to shape the ecological function of these beneficial microbes. However, while certain families of lipopeptides are well-characterized, others remain elusive. Herein, we describe the characterization of the kurstakins, a family of lipopeptides associated with promising biocontrol properties but that lack adequate characterization. Metabolomic analyses of a semipurified Bacillus cereus EM195W extract fraction revealed the presence of approximately 50 cyclic- and linear-peptide analogs. Deeper analyses revealed that the chemical diversity stems from the diverse lipid tails, including linear, iso-, and anteiso-lipid tails ranging from C8-C18, along with several hydroxylated lipid tails. Isolation and complete structural analysis of two new analogs represented the first kurstakin analogs characterized by NMR and provided the first experimental analyses for deducing their absolute configuration. Finally, analysis of publicly available genomic and MS data provided insights into the true chemical diversity and distribution of the kurstakins. These results expand our understanding of this family of compounds, opening the door for determining their ecological functions and the role they play in the broader activity of biocontrol agents.}, }
@article {pmid41307322, year = {2025}, author = {Baima, G and Dabdoub, S and Thumbigere-Math, V and Ribaldone, DG and Caviglia, GP and Tenori, L and Fantato, L and Vignoli, A and Romandini, M and Ferrocino, I and Aimetti, M}, title = {Multi-Omics Signatures of Periodontitis and Periodontal Therapy on the Oral and Gut Microbiome.}, journal = {Journal of periodontal research}, volume = {60}, number = {12}, pages = {1237-1253}, pmid = {41307322}, issn = {1600-0765}, support = {CUP B83C22004800006//Next Generation EU/ ; DM 1557 11.10.2022//Next Generation EU/ ; Prot. P2022YEX5R//Next Generation EU Program and the Italian Ministry of University and Research/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Saliva/microbiology ; *Periodontitis/microbiology/therapy/metabolism ; Male ; Feces/microbiology ; Female ; Metabolomics ; Adult ; Middle Aged ; *Mouth/microbiology ; Multiomics ; }, abstract = {AIM: To characterize the impact of periodontitis and of Steps I-II of periodontal therapy on microbiome composition, function, and metabolic output across the oral and gut environments.<br><br>METHODS: A multi-omics analysis was performed on saliva and stool samples collected from 50 systemically healthy individuals with and without Stage III-IV periodontitis. For participants with periodontitis, samples were analyzed both at baseline and 3&#x2009;months after Steps I-II of periodontal therapy. High-throughput whole metagenome sequencing was used to profile microbial taxa and functional genes, NMR-based metabolomics profiled host-microbial metabolites. Single-omic differential abundance analysis between healthy samples and periodontitis samples was performed with MaAsLin2, while analysis between pre- and post-treatment was conducted with timeOmics. Variable selection and subsequent supervised multivariate analysis to determine group-separating markers utilized multi-level sparse Partial Least Squares Discriminant Analysis (sPLS-DA) through mixOmics. KEGG pathway enrichment was analyzed using clusterProfiler, whereas multi-omic data integration was performed with multi-block Partial Least Squares regression analysis.<br><br>RESULTS: Periodontitis was associated with significant compositional and functional changes in both saliva and stool, with increased abundance of pathobionts and loss of health-associated taxa in both niches. A subset of species was shared across oral and gut habitats, with detectable differences across clinical groups. As functional potential, periodontitis enriched microbial pro-inflammatory pathways (lipopolysaccharide biosynthesis, bacterial motility) and depleted beneficial short-chain fatty acid (SCFA)- and vitamin-producing functions. Metabolomic profiles revealed reduced SCFAs and amino acids in periodontitis, with elevated pro-inflammatory metabolites (succinate, trimethylamine) in both saliva and stool. Following therapy, microbial communities and their metabolic output partially reverted toward health-associated profiles, particularly in saliva. Stool samples showed subtler but consistent shifts, including a decrease in some typically oral species and decreased succinate and methylamine and restoration of amino acid and SCFA-related metabolites.<br><br>CONCLUSIONS: Periodontitis is associated with coordinated microbial and metabolic signatures across the oral and gut environments. Non-surgical periodontal therapy promotes partial ecological restoration in both niches, supporting the view of oral health as a modifiable target for influencing systemic microbial homeostasis.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov identification number: NCT04826926.}, }
@article {pmid41304309, year = {2025}, author = {Paoli, JE and Thongthum, T and Bassett, M and Beardsley, J and Tagliamonte, MS and Cash, MN and Spertus Newman, J and Smith, LM and Anderson, BD and Salemi, M and Subramaniam, K and von Fricken, ME and Braun de Torrez, E and Mathis, V and Mavian, CN}, title = {Virome and Microbiome of Florida Bats Illuminate Viral Co-Infections, Dietary Viral Signals, and Gut Microbiome Shifts.}, journal = {Microorganisms}, volume = {13}, number = {11}, pages = {}, pmid = {41304309}, issn = {2076-2607}, support = {Department of Pathology EPIG RAS 2021-2022//University of Florida/ ; Florida Informatics Institute SEED 2022-2023//University of Florida/ ; Biodiversity Institute SEED 2022-2023//University of Florida/ ; }, abstract = {Florida's bat virome remains poorly characterized despite the state's high bat species diversity and conservation importance. We characterized viral metagenomes from rectal tissues, anal swabs, and feces of Myotis austroriparius and Tadarida brasiliensis sampled across north Florida. We recovered a near-complete Hubei virga-like virus 2 (HVLV2) genome from T. brasiliensis feces, a finding consistent with an arthropod-derived dietary signal rather than active bat infection. An Alphacoronavirus (AlphaCoV) was detected in two M. austroriparius specimens, including one with a putative co-infection involving an Astrovirus (AstV), the first detection of AstV in Florida bats to date. Parallel profiling of the M. austroriparius gut microbiome highlighted compositional differences in the co-infected individual relative to AlphaCoV-only and virus-negative bats, suggestive of potential associations between viral detection and gut microbial shifts. Our study expands the known viral diversity in Florida bat populations, and demonstrates how metagenomics can simultaneously illuminate host diet, viral exposure, and gut microbial ecology. This approach provides a scalable framework for monitoring how diet, microbiome composition, and environmental pressures shape the bat virome, and inform conservation and zoonotic risk assessments.}, }
@article {pmid41302669, year = {2025}, author = {de Freitas, PP and Lopes, MS and Ferreira, NL and Peixoto, SV and Lopes, ACS}, title = {Community Food Environment in Brazilian Medium-Sized Municipality After the Ore Dam Break: Database Creation and Diagnosis.}, journal = {International journal of environmental research and public health}, volume = {22}, number = {11}, pages = {}, pmid = {41302669}, issn = {1660-4601}, support = {Processo 25000.127551/2019-69//Minist&#xe9;rio da Sa&#xfa;de/ ; Productivity Scholarship SVP and ACSL//National Council for Scientific and Technological Development/ ; }, mesh = {Brazil ; *Databases, Factual ; *Food Supply/statistics &amp; numerical data ; Humans ; Mining ; Cities ; }, abstract = {This study proposed a methodology for obtaining a valid database of food retail establishments and characterized the community food environment, understood as the distribution and type of food outlets, in a Brazilian medium-sized municipality after the collapse of a mining tailings dam. An ecological study was conducted with establishments selling food for home consumption (butcher shops, fish markets; fruit and vegetable specialty markets; large- and small-chain supermarkets; bakeries and local markets) and immediate consumption (bars, snack bars, and restaurants). For home-consumption establishments, data were requested from governments and completed with website/app searches, virtual audits (Google Street View), and on-site audits. For immediate-consumption establishments, only on-site audit was used due to the low quality of the secondary databases. Agreement between databases was assessed with the Kappa statistic. Density (d) was calculated by the area (in km[2]) of the sampling stratum. Public databases presented low validity (23.0%; Kappa -0.388; p = 1.000), even after virtual auditing (31.4%; Kappa 0.37; p < 0.001). 96 establishments for home consumption and 261 for immediate consumption were identified, with predominance of local markets (35.4%), bars (35.2%), and snack bars (29.1%). The region with the highest density of establishments was the "Other Areas" stratum (d = 4.7 for home-consumption establishments and d = 13.2 for immediate-consumption establishments). Audit proved most effective, especially for small establishments. The lack of governmental databases and the identified food environment should inform municipal policies to promote food and nutrition security and reduce inequalities after the disaster.}, }
@article {pmid41299059, year = {2025}, author = {Sharma, AK and Jani, AD and Brunnengraeber, E and Choi, J and Fife, R and Gandhok, S and Huie, K and Ilano, AB and Lopez, E and Lopez, M and McMillan, O and Parra, A and Pollock, T and Woodbridge, D and Young, R}, title = {Deep learning classification of INSV-associated weeds in Monterey county using a curated RGB image dataset.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {45395}, pmid = {41299059}, issn = {2045-2322}, mesh = {*Deep Learning ; *Plant Weeds/classification/virology ; *Image Processing, Computer-Assisted/methods ; *Convolutional Neural Networks ; Plant Diseases/virology ; Malva ; Sonchus ; California ; Datasets as Topic ; }, abstract = {Weeds, defined by their ecological and economic impact rather than taxonomy, present a major challenge to agriculture by competing with crops for limited resources and serving as vectors for disease. In Monterey County, California, one of the most productive farming regions in the United States, Sonchus oleraceus (annual sowthistle) and Malva parviflora (little mallow) have been linked to over $150 million in crop losses due to their role in spreading Impatiens Necrotic Spot Virus (INSV). As precision agriculture becomes more important in high-value production systems, deep learning and image-based classification offer promising tools for early weed detection and disease prevention. To address the absence of region-specific image datasets, this study presents the first curated, high-resolution image collection of INSV-associated weeds from Monterey County, captured under greenhouse conditions designed to mimic field variability. This dataset fills a documented gap in existing global repositories such as PlantCLEF and DeepWeeds, which lack representation of California's high-value crop systems. This study compares three convolutional neural networks-ResNet-50, ResNet-101, and DenseNet-121-for classifying these visually similar weeds under controlled conditions that approximate real field environments. RGB images were augmented to improve model robustness, and training was conducted across ten independent stratified data splits.Among the tested architectures, ResNet-101 achieved the highest median classification accuracy (91%) and Cohen's Kappa (0.87), while DenseNet-121 demonstrated the strongest F1-score and AUC values exceeding 0.99. These results confirm that dataset augmentation substantially enhanced model generalization. The results demonstrate that deep learning can support accurate and reliable weed identification, paving the way for real-time detection systems and more targeted, sustainable weed control practices in precision agriculture.}, }
@article {pmid41298935, year = {2025}, author = {Farooq, MA and Hannan, F and Zou, HX and Zhou, W and Zhao, DS and Ayyaz, A and Ullah Asad, MA and Ahmad, R and Yan, X}, title = {Microplastics in soil-plant systems: impacts on soil health, plant toxicity, and multiomics insights.}, journal = {Plant cell reports}, volume = {44}, number = {12}, pages = {283}, pmid = {41298935}, issn = {1432-203X}, support = {2022YFE0108300//Key Technologies Research and Development Program/ ; }, mesh = {*Microplastics/toxicity ; *Soil/chemistry ; *Soil Pollutants/toxicity ; *Plants/drug effects/metabolism ; Proteomics ; Metabolomics ; Oxidative Stress/drug effects ; Multiomics ; }, abstract = {Microplastic pollution has emerged as a critical environmental concern, particularly in agricultural soils, where various MP types, including polyethylene, polystyrene and polyvinyl chloride accumulate due to plastic mulch degradation, irrigation, and biosolid application. This review synthesizes current knowledge on the impacts of MPs on soil integrity and function, highlighting the degradation of soil structure, disruption of nutrient cycles and shifts in microbial community composition and enzymatic activity. Furthermore, MPs can be taken up by plants, with submicrometer sized particles infiltrating root tissues, triggering phytotoxic effects such as oxidative stress, impaired growth, and reduced photosynthesis. In response plants deploy tolerance mechanisms involving antioxidant defense and altered nutrient metabolism to mitigate MP-induced stress. Advanced omics technologies, including transcriptomics, metabolomics, and proteomics provide valuable insights into the molecular responses of plants to MP exposure, uncovering stress responsive genes, metabolite shifts and protein alterations linked to MP toxicity. This review synthesizes current knowledge on MP contamination in agricultural soil, its impact on soil health and plant physiology, and the application of multiomics approaches to elucidate MP-induced toxicity, paving the way for sustainable strategies to mitigate MP pollution in agroecosystems.}, }
@article {pmid41298300, year = {2025}, author = {Wang, ZQ and Gong, LX and Si, M and Huang, ZL and Wu, H and Feng, J and Jiang, TL}, title = {Seasonal changes in 3D space use and foraging strategies in the avivorous bat Ia io.}, journal = {Zoological research}, volume = {46}, number = {6}, pages = {1465-1476}, pmid = {41298300}, issn = {2095-8137}, mesh = {Animals ; *Chiroptera/physiology ; *Seasons ; *Feeding Behavior/physiology ; Ecosystem ; Geographic Information Systems ; }, abstract = {To cope with seasonal changes in food availability, animals need to optimize their behaviors, including shifts in temporal activity patterns and spatial use in habitats. Most studies focused on the temporal activity pattern or habitat use in two-dimensional (2D) space. However, studies on the simultaneous changes in temporal activity patterns and habitat use in three-dimensional (3D) space are limited. In this study, we used the great evening bat (Ia io) to investigate differences in the activity pattern and space use during the summer and autumn. We collected and analyzed the Global Positioning System (GPS) data and activity data obtained from accelerometers. The results showed that bats displayed seasonal variations in their movement patterns. Specifically, compared with summer, I. io individuals were found to extend their foraging duration and adopt a low-energy consumption pattern of activity in autumn. Furthermore, there was a notable increase in the vertical extent of the 3D habitat utilization range for these bats, although the 2D habitat size in autumn remained similar to that in summer. These changes manifested both temporally and spatially, potentially as a response to the reduced availability of insect resources from summer to autumn, and the arrival of migratory birds in autumn as an alternative food source. Our results suggest that I. io seasonally adjust their foraging strategies and spatial use from two to three dimensions. Our study provides important insights into the seasonal behaviour dynamics of bats during summer and autumn, which may contribute to understanding their ecological strategies and inform conservation efforts.}, }
@article {pmid41297621, year = {2025}, author = {Houmenou, CT and Sokhna, C and Fenollar, F and Mediannikov, O}, title = {Advancements and challenges in bioinformatics tools for microbial genomics in the last decade: Toward the smart integration of bioinformatics tools, digital resources, and emerging technologies for the analysis of complex biological data.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {136}, number = {}, pages = {105859}, doi = {10.1016/j.meegid.2025.105859}, pmid = {41297621}, issn = {1567-7257}, mesh = {*Computational Biology/methods ; *Genomics/methods ; High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; Humans ; Animals ; }, abstract = {Over the past decade, microbial genomics has been transformed by advances in sequencing technologies and bioinformatics, enabling the transition from targeted gene markers to complete genome assemblies and ecological scale metagenomic surveys. This review presents a comprehensive overview of the bioinformatics pipelines that structure this field, from sample preparation, PCR amplification, and next-generation sequencing (NGS) to read preprocessing, genome assembly, polishing, structural and functional annotation, and submission to public databases. We highlight the major tools that have become standards at each stage, including FastQC, SPAdes, Prokka, Bakta, CARD, GTDB-Tk, QIIME 2, and Kraken2, while also emphasizing recent innovations such as hybrid assemblers, ontology-driven annotation frameworks, and automated workflows (nf-core, Bactopia). Applications extend across microbiology, from antimicrobial resistance surveillance and phylogenetic classification to ecological studies, exemplified here by three case studies: termite gut microbiota profiling by 16S metabarcoding, the description of new Bartonella species from bats, and the genomic characterization of rare Salmonella enterica serovars from primates. Despite these advances, persistent challenges remain, including incomplete and biased reference databases, computational bottlenecks, and economic disparities in sequencing and storage capacities. In response, international initiatives increasingly promote open, interoperable, and reusable bioinformatics infrastructures. Conforming to the Findable, Accessible, Interoperable, Reusable (FAIR) principles and global frameworks such as Global Alliance for Genomics and Health (GA4GH), these efforts are driving greater standardization, transparency, and data sharing across the microbial genomics community. Future perspectives point toward the integration of artificial intelligence, long-read and telomere-to-telomere (T2T) sequencing, cloud-native infrastructures, and even quantum computing, paving the way for a predictive, reproducible, and globally inclusive microbial genomics.}, }
@article {pmid41297421, year = {2025}, author = {Yang, H and Luo, X and Liao, Z and Gu, Y and Qian, J and Wang, Y and Guo, H and Shi, L and Peng, J and Liu, M and Wan, X and Chen, L and He, F and Huang, X}, title = {Integrative multi-omics reveal the regulatory mechanism of golden-thread wood color in Phoebe zhennan.}, journal = {Plant physiology and biochemistry : PPB}, volume = {229}, number = {Pt E}, pages = {110781}, doi = {10.1016/j.plaphy.2025.110781}, pmid = {41297421}, issn = {1873-2690}, mesh = {*Wood/genetics/metabolism ; Gene Expression Regulation, Plant ; Plant Proteins/genetics/metabolism ; Flavonoids/metabolism/biosynthesis ; *Pigmentation/genetics ; *Poaceae/genetics/metabolism ; Color ; Genome, Plant ; Metabolomics ; Multiomics ; }, abstract = {Wood color serves as a crucial indicator of timber quality and economic value. Phoebe zhennan is well known for its golden-thread wood color. Nonetheless, the absence of genomic information precludes a comprehensive understanding of the genetic basis of wood color development in this species. In this study, we produced a chromosome-scale genome sequence for P. zhennan, investigated the molecular processes associated with the development of golden-thread wood color, and examined population dynamics over evolutionary time. The genome, with a size of 1001.05 Mb (contig N50 = 4.32 Mb, 2n = 24), comprises 27,284 protein-coding genes. Metabolomic studies revealed seven flavonoids, including cycloheterophyllin, astraganoside, and licoricone, that contribute to the development of golden-thread wood color. Additionally, we reconstructed the flavonoid biosynthetic pathway, which plays a significant role in the development of golden-thread wood color. In this process, transcription factors such as PzMYB2, PzNAC6, and PzWRKY12 were identified as core regulators that activate the expression of crucial enzyme-encoding genes, including PzGT2, PzGT3, and PzF2H3. Moreover, PzNAC6 may regulate flavonoid accumulation during wood development through direct interactions with PzHSF3, PzC3H8 and PzMYB2. In summary, comprehensive genome assembly, metabolomic, transcriptomic, and population genomic data will significantly enhance Phoebe genomic resources, aid in conservation biology studies, and offer vital insights for a deeper understanding of the mechanisms that drive wood color development.}, }
@article {pmid41295546, year = {2025}, author = {Calvo, A and Hall, S and Melgar Cossich, VB and Andreadakis, J and López Castillo, H and Pinto, D and Hewitt, I}, title = {HPV Vaccine Uptake and Cervical Cancer Trends in Panama: A Reference Point for Future Impact Studies.}, journal = {Vaccines}, volume = {13}, number = {11}, pages = {}, pmid = {41295546}, issn = {2076-393X}, abstract = {Background: Cervical cancer (CC) continues to be an important public health concern in Latin America, where it is the second cause of cancer-related deaths among women. With its strong culture of vaccination, Panama was the first country to implement the HPV vaccine as part of its Essential Program on Immunization (EPI). Recently, the government implemented the 90:70:90 PAHO/WHO strategy to reach milestones toward CC elimination. Objective: This analysis triangulates and assesses national data on HPV vaccination coverage, screening practices, and cervical cancer incidence and mortality in Panama, to understand historical tendencies to date and establish a comprehensive foundation for future impact evaluations and research studies. The analysis aims to identify trends and gaps in prevention efforts and to serve as a reference point for future research on HPV-associated cancers. Methods: Population-based, descriptive, observational, ecological study where four, aggregate, de-identified data sources by various curators in Panama were match-merged by year, sex, and administrative division. Reported outcomes include HPV vaccine coverage, CC incidence and mortality rates, screening Pap tests, and CC behavior at diagnosis (in situ vs. invasive). Results: Panama has high HPV vaccine uptake (≥85% most years) in spite of low Pap test coverage (~10%). A decreasing trend in CC incidence has been observed continuously since the 1990s, counterintuitively to significantly increasing CC mortality rates, with most cases diagnosed as invasive and among younger women (30-69 years old). Conclusions: This report provides a comprehensive foundation for understanding trends in HPV vaccination coverage, cervical cancer incidence and mortality, and screening practices in Panama. While high vaccine uptake and declining incidence trends are encouraging, persistent low screening rates and elevated mortality-particularly at invasive stages among younger women-highlight critical gaps in prevention efforts. The need for integrated strategies that strengthen data systems, improve early detection, and address structural and sociocultural barriers are discussed, framed within Panama's progress toward achieving the 90:70:90 targets. Future studies should focus on understanding non-medical influences on health and further vaccine impact with patient-level data, and other forms of HPV-related cancers in immunosuppressed populations. Public strategies would benefit from the implementation of real-life data and efficient data management, consolidation systems, systematic health promotion interventions, and an increase in resource allocation for women at the highest risk.}, }
@article {pmid41294456, year = {2025}, author = {Jacobs, S and Zhang, J and Wolf, E and Porter, E and Bohn, SJ and Sparks, AM and Eggermont, M and Summers, M and Rivera Cárdenas, CI and Clitheroe, H and Gillis, D and Smith, MA and Benessaiah, K and Jones, A and Davies, A and Helms, M and Bazely, D and Lipton, M and Dowhaniuk, D and van Vierssen Trip, N and Zampaki, N and Karpouzou, P and Wanieck, K}, title = {Are Ecosystem Services Replaceable by Technology Yet? Bio-Inspired Technologies for Ecosystem Services: Challenges and Opportunities.}, journal = {Biomimetics (Basel, Switzerland)}, volume = {10}, number = {11}, pages = {}, pmid = {41294456}, issn = {2313-7673}, support = {2022-00491//New Frontiers in Research - Canadian Federal Government/ ; }, abstract = {As ecological collapse accelerates under the pressures of anthropogenic climate change, adaptation strategies increasingly include technological proxies for nature's functions. But can ecosystem services (ES) be meaningfully replaced by technology? Revisiting this urgent question first posed by Fitter (2013), we assess the extent to which bio-inspired design-particularly biomimetics-has advanced the capacity to support, enhance, or replace natural ES. We convened an interdisciplinary team to synthesize and refine a comprehensive list of 22 ecosystem services, integrating often-overlooked cultural and relational dimensions. Using this framework, we conducted a large-scale analysis of over 68,000 peer-reviewed publications from the biomimetics and bio-inspired design literature between 2004 and 2025, applying AI-assisted classification to evaluate whether, and how, these technologies map onto specific ES functions and benefits. Our findings reveal both promise and profound limitations. Bio-inspired research engages with 20 of the 22 ES, but over 78% of this work concentrates on five technologically tractable functions-biochemicals, disease regulation, waste treatment, fibre/hide/wood, and fuel. Foundational supporting and regulating services such as pollination, soil formation, and nutrient cycling are almost entirely absent. Moreover, only 3% of technologies described in the academic literature aim to support existing systems; the overwhelming emphasis on enhancement (39%) and replacement (58%) suggests a design paradigm skewed toward substitution rather than coexistence. Intangible, co-produced services-particularly those related to culture, identity, and meaning-remain outside the current reach of biomimetic design. This skew reveals a dangerous imbalance: while certain ES can be technologically approximated, the relational, emergent, and systemic qualities of ecosystems elude replication. Technological replacement must not become a substitute for preservation. Instead, bio-inspired design should be mobilized as a tool for adaptation that amplifies and protects the living systems on which human and more-than-human futures depend.}, }
@article {pmid41293965, year = {2026}, author = {Navarro, D and Latch, EK and Tallon, AK and Ott-Conn, CN and DeYoung, RW and Walsh, DP and Euclide, PT and R G, C and Larson, WA and Seetharam, AS and Severin, AJ and Reecy, JM and Hu, ZL and Cantrell, JR and Carstensen, M and Caudell, JN and Killmaster, CH and Lockwood, ML and McKinley, WT and Norton, AS and Schuler, KL and Storm, DJ and Sumners, JA and Walter, WD and Blanchong, JA}, title = {Development of High-Throughput Genomic Resources to Inform White-Tailed Deer Population and Disease Management.}, journal = {Molecular ecology resources}, volume = {26}, number = {1}, pages = {e70085}, pmid = {41293965}, issn = {1755-0998}, support = {//Association of Fish and Wildlife Agencies/ ; //Michigan Department of Natural Resources/ ; //Michigan State University/ ; //Iowa State University/ ; //State of Iowa/ ; }, mesh = {Animals ; *Deer/genetics/classification ; Polymorphism, Single Nucleotide ; *Genomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Wasting Disease, Chronic/prevention &amp; control ; *Genetics, Population/methods ; Genotyping Techniques/methods ; North America ; }, abstract = {White-tailed deer (Odocoileus virginianus) are the most abundant and widespread cervid in North America. Genetic data are used as a tool to monitor populations and make management decisions for this game species. However, the development and use of genomic tools that can generate a set of markers suitable for longitudinal genomic data collection, whether for management purposes or to study the demographic and evolutionary processes of widely distributed species, have been challenging. This is mainly due to the cost required to fully implement and interpret the data produced. Here, we generated whole genome resequencing data for 44 free-ranging deer from three regions in their central and eastern North American range and identified over 89 million single nucleotide polymorphisms (SNPs). We used a subset of these SNPs to develop two nested SNP tools, a high-density array (702,183 SNPs) and a medium-density array (72,723 SNPs) to support deer and chronic wasting disease (CWD) management and research. SNPs were selected to ensure an even distribution across scaffolds of the reference genome and include SNPs associated with CWD susceptibility. Using genotyping results for 469 deer from 15 states in the US and Mexico generated by the high-density array and 1335 deer from 18 states generated by the medium-density array, we assessed genotyping success across different populations and explored some insights into population structure. These genomic tools offer a standard set of markers that will enable researchers and managers to address important questions related to white-tailed deer and CWD management. Our SNP arrays also offer the opportunity to examine aspects of white-tailed deer ecology and evolutionary history that were previously difficult to address.}, }
@article {pmid41293580, year = {2025}, author = {Siminiuc, R and Țurcanu, D and Siminiuc, S}, title = {Energy intake and dietary fiber as principal determinants of obesity in Eastern Europe, 2010-2022: an ecological panel study.}, journal = {Frontiers in public health}, volume = {13}, number = {}, pages = {1698838}, pmid = {41293580}, issn = {2296-2565}, mesh = {*Dietary Fiber/administration &amp; dosage ; Humans ; *Obesity/epidemiology ; *Energy Intake ; Europe, Eastern/epidemiology ; Female ; Male ; Adult ; Exercise ; Prevalence ; Overweight/epidemiology ; Middle Aged ; Diet/statistics &amp; numerical data ; }, abstract = {BACKGROUND: Obesity is a major global health challenge, with Eastern Europe standing out for rapid nutrition transitions and persistent social and economic inequalities. Despite its high prevalence, longitudinal ecological evidence on the structural determinants of obesity in this region remains limited.<br><br>OBJECTIVE: To examine population-level associations between dietary energy availability, dietary fiber intake, macronutrient composition, and insufficient physical activity with obesity and overweight prevalence in Eastern Europe during 2010-2022.<br><br>METHODS: Data from FAOSTAT and the World Health Organization were assembled into a balanced panel of 130 country-year observations. Analyses combined descriptive statistics and Pearson correlations with two-way fixed-effects regressions (country and year), using robust standard errors and one-year lagged predictors to test for robustness.<br><br>RESULTS: Higher energy availability was positively associated with both obesity and overweight, while dietary fiber consistently showed a protective effect. Marginal estimates indicated that an additional 100&#x202f;kcal/day predicted an increase of nearly one percentage point in obesity, whereas +5&#x202f;g/day of fiber corresponded to an approximate two-percentage-point reduction. Neither macronutrient shares nor insufficient physical activity showed significant associations.<br><br>CONCLUSION: Dietary energy and fiber emerge as the primary structural correlates of obesity in Eastern Europe. These findings underscore the need for region-specific, data-driven nutrition and public health policies to address obesogenic environments and reduce socio-economic disparities in diet quality.}, }
@article {pmid41291465, year = {2025}, author = {Leber, W and Farooq, HZ and Panovska-Griffiths, J and Larvin, H and Baggaley, RF and Divall, P and Haigh, D and Davies, EA and Choudhry, S and Hicks, SR and Goodwin, L and Foster, GR and Orkin, CM and Zenner, D and Vickerman, P and Hickman, M and Reid, L and Worrall, S and Pareek, M and Lais, S and Anderson, J and Robson, J and Griffiths, CJ}, title = {Risk prediction models for targeted testing of HIV, hepatitis B and hepatitis C: a systematic review and meta-analysis.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {1648}, pmid = {41291465}, issn = {1471-2334}, abstract = {BACKGROUND: Diagnosing human immunodeficiency virus (HIV), hepatitis B virus (HBV), and hepatitis C virus (HCV) infections in general population settings is challenging. We conducted a systematic review and meta-analysis of prediction tools designed to help identify individuals at risk of these blood-borne viruses.<br><br>METHODS: We included studies on individuals of any age at risk of blood-borne viruses from healthcare, community settings, and national databases. We searched the Web of Science, MEDLINE, EMBASE, and CENTRAL databases (from database inception to 2023) and used the Prediction model Risk Of Bias ASsessment Tool (PROBAST) to evaluate the quality and systematic risk of bias of these studies. We extracted model accuracy using the area under the receiver operating characteristic curve (AUC), sensitivity, and specificity. A mixed-effects model (for AUC) and bivariate random-effects model (for sensitivity/specificity) were used to generate pooled values for these studies.<br><br>RESULTS: Of the 41,585 records, 71 were included, covering over 31 million participants and more than 65,000 cases of blood-borne viruses. We examined 67 models: 47 for HIV, 13 for HCV, 5 for HBV, and 2 from studies that assessed multiple viruses separately. The studies were conducted in 41 low- and middle-income and 30 high-income countries. They covered 11 different populations (including men who have sex with men, the general population, and women), 8 types of settings (including sexual health, secondary care, and primary care) and 7 types of risk factors (behavioural, clinical, and demographic). The methods comprised traditional regression (n&#x2009;=&#x2009;50), machine-learning models (n&#x2009;=&#x2009;17), and others (n&#x2009;=&#x2009;4). The risk of bias was high in 64 studies and low in seven. Among 33 studies reporting mean and 95% CI, pooled AUC values were 0.73 (95% CI:0.67&#x2013;0.80, [Formula: see text]&#x2009;=&#x2009;74%) across HIV studies (including 8 machine-learning models), 0.80 (0.73&#x2013;0.86, [Formula: see text]&#x2009;=&#x2009;86%) for HCV (including 2 machine-learning models) and 0.79 (0.76&#x2013;0.81, [Formula: see text]&#x2009;=&#x2009;93%) for HBV (including 3 machine-learning models).<br><br>CONCLUSIONS: Significant heterogeneity exists in blood-borne virus prediction accuracy across diverse settings and populations, with a high risk of bias. Contributions from primary care were limited, and evaluation and reporting were inconsistent. Developing and evaluating effective models for the combined risk assessment of HIV, HBV, and HCV in general population settings remains a priority.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12879-025-11921-3.}, }
@article {pmid41290686, year = {2025}, author = {Niedostatek, M and Baptista, A and Yamamoto, J and Kurths, J and Sanchez Garcia, R and MacArthur, BD and Bianconi, G}, title = {Mining higher-order triadic interactions.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {11613}, pmid = {41290686}, issn = {2041-1723}, mesh = {Humans ; Algorithms ; Leukemia, Myeloid, Acute/genetics/metabolism ; *Data Mining/methods ; Neural Networks, Computer ; }, abstract = {Complex systems often involve higher-order interactions that go beyond pairwise networks. Triadic interactions, where one node regulates the interaction between two others, are a fundamental form of higher-order dynamics found in many biological systems, from neuron-glia communication to gene regulation and ecosystems. However, triadic interactions have so far been mostly neglected. In this article, we propose the Triadic Perceptron Model (TPM) which shows that triadic interactions can modulate the mutual information between the dynamical states of two connected nodes. Leveraging this result, we formulate the Triadic Interaction Mining (TRIM) algorithm to extract triadic interactions from node metadata, and we apply this framework to gene expression data, finding new candidates for triadic interactions relevant for Acute Myeloid Leukemia. Our findings highlight crucial aspects of triadic interactions that are often ignored, offering a framework that can deepen our understanding of complex systems across biology, ecology, and climate science.}, }
@article {pmid41290171, year = {2025}, author = {Becker, JA and Ortega, AC and Beck, J and Buchanan, CB and Bills, T and Hall, LE and Hennig, JD and Hnilicka, P and Huggler, K and Kauffman, M and Middleton, A and Mong, TW and Monteith, KL and Reinking, A and Sawyer, H and Scasta, J and Scurlock, BM and Merkle, JA}, title = {The role of spatiotemporal variation in resources in the diverse movement strategies of temperate ungulates.}, journal = {Proceedings. Biological sciences}, volume = {292}, number = {2059}, pages = {20251973}, pmid = {41290171}, issn = {1471-2954}, support = {//Wyoming Governor's Big Game License Coalition/ ; //U.S. Geological Survey/ ; //George B. Storer Foundation/ ; //Wyoming Game and Fish Department/ ; //University of Wyoming-Reclamation and Restoration Center/ ; //Memorial Resource Development/ ; //Pinedale Anticline Project Office/ ; //National Geographic Society/ ; //University of Wyoming-School of Energy Resources/ ; //Bureau of Land Management/ ; //University of Wyoming-Haub School/ ; //Wyoming Sage Grouse Conservation Funds/ ; //Native Range Capture Services/ ; //Marathon Oil/ ; //Anadarko Petroleum Company/ ; //Petro-Canada/ ; //PacifiCorp/ ; //L. Floyd Clarke Greater Yellowstone Scholarship/ ; //Grand Teton Association/ ; //Samson Resources/ ; //Rawlins Field Office/ ; //Wyoming State Legislature/ ; //The Greater Yellowstone Coordinating Committee/ ; //Knobloch Family Foundation/ ; //Nature Conservancy/ ; //Brucellosis-Feedground-Habitat Program/ ; //Black Diamond Minerals LLC/ ; //The Greater Yellowstone Coalition/ ; //British Petroleum North America/ ; //Rocky Mountain Elk Foundation/ ; //Wyoming Chapter of The Wildlife Society/ ; //Sky Aviation/ ; //Leading Edge Aviation, LLC/ ; //Warren Resources/ ; //Wyoming Animal Damage Management Board/ ; //Linn Energy/ ; //University of Wyoming/ ; //Devon Energy Corporation/ ; //Community Forestry and Environmental Research Partnership Fellowship/ ; //Yellowstone Center for Resources/ ; //Greater Yellowstone Interagency Brucellosis Committee/ ; }, mesh = {Animals ; *Animal Migration ; *Deer/physiology ; Wyoming ; Seasons ; Climate ; Geographic Information Systems ; *Antelopes/physiology ; }, abstract = {Animal movement strategies are thought to be determined by the spatiotemporal variation of resources in an environment. Observations of various species indicate that the occurrence of migratory versus resident movements depends on resource predictability and the associated costs and benefits of tracking resource availability versus remaining in a familiar range. Here, we use 21 years of GPS data from seven populations (n = 239) of pronghorn (Antilocapra americana) and 12 populations (n = 283) of elk (Cervus canadensis) across Wyoming, USA to test if resource-based hypotheses predict individual movement strategies within a common geographic range. We identified three distinct movement strategies in each species-residents, dual-range migrants and multi-range migrants. Spatiotemporal variation in resources did explain variation in strategies in both pronghorn and elk, with residents experiencing less spatial and greater year-to-year variation than migratory individuals. However, spatiotemporal variation did not predict differentiation between dual- and multi-range migrants in either species. Climatic conditions were also important, especially in elk, where individuals were less likely to be resident when they experienced worse winters. Our findings demonstrate that the movement strategies of temperate ungulates are consistently linked to spatiotemporal resource variation across scales, but additional mechanisms can also facilitate localized behavioural differences.}, }
@article {pmid41289675, year = {2026}, author = {Zou, D and Fancello, G and Montanari, A and Zhou, S and Chaix, B}, title = {Momentary associations between time-varying social contacts and depressive symptomatology in older adults: A GPS-based mobility survey study.}, journal = {Social science &amp; medicine (1982)}, volume = {389}, number = {}, pages = {118834}, doi = {10.1016/j.socscimed.2025.118834}, pmid = {41289675}, issn = {1873-5347}, mesh = {Humans ; Male ; Female ; Aged ; *Depression/psychology/epidemiology ; France/epidemiology ; Ecological Momentary Assessment ; Bayes Theorem ; Geographic Information Systems/statistics &amp; numerical data ; Surveys and Questionnaires ; Aged, 80 and over ; Time Factors ; Middle Aged ; *Interpersonal Relations ; }, abstract = {Studies often investigate the long-term impact of social contacts on mental health in older adults, neglecting momentary effects. This research, grounded in the consideration of daily activity, explores how time-varying social contacts associate with momentary depressive symptoms among 216 older adults in the Île-de-France region. Employing a geographically-explicit ecological momentary assessment approach (GEMA), we collected participants' depressive symptoms, mobility locations, and social contacts data via smartphone surveys, GPS receivers, and mobility survey over 7 days. Bayesian mixed models with random effects at individual and daily levels, considering time autocorrelation, were employed. Participants engaging with social contacts exhibited lower depression not only immediately but also in the following hours. Interestingly, a longer duration of time spent with social contacts did not lead to a sharper decrease in depression levels. Notably, larger decreases were observed when the number of social contacts increased from one to two, especially with friends or family members.}, }
@article {pmid41289307, year = {2025}, author = {Guang, A and Dunn, CW and Novitsky, V and Howison, M and Kantor, R}, title = {T-shaped alignments integrating HIV-1 near full-length genome and partial pol sequences can improve phylogenetic inference of transmission clusters.}, journal = {PLoS computational biology}, volume = {21}, number = {11}, pages = {e1013676}, pmid = {41289307}, issn = {1553-7358}, support = {K24 AI134359/AI/NIAID NIH HHS/United States ; P20 GM109035/GM/NIGMS NIH HHS/United States ; P30 AI042853/AI/NIAID NIH HHS/United States ; R01 AI136058/AI/NIAID NIH HHS/United States ; }, mesh = {*HIV-1/genetics/classification ; *Phylogeny ; Humans ; *HIV Infections/transmission/virology/epidemiology ; *Genome, Viral/genetics ; *Sequence Alignment/methods ; Computational Biology/methods ; Cluster Analysis ; Algorithms ; }, abstract = {Molecular epidemiology and HIV-1 transmission networks reconstruction can provide insights into transmission dynamics and inform public health strategies. Long HIV sequences, such as near full-length (nFL) genomes, can improve the accuracy of phylogenetic inference. However, relatively short pol sequences are still broadly used for inferring molecular HIV clusters. Whether a mix of long and short HIV-1 sequences can improve phylogenetic inference of molecular HIV clusters remains unknown. We propose a flexible approach called T-shaped alignments that incorporates both nFL HIV-1 genomes and partial pol sequences, and investigate whether this approach improves phylogenetic reconstruction of molecular clusters. Under the assumption that clustering from 100% of long sequences is the most accurate, we obtained 1196 subtype B nFL HIV-1 sequences from the Los Alamos National Laboratory Database and a single-study subset, varied the proportion of long and short sequences in our T-shape alignments, systematically masked all non-pol regions with missing characters in proportional increments, and compared tree similarity and cluster inference among datasets. With the full dataset, we found that when more than 50% of available sequences are nFL, the T-shaped alignment gradually yields results closer to the 100% n, with more and larger clusters identified. However, below the 50% threshold accuracy did not increase. Stringent bootstrap thresholds decreased cluster accuracy gaps but also decreased number of clusters found and mean cluster size. For the subset dataset, we found that the introduction of nFL sequences to the T-shaped alignment improves accuracy in clustering either after a 30% threshold or immediately depending on bootstrap choice. Our new approach and results suggest that using T-shape alignments to mix HIV-1 sequences of different lengths can improve phylogenetic and clustering accuracy, with needed nFL proportion depending on analysis goals. The T-shape alignment provides a straightforward method for utilizing all available sequences to improve phylogenetic analysis.}, }
@article {pmid41288576, year = {2025}, author = {Li, J and Cai, X and Li, M and Zhang, D and Li, B and Jin, LN and Luo, C and Zhang, G}, title = {In situ degradation of 2-methylnaphthalene by a soil Penicillium strain associated with fungal-bacterial interactions.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {41288576}, issn = {1751-7370}, support = {42192513//National Natural Science Foundation of China/ ; 42277210//National Natural Science Foundation of China/ ; 42477262//National Natural Science Foundation of China/ ; 2023B1515020038//Natural Science Foundation of Guangdong Province, China/ ; 2023B1212060049//Guangdong Foundation for Program of Science and Technology Research/ ; 2023368//Youth Innovation Promotion Association CAS/ ; }, mesh = {*Penicillium/metabolism/genetics/isolation &amp; purification/classification ; Biodegradation, Environmental ; *Soil Microbiology ; *Naphthalenes/metabolism ; *Bacteria/metabolism/genetics ; *Microbial Interactions ; *Soil Pollutants/metabolism ; Metabolic Networks and Pathways/genetics ; }, abstract = {Fungi play critical but underappreciated roles comparing to bacteria in the bioremediation of organic pollutants, particularly emerging contaminants. Numerous fungal species, along with their functional genes and metabolic pathways, remain largely unexplored. Here, we integrate single-cell Raman-activated cell sorting with stable isotope probing to identify and characterize in situ active fungi involved in emerging contaminant degradation. This approach enabled the isolation of a Penicillium sp. strain LJD-20, previously unreported, which acts as an active degrader of 2-methylnaphthalene, a model emerging pollutant. Genomic analyses revealed that LJD-20 harbors a diverse repertoire of degradation-related genes, including those encoding dioxygenases, methyl hydroxylases, and cytochrome P450 monooxygenases, highlighting its versatile metabolic potential. Single-cell genome sequencing also uncovered a potential close fungal-bacterial co-occurrence, suggesting possible ecological or metabolic interactions. In bioaugmentation trials, strain LJD-20 independently degraded 2-methylnaphthalene and simultaneously promoted the enrichment of other microorganisms involved in its removal. These findings highlight the metabolic versatility and ecological importance of fungi in pollutant degradation and demonstrate the utility of combining single-cell and isotopic approaches to explore microbial function and interaction in complex environments.}, }
@article {pmid41285988, year = {2025}, author = {Li, M and Li, Z and Xu, C and Chen, Y}, title = {Semi-supervised medical image segmentation of bladder tumors based on supervised branches and uncertainty estimation.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {41517}, pmid = {41285988}, issn = {2045-2322}, support = {No. 2019YFC0117800//National Key Research and Development Program of China/ ; No. 2019YFC0117800//National Key Research and Development Program of China/ ; No. 2019YFC0117800//National Key Research and Development Program of China/ ; No. 2019YFC0117800//National Key Research and Development Program of China/ ; }, mesh = {*Urinary Bladder Neoplasms/diagnostic imaging/pathology ; Humans ; Uncertainty ; Algorithms ; *Image Processing, Computer-Assisted/methods ; *Supervised Machine Learning ; *Image Interpretation, Computer-Assisted/methods ; Reproducibility of Results ; }, abstract = {Supervised learning has excellent segmentation performance in bladder tumor segmentation, but it relies on a large amount of labeled data. To learn the features of bladder tumors from limited labeled data and obtain accurate segmentation results, we propose a semi-supervised segmentation method for bladder tumors, UDS-MT. The method consists of a Mean Teacher network and a guided branch, which respectively undertake the tasks of segmentation prediction and supervision of prediction results. Mean teacher network uses the exponential moving average (EMA) mechanism to update the teacher network parameters to achieve fine-grained capture of the target shape; the guided branch uses uncertainty estimation to filter out pixel blocks with high confidence to obtain more reliable masks, and it suppresses overfitting on some certain extent. In addition, we propose a defend loss term that only calculates the loss for pixels with high prediction confidence of the model, thereby improving the reliability of the pseudo-label. After evaluation on a bladder tumor clinical medical image dataset, when the labeled data is limited to 15%, the Dice coefficient of the network segmentation target shape can reach up to 80.04%, which is at least 2.81% higher than other methods.}, }
@article {pmid41285897, year = {2025}, author = {Dalisay, DS and Mateo, JC and Teodosio, JJR and Jusa, LMS and Baladjay, DMS and de Guzman, LS and Balida, LAP and Jamal, JA}, title = {Identification of SARS-CoV-2 3CLpro inhibitors from marine actinomycetes through integrated phylogeny-based metabolomics with functional screening and bioinformatic analysis.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {41503}, pmid = {41285897}, issn = {2045-2322}, mesh = {*Actinobacteria/chemistry/metabolism/genetics/classification ; *SARS-CoV-2/drug effects/enzymology ; Phylogeny ; Metabolomics/methods ; *Antiviral Agents/pharmacology/chemistry ; Computational Biology/methods ; *Coronavirus 3C Proteases/antagonists &amp; inhibitors/metabolism/chemistry ; Humans ; COVID-19/virology ; Molecular Docking Simulation ; *Protease Inhibitors/pharmacology/chemistry ; COVID-19 Drug Treatment ; }, abstract = {As the acute threat of the COVID-19 pandemic diminishes globally, advancing the research and development of antiviral agents remains crucial for ensuring preparedness for future outbreaks. This study investigates the inhibitory effects of marine sediment-derived actinomycetes on the SARS-CoV-2 main protease (3CLpro), a key enzyme involved in viral replication and transcription. Extracts of 75 actinomycete strains from two locations, Nogas Island in Antique and Tubbataha Reefs Natural Park in Palawan, Philippines, were evaluated for their ability to inhibit 3CLpro, with 36% of the extracts showing more than 90% inhibition. Further examination of 27 extracts revealed IC50 values between 2 and 8 µg/mL, suggesting notable inhibitory strength. Phylogenetic analysis grouped the active strains into seven distinct clades, with Clades 1, 5, and 6, closely related to Streptomyces enissocaesilis, S. geysiriensis, S. ardesiacus, and S. indicus, exhibiting antiviral activity. Metabolomic profiling using LCMS-QTOF, coupled with principal component analysis (PCA) and hierarchical clustering, revealed that metabolic signatures were consistent with clade classification. Shared features among the active clades included a biohopanoid, fatty acid amides, diketopiperazines, lipid derivatives, and aromatic compounds. Supervised analysis using orthogonal partial least squares discriminant analysis (OPLS-DA) identified 17 discriminant metabolites produced by Streptomyces strains associated with antiviral activity, including a bicyclic sesquiterpenoid, an aromatic polyketide, an alkylphenol, fatty acid derivatives, alkylated aromatic amines, lipid-derived metabolites, and a carbazole alkaloid. Among the identified compounds, streptocarbazole C showed a strong predicted binding affinity to SARS-CoV-2 3CLpro (- 9.8 ± 0.30 kcal/mol) in molecular docking analysis, with favorable interactions at the enzyme's catalytic dyad (HIS41 and CYS145). In silico toxicity predictions suggested a generally favorable safety profile, although some limitations were noted. These findings highlight the biosynthetic and functional potential of marine sediment-derived Streptomyces against SARS-CoV-2 3CLpro, providing a framework for the discovery of antiviral natural products through the integration of ecological, phylogenetic, metabolomics, and computational analyses.}, }
@article {pmid41285770, year = {2025}, author = {Gamaarachchi, H and Stevanovski, I and Hammond, JM and M Reis, AL and Rapadas, M and Jayasooriya, K and Russell, T and Yeow, D and Hort, Y and Patel, C and Mallett, AJ and Stackpoole, E and Roman, L and Silver, LW and Hogg, CJ and Streeting, LM and Bogdanovic, O and Coelho Rodrigues Noronha, R and Santos do Nascimento, LA and Lima Cardoso, A and Georges, A and Cheng, H and Patel, HR and Kumar, KR and Mallawaarachchi, AC and Deveson, IW}, title = {Targeted sequencing and iterative assembly of near-complete genomes.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10406}, pmid = {41285770}, issn = {2041-1723}, mesh = {Humans ; *Genome, Human/genetics ; *Nanopore Sequencing/methods ; Animals ; *Sequence Analysis, DNA/methods ; Algorithms ; High-Throughput Nucleotide Sequencing/methods ; *Genomics/methods ; }, abstract = {Advances in long-read sequencing (LRS) and assembly algorithms have made it possible to create highly complete genome assemblies for humans, animals and plants. However, ongoing development is needed to improve accessibility, affordability, and assembly quality and completeness. 'Cornetto' is a new strategy in which we use programmable selective nanopore sequencing to focus LRS data production onto the unsolved regions of a nascent assembly. This improves assembly quality and streamlines the process, both for humans and non-human vertebrates. Cornetto enables us to generate highly complete diploid human genome assemblies using only nanopore LRS data, surpassing the quality of previous efforts at a fraction of the cost. Cornetto enables genome assembly from challenging sample types like human saliva. Finally, we obtain accurate assemblies for clinically-relevant repetitive loci at the extremes of the genome, demonstrating valid approaches for genetic diagnosis in facioscapulohumeral muscular dystrophy (FSHD) and MUC1-autosomal dominant tubulointerstitial kidney disease (MUC1-ADTKD).}, }
@article {pmid41285720, year = {2025}, author = {Li, J and Liao, Q and Zhou, H and Hu, R and Li, Y and Hu, Z and Yu, B and Liu, P and Zheng, Q and Pu, W and Sheng, S and Liu, Y and Wu, S and Liu, T and Xiao, Q and Duan, S and Gao, J and Li, X and Wang, S and Xiao, H and Zhou, Z and Lu, Z and Yang, J and Yan, J}, title = {Multi-omics analyses reveal regulatory networks underpinning metabolite biosynthesis in Nicotiana tabacum.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10339}, pmid = {41285720}, issn = {2041-1723}, support = {32425011//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32502746//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Nicotiana/genetics/metabolism ; Gene Expression Regulation, Plant ; *Gene Regulatory Networks ; Metabolomics/methods ; Plant Leaves/metabolism/genetics ; Transcriptome ; Plant Proteins/genetics/metabolism ; Metabolome ; Metabolic Networks and Pathways/genetics ; Gene Expression Profiling ; Metabolic Engineering ; Multiomics ; }, abstract = {Tobacco is a significant industrial crop, serving as a model for plant science and a promising specie for the production of proteins and small molecules. However, system biology studies of tobacco under natural field cultivation conditions remain scarce. Here, we construct a genome-scale metabolic regulatory network through integration of dynamic transcriptomic and metabolomic profiles from field-grown tobacco leaves across two ecologically distinct regions. We map 25,984 genes and 633 metabolites into 3.17 million regulatory pairs using multi-algorithm integration. This network reveals three pivotal transcriptional hubs, including NtMYB28 (promoting hydroxycinnamic acids synthesis by modifying Nt4CL2 and NtPAL2 expression), NtERF167 (amplifying lipid synthesis via NtLACS2 activation) and NtCYC (driving aroma production through NtLOX2 induction). These transcriptional hubs achieve substantial yield improvements of target metabolites by rewiring metabolic flux. The present work provides a systems-level atlas of tobacco metabolic regulation and may help to guide metabolic engineering.}, }
@article {pmid41283812, year = {2025}, author = {Shang, J and Peng, C and Guan, J and Cai, D and Wang, D and Sun, Y}, title = {From genomic signals to prediction tools: a critical feature analysis and rigorous benchmark for phage-host prediction.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {6}, pages = {}, pmid = {41283812}, issn = {1477-4054}, support = {//Hong Kong Research Grants Council/ ; 11209823//General Research Fund/ ; 9667256//City University of Hong Kong/ ; 9678241//City University of Hong Kong/ ; 217310019//Open Research Fund of Guangdong Provincial Key Laboratory of Wastewater Information Analysis and Early Warning/ ; }, mesh = {*Bacteriophages/genetics/physiology ; *Genomics/methods ; *Computational Biology/methods ; Benchmarking ; *Host-Pathogen Interactions ; Genome, Viral ; }, abstract = {Accurate prediction of virus-host interactions is critical for understanding viral ecology and developing applications like phage therapy. However, the growing number of computational tools has created a complex landscape, making direct performance comparison challenging due to inconsistent benchmarks and varying usability. Here, we provide a systematic review and a rigorous benchmark of 27 virus-host prediction tools. We formulate the host prediction task into two primary frameworks-link prediction and multi-class classification-and construct two benchmark datasets to evaluate tool performance in distinct scenarios: a database-centric dataset (RefSeq-VHDB) and a metagenomic discovery dataset (MetaHiC-VHDB). Our results reveal that no single tool is universally optimal. Performance is highly context-dependent, with tools like CHERRY and iPHoP demonstrating robust, broad applicability, while others, such as RaFAH and PHIST, excel in specific contexts. We further identify a critical trade-off between predictive accuracy, prediction rate, and computational cost. This work serves as a practical guide for researchers and establishes a standardized benchmark to drive future innovation in deciphering complex virus-host interactions.}, }
@article {pmid41281954, year = {2025}, author = {Johnston, PI and Chizani, K and Chirwa, E and Dale, H and Patel, P and Silungwe, N and Mkwangwanya, C and Kachala, T and Mhango, C and Nyirenda, G and Diness, Y and Mpesi, S and Wachepa, R and Shumba, F and Mwakiseghile, F and Rashid, V and Misiri, T and Ashton, PM and Chunga, A and Cocker, D and Cunningham-Oakes, E and Jewell, C and Feasey, N and Gordon, MA and Nyirenda, T}, title = {Transmission dynamics for invasive Non-Typhoidal S almonella serovars (TiNTS): protocol for a household study of transmission and immune response to non-typhoidal Salmonella in Malawi.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {581}, pmid = {41281954}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {BACKGROUND: Invasive non-typhoidal Salmonella (iNTS) disease is a leading cause of community-onset bloodstream infection in Africa, driving high morbidity in young children. The World Health Organization has published preferred product characteristics for an iNTS vaccine, but lack of transmission data is an impediment to vaccine licensure. Enteric NTS (eNTS) is the asymptomatic carriage of NTS in stool that precedes invasive disease. We do not know how long eNTS shedding lasts, how often infection spreads in endemic settings, or how an eNTS episode shapes immunity against later invasion. These gaps make it difficult to define trial sites, select cohorts, refine target product profiles, and build reliable models of vaccine impact. Here we describe TiNTS, a prospective household study in Blantyre, Malawi, which will measure real-time eNTS incidence, transmission, and antibody responses to close these evidence gaps and accelerate rational vaccine deployment.<br><br>METHODS: We will recruit all members of at least 60 households in Ndirande, Blantyre, Malawi. Stool samples will be collected every other day for at least four weeks and tested for NTS using culture and pan- Salmonella PCR on growth media. Environmental samples collected at enrolment will be tested using the same methods. Symptoms and exposure risks will be recorded throughout.We will collect blood samples at enrolment, after four weeks, and four weeks after the first eNTS episode in each household. We will measure serum IgG responses to Salmonella Typhimurium and Enteritidis LPS antigens. We will extend follow-up if participants continue shedding or if the first household case occurs with fewer than 14 days of follow-up remaining.All culture-positive isolates and PCR-positive broths will undergo Illumina sequencing to enable genome and metagenome reconstruction for transmission inference.<br><br>CONCLUSIONS: TiNTS will define the burden, transmission patterns, and immune response to eNTS. Findings will inform vaccine modelling, trial design, and targeted introduction strategies.}, }
@article {pmid41280341, year = {2025}, author = {Ma, J and Xu, L and Han, Q and Gao, J and Yuan, H and Dong, K and Huang, C and Zhou, C and Ji, JS and Zhang, C and Zeng, H and Guo, Y and Luo, L and Zhang, X and Luo, Y and Liu, Q and Stenseth, NC and Liang, W}, title = {The Indian Ocean Dipole drives imported-dominated dengue outbreaks in China: Mechanisms and predictions.}, journal = {PNAS nexus}, volume = {4}, number = {11}, pages = {pgaf350}, pmid = {41280341}, issn = {2752-6542}, abstract = {Dengue fever, influenced by climate dynamics and human mobility in nonendemic regions, remains poorly understood. We assessed the effects of large-scale climate features on domestic dengue outbreaks using data from China (2013-2021) and projections for 2023-2028, incorporating climate, human mobility, and environmental factors. A significant positive correlation (r = 0.89, P < 0.01) was found between domestic dengue incidence and overseas imported cases. Significant associations were also noted with domestic (F 2.96, 25.78 = 518.03, P < 0.01) and international human mobility (F 2.77, 25.78 = 66.84, P < 0.01), the Indian Ocean Dipole (IOD) index (F 2.98, 25.78 = 522.84), and vectorial capacity (F 2.92, 25.78 = 338.74, P < 0.01). IOD is the most influential climate feature, with a trend of intensification over time. The Extreme Gradient Boosting (XGBoost) algorithm incorporating IOD (r [2] = 0.56) predicted outbreaks in 2025, 2026, and 2028. Our findings reveal that large-scale climate phenomenon, notably the IOD, and human mobility significantly influence dengue domestic outbreaks in China through a "dislocated impact."}, }
@article {pmid41279688, year = {2025}, author = {Tchourine, K and Carballo-Pacheco, M and Vitkup, D}, title = {Macroecological Laws Can Naturally Arise from Chaotic Internal Species Dynamics.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41279688}, issn = {2692-8205}, support = {R01 DK118044/DK/NIDDK NIH HHS/United States ; R35 GM131884/GM/NIGMS NIH HHS/United States ; }, abstract = {Macroecological relationships that connect various statistical descriptors of long-term and short-term species dynamics represent some of the most general laws in ecology and biology. These macroecological laws have been observed across diverse ecologies of plants and animals, and more recently, also in microbiota. Yet it remains unclear why strikingly similar macroecological relationships often arise in very different biological communities and various environmental contexts. Here, we investigated whether chaotic internal dynamics in spatially heterogeneous communities could underlie multiple macroecological relationships. Our analyses reveal that very general constraints on species interactions and spatial migration parameters can simultaneously lead to multiple macroecological laws found in microbial ecosystems without requiring external sources of noise. Our study also identifies the mechanistic origins of many empirically observed macroecological relationships, such as Taylor's law, anomalous abundance diffusion, the Laplace distribution of short-term abundance changes, and the distribution of species residence times. Overall, we demonstrate how macroecological laws can arise from interaction-driven chaotic dynamics and common ecological constraints, thereby providing a unifying explanation for their widespread prevalence in nature.}, }
@article {pmid41279534, year = {2025}, author = {McCrone, JT and Baele, G and Omah, IF and Kinganda-Lusamaki, E and Brew, JA and Carvalho, LM and Dudas, G and Mbala-Kingebeni, P and Suchard, MA and Rambaut, A}, title = {Evidence of latency reshapes our understanding of Ebola virus reservoir dynamics.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41279534}, issn = {2692-8205}, support = {/WT_/Wellcome Trust/United Kingdom ; R01 AI153044/AI/NIAID NIH HHS/United States ; R01 AI162611/AI/NIAID NIH HHS/United States ; }, abstract = {Ebola virus (EBOV) has caused severe outbreaks of haemorrhagic fever in Central and West Africa since the first observed zoonotic epidemic in the late 1970s. While recent outbreaks have revealed much about the epidemiological dynamics that sustain human-to-human transmission, the mechanisms by which the virus persists between outbreaks are unknown. Previously, phylogenetic approaches have been used to characterise the EBOV reservoir from the evolutionary relationships among observed human outbreaks. We here employ a novel phylogenetic latency model - inspired by recent observations of extreme EBOV evolutionary rate heterogeneity in humans - to characterise the natural history of EBOV and by extension its reservoir. We find the prevailing model of EBOV reservoir dynamics is deficient, and the long-term EBOV evolutionary rate is slower than previously believed. The hypothesis that EBOV diversity dates back to a bottleneck event just prior to the first human outbreak is not supported by the data. Further, our results suggest that EBOV undergoes extended periods of quiescence in the reservoir, similar to that observed in a small fraction of human infections. These findings have significant implications for understanding the source of EBOV outbreaks, characterising the EBOV reservoir, and uncovering the factors that contribute to EBOV outbreaks in humans.}, }
@article {pmid41278887, year = {2025}, author = {Rühlemann, M and Szánthó, LL and Waschina, S and Moitinho-Silva, L and Mews, LK and Camarena, JF and Jebens, H and Costa, J and Juimo, V and Fezeu, A and Agyei, A and Afihene, MY and Asibey, SO and Awuku, YA and Duah, A and Nartey, YA and Ibrahim, F and Lim, YAL and Pin, TM and Onyekwere, C and Rusine, J and Mwikarago, IE and Baines, J and Franke, A and Szöllősi, GJ and Xavier, R and Alm, EJ and Groussin, M and Poyet, M}, title = {Convergent genomic responses of human gut bacteria to variations in industrialization.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41278887}, issn = {2692-8205}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; }, abstract = {To what extent gut bacteria respond to the distinct ecological pressures imposed by human lifestyle remains unclear. Here, we investigate how genomic adaptation in gut bacteria differ between industrialized and non-industrialized human populations. We generated a broad collection of isolate genomes spanning diverse host geographies, lifestyles, species, and strains. We first found that compared to MAGs, paired isolate genomes recover more functional elements and signals of horizontal gene transfers (HGTs). Leveraging isolate genomes from multiple species, we find that strains from industrialized hosts experience an expansion of proteome size and harbor greater pangenome fluidity, driven by recent events of HGTs. Gene- and variant-level analyses reveal convergent patterns of lifestyle-specific adaptation in functions that are critical for ecological adaptation, such as stress response, cell envelope remodeling and central metabolism. Our results demonstrate that industrialization imprints evolutionary signatures on gut bacterial genomes, illuminating the effects of rapidly changing environments on human biology.}, }
@article {pmid41278536, year = {2025}, author = {Petrovič, M and Bartas, M and Garratt, AN and Pečinka, P and Dobrovolná, M and Koňaříková, K and Trenz, O and Brázda, V and Šťastný, J}, title = {Z-DNA Hunter tool for straightforward detection of Z-DNA forming regions and a case study in Drosophila.}, journal = {NAR genomics and bioinformatics}, volume = {7}, number = {4}, pages = {lqaf166}, pmid = {41278536}, issn = {2631-9268}, mesh = {Animals ; *Drosophila melanogaster/genetics ; *Software ; Algorithms ; Genome, Insect ; DNA ; }, abstract = {Z-DNA is a left-handed DNA conformation linked to gene regulation, chromatin dynamics, and immunity. Despite its importance, genome-wide prediction of Z-DNA forming sequences (ZFS) remains limited by the absence of fast and accessible tools. Here, we present Z-DNA Hunter, a user-friendly web server for genome-scale ZFS prediction utility. The algorithm employs a pattern-based approach optimized for canonical motifs such as (GC)n and (CA)n repeats, with adjustable parameters for detection stringency. Compared with existing methods, Z-DNA Hunter achieves similar or higher accuracy while reducing runtime from hours to seconds, making large-scale analyses feasible. To demonstrate its application, we analyzed the Drosophila melanogaster genome and uncovered a pronounced enrichment of long ZFS on the X chromosome, contrasting with their near absence on the satellite repeat- and transposable element-rich Y chromosome. These findings illustrate both the scalability of Z-DNA Hunter and its potential to reveal biologically meaningful patterns of non-B-DNA. The tool provides direct visualization and export options (e.g. BedGraph for UCSC Genome Browser) and is freely available at https://bioinformatics.ibp.cz/#/analyse/zdna.}, }
@article {pmid41278531, year = {2024}, author = {Morales, HE and van Oosterhout, C and Whitford, H and Tatayah, V and Ruhomaun, K and Groombridge, JJ and Gilbert, MTP and ,  and ,  and ,  and , }, title = {The genome sequence of the Pink Pigeon, Nesoenas mayeri (Prévost, 1843).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {336}, pmid = {41278531}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Nesoenas mayeri (the Pink Pigeon; Chordata; Aves; Columbiformes; Columbidae). The genome sequence is 1,183.3 megabases in span. Most of the assembly is scaffolded into 40 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 16.97 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,730 protein coding genes. The primary assembly achieves the Earth Biogenome Project reference standard of 6.C.Q62.}, }
@article {pmid41277831, year = {2025}, author = {Rahmdel, S and Türkoglu, T and Nikjoo, N and Babaali, E and Moradi Mirhesari, D and Nega, M and Brüggemann, H and Huang, L and Witte Paz, M and Nieselt, K and Götz, F}, title = {Beyond commensalism: genomic insights into micrococcin P1-producing Staphylococcus chromogenes.}, journal = {mSphere}, volume = {10}, number = {12}, pages = {e0073325}, pmid = {41277831}, issn = {2379-5042}, support = {Germany's Excellence Strategy-EXC 2124-390838134 'Controlling Microbes to Fight Infections' (CMFI)//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Bacteriocins/genetics/biosynthesis/pharmacology ; *Staphylococcus/genetics/metabolism ; Animals ; *Genome, Bacterial ; Multigene Family ; Whole Genome Sequencing ; Female ; Symbiosis ; Anti-Bacterial Agents/pharmacology ; Virulence Factors/genetics ; Genomics ; Staphylococcal Infections/microbiology/veterinary ; Cattle ; Virulence/genetics ; Microbial Sensitivity Tests ; }, abstract = {UNLABELLED: Staphylococcus chromogenes (S. chromogenes) is a predominant non-aureus staphylococcal species colonizing the teat skin and mammary gland of dairy ruminants. Although often linked to mild or subclinical mastitis, specific strains may also play protective roles against major udder pathogens. In this study, we characterized two S. chromogenes isolates (4S77 and 4S90) that displayed antimicrobial activity against Gram-positive bacteria. Complete genome sequencing revealed a conserved, plasmid-encoded biosynthetic gene cluster for the thiopeptide bacteriocin micrococcin P1 (MP1). All genes necessary for MP1 biosynthesis, modification, export, and immunity were identified, and compound production was confirmed by high-performance liquid chromatography and liquid chromatography-mass spectrometry. Comparative analysis with publicly available S. chromogenes genomes revealed that the MP1 cluster appears unique to these isolates. Both strains showed full phenotypic susceptibility to tested antibiotics, despite 4S90 carrying the lnuA gene, which did not confer detectable resistance under standard conditions. Classical staphylococcal toxin genes were also absent. Virulence gene profiling revealed a conserved repertoire of colonization- and persistence-associated genes, including factors involved in adhesion, capsule formation, and iron acquisition, but no markers of aggressive pathogenicity. Mobile genetic elements, including prophages and genomic islands, were common but did not carry antimicrobial resistance or virulence genes, suggesting a low risk of transmission of new pathogenic traits to the endogenous microbiome, including opportunistic bacteria. These findings suggest that MP1-producing S. chromogenes strains combine antimicrobial functionality with low virulence potential, highlighting their potential ecological role as protective commensals on the teat skin and in the broader mammary ecosystem of dairy ruminants.<br><br>IMPORTANCE: Staphylococcus chromogenes is one of the most prevalent bacteria isolated from the mammary glands of dairy animals and is primarily considered a causative agent of subclinical mastitis. However, certain strains may also act as microbial competitors that inhibit more harmful pathogens. In this study, we identified two goat-derived S. chromogenes strains that produce micrococcin P1 (MP1), a potent antimicrobial compound effective against Gram-positive bacteria, including major mastitis pathogens. Genomic and phenotypic analyses revealed that these strains possess low virulence potential and retain antibiotic susceptibility, suggesting a possible protective role within the mammary microbiome. This is the first report of MP1 production in this species. Our findings highlight the functional diversity within S. chromogenes and suggest its potential application in microbiota-based strategies for mastitis prevention and antimicrobial stewardship in livestock.}, }
@article {pmid41276529, year = {2025}, author = {Martin, C and Gitter, A and Anantharaman, K}, title = {Protein Set Transformer: a protein-based genome language model to power high-diversity viromics.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {11123}, pmid = {41276529}, issn = {2041-1723}, support = {R35 GM143024/GM/NIGMS NIH HHS/United States ; R35GM143024//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, mesh = {*Genome, Viral/genetics ; *Genomics/methods ; *Viruses/genetics ; *Viral Proteins/genetics/chemistry/metabolism ; Capsid Proteins/genetics ; }, abstract = {Exponential increases in microbial and viral genomic data demand transformational advances in scalable, generalizable frameworks for their interpretation. Standard homology-based functional analyses are hindered by the rapid divergence of microbial and especially viral genomes and proteins that significantly decreases the volume of usable data. Here, we present Protein Set Transformer (PST), a protein-based genome language model that models genomes as sets of proteins without considering sparsely available functional labels. Trained on >100k viruses, PST outperforms other homology- and language model-based approaches for relating viral genomes based on shared protein content. Further, PST demonstrates protein structural and functional awareness by clustering capsid-fold-containing proteins with known capsid proteins and uniquely clustering late gene proteins within related viruses. Our data establish PST as a valuable method for diverse viral genomics, ecology, and evolutionary applications. We posit that the PST framework can be a foundation model for microbial genomics when trained on suitable data.}, }
@article {pmid41276033, year = {2026}, author = {Liu, XY and He, FX and Qu, TC and Weng, ZH and Li, PF and Ye, J and Fu, HY}, title = {Integrated physiological and multi-omics insights into Chlorella mutagenized by atmospheric and room temperature plasma for enhanced saline aquaculture wastewater treatment and bioresource production.}, journal = {Bioresource technology}, volume = {442}, number = {}, pages = {133694}, doi = {10.1016/j.biortech.2025.133694}, pmid = {41276033}, issn = {1873-2976}, mesh = {*Chlorella/genetics/physiology/metabolism/drug effects ; *Wastewater/chemistry ; *Aquaculture/methods ; *Water Purification/methods ; *Mutagenesis ; *Plasma Gases/pharmacology ; Nitrogen ; Salinity ; Photosynthesis ; Temperature ; Biological Oxygen Demand Analysis ; Phosphorus ; *Metabolomics/methods ; Chlorophyll/metabolism ; Multiomics ; }, abstract = {The salinity of aquaculture wastewater varies considerably across farming systems, limiting the applicability of conventional Chlorella strains. To enhance salt tolerance and application potential, atmospheric and room temperature plasma (ARTP) mutagenesis was employed for its high mutation efficiency and ability to generate genetically stable mutants via a non-thermal plasma process. Among five mutant strains evaluated, strain AMC-2 exhibited the best performance, with enhanced growth, photosynthesis, nutrient removal, and bioresource accumulation. Within 8 days, strain AMC-2 removed over 90 % of total nitrogen (TN) and total phosphorus (TP) and chemical oxygen demand (COD), with algal density and chlorophyll content increased by 110 % and 134 %, respectively. The maximum quantum yield of PSII photochemistry reached 0.78, and the maximum electron transport rate increased by 69 %. Protein, polysaccharide, and lipid contents were also elevated by 83 %, 32 %, and 12 %, respectively. Compared to the wild-type, transcriptomic and metabolomic analyses of AMC-2 revealed coordinated upregulation of key genes (e.g., LHCB1, rbcS, ALDO, GOT2, Nrt, and NR) and elevated levels of metabolites such as citric acid, isocitric acid, γ-aminobutyric acid, and glycerophospholipids. These changes indicate systemic reprogramming of photosynthesis, carbon and nitrogen metabolism, and membrane composition. Functional validation in saline aquaculture wastewater demonstrated that AMC-2 sustained stable growth, photosynthetic activity, and nutrient removal at salinities up to 15 ppt, confirming its enhanced environmental adaptability. Collectively, these results highlight AMC-2 as a promising microalgal candidate for integrated bioremediation and bioresource production in brackish aquaculture systems, and exemplify the effectiveness of ARTP mutagenesis for improving microalgal performance under challenging conditions.}, }
@article {pmid41275375, year = {2025}, author = {Su, Z and Zhang, X and Wang, Q and Tang, Q and Yang, D and Liu, Y}, title = {amplysis: an R package for microbial composition and diversity analysis using 16S rRNA amplicon data.}, journal = {Briefings in functional genomics}, volume = {24}, number = {}, pages = {}, pmid = {41275375}, issn = {2041-2657}, support = {//Guangxi Education Agency/ ; //Guangxi Province Talent Project/ ; 42377012//National Natural Science Foundation of China/ ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; *Software ; *Microbiota/genetics ; *Computational Biology/methods ; Biodiversity ; Bacteria/genetics/classification ; }, abstract = {The downstream analysis of 16S rRNA sequencing data remains a significant challenge for researchers lacking extensive bioinformatics expertise, often requiring proficiency in diverse tools and methodologies. To address this, we present amplysis, an R package designed to streamline the analysis and visualization of 16S rRNA amplicon sequencing data through an intuitive, code-light workflow. amplysis integrates data importing, processing, statistical analysis, and visualization into a unified framework. Key features include data normalization, microbial composition profiling, alpha/beta diversity analysis, ordination methods (e.g. Principal Component Analysis), and publication-ready visualization tools. The package's utility was demonstrated through three case studies, one of which analyzed microbial community responses to hexachlorocyclohexane (HCH) degradation in groundwater environments. Using amplysis, we efficiently generated phylum/genus-level abundance plots, alpha-diversity indices, and Principal Coordinates Analysis ordination, revealing significant shifts in community structure and diversity under HCH stress. The other case studies utilized publicly available data from published studies by other researchers. These results underscore the package's ability to simplify complex analyses while ensuring reproducibility and high-quality output. By integrating modular, user-friendly functions, amplysis lowers the barrier to robust microbiome data exploration. The package is available on GitHub (https://github.com/min-perilla/amplysis), offering a valuable resource for researchers in microbial ecology and environmental genomics.}, }
@article {pmid41271865, year = {2025}, author = {Pottier, P and Oh, RRY and Pollo, P and Rivera-Villanueva, AN and Yang, Y and Varon, S and Longo, AV and Burke, S and Lin, HY and Valdebenito, JO and Amano, T and Drobniak, SM and Nakagawa, S and Claunch, N}, title = {AmphiTherm: a comprehensive database of amphibian thermal tolerance and preference.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1987}, pmid = {41271865}, issn = {2052-4463}, support = {Scientia PhD Scholarship//University of New South Wales (UNSW Australia)/ ; Scientia PhD scholarship//University of New South Wales (UNSW Australia)/ ; DP230101248//Department of Education and Training | Australian Research Council (ARC)/ ; FT220100276//Department of Education and Training | Australian Research Council (ARC)/ ; FT180100354//Department of Education and Training | Australian Research Council (ARC)/ ; DE180100202//Department of Education and Training | Australian Research Council (ARC)/ ; UPD2024-0239//Wenner-Gren Foundation (Wenner-Gren Foundation for Anthropological Research, Inc.)/ ; DFG-FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; IOS-2011278//National Science Foundation (NSF)/ ; 2109663//National Science Foundation (NSF)/ ; 3220722//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico (National Fund for Scientific and Technological Development)/ ; }, mesh = {Animals ; *Amphibians/physiology ; *Thermotolerance ; Biodiversity ; Databases, Factual ; }, abstract = {Thermal traits are crucial to our understanding of the ecology and physiology of ectothermic animals. While rising global temperatures have increasingly pushed research towards the study of upper thermal limits, lower thermal limits and thermal preferences are essential for defining the thermal niche of ectotherms. Through a systematic review of the literature in seven languages, we expanded an existing database of amphibian heat tolerance by adding 1,009 estimates of cold tolerance and 816 estimates of thermal preference across 375 species. AmphiTherm is a comprehensive and reproducible database that contains 4,899 thermal trait estimates from a diverse sample of 659 species (~7.5% of all described amphibians) spanning 38 families. Despite its broad geographic coverage, we report evident gaps across amphibian biodiversity hotspots in Africa, most regions of Asia, central South America, and Western Australia. By providing a more holistic understanding of amphibian thermal tolerance and preferences, AmphiTherm is a valuable resource for advancing research in evolutionary biology, ecophysiology, and biogeography of amphibians, offering insights that are increasingly needed in changing climates.}, }
@article {pmid41270500, year = {2025}, author = {Li, C and Chen, Z and Chen, L and Yu, J and Wang, Z and Wang, G}, title = {Multi-omics insight into the adaptation mechanism of desert cyanobacterium Chroococcidiopsis sp. ASB-02 under salinity stress.}, journal = {Plant physiology and biochemistry : PPB}, volume = {229}, number = {Pt D}, pages = {110769}, doi = {10.1016/j.plaphy.2025.110769}, pmid = {41270500}, issn = {1873-2690}, mesh = {*Cyanobacteria/metabolism/genetics/physiology ; *Salt Stress ; Desert Climate ; *Adaptation, Physiological ; Salt Tolerance ; Salinity ; Phylogeny ; Multiomics ; }, abstract = {Soil salinity is an environmental stress severely restricting organism growth and causing ecological deterioration. However, Chroococcidiopsis sp. can grow in various salt-rich deserts and is known for extreme environmental tolerance. Currently, there is little information about its salt adaptation mechanism. To address this issue, we conducted investigation at multiple levels, including phylogenetics, physiology, transcriptomics, and metabolomics, to gain understanding of its evolution, degree of salt tolerance, and study salt adaptation mechanism of Chroococcidiopsis sp. ASB-02. The results showed that Chroococcidiopsis sp. ASB-02 exhibited high survival rates under high salt stress and could grow even in 600 mM NaCl, which is 3-6 times than the salt limit of other desert cyanobacteria. Multi-omics analyses revealed that high salt enhanced the expression of PSII repair genes, activated SuS sucrose synthesis and TreS trehalose synthesis pathways, which help to reduce PSII damage, maintaining stable PSII activity, and facilitating osmoregulation. In addition, in response to higher salt concentration (600 mM NaCl), Chroococcidiopsis sp. ASB-02 activated Na[+]/H[+] transporters and ion channel genes to regulate intracellular ion concentrations. To counter salt-induced oxidative stress, Chroococcidiopsis sp. ASB-02 employed distinct antioxidant strategies based on salt concentration. At 300 mM NaCl, sodA2 and katG genes mainly played roles, whereas at 600 mM NaCl, gor2 and grxB of glutaredoxin system, as well as trxB and ntrC of thioredoxin system played key roles in mitigating oxidative damage. This study clarified the salt adaptation mechanism of Chroococcidiopsis sp. ASB-02 and revealed crucial biological pathways with multi-omics insight, which may be helpful to develop salinization bioremediating with cyanobacteria.}, }
@article {pmid41266326, year = {2025}, author = {Stanislawski, MA and Litkowski, E and Arehart, CH and Luo, K and Gilmore, N and Lange, LA and Lange, EM and Barnes, K and Avery, CL and Meyer, KA and Holguin, F and North, KE and Burk, RD and Kaplan, RC}, title = {Relationships among host genetics, gut microbiota, and asthma in US Hispanic/Latino adults.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10223}, pmid = {41266326}, issn = {2041-1723}, support = {R01 DK120870/DK/NIDDK NIH HHS/United States ; N01 HC065236/HL/NHLBI NIH HHS/United States ; K01HL157658//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R01 HL105756/HL/NHLBI NIH HHS/United States ; R61 HL157069/HL/NHLBI NIH HHS/United States ; R01 HL060712/HL/NHLBI NIH HHS/United States ; N01 HC065237/HL/NHLBI NIH HHS/United States ; R01HL136266//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; HHSN268200625235C//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R33 HL157069/HL/NHLBI NIH HHS/United States ; N01 HC065233/HL/NHLBI NIH HHS/United States ; R01 MD011389/MD/NIMHD NIH HHS/United States ; N01 HC065235/HL/NHLBI NIH HHS/United States ; R01 DK119268/DK/NIDDK NIH HHS/United States ; R01HL157069//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R01AI152504//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; 1OT3HL14715//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; OT3 HL147154/HL/NHLBI NIH HHS/United States ; P30 DK111022/DK/NIDDK NIH HHS/United States ; N01 HC065234/HL/NHLBI NIH HHS/United States ; R01 AI152504/AI/NIAID NIH HHS/United States ; R01 DK134672/DK/NIDDK NIH HHS/United States ; R01 AG085320/AG/NIA NIH HHS/United States ; R01 HL140976/HL/NHLBI NIH HHS/United States ; K01 HL157658/HL/NHLBI NIH HHS/United States ; R01 HL136266/HL/NHLBI NIH HHS/United States ; R01MD011389//U.S. Department of Health &amp; Human Services | NIH | National Institute on Minority Health and Health Disparities (NIMHD)/ ; }, mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Asthma/genetics/microbiology/epidemiology/ethnology ; Body Mass Index ; Cross-Sectional Studies ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; *Hispanic or Latino/genetics ; Obesity/microbiology/genetics/complications ; Risk Factors ; United States/epidemiology ; }, abstract = {Asthma is a heterogeneous condition that is often comorbid with obesity and influenced by diverse risk factors. Elucidating the association of gut microbial characteristics with asthma could improve our understanding of the pathophysiology. Here, we investigate relationships of host genetics and stool microbiota characteristics with asthma among US Hispanic/Latino adults, while considering the influence of obesity status, using host whole genome sequencing and stool shotgun metagenomic microbiota data from participants of the Hispanic Community Health Study/Study of Latinos. We evaluate cross-sectional associations of microbiota characteristics with asthma and analyse whether they are modified by obesity status (body mass index≥30 kg/m[2]). We assess differences in alpha diversity, beta diversity, and taxonomic abundance with asthma, independent of obesity, and interactions between asthma and obesity using covariate-adjusted regression-based methods. We generate an asthma polygenic risk score (PRS) and compare the classification accuracy of genetic and microbial factors for asthma status. We report that asthma is associated with differences in overall taxonomic composition (beta diversity; p = 0.001), which is not dependent on obesity status (p = 0.31). Asthma is not associated with alpha diversity metrics (p > 0.17), though obesity is associated with lower alpha diversity (p < 0.01). We identify multiple taxa that are associated with asthma, including decreased abundance of Lactobacillus and Enterococcus species, and some taxonomic associations vary by obesity status. Compared to models including baseline risk factors and an asthma PRS, microbial information improves classification accuracy of asthma (p = 0.04). Our results support that there are microbiota characteristics associated with asthma in Hispanic/Latino adults independent of obesity.}, }
@article {pmid41264985, year = {2026}, author = {Singh, CL and Spuur, K and Rose, L and Jones, D and Irwin, P and Yun, J}, title = {Documentation of contrast hypersensitivity reactions: a socio-ecological scoping review.}, journal = {European journal of radiology}, volume = {194}, number = {}, pages = {112539}, doi = {10.1016/j.ejrad.2025.112539}, pmid = {41264985}, issn = {1872-7727}, mesh = {Humans ; *Contrast Media/adverse effects ; *Documentation/statistics &amp; numerical data/standards ; *Drug Hypersensitivity/epidemiology/diagnosis ; }, abstract = {PURPOSE: To investigate the critical yet often overlooked challenge of documentation of hypersensitivity reactions to contrast media. Inaccurate documentation not only informs future imaging events but also impacts other areas in medicine. This study applies Bronfenbrenner's adapted socio-ecological model to examine the literature related to contrast hypersensitivity documentation, highlighting systemic issues that perpetuate suboptimal practice.<br><br>METHOD: A scoping review was conducted following the Arksey and O'Malley framework with adaptations for a socio-ecological lens. A search was conducted across Ovid MEDLINE, SCOPUS, ProQuest and CINAHL Plus (2000-present), identifying 673 articles. Seven studies met the inclusion criteria and were analysed using NVIVO software to identify key themes across Bronfenbrenner's system levels of micro, meso, exo, macro and chrono.<br><br>RESULTS: Findings revealed inconsistencies in documentation practices across all levels of healthcare. At the micro level, patient-practitioner communication is often hindered by the patient's inability to provide an accurate history. At the meso and macro levels, fragmented systems, lack of interoperability and inconsistent terminology contribute to the problem. At the chrono level, the impact of the evolution of documentation practices, standards, and policies over time have influenced current practices. This includes perpetuating a cycle of inaccurate information being utilised in clinical decision making, compromising patient outcomes and increasing healthcare costs.<br><br>CONCLUSION: This review is the first to highlight the systemic nature of contrast hypersensitivity documentation challenges using the socio-ecological lens. All medical and allied professionals who document and communicate medical histories can break this self-perpetuating cycle with simple actions such as accurately recording of contrast agent name, details of the reaction, severity, treatment and timelines. Further research is required to develop strategies to drive systemic change, ultimately to benefit patient safety.}, }
@article {pmid41263111, year = {2026}, author = {Feng, X and Li, Y and Zheng, J and Chen, X and Yang, S and Chen, Y and Li, SC}, title = {MicrobialScope: an integrated genomic resource with rich annotations across bacteria, archaea, fungi, and viruses.}, journal = {Nucleic acids research}, volume = {54}, number = {D1}, pages = {D842-D851}, pmid = {41263111}, issn = {1362-4962}, support = {C2004-23Y//Young Collaborative Research/ ; JCYJ20220818101201004//Shenzhen Science and Technology Program/ ; 32300527//National Natural Science Foundation of China/ ; 32470695//National Natural Science Foundation of China/ ; 2022A1515110784//Guangdong Basic and Applied Basic Research Foundation/ ; 2023B0303040004//Key-Area Research and Development Program of Guangdong Province/ ; TC2024JC43//Basic Research Programs of Taicang, 2024/ ; //Shenzhen-Hong Kong Institute of Brain Science/ ; //SIAT-HKUST Joint Laboratory of Brain Science/ ; }, mesh = {*Molecular Sequence Annotation ; Archaea/genetics ; *Databases, Genetic ; Fungi/genetics ; Genome, Viral ; Genome, Archaeal ; Bacteria/genetics ; Viruses/genetics ; *Genomics/methods ; *Software ; Genome, Fungal ; Genome, Bacterial ; Computational Biology/methods ; Metagenome ; }, abstract = {Microorganisms, including bacteria, archaea, fungi, and viruses, are the most taxonomically diverse and ecologically dominant life forms on Earth, playing critical roles in ecosystems, human health, and industrial applications. While existing microbial databases such as BV-BRC and IMG archive both monoisolate and metagenome-assembled genomes (MAGs) across domains, challenges remain in standardized, multi-level annotations and interactive tools for all microbial groups. Here, we present MicrobialScope (https://microbial.deepomics.org/), a comprehensive microbial genomic platform that integrates large-scale genome collections, multilevel annotations, and interactive visualizations. MicrobialScope harbors 2 411 503 bacterial, 24 472 archaeal, 20 203 fungal, and 188 267 viral genomes derived from both monoisolate assemblies and MAGs. Integrating 15 state-of-the-art bioinformatics tools and 10 specialized databases, MicrobialScope provides extensive annotations encompassing basic genomic features, genomic element prediction (e.g., genes, tRNAs, tmRNAs, CRISPR-Cas and anti-CRISPR elements, secondary metabolite biosynthetic clusters, signal peptides, and transmembrane proteins), and functional and structural annotations. This includes 1 072 114 935 proteins with diverse annotations, 24 640 186 tRNAs and tmRNAs, 140 888 CRISPR-Cas systems, 173 256 anti-CRISPR elements, 105 121 secondary metabolite biosynthetic clusters, 13 235 096 signal peptides, and 50 811 729 transmembrane proteins. In addition, MicrobialScope offers unrestricted access to all data resources, interactive visualization tools, and built-in online analytical modules for intuitive exploration and comparative analysis. With its extensive genome collection, comprehensive annotations, and user-friendly interface, MicrobialScope serves as a scalable platform to advance genome research across diverse microbial domains.}, }
@article {pmid41261971, year = {2025}, author = {Ye, JF and Liu, PL and Guo, H}, title = {Disparities in Healthcare Services Efficiency and Patient-Provider Communication Quality Among Deaf and Hard-of-Hearing Patients in the U.S.: A Multi-Year Cross-Sectional Analysis (2017-2020).}, journal = {Health communication}, volume = {}, number = {}, pages = {1-13}, doi = {10.1080/10410236.2025.2589346}, pmid = {41261971}, issn = {1532-7027}, abstract = {The marginalization of the Deaf and Hard of Hearing (D/HH) group arises from barriers at multiple levels of the socio-ecological matrix. This is primarily reflected in challenges related to effective healthcare services delivery and high-quality patient-provider communication. Utilizing national data from the Health Information National Trends Survey (HINTS) from 2017 to 2020, we examined the difference between D/HH adults and hearing-abled adults in terms of healthcare services efficiency, patient-provider communication quality, health self-efficacy, and psychological health. The findings revealed that D/HH adults consistently exhibited lower levels than hearing adults in healthcare services efficiency, health self-efficacy, and psychological health, and these differences remained evident from 2017 to 2020. However, the difference in patient-provider communication quality between the two groups was not significant. The study further investigates health self-efficacy as a potential mediator influencing the efficiency of healthcare services and quality of patient-provider communication in their relationship with psychological health. Our findings highlight the imperative to devise specialized communication strategies and enhance healthcare services for the D/HH group.}, }
@article {pmid41261732, year = {2026}, author = {Fullam, A and Letunic, I and Maistrenko, OM and Castro, AA and Coelho, LP and Grekova, A and Schudoma, C and Khedkar, S and Robbani, M and Kuhn, M and Schmidt, TSB and Bork, P and Mende, DR}, title = {proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes.}, journal = {Nucleic acids research}, volume = {54}, number = {D1}, pages = {D852-D857}, pmid = {41261732}, issn = {1362-4962}, support = {FT230100724//Australian Research Council/ ; //Deutsche Forschungsgemeinschaft/ ; 460129525//German Research Foundation/ ; LIBIS/de.NBI//Ministry of Science, Research and Art Baden-W&#xfc;rttemberg/ ; //MEXT/ ; //Keio University/ ; }, mesh = {*Molecular Sequence Annotation/methods ; *Genome, Bacterial ; *Software ; *Databases, Genetic ; *Genomics/methods ; *Genome, Archaeal ; *Genome, Microbial ; Multigene Family ; }, abstract = {The pervasive availability of publicly available microbial genomes has opened many new avenues for microbiology research, yet it also demands robust quality control and consistent annotation pipelines to ensure meaningful biological insights. proGenomes4 (prokaryotic Genomes v4) addresses this challenge by providing a resource of nearly 2 million high-quality microbial genomes, a doubling in scale from previous versions, encompassing over 7 billion genes. Each genome underwent rigorous quality assessment and comprehensive functional annotation by applying multiple standardized annotation workflows, including the systematic identification of mobile genetic elements and biosynthetic gene clusters. proGenomes4 contains 32 887 species with ecological habitat metadata as well as precomputed pan-genomes. This substantially expanded resource provides the microbiology community with a foundation for large-scale comparative studies and is freely accessible via a newly developed command line interface and at https://progenomes.embl.de/.}, }
@article {pmid41261182, year = {2025}, author = {Prusty, G and Prasad, BR and Polaki, S and Mereddy, S}, title = {Integrative multi-omics characterization of the gut microbiome in Pila globosa: functional insights into nutrient cycling and detoxification potential.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {41}, number = {12}, pages = {464}, pmid = {41261182}, issn = {1573-0972}, mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Metagenomics/methods ; Proteomics/methods ; *Snails/microbiology ; Phylogeny ; Metagenome ; Multiomics ; }, abstract = {Pila globosa, a freshwater snail endemic to Indian aquatic ecosystems, plays a pivotal role in nutrient cycling and organic matter turnover. In this study, we present the first integrative multi-omics characterization of its gut microbiome using shotgun metagenomics, metaproteomics, and genome-resolved analyses. The gut microbiota was taxonomically diverse yet compositionally stable, dominated by Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, with core genera including Pseudomonas, Clostridium, Bacillus, and Streptomyces. Alpha diversity metrics (Shannon = 4.22 ± 0.15; Simpson = 0.90 ± 0.01) and low Bray-Curtis dissimilarity (0.12-0.15) indicated a conserved core microbiome across replicates. Functional profiling through HUMAnN2 and metaproteomic validation revealed enrichment of pathways related to carbohydrate metabolism, short-chain fatty acid (SCFA) synthesis, amino-acid biosynthesis, and oxidative phosphorylation, reflecting the community's contribution to host nutrition and metabolic balance. Genes and proteins associated with xenobiotic degradation (benzoate, toluene metabolism) and oxidative stress response (superoxide dismutase, catalase, glutathione S-transferase) were abundant, suggesting microbial support for redox regulation and detoxification. Twelve high-quality metagenome-assembled genomes (MAGs) reconstructed from dominant taxa encoded traits for secondary metabolite production, metal resistance, and stress tolerance, underscoring their ecological versatility. Together, these results establish a foundational reference for understanding the functional potential of the P. globosa gut microbiome and its possible role in nutrient transformation and pollutant processing in freshwater systems. The study provides baseline data for future comparative and ecotoxicological investigations of gastropod holobionts.}, }
@article {pmid41260397, year = {2026}, author = {Abbasi, E}, title = {Metagenomic surveillance of emerging viruses in mosquito populations from high-risk regions of Iran.}, journal = {Journal of virological methods}, volume = {340}, number = {}, pages = {115301}, doi = {10.1016/j.jviromet.2025.115301}, pmid = {41260397}, issn = {1879-0984}, mesh = {Animals ; Iran/epidemiology ; *Culicidae/virology ; *Metagenomics ; Phylogeny ; *Arboviruses/genetics/classification/isolation &amp; purification ; *Mosquito Vectors/virology ; *Virome ; High-Throughput Nucleotide Sequencing ; Epidemiological Monitoring ; Computational Biology ; RNA, Viral/genetics ; }, abstract = {BACKGROUND: Mosquito-borne arboviruses pose a growing threat to public health, particularly in ecologically vulnerable and climatically dynamic regions. This study aimed to investigate the diversity of emerging arboviruses in mosquito populations from high-risk provinces in southern and southeastern Iran using a metagenomic surveillance approach.<br><br>METHODS: Adult mosquitoes were collected from 36 sites across Hormozgan, Sistan and Baluchestan, and Khuzestan provinces. Specimens were pooled by species and location, followed by RNA extraction and high-throughput sequencing. Bioinformatics analysis was performed to identify viral taxa and assess phylogenetic relationships.<br><br>RESULTS: A total of 4275 mosquitoes representing six species were analyzed. Virome analysis revealed 43 viral taxa, including medically important arboviruses such as dengue virus serotype 2 (DENV-2), chikungunya virus (CHIKV), and West Nile virus (WNV). Multiple novel viral sequences were also detected, including putative members of Phenuiviridae and Orthomyxoviridae. Viral diversity was highest in Hormozgan province and positively correlated with ambient temperature.<br><br>CONCLUSION: This study provides the first comprehensive metagenomic insight into mosquito viromes in Iran, revealing both endemic and potentially novel arboviruses. These findings underscore the need for integrated genomic surveillance and regional vector-borne disease preparedness.}, }
@article {pmid41259569, year = {2025}, author = {Pereira, JFG and Nascimento, LFC}, title = {Preventable neonatal mortality in the state of São Paulo: a spatial approach.}, journal = {Revista paulista de pediatria : orgao oficial da Sociedade de Pediatria de Sao Paulo}, volume = {43}, number = {}, pages = {e2024294}, pmid = {41259569}, issn = {1984-0462}, mesh = {Humans ; Brazil/epidemiology ; Infant, Newborn ; *Infant Mortality/trends ; Female ; Pregnancy ; Spatial Analysis ; Infant ; Socioeconomic Factors ; Prenatal Care/statistics &amp; numerical data ; Adolescent ; Apgar Score ; }, abstract = {OBJECTIVE: Identify spatial patterns for preventable neonatal deaths in municipalities in the state of São Paulo between the years of 2015 and 2019, looking for possible correlations with socioeconomic and demographic indices.<br><br>METHODS: This is an ecological study, with data obtained from the Department of Informatics of the Unified Health System (DATASUS), from the of Mortality Information System (SIM) and Live Birth Information System (SINASC), regarding preventable deaths due to adequate care for women during pregnancy, childbirth and for the newborns, were analysed. Proportions per thousand live births were built. The independent variables used were the proportion of adolescent mothers; insufficient number of antenatal consultations (0-6 consultations); low birthweight (500-2499 g); low Apgar score in the 1st and 5th minute of life (0-7), all of which were used to calculate the Univariate Moran Index (IMU). The Social Vulnerability Index (SVI) and the Municipal Human Development Index (MHDI) were used to calculate the Bivariate Moran Index (IM). The Univariate and Bivariate Moran's indexes were calculated, thematic maps and box maps were constructed, and a significance level of &#x3b1; < 5% was adopted.<br><br>RESULTS: There were four thematic maps, and three box maps created to analyse the dependent variables, mentioned above. SVI and MHDI, inadequate antenatal care and reduced Apgar score at the 1st and 5th minute showed IM significant with preventable deaths in the neonatal population. A concentration of preventable deaths was identified in the southern region of the state.<br><br>CONCLUSIONS: The data presented can support municipal managers, demonstrating the need for investment in maternal and child health.}, }
@article {pmid41258717, year = {2025}, author = {Cheng, R and Lv, T and Ji, P and Ma, B and Wang, M and Matsumoto, H}, title = {Multi-omics analyses reveal the virulence differentiation underlying natural variation in Burkholderia gladioli.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {12}, pages = {e0168525}, pmid = {41258717}, issn = {1098-5336}, support = {2024SZRZDC130001//Natural Science Foundation of Hangzhou/ ; LD25C140002//Zhejiang Provincial Natural Science Foundation of China/ ; U21A20219//National Natural Science Foundation of China/ ; W2533054//National Natural Science Foundation of China/ ; 2024M762853//China Postdoctoral Science Foundation/ ; }, mesh = {*Burkholderia gladioli/genetics/pathogenicity ; *Oryza/microbiology ; Virulence/genetics ; *Plant Diseases/microbiology ; *Genetic Variation ; Bacterial Proteins/genetics/metabolism ; Genome, Bacterial ; Transcriptome ; Multiomics ; }, abstract = {UNLABELLED: Burkholderia gladioli is a critical pathogen causing bacterial panicle blight in rice, severely threatening global rice yield and grain quality. Here, B. gladioli strains were isolated and identified from two rice fields exhibiting markedly different severities of bacterial panicle blight. Although the two strains belong to the same species, they displayed significant differences in phenotype and pathogenicity. Comparative genomic and transcriptomic analyses revealed that natural variation between the strains not only arose from 79 single-nucleotide polymorphisms (SNPs), 12 insertions/deletions (INDELs), and 3 structural variations (SVs) across 27 mutated genes, which may affect protein function and stability, but also coincided with the significant downregulation of genes in multiple virulence-associated pathways, such as two-component systems, bacterial chemotaxis, quorum sensing, and flagellar assembly at the transcriptional level. The combined effects of genetic variation and transcriptional regulation ultimately contributed to the observed differences in pathogenicity. This study uncovers the potential mechanisms by which natural variation in B. gladioli influences pathogenicity, providing a theoretical basis and potential molecular targets for the precise control of rice bacterial panicle blight.<br><br>IMPORTANCE: This study demonstrates that natural variation in Burkholderia gladioli, a major pathogen responsible for bacterial panicle blight in rice, has a significant impact on its pathogenicity and further explores the underlying mechanisms. These findings expand our understanding of how phytopathogens' virulence differentiates conditions of natural variation, and provide potential molecular targets for the development of novel bactericides. The identification of low-virulence strains and their associated gene variations in this study offers both theoretical and practical foundations for ecological disease management and biocontrol of rice bacterial diseases, highlighting their importance for promoting precision agriculture and sustainable development.}, }
@article {pmid41257544, year = {2025}, author = {Agany, DD and Callegari, EA and Paez, MD and Pietri, JE}, title = {Multi-omics of cockroaches infected with Salmonella Typhimurium identifies molecular signatures of vector colonization.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {1118}, pmid = {41257544}, issn = {1471-2164}, support = {P20 GM103443/GM/NIGMS NIH HHS/United States ; R01 AI171014/AI/NIAID NIH HHS/United States ; R01AI171014/NH/NIH HHS/United States ; P20GM103443/NH/NIH HHS/United States ; }, mesh = {Animals ; *Salmonella typhimurium/physiology ; *Cockroaches/microbiology/genetics/metabolism ; *Proteomics/methods ; Host-Pathogen Interactions ; Transcriptome ; Gene Expression Profiling ; *Insect Vectors/microbiology/genetics ; Multiomics ; }, abstract = {BACKGROUND: German cockroaches (Blattella germanica) are prevalent indoor pests that have long been associated with the spread of enteric human pathogens. Recent work investigating the relationship between these insects and Salmonella enterica serovar Typhimurium (S. Typhimurium), a model pathogen of global concern, demonstrated that S. Typhimurium colonizes the cockroach gut. S. Typhimurium has a broad host range, but mechanistic molecular insight into how ecologically relevant invertebrate hosts interact with this pathogen is lacking. Here, we applied a multi-omic (transcriptomic and proteomic) approach to infected cockroaches to examine the molecular variables that govern cockroach-borne S. Typhimurium transmission.<br><br>RESULTS: Our results reveal enriched monocarboxylic acid transport and metabolism, increased long-chain fatty acid transport, increased triglyceride metabolism, and an increased response to reactive oxygen species and free radicals as host signatures of a metabolic shift in the cockroach gut during infection. Surprisingly, downregulation of the immune deficiency (IMD) pathway transcription factor relish, and upregulation of xenobiotic detoxification (glutathione-s-transferase) and known allergens (Blag5 &amp; Blag8, myosin, tropomyosin) were also evident in infected guts.<br><br>CONCLUSIONS: To our knowledge, this study is both the first omics study of enteric human pathogen infection in a cockroach vector and the first omics study of S. Typhimurium in an ecologically relevant insect host, representing a seminal contribution to the field of vector-borne infectious disease. This work provides novel fundamental knowledge regarding the response of insect hosts to S. Typhimurium infection and the evolution of vector-pathogen relationships with the potential to inform mitigation of the public health impacts of cockroaches.}, }
@article {pmid41257449, year = {2025}, author = {Wei, Y and Siddique, J and Spring, B and Hedeker, D}, title = {A Bayesian Two-Step Multiple Imputation Approach Based on Mixed Models for Missing EMA Data.}, journal = {Statistics in medicine}, volume = {44}, number = {25-27}, pages = {e70325}, pmid = {41257449}, issn = {1097-0258}, support = {R01DK125414/DK/NIDDK NIH HHS/United States ; }, mesh = {Bayes Theorem ; Humans ; *Models, Statistical ; Computer Simulation ; *Ecological Momentary Assessment ; Data Interpretation, Statistical ; Linear Models ; Longitudinal Studies ; Logistic Models ; }, abstract = {Ecological Momentary Assessments (EMA) capture real-time thoughts and behaviors in natural settings, producing rich longitudinal data for statistical analyses. However, the robustness of these analyses can be compromised by the large amount of missing data in EMA studies. To address this, multiple imputation, a method that replaces missing values with several plausible alternatives, has become increasingly popular. In this article, we introduce a two-step Bayesian multiple imputation framework which leverages the configuration of mixed models. We adopt and compare: (1) the Random Intercept Linear Mixed model; (2) the Mixed-effect Location Scale (MELS) model which accounts for subject variance influenced by covariates and random effects; and (3) the Shared Parameter MELS model which additionally links the missing data to the response variable through a random intercept logistic model. Each of these three can be used to complete the posterior distribution within the framework. In the simulation study, we extend this two-step Bayesian multiple imputation strategy to handle simultaneous missing variables in EMA data and compare the effectiveness of the multiple imputations across the three mixed models. Our analyses highlight the advantages of multiple imputations over single imputations and underscore the importance of selecting an appropriate model for the imputation process. Specifically, modeling within-subject variance and linking the missingness mechanism to the response will greatly improve the performance in certain scenarios. Furthermore, we applied our techniques to the "Make Better Choices 1 (MBC1)" study, highlighting the distinction, in particular, of imputation results between the Random Intercept Linear Mixed model and the two MELS models in terms of modeling within-subject variance.}, }
@article {pmid41256502, year = {2025}, author = {Castillo-Neyra, R and Díaz, EW and Bellotti, BR and Morucci, K and De la Puente-León, M and Ortiz-Cam, L and Levy, MZ}, title = {Cave dogs around major urban areas threaten rabies elimination program.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41256502}, issn = {2692-8205}, support = {D43 TW012741/TW/FIC NIH HHS/United States ; K01 AI139284/AI/NIAID NIH HHS/United States ; }, abstract = {BACKGROUND: In the city of Arequipa, Peru, the government has implemented control measures against dog rabies virus since the detection of its reintroduction in 2015. The city was previously considered free of animal reservoirs other than owned and stray dogs within its urban boundaries. However, multiple reports from peri-urban residents have suggested the presence of feral dogs living in caves on the city's outskirts. We aim to document the presence and dietary patterns of feral dogs adjacent to the city margins.<br><br>METHODS: We conducted monthly field visits to four peri-urban localities in eastern Arequipa, an area where the presence of feral dogs had been previously reported. Dog caves were identified by tracking footprints and other field signs left by dogs, and their locations were georeferenced. Each cave was revisited monthly three times to record the presence of live and dead dogs, and puppies. Fecal samples collected around the caves were analyzed to assess dietary patterns.<br><br>RESULTS: We observed that feral dogs use caves for resting, hiding, and reproduction-some of which appear to be constructed by the dogs themselves. The high number of puppies and dead adult dogs indicates a high population turnover. Dietary analysis revealed that these dogs feed on local fauna, including birds, rodents, cats, sheep, and, notably, other dogs.<br><br>CONCLUSIONS: These unowned, cave-dwelling dogs are not reached by mass rabies vaccination or sterilization programs. Moreover, they exist outside the jurisdiction of health inspectors responsible for rabies surveillance, resulting in a lack of data on rabies infection in this subpopulation. Our findings highlight the need for integrated One Health strategies to address the challenges posed by feral dog populations in rabies elimination efforts.}, }
@article {pmid41255279, year = {2025}, author = {Mack, JM and Bely, AE}, title = {Regeneration physiology of invertebrates.}, journal = {The Journal of experimental biology}, volume = {228}, number = {22}, pages = {}, doi = {10.1242/jeb.250750}, pmid = {41255279}, issn = {1477-9145}, support = {//University of Maryland/ ; //University of Maryland/ ; IOS-1923429//National Science Foundation/ ; }, mesh = {Animals ; *Invertebrates/physiology ; *Regeneration/physiology ; }, abstract = {One of the great puzzles in biology is to understand the mechanisms underlying animal regeneration. Most recent efforts have used developmental and informatics approaches to understand how regenerated structures are formed, framing regeneration as a developmental outcome. However, regeneration is a complex process that also involves dynamic physiological mechanisms that support and fuel the rebuilding of lost structures. To develop a full understanding of regeneration, including how it relates to the ecology and evolution of organisms, it is essential to understand regeneration physiology. Despite the importance of physiological processes for regeneration, studies of regeneration focused on energetics, metabolism and environmental effects are scarce and have not been synthesized. This Review discusses the current understanding of regeneration physiology, focusing specifically on data from invertebrate animals where such information is especially dispersed and in need of synthesis. Considering data from diverse animal phyla, we review evidence for the consumption of different nutritional substrates during regeneration, summarize how aerobic and anaerobic metabolism appear to be broadly important to regeneration across animal phyla, and discuss how environmental and biotic factors can affect regeneration outcomes. We also introduce the concept of the 'physiological regeneration niche', describing the abiotic and biotic parameters where regeneration is possible, to expand consideration of regeneration in an ecological context. Significant gaps remain in understanding the physiological processes that underlie invertebrate regeneration, and we highlight some of these, including the need for broader taxonomic sampling, assessments of anaerobic metabolism during regeneration, investigations of multiple stressor effects on regeneration and comparisons between regenerators and non-regenerators.}, }
@article {pmid41253964, year = {2025}, author = {Yang, F and Wang, Z and Yang, X and Sun, Y and Wang, Q and Yu, X}, title = {Analyzing and predicting the effects of urban spatial planning on the gradient differentiation of production-living-ecological land and carbon storage.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {40605}, pmid = {41253964}, issn = {2045-2322}, support = {ZR2021QD128//Shandong Provincial Natural Science Foundation/ ; }, abstract = {Carbon storage (CS) of terrestrial ecosystems is strongly associated with space utilization changes. However, effects of urban spatial planning on the spatio-temporal heterogeneity of production-living-ecological land (PLEL) and CS remain unclear. To bridge this gap, we developed a new PGIP framework that combines PLEL theory, gradient analysis, the InVEST model, and the PLUS model. This integrated approach offers a comprehensive tool for assessing and simulating how urban planning influences CS. We applied this framework in Jinan, China, where we defined four urban gradient zones to examine the gradient differentiation of PLEL and CS. By integrating dynamic driving factors and urban spatial planning, the PLEL and CS in 2030 were simulated under different scenarios. Results revealed significant gradient-based variations in PLEL between 1980 and 2020. The urban living land (ULL) within 10 km of the city center increased by 117.60%. The CS has decreased by 8.14 × 10[6] t, and the spatial heterogeneity of CS in the southeastern gradient zone was the strongest. More than 50% of the rise in CS resulted from the shift of rural living land to cultivated production land (CPL), while over 41% of the decrease in CS was caused by the conversion of CPL to ULL. By 2030, urban spatial planning is projected to significantly affect CS pattern, especially in downtown, far suburban, and southeastern gradient zone. Compared with unconstrained development scenario, under spatial planning-guided scenario, high-value clusters of CS will increase by 14.86 km[2], while low-value clusters will decrease by 3.99 km[2]. This study provides a spatially explicit, policy-relevant framework for understanding and planning CS across urban-rural gradients, integrating planning scenarios and mechanistic insights to support low-carbon land use strategies.}, }
@article {pmid41253877, year = {2025}, author = {Wang, C and Lu, Y and Fang, C and Gan, X and Yang, L and He, S}, title = {Chromosome-level genome assembly of the Chinese algae eater Gyrinocheilus aymonieri.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1805}, pmid = {41253877}, issn = {2052-4463}, support = {91731301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32170438//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {China ; *Chromosomes ; *Genome ; Molecular Sequence Annotation ; *Cypriniformes/genetics ; Animals ; Datasets as Topic ; }, abstract = {Gyrinocheilus aymonieri is endemic to Yunnan Province, China. Its mouth has evolved a specialized sucker-like structure as an adaptation to fast-flowing aquatic habitats, representing a remarkable evolutionary example of environmental adaptation. Here, we present a chromosome-level genome assembly of G. aymonieri (507 Mb) integrating HiFi, Illumina, and Hi-C sequencing data. The assembly comprises 24 chromosomes with 92.3% anchoring efficiency. Genome annotation revealed 23.02% repetitive elements, 24,078 protein-coding genes, and 55,943 transcript isoforms. The good genomic collinearity also demonstrates the accuracy of the G. aymonieri genome assembly at the macroscale. This high-quality genome will provide a crucial resource for understanding cypriniform evolution and different ecological adaptation mechanisms.}, }
@article {pmid41249177, year = {2025}, author = {Zhang, D and Hu, Q and Zhou, Y and Yu, H and Cong, W and Cheng, M and Wang, J and Liu, X and Zou, K and Long, S and Zhao, C and Jiang, J and Zhang, Y}, title = {Multi-omic profiling reveals distinct gut microbial and metabolic landscapes in golden snub-nosed monkeys under contrasting conservation strategies.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {209}, pmid = {41249177}, issn = {2055-5008}, support = {2020BCA081//Key Research and Development Project of Hubei Province/ ; 2013BAD03B02//National Key Technology R&amp;D Program of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology/chemistry ; Metagenomics/methods ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Conservation of Natural Resources/methods ; Metabolomics/methods ; Metabolome ; *Colobinae/microbiology ; Endangered Species ; Multiomics ; }, abstract = {Gut microbiota are crucial for the fitness of endangered wildlife, yet how different conservation strategies affect these microbial ecosystems and their metabolic activities remains insufficiently understood. This study employed integrated metagenomic and metabolomic analyses to compare the gut microbial communities and fecal metabolomes of endangered golden snub-nosed monkeys (Rhinopithecus roxellana) under three distinct conservation scenarios: natural wild, food provisioning, and captivity. We established a comprehensive species-specific gut microbial gene catalog and observed significant microbial and metabolic divergence associated with each conservation strategy. Monkeys in managed settings (captive and provisioned) exhibited larger gut microbial gene catalogs than wild individuals. While alpha diversity was highest in the provisioned group, both captive and provisioned groups showed notably altered microbial community structures and co-occurrence networks compared to the wild baseline. Captivity was linked to the most pronounced shifts, including a microbiome assembly more strongly governed by deterministic processes, reduced network stability, and an enrichment of habitat specialists, alongside an increased abundance of antibiotic resistance genes (ARGs) and virulence factors (VFs), and distinct alterations in microbiota-metabolite co-variation patterns, particularly concerning amino acid metabolism. These findings highlight that food provisioning, when managed to emulate natural conditions, is associated with a less disruptive microbial and metabolic profile than intensive captivity, offering crucial insights for developing microbiome-informed conservation practices to enhance the health and long-term viability of this endangered primate.}, }
@article {pmid41248381, year = {2025}, author = {Norris, LE and Lemin, M and Kelly-Hope, LA}, title = {Spatial-temporal analysis of natural hazards and disasters in the Greater Horn of Africa between 2010 and 2024 to inform disaster risk reduction, and surveillance and control strategies for climate and environmentally sensitive diseases.}, journal = {BMJ open}, volume = {15}, number = {11}, pages = {e104998}, pmid = {41248381}, issn = {2044-6055}, mesh = {Humans ; Retrospective Studies ; Cross-Sectional Studies ; Spatio-Temporal Analysis ; *Disasters/statistics &amp; numerical data ; *Disease Outbreaks/prevention &amp; control ; Floods/statistics &amp; numerical data ; *Natural Disasters ; Ethiopia ; Climate Change ; Somalia ; Droughts/statistics &amp; numerical data ; }, abstract = {OBJECTIVE: To determine the spatial-temporal patterns of natural hazards and disasters in the Greater Horn of Africa, including climate and environmentally sensitive diseases, and compare the reporting consistencies across multiple open-access databases.<br><br>DESIGN: Cross-sectional retrospective secondary analysis of natural hazard and disaster data.<br><br>SETTING: Djibouti, Eritrea, Ethiopia, Kenya, Somalia, Sudan, South Sudan and Uganda.<br><br>DATA SOURCES: Primary data from Emergency Events Database (EM-DAT), and comparative data from ReliefWeb, WHO Disease Outbreak News (WHO-DON), FloodList and Global Unique Disaster Identifier Number (GLIDE).<br><br>RESULTS: EM-DAT reported 228 natural hazards and disasters affecting 145.7&#x2009;million people; highest numbers reported in Uganda (n=48), Kenya (n=46), Somalia (n=38) and Ethiopia (n=35); 175 geophysical, hydrological, meteorological and climatological hazards reported, including 118 floods, 26 droughts, 11 storms and 17 landslides; 46 epidemics reported, primarily bacterial (eg, cholera) or viral (eg, yellow fever, measles) diseases, with 20% preceded by a flood, drought or landslide within the previous 3&#x2009;months. Reporting consistency and content varied considerably across the five databases.<br><br>CONCLUSION: Natural hazards and disasters affect millions of people. There is an urgent need to improve database connectedness to facilitate better monitoring and mapping, which can inform disease forecasting and decision tools to develop preparedness and intervention strategies.}, }
@article {pmid41247083, year = {2026}, author = {Galtier, N and Belkhir, K and Antoine, PO and Bibal, C and Boëte, C and Delsuc, F and Huchard, E and Kéfi, S and Maeder, C and Paradis, L and Puechmaille, SJ and Queffelec, A and Scornavacca, C and Smadja, CM}, title = {Time to publish responsibly: DAFNEE, a database of academia-friendly journals in ecology and evolutionary biology.}, journal = {Journal of evolutionary biology}, volume = {39}, number = {2}, pages = {190-199}, doi = {10.1093/jeb/voaf143}, pmid = {41247083}, issn = {1420-9101}, support = {//CNRS Ecology &amp; Environment/ ; //University of Montpellier/ ; //DAFNEE/ ; }, mesh = {*Biological Evolution ; *Periodicals as Topic ; *Publishing ; *Ecology ; *Databases, Factual ; Academia ; }, abstract = {The current economics of scientific publishing reveal a profound imbalance: academia pays prices far exceeding the actual costs of publication. Rather than supporting research, much of this expenditure sustains the profits of a few dominant commercial publishers. Transitioning to responsible publishing is a collective challenge that requires raising awareness among scientists about the problem and the solutions available. We present DAFNEE, a database of academia-friendly journals in ecology, evolutionary biology and archaeology (https://dafnee.isem-evolution.fr/). DAFNEE includes information on over 600 journals (co)run by academic or non-profit institutions, aiming at helping to keep publishing funds within the academic community. The database details these journal's business models, article processing charges, citation rates and partnerships. We show that DAFNEE journals compare favourably to non-DAFNEE ones in terms of editorial and financial policy, while offering similar citation rates. Finally, we offer several recommendations aimed at encouraging authors, reviewers, and evaluators to adopt more responsible publishing practices.}, }
@article {pmid41246445, year = {2025}, author = {Crnobrna, B and Champagne, PS and Williams, HF and Turner, H and Panduro Pisco, G}, title = {Occurrence dataset of reptiles and amphibians from two old-growth forest localities along the Las Piedras River, Tambopata Province, Peru.}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e154136}, pmid = {41246445}, issn = {1314-2828}, abstract = {BACKGROUND: This study presents the first watershed-wide checklist and geo-referenced dataset of amphibians and reptiles from two primary forest localities along the Las Piedras River, Madre de Dios, Peru. Compiled from pitfall traps, quadrats, transects and opportunistic observations between 2004 and 2024, the dataset contains 2,327 records across 165 species, including several new distribution records from the central basin near the Huascar River. The Madre de Dios region in south-eastern Peru is renowned for its biodiversity and old-growth rainforests, hosting diverse flora and fauna. Protected areas like the Tambopata National Reserve and Manu National Park are vital refuges for wildlife and research hubs. The region faces threats from deforestation and illegal mining, necessitating urgent conservation efforts. Despite being one of the most diverse regions for herpetofauna globally, biogeography reports from the Las Piedras River are limited. Notably, sixty non-volant mammal species and 144 fish species have been documented, along with 59 frog and 11 reptile species at the Las Piedras Biodiversity Station (LPBS). However, a comprehensive review of reptile diversity in the watershed is lacking. This study presents a survey and occurrence dataset for reptile and amphibian species at LPBS and the Amazon Research and Conservation Centre (ARCC), including opportunistic records to provide complete taxonomic coverage. Furthermore, we review and compile other reported occurrences. This dataset and review offer detailed species and geographical information, supporting further research on herpetofauna biogeography and ecology and aiding conservation efforts on the Las Piedras River.<br><br>NEW INFORMATION: This list of reptile and amphibian species from the Las Piedras River in Peru includes new records from the basin's central area, near the Huascar River's confluence. It unifies data from early efforts to find herpetofauna at the Las Piedras Biodiversity Station spanning more than ten years. Over a decade of sampling, combined with opportunistic records, comprehensive taxonomic coverage of herpetofauna on the tributary has been provided. Our dataset contains 2,327 distinct geo-referenced records, categorised into Anura (1788), Crocodilia (10), Gymnophiona (1), Squamata (517) and Testudines (11). These records span 165 identified species, along with one entry recorded at the genus level (Chironius). This dataset was structured and managed using Microsoft Excel, where geo-referenced species occurrence data were organised into standardised formats compatible with GBIF publishing requirements. The dataset was subsequently validated and formatted as a Darwin Core Archive (DwC-A), the standard format for biodiversity data sharing, using GBIF's Integrated Publishing Toolkit (IPT). This structured approach ensures interoperability and compliance with global biodiversity informatics standards, supporting its integration into herpetofauna biogeography and conservation efforts. This dataset also includes new records from the central basin of the Las Piedras River near the Huascar River confluence. By offering 2,327 distinct geo-referenced records, this dataset (https://doi.org/10.15468/sa8m3q) supports ongoing research into herpetofauna biogeography and conservation efforts in a region under increasing pressure from deforestation and other human activities.Based on our dataset and an accompanying review of historical records and publications, we document a total of 175 herpetofauna species in the Las Piedras River watershed. This total includes 96 reptile species (ARCC = 70, LPBS = 76) and 79 amphibian species (ARCC = 64, LPBS = 69), from both geo-referenced and literature-confirmed sources.}, }
@article {pmid41238729, year = {2025}, author = {Lee, KY and Shin, SH and Park, G and Kang, SH and Kang, HJ and Kim, J and Lee, JJ and Son, GH and Hong, JY}, title = {Shotgun metagenomics of the vaginal microbiome in cervical shortening and preterm birth risk.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {39988}, pmid = {41238729}, issn = {2045-2322}, support = {HI21C1624//Korea Health Industry Development Institute (KHIDI)/ ; HI21C1624//Korea Health Industry Development Institute (KHIDI)/ ; RS-2023-00252948//Korea government (the Ministry of Science and ICT, the Ministry of Trade, Industry and Energy, the Ministry of Health &amp; Welfare, the Ministry of Food and Drug Safety)/ ; }, mesh = {*Premature Birth/epidemiology/microbiology/physiopathology/prevention &amp; control ; *Vagina/microbiology ; *Cervix Uteri/microbiology/physiopathology ; Humans ; Female ; Microbiota/genetics ; *Metagenomics ; Cervical Length Measurement ; Risk Factors ; East Asian People/statistics &amp; numerical data ; Risk Assessment/methods ; Prospective Studies ; DNA, Bacterial/genetics/isolation &amp; purification ; Pregnancy ; Adult ; }, abstract = {Preterm birth (PTB), a leading cause of neonatal morbidity and mortality, is frequently associated with premature cervical remodeling and vaginal microbiome dysbiosis. Cervical shortening in mid-pregnancy is a well-established risk factor for spontaneous PTB (sPTB), yet the microbial signatures underlying this condition remain underexplored, especially in Asian populations. In this study, we conducted shotgun metagenomic analysis of vaginal samples from 35 East Asian pregnant women with a short cervix and 12 with normal cervical length. Species-level taxonomic profiling and functional pathway analysis revealed reduced Lactobacillus dominance, increased microbial diversity, and enrichment of non-optimal CST IV species, such as Fannyhessea vaginae, Bifidobacterium breve, and Mycobacterium canetti in the short cervix group. Functional profiling showed group differences in pathways related to folate biosynthesis, carbohydrate metabolism, and epithelial barrier regulation. Among women with a short cervix, those who delivered preterm had vaginal microbiomes enriched in opportunistic pathogens, including Peptoniphilus equinus, Treponema spp., and Staphylococcus hominis. Conversely, B. breve, Lactobacillus gasseri, and Lactobacillus paragasseri were associated with full-term delivery. Functions related to glycosylation, structural stability, and degradation of cervical mucin were enriched in the sPTB group. Network analysis identified distinct microbial interactions between Lactobacillus-dominated clusters and CST IV-associated taxa, providing ecological insights that may reflect competitive dynamics and potential influences on cervicovaginal barrier integrity. These findings enhance our understanding of the taxonomic and functional profiles of the vaginal microbiome linked to cervical shortening and sPTB, contributing to improved risk stratification and management strategies for PTB, particularly in women with cervical shortening.}, }
@article {pmid41237217, year = {2025}, author = {Billings, WZ and Ge, Y and Skarlupka, AL and Miller, SL and Hemme, H and John, M and Dean, NE and Cobey, S and Cowling, BJ and Shen, Y and Ross, TM and Handel, A}, title = {Different antigenic distance metrics generate similar predictions of influenza vaccine response breadth despite moderate correlation.}, journal = {PLoS computational biology}, volume = {21}, number = {11}, pages = {e1013720}, pmid = {41237217}, issn = {1553-7358}, support = {R01 AI139761/AI/NIAID NIH HHS/United States ; R01 AI170116/AI/NIAID NIH HHS/United States ; 75N93019C00052/AI/NIAID NIH HHS/United States ; R35 GM146612/GM/NIGMS NIH HHS/United States ; U01 AI150747/AI/NIAID NIH HHS/United States ; }, mesh = {*Influenza Vaccines/immunology ; Humans ; *Influenza, Human/immunology/prevention &amp; control/virology ; *Antigens, Viral/immunology ; Computational Biology ; Bayes Theorem ; Antibodies, Viral/immunology ; Vaccine Efficacy ; Influenza A Virus, H3N2 Subtype/immunology ; Antigenic Variation/immunology ; Influenza A Virus, H1N1 Subtype/immunology ; }, abstract = {INTRODUCTION: Influenza continuously evolves to escape population immunity, which makes formulating a vaccine challenging. Antigenic differences between vaccine strains and circulating strains can affect vaccine effectiveness (VE). Quantifying the antigenic difference between vaccine strains and circulating strains can aid interpretation of VE, and several antigenic distance metrics have been discussed in the literature. Here, we compare how the predicted breadth of vaccine-induced antibody response varies when different metrics are used to calculate antigenic distance.<br><br>METHODS: We analyzed data from a seasonal influenza vaccine cohort that collected serum samples from 2013/14 - 2017/18 at three study sites. The data include pre- and post-vaccination HAI titers to the vaccine strains and a panel of heterologous strains. We used that data to calculate four different antigenic distance measures between assay strains and vaccine strains: difference in year of isolation (temporal), p-Epitope (sequence), Grantham's distance (biophysical), and antigenic cartography distance (serological). We analyzed agreement between the four metrics using Spearman's correlation and intraclass correlation. We then fit Bayesian generalized additive mixed-effects models to predict the effect of antigenic distance on post-vaccination titer after controlling for confounders and analyzed the pairwise difference in predictions between metrics.<br><br>RESULTS: The four antigenic distance metrics had low or moderate correlation for influenza subtypes A(H1N1), B/Victoria, and B/Yamagata. A(H3N2) distances were highly correlated. We found that after accounting for pre-vaccination titer, study site, and repeated measurements across individuals, the predicted post-vaccination titers conditional on antigenic distance and subtype were nearly identical across antigenic distance metrics, with A(H3N2) showing the only notable deviation between metrics, despite higher agreement for that subtype.<br><br>DISCUSSION: Despite moderate correlation among metrics, we found that different antigenic distance metrics generated similar predictions about breadth of vaccine response. Costly titer assays for antigenic cartography may not be needed when simpler sequence-based metrics suffice for quantifying vaccine breadth.}, }
@article {pmid41237195, year = {2025}, author = {Kertesz, SG and Varley, AL and Hoge, AE and Joiner, TE and Darnall, BD and Nicholson, KM and Fuqua, LA and Gilmore, MF and Riggs, KR and Gamble, SA and Gordon, AJ and Dwivedi, Y and Flower, M and Veasley, CS and Patton, CS and Leal, AS and Gibson, DM and Elliott, JE and McCullough, MB}, title = {Protocol for research examination of individual suicides occurring in chronic pain: A qualitative approach to psychological autopsy methodology.}, journal = {PloS one}, volume = {20}, number = {11}, pages = {e0329874}, pmid = {41237195}, issn = {1932-6203}, mesh = {Humans ; *Chronic Pain/psychology/drug therapy ; *Suicide/psychology ; Analgesics, Opioid/therapeutic use/adverse effects ; United States ; Male ; Female ; Autopsy/methods ; Qualitative Research ; Risk Factors ; Veterans/psychology ; Adult ; Middle Aged ; }, abstract = {INTRODUCTION: In the United States, taper and discontinuation of opioids prescribed for long-term pain have emerged as statistical correlates of suicidal events. Suicide is a complex and multidetermined event reflecting a combination of risks occurring over time in a particular narrative context. Prevention of suicides should be informed by a detailed understanding of life events, pain-related and other risk factors contributing to these tragedies. To date, there have been no efforts to qualitatively profile these suicides through interview of bereaved survivors or review of medical records. This method is usually termed "psychological autopsy.".<br><br>AIMS: This paper summarizes the protocol for the Clinical Context of Suicide Following Opioid Transitions (CSI:OPIOIDs) study. The study seeks to qualitatively characterize patient and clinical context factors associated with suicide among persons who died by suicide in the context of opioid stoppage or reduction, and to compare findings between Veteran and non-Veteran decedents.<br><br>METHODS: In the United States, there is no master list for suicide deaths linked to an antemortem health care event. For this reason, recruitment requires public advertising followed by screening of bereaved individuals who wish to participate. Data collection and interpretation are guided by the Social-Ecological Model for suicide. The study involves a collaboration of persons with lived experience and disciplinary experts in suicide, primary care, pain, health services, and medical anthropology.<br><br>CONCLUSIONS: This study aims to deliver the first in-depth analysis of suicide events occurring in persons with chronic pain who died by suicide in the context of a prescription opioid reduction or stoppage. The results should provide insights that can guide alterations to care by health systems and by individual practitioners.}, }
@article {pmid41235392, year = {2024}, author = {Ravenswater, HM and Greco, F and Burthe, SJ and Cunningham, EJA and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the European shag, Gulosus aristotelis (previously Phalacrocorax aristotelis) (Linnaeus, 1761).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {144}, pmid = {41235392}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Gulosus aristotelis, previously known as Phalacrocorax aristotelis, (the European shag; Chordata; Aves; Pelecaniformes; Phalacrocoracidae). The genome sequence is 1,279.1 megabases in length. Most of the assembly is scaffolded into 36 chromosomal pseudomolecules, including the Z and W sex chromosomes. Gene annotation of this assembly on Ensembl identified 16,474 protein coding genes. The mitochondrial genome has also been assembled and is 18.61 kilobases in length.}, }
@article {pmid41234513, year = {2025}, author = {Crowley, LM and Boyes, D and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Tawny Oak Tortrix, Acleris ferrugana (Denis &amp; Schiffermüller), 1775 (Lepidoptera: Tortricidae).}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {507}, pmid = {41234513}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Acleris ferrugana (Tawny Oak Tortrix; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence has a total length of 480.03 megabases. Most of the assembly (99.03%) is scaffolded into 31 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled, with a length of 16.58 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.}, }
@article {pmid41232106, year = {2025}, author = {Wang, LC and Pike, KC and Conway, M and Chen, AT}, title = {Identifying Stigma Phenotypes in Social Media Narratives of Substance Use: Observational Study.}, journal = {Journal of medical Internet research}, volume = {27}, number = {}, pages = {e68695}, pmid = {41232106}, issn = {1438-8871}, mesh = {Humans ; *Substance-Related Disorders/psychology ; *Social Stigma ; *Social Media ; Phenotype ; Narration ; }, abstract = {BACKGROUND: Individuals with substance use problems experience stigma in different contexts. Identifying characteristic situations in which stigma occurs or manifests-stigma phenotypes-can serve as important leverage points for future intervention.<br><br>OBJECTIVE: This paper aims to (1) identify stigma phenotypes expressed in social media narratives related to substance use stigma and (2) explore the similarities and differences between the stigma phenotypes from a social ecological perspective.<br><br>METHODS: We collected Reddit posts pertaining to 3 substances-alcohol, cannabis, and opioids. We performed feature engineering using a combination of content analysis, machine learning, and keyword-based methods to predict variables at different levels of the social ecological framework. Leveraging these features, we applied the fuzzy c-means clustering algorithm on the subset of posts containing stigma to extract stigma phenotypes, where a phenotype is defined by four main dimensions: (1) the stigma mechanism present (eg, internalized stigma, anticipated stigma, or enacted stigma), (2) the substance used (eg, alcohol, cannabis, or opioids), (3) the settings involved (eg, work, school, or home), and (4) the actors involved (eg, family, friends, or partners). Finally, we used Kruskal-Wallis and Dunn post hoc tests to examine the differences between stigma phenotypes with respect to specific ecological factors.<br><br>RESULTS: We derived 7 stigma phenotypes from stigma-related posts by 8627 authors. The phenotypes can be categorized into 4 groups: internalized stigma-only, anticipated stigma, enacted stigma-only, and mixed-stigma phenotypes. Narratives on internalized stigma phenotypes focused on the self, with minimal reference to settings and actors. One phenotype focused on anticipated stigma and was characterized by a high proportion of opioid use mentions (707/1217, 58.09% of the authors) and references to the health care setting (647/1217, 53.16% of the authors). Posts associated with the enacted stigma-only phenotypes included substantial representation of settings and actors. Narratives in the mixed-stigma phenotypes often involved more than one stigma mechanism, setting, and actor, with home and family being the most salient factors. The phenotypes differed from one another with respect to social ecological factors, including loneliness and social isolation, use of treatment services, presence of health care providers, community and support groups, society, and legalization.<br><br>CONCLUSIONS: These findings provide valuable insights that help inform the design and development of interventions targeted at different stigma phenotypic groups from a social ecological perspective.}, }
@article {pmid41231796, year = {2025}, author = {Baral, T and Maile, A and Adimurthy, NH and Saravu, K and Kudru, CU and Singh, J and Mukhopadhyay, C and Rao, M and Manu, MK and Sekhar Miraj, S}, title = {Exploring gut microbiota and its predicted functions in pulmonary tuberculosis: A multi-regional study using public 16S datasets.}, journal = {PloS one}, volume = {20}, number = {11}, pages = {e0336337}, pmid = {41231796}, issn = {1932-6203}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics/drug effects ; *Tuberculosis, Pulmonary/microbiology/drug therapy ; Phylogeny ; *RNA, Ribosomal, 16S/genetics ; Antitubercular Agents/therapeutic use ; Male ; Female ; Mycobacterium tuberculosis/genetics ; Middle Aged ; Adult ; }, abstract = {BACKGROUND: Pulmonary tuberculosis, caused by the bacillus Mycobacterium tuberculosis, remains a major global health challenge, particularly in developing countries. In this study, we analyzed publicly available 16S amplicon sequencing datasets from four geographical locations using a single workflow.<br><br>METHODS: We employed Quantitative Insights Into Microbial Ecology v.2 for microbial diversity analysis and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States v.2 for functional pathway predictions of the gut microbiota in patients with PTB and antitubercular therapy.<br><br>RESULTS: Our analysis revealed statistically significant alpha diversity differences in West Africa with decreased microbial diversity in pulmonary tuberculosis patients after two months of antitubercular therapy. Additionally, there were no statistically significant differences observed in pairwise comparisons within the same location or in the aggregate beta diversity of the datasets. The predicted microbial metabolic pathways related to vitamin biosynthesis, amino acid synthesis, and energy production were depleted in pulmonary tuberculosis patients following antitubercular therapy.<br><br>CONCLUSIONS: The observed alterations of gut microbial diversity and predicted functional profile underscores the influence of antitubercular therapy on gut health, suggesting that longer treatment durations may aggravate these alterations in gut microbial function. Moreover, geographical location exerts a more significant impact on microbial diversity than the disease state in a specific location, highlighting the potential for precision medicine to tailor interventions based on individual or regional microbiome characteristics.}, }
@article {pmid41231440, year = {2025}, author = {Lee, J and Nam, KH and Suh, Y and Lee, Y and Lee, D}, title = {Factors Associated With Patient Safety Activities of Clinical Nurses: A Cross-Sectional Secondary Data Analysis.}, journal = {International nursing review}, volume = {72}, number = {4}, pages = {e70127}, pmid = {41231440}, issn = {1466-7657}, support = {2022-22-0274//Ministry of Education/ ; //National Research Foundation of Korea/ ; }, mesh = {Humans ; Cross-Sectional Studies ; *Patient Safety ; Republic of Korea ; *Nursing Staff, Hospital/psychology/education ; Female ; Male ; Adult ; Organizational Culture ; Middle Aged ; Surveys and Questionnaires ; *Clinical Competence ; *Safety Management ; Secondary Data Analysis ; }, abstract = {AIMS: To examine the associations between patient safety silence, culture, competency, and activities among clinical nurses.<br><br>BACKGROUND: Patient safety ensures harm prevention and quality of care. Factors such as silence, culture, and competency are widely recognized as significantly associated with patient safety activities, but limited research has examined their interrelationships.<br><br>DESIGN: Cross-sectional secondary data analysis.<br><br>METHODS: This study used data from a study that investigated the patient safety educational needs of 291 nurses from general hospitals located in the Busan, Ulsan, and Gyeongsangnamdo regions of South Korea. To assess patient safety activities, silence, culture, and competency, the study employed the Patient Safety Activities Questionnaire, Patient Safety Silence Scale, Hospital Survey on Patient Safety Culture, and Patient Safety Competency Self-Evaluation Tool, respectively. The analysis involved descriptive statistics, correlation analysis, and multiple regression using SPSS 27.0.<br><br>RESULTS: The factors of silence and receiving patient safety education only once were negatively associated with patient safety activities. Positive associations were found for teamwork within the culture subdomain, skills within the competency subdomain, and hospital size.<br><br>CONCLUSIONS: These findings provide a basis for educational programs to improve nursing skills and highlight the need to build an open and collaborative organizational culture.<br><br>IMPLICATIONS FOR NURSING: Clinical nurses should develop patient safety skills, report patient safety incidents, and collaborate with team members to foster an open and cooperative organizational culture.<br><br>To minimize silence, while strengthening teamwork, organizations actively foster a culture of openness and collaboration. Education should be managed to meet minimum standards, and hospital-specific policies should be tailored according to each institution's size and characteristics.}, }
@article {pmid41230929, year = {2026}, author = {Chen, Z and Vončina, K and Sigwart, JD}, title = {Evaluating Probe Design for Phylogenomics Across Taxonomic Scales: First Steps for Applying Ultraconserved Elements in an Understudied Class (Mollusca: Polyplacophora).}, journal = {Molecular ecology resources}, volume = {26}, number = {1}, pages = {e70076}, pmid = {41230929}, issn = {1755-0998}, support = {P123//Leibniz project PHENOME/ ; }, mesh = {Animals ; *Phylogeny ; *Genomics/methods ; *Conserved Sequence ; *Mollusca/genetics/classification ; Transcriptome ; Computational Biology/methods ; }, abstract = {Ultraconserved elements (UCEs) have become a powerful tool for phylogenomics, but probe sets optimized for one lineage often perform inconsistently when applied in others. Here, we designed and tested new UCE probe sets derived from both genome and transcriptome data of an understudied molluscan class, Polyplacophora (chitons). In this study, we identified 5730 ultra-conserved elements (UCEs) from available chiton genomes and transcriptomes, and designed a set of 19,080 probes. These probes showed an average efficiency of 55% in the genome and 20% in transcriptomes, significantly outperforming available molluscan probe sets. A coalescence-based phylogenetic tree based on in silico extractions of UCEs from transcriptome and genome data successfully resolved chiton phylogeny at the species level. Relatively shorter flanking regions performed best. Where genome and transcriptome data were available for the same species, they did not always resolve as sister taxa in non-optimized methods; instead, genome- and transcriptome-derived sequences tended to form separate clades. This offers a caution for combining data harvested from published datasets. Quantifying phylogenetic signal at individual UCE loci demonstrates that the dataset retains topological stability across a range of filtering stringencies. This resource provides a foundation for integrating new genomic and transcriptomic datasets and has the potential to enable targeted sequencing of historical museum specimens. More broadly, our study highlights the importance of tailored probe design for phylogenomic studies in understudied lineages and the challenges of combining diverse molecular data types.}, }
@article {pmid41228769, year = {2025}, author = {Tanabe, R and Kikuchi, R and Zou, M and Suehiro, K and Takahashi, N and Saito, H and Kobayashi, T and Satake, H and Sato, N and Kageyama, Y}, title = {Emotion Recognition Using Temporal Facial Skin Temperature and Eye-Opening Degree During Digital Content Viewing for Japanese Older Adults.}, journal = {Sensors (Basel, Switzerland)}, volume = {25}, number = {21}, pages = {}, pmid = {41228769}, issn = {1424-8220}, support = {JP22K12215//JSPS KAKENHI/ ; JP25K15297//JSPS KAKENHI/ ; }, mesh = {Humans ; *Emotions/physiology ; *Skin Temperature/physiology ; Female ; Male ; Aged ; Thermography/methods ; *Eye Movements/physiology ; Facial Expression ; Face/physiology ; Japan ; Middle Aged ; East Asian People ; }, abstract = {Electroencephalography is a widely used method for emotion recognition. However, it requires specialized equipment, leading to high costs. Additionally, attaching devices to the body during such procedures may cause physical and psychological stress to participants. These issues are addressed in this study by focusing on physiological signals that are noninvasive and contact-free, and a generalized method for estimating emotions is developed. Specifically, the facial skin temperature and eye-opening degree of participants captured via infrared thermography and visible cameras are utilized, and emotional states are estimated while Japanese older adults view digital content. Emotional responses while viewing digital content are often subtle and dynamic. Additionally, various emotions occur during such situations, both positive and negative. Fluctuations in facial skin temperature and eye-opening degree reflect activities in the autonomic nervous system. In particular, expressing emotions through facial expressions is difficult for older adults; as such, emotional estimation using such ecological information is required. Our study results demonstrated that focusing on skin temperature changes and eye movements during emotional arousal and non-arousal using bidirectional long short-term memory yields an F1 score of 92.21%. The findings of this study can enhance emotion recognition in digital content, improving user experience and the evaluation of digital content.}, }
@article {pmid41227447, year = {2025}, author = {Götz, S and Reiter, K and Wensch-Dorendorf, M and von Borell, E and Raoult, CMC}, title = {Role of Illumination and Light Colour Temperature in the Preference Behaviour of Weaned Piglets.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {21}, pages = {}, pmid = {41227447}, issn = {2076-2615}, support = {820 204, 2017//German Government's Special Purpose Fund (Landwirtschaftliche Rentenbank)/ ; }, abstract = {This study investigated the preference behaviour of 24 four-week-old weaned piglets under different lighting conditions (0 lux with 0 Kelvin vs. 80 lux with 3000 Kelvin vs. 6500 Kelvin). Two trials with 12 piglets each were conducted over five weeks in a room with four interconnected pens, allowing free movement between the pens. Pens A and B were nearly dark (~0 lux), while pen C (80 lux, 3000 Kelvin) and pen D (80 lux, 6500 Kelvin) were illuminated. On three days in weeks 1, 3 and 5, behaviour (lying, eating and activity) was recorded using video observations and a 5 min time sampling method. Cleanliness was also monitored daily. In the first week, piglets in the first batch preferred the darkened pens, whereas piglets in the second batch preferred illuminated pens, especially when the colour temperature was 3000 Kelvin. By the third week, piglets in the second batch now preferred darker areas. In the fifth week, the piglets spent more time in the dark in the mornings and evenings but showed no preference for colour temperature. The darkened pens remained mostly clean, whereas pen D, which had a light colour temperature of 6500 Kelvin, was the most soiled. The results show that piglet behaviour changes with age and the time of day, suggesting that lighting concepts can be adapted to improve both animal welfare and pen hygiene.}, }
@article {pmid41225921, year = {2025}, author = {Alrhmoun, M and Sulaiman, N and Bajrami, A and Hajdari, A and Pieroni, A and Sõukand, R}, title = {The Resilience and Change in the Biocultural Heritage of Wild Greens Foraging Among the Arbëreshë Communities in Argolis and Corinthia Areas, Peloponnese, Greece.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {21}, pages = {}, pmid = {41225921}, issn = {2223-7747}, abstract = {The transformation of Local Ecological Knowledge (LEK) among minority populations undergoing cultural and linguistic assimilation over time is poorly understood. Arbëreshë communities in Greece, who have preserved Albanian-derived traditions for centuries, offer a unique opportunity to examine how folk plant knowledge adapts over time. This study examines the linguistic labels and culinary uses of wild greens among Arbëreshë (or Arvanites), an ethno-linguistic minority traditionally speaking Arbërisht or Arvanitika, the Tosk dialect of Albanian, who have resided in the Argolis and Corinthia regions of the Peloponnese for several centuries. In 2025, fieldwork was conducted in four rural Arbëreshë villages in the Argolis and Corinthia regions of Greece, combining semi-structured interviews with 24 elderly participants, participant observation, and the collection and identification of botanical specimens. The contemporary dataset was compared with historical ethnobotanical records from the 1970s to assess temporal changes in the use of wild vegetables and folk plant nomenclature. Our results reveal that current Arbëreshë ethnobotanical heritage has undergone profound Hellenisation, with 62% of folk plant names of Greek origin, 14% Albanian, and 24% hybrid, reflecting strong linguistic and cultural assimilation over the past half-century. The traditional boiled green mix (lakra in Arbëreshë, chorta in Greek) remains central to the local cuisine, which is rooted in foraged plants, although its culinary applications have diversified. In total, 37 taxa of wild vegetables across 37 genera and 14 families were documented in 2025, compared with 21 taxa across 21 genera in the filtered 1970 dataset. Core families, such as Asteraceae and Brassicaceae, remained dominant, while new families, like Malvaceae and Portulacaceae, appeared, possibly indicating both ecological and culinary changes. These findings raise questions about whether the Arbëreshë wild vegetable heritage was strongly influenced by the surrounding Greek majority or primarily acquired after migration, potentially facilitated by intermarriages and shared Orthodox Christian affiliation. Overall, our study highlights a largely Hellenised Arbëreshë biocultural heritage and underscores the urgent need for national and regional stakeholders to recognise and celebrate the remaining minority's linguistic and ethnobotanical diversity. The transformation of local ethnobotanical knowledge over the past fifty years appears influenced by ecological availability, socio-cultural dynamics, and changing taste preferences.}, }
@article {pmid41223204, year = {2025}, author = {Bateux, Q and Koss, J and Sweeney, PW and Edwards, E and Rios, N and Dollar, AM}, title = {Improving the accuracy of automated labeling of specimen images datasets via a confidence-based process.}, journal = {PLoS computational biology}, volume = {21}, number = {11}, pages = {e1013650}, pmid = {41223204}, issn = {1553-7358}, mesh = {Humans ; *Image Processing, Computer-Assisted/methods ; Neural Networks, Computer ; Computational Biology/methods ; Machine Learning ; Algorithms ; Databases, Factual ; Deep Learning ; }, abstract = {The digitization of natural history collections over the past three decades has unlocked a treasure trove of specimen imagery and metadata. There is great interest in making this data more useful by further labeling it with additional trait data, and modern "deep learning" machine learning techniques utilizing convolutional neural nets (CNNs) and similar networks show particular promise to reduce the amount of required manual labeling by human experts, making the process much faster and less expensive. However, in most cases, the accuracy of these approaches is too low for reliable utilization of the automatic labeling, typically in the range of 80-85% accuracy. In this paper, we present and validate an approach that can greatly improve this accuracy, essentially by examining the "confidence" that the network has in the generated label as well as utilizing a user-defined threshold to reject labels that fall below a chosen level. We demonstrate that a naive model that produced 86% initial accuracy can achieve improved performance - over 95% accuracy (rejecting about 40% of the labels) or over 99% accuracy (rejecting about 65%) by selecting higher confidence thresholds. This gives flexibility to adapt existing models to the statistical requirements of various types of research and has the potential to move these automatic labeling approaches from being unusably inaccurate to being an invaluable new tool. After validating the approach in a number of ways, we annotate the reproductive state of a large dataset of over 600,000 herbarium specimens. The analysis of the results points at under-investigated correlations as well as general alignment with known trends. By sharing this new dataset alongside this work, we want to allow biologists to gather insights for their own research questions, at their chosen point of accuracy/coverage trade-off.}, }
@article {pmid41219229, year = {2025}, author = {Berto, D and Fanelli, E and Vizzini, S and Rampazzo, F and Da Ros, Z and Noventa, S and Fortibuoni, T and Antonini, C and Cilluffo, G and Signa, G and Premici, A and Bardelli, R and Raicevich, S}, title = {ISOMED - A Stable ISOtope database of MEDiterranean marine food web components.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1768}, pmid = {41219229}, issn = {2052-4463}, support = {101059877//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101059877//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101059877//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; }, mesh = {*Food Chain ; Nitrogen Isotopes/analysis ; Carbon Isotopes/analysis ; Mediterranean Sea ; Databases, Factual ; Animals ; }, abstract = {Marine food webs shape the ecological dynamics of energy flows and predator-prey relationships. Their study is crucial to understanding human impacts that are monitored within environmental policies, such as the European Marine Strategy Framework Directive. One of the most used methods to assess the structure and functioning of marine food webs relies on the use of carbon and nitrogen stable isotopes (δ[13]C and δ[15]N), which are particularly useful for a vast range of taxa whose diet composition may be impractical to evaluate through traditional approaches (i.e., stomach content analysis). However, such data are sparse and have not been consistently collected, making it often difficult to assess the status of marine food webs. Here, we present ISOMED, a georeferenced database of published δ[13]C and δ[15]N values and carbon and nitrogen elemental composition of basal sources of organic matter and consumers collected in the Mediterranean Sea. The information reported includes estimates for 4959 records. ISOMED provides a unique tool for investigating trophic interactions and energy flow within Mediterranean food web components.}, }
@article {pmid41216995, year = {2026}, author = {Trepel, J and Atkinson, J and le Roux, E and Abraham, AJ and Aucamp, M and Greve, M and Greyling, M and Kalwij, JM and Khosa, S and Lindenthal, L and Makofane, C and Mokoena, L and Oosthuizen, A and Rech, BJ and Lundgren, E and Svenning, JC and Buitenwerf, R}, title = {Large herbivores are linked to higher herbaceous plant diversity and functional redundancy across spatial scales.}, journal = {The Journal of animal ecology}, volume = {95}, number = {1}, pages = {230-242}, pmid = {41216995}, issn = {1365-2656}, support = {DNRF173//Danmarks Grundforskningsfond/ ; 0135-00225B//Danmarks Frie Forskningsfond/ ; }, mesh = {*Herbivory ; Animals ; South Africa ; *Biodiversity ; Grassland ; *Food Chain ; *Plants/classification ; }, abstract = {Large herbivores can strongly influence plant communities. However, these effects are highly variable, potentially depending on the herbivore regime, that is, herbivore diversity and density. However, the role of the herbivore regime has been challenging to evaluate across spatial scales due to widespread defaunation and a lack of data on herbivore communities and their densities. Here, we investigated the effects of large herbivores along a gradient of trophic complexity (low to high herbivore diversity) and herbivory intensity (estimated from herbivore biomass and visitation frequency) on plant taxonomic and functional diversity at different scales (plot [n = 250], site [n = 50] and landscape [n = 10]) in 10 reserves in the savanna biome in South Africa. We found higher total plant species richness, driven by higher herbaceous (but not woody) plant species richness, in areas with higher herbivory intensity across multiple scales. While herbivores had no significant relationship with plant functional richness, we observed higher functional redundancy at all scales in areas more frequently visited by herbivores. Overall, herbivore-vegetation relationships were largely consistent across scales, and the strongest effects emerged at the largest scale. Our results show a positive relationship between large herbivores and both herbaceous plant species richness and plant functional redundancy, the latter suggesting higher vegetation resilience (the capacity of ecosystems to quickly recover from disturbances as different species compensate for the loss or decline of others). These effects are largely consistent across scales, indicating that the impact of herbivore regimes on plant communities is predominantly scale-independent and that large herbivores drive vegetation dynamics at both local and large scales. However, the stronger effects observed at the landscape scale imply that herbivore impacts manifest most prominently at larger scales. Altogether, our results suggest that restoring large herbivore populations can be expected to promote herbaceous plant diversity and ecosystem resilience.}, }
@article {pmid41214799, year = {2025}, author = {Ahuekwe, EF and Taiwo, DI}, title = {Performance assessment of Bayesian meta-analytic predictive model on kdr mutation in insecticide-resistant malarial vectors in sub-Saharan Africa.}, journal = {Malaria journal}, volume = {24}, number = {1}, pages = {391}, pmid = {41214799}, issn = {1475-2875}, mesh = {Africa South of the Sahara ; Bayes Theorem ; *Insecticide Resistance/genetics ; *Anopheles/genetics/drug effects ; *Mosquito Vectors/genetics/drug effects ; Animals ; *Mutation ; Malaria/transmission ; *Insecticides/pharmacology ; Pyrethrins/pharmacology ; }, abstract = {Mosquito populations' selective pressure arising from the widespread and prolonged use of insecticides, especially pyrethroids, for both agricultural usages and public health outcomes, has immensely contributed to the emergence and heavily spread of insecticide resistance. In this study, a systematic review identified eight eligible case-control or cohort studies published between 2015 and 2025 across sub-Saharan Africa that reported both allele and/or genotype frequencies of L1014F and L1014S. The predictive performance and inferential robustness of a Bayesian meta-analytic model were applied and evaluated on two knockdown resistance (kdr) mutations, L1014F and L1014S, in the Anopheles mosquito populations. Using the Markov Chain Monte Carlo (MCMC) sampling to compute pooled concordance statistics, odds ratios, and perform funnel plot asymmetry tests (Egger, Macaskill, Debray). The results revealed that L1014F showed a stronger and more consistent association with phenotypic resistance compared to L1014S, with odds ratios (OR) as high as 4.44 (95% CI 3.40-5.80). However, concordance statistics for both mutations demonstrated wide confidence intervals (L1014F: 0.141; CI - 0.095 to 0.459; L1014S: 0.169; CI - 0.399 to 0.688), indicating moderate predictive reliability. The Bayesian framework effectively synthesized complex and heterogeneous resistance data, confirming the operational relevance of KDR mutations in resistance surveillance. The global significance of these results enhances the predictive analytics in resistance management, such that resistance evolution is temporally and spatially dynamic. The integration of Bayesian modelling into existing entomological surveillance systems shifts the paradigm towards more adaptive and anticipatory management. Although data sparsity and regional heterogeneity warrant cautious interpretation, integrating ecological and thermodynamic variables into predictive models is essential for enhancing future resistance forecasting.}, }
@article {pmid41213900, year = {2025}, author = {Bu, C and Zhang, H and Zhang, F and Liang, W and Gao, H and Zhao, J and Lv, F and Xue, R and Liu, Q and Zhang, Z and Jin, Z and Xiao, J}, title = {PGAP2: A comprehensive toolkit for prokaryotic pan-genome analysis based on fine-grained feature networks.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {9865}, pmid = {41213900}, issn = {2041-1723}, support = {32170669//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Software ; *Genome, Bacterial/genetics ; *Genomics/methods ; Genetic Variation ; *Computational Biology/methods ; Phylogeny ; }, abstract = {Pan-genome analysis is a crucial method for studying genomic dynamics. By creating pan-genome maps for prokaryotic organisms, we can gain valuable insights into their genetic diversity and ecological adaptability. However, current analytical methods often struggle to balance accuracy and computational efficiency, and they tend to provide primarily qualitative results. This study introduces PGAP2, an integrated software package that simplifies various processes, including data quality control, pan-genome analysis, and result visualization. PGAP2 facilitates the rapid and accurate identification of orthologous and paralogous genes by employing fine-grained feature analysis within constrained regions. Our systematic evaluation with simulated and gold-standard datasets demonstrates that PGAP2 is more precise, robust, and scalable than state-of-the-art tools for large-scale pan-genome data. Furthermore, PGAP2 introduces four quantitative parameters derived from the distances between or within clusters, enabling detailed characterization of homology clusters. Finally, we validate our quantitative findings by applying PGAP2 to construct a pan-genomic profile of 2794 zoonotic Streptococcus suis strains. This analysis offers new insights into the genetic diversity of S. suis, thereby enhancing our understanding of its genomic structure. PGAP2 is freely available at https://github.com/bucongfan/PGAP2 .}, }
@article {pmid41212859, year = {2025}, author = {Hendawy, E and Belal, AA and Rebouh, NY and Shokr, MS and Sheta, AEAS and Saleh, AM and Abou-Hadid, AF}, title = {Health risk assessment of heavy metals in arid soils of the Nile Delta, Egypt using GIS and multivariate statistical analyses.}, journal = {PloS one}, volume = {20}, number = {11}, pages = {e0335394}, pmid = {41212859}, issn = {1932-6203}, mesh = {Egypt ; *Metals, Heavy/analysis/toxicity ; *Geographic Information Systems ; Humans ; *Soil Pollutants/analysis/toxicity ; Risk Assessment ; *Soil/chemistry ; Multivariate Analysis ; Environmental Monitoring/methods ; }, abstract = {Economic expansion has led to an increase in new toxins in the environment, creating a global problem for managing both environmental and human health. This study aimed to quantify the concentration of heavy metals (HMs) in soils of the Kafr El-Sheikh Governorate, located in the northern Nile Delta, Egypt, and to evaluate potential health risks by integrating Geographic Information Systems (GIS) with multivariate statistical analyses. Soil samples from 27 sites were analysed for potentially toxic elements (As, Cd, Co, Cu, Fe, Mn, Ni, Pb, and Zn) using Inductively Coupled Plasma Mass Spectrometry. Soil pollution indices such as enrichment factor (EF), contamination factor (CF), and geoaccumulation index (Igeo) were assessed. In addition, non-carcinogenic and cancer risk indices were calculated. To identify the origins of HMs in the research area, Pearson's bivariate correlation, principal component, and hierarchical cluster analyses (PCA) were used. The findings revealed that the mean HM concentrations (mg kg-1) were in the following order: Fe (10706 ± 2855)>Mn (697.53 ± 138.46)> As(210.07 ± 20.23)> Zn (207.40 ± 216.76)>Ni(112.43 ± 13.68)> Cu (87.15 ± 47.69)> Pb(31.11 ± 8.66)> Co(23.97 ± 5.96)> Cd (6.50 ± 5.62). The EF, CF, and Igeo indices indicated that the soils in the study area were contaminated with metals. The risk index values indicated moderate, considerable, and very high ecological risk, with a median value of 2060.40 (range: 192.95-5006.97). From PCA results, the possible sources of the metals in the arid soils included pesticides and chemical fertilizers, except for Mn, which appeared to originate from geogenic sources. Both children and adults had hazard quotient and Hazard index values less than one in all three exposure pathways, except for As in the ingestion pathway for children.. Furthermore, the total cancer risk (sum of ingestion, inhalation, and dermal contact pathways for each element) associated with children's exposure to the elements under investigation was as follows: Pb (4.5E-02)> As (4.1E-03)> Ni (2.6E-03)> Cd (4.7E-05). Consequently, the largest cancer risk was determined to be from Pb. These results provide valuable information that emphasizes the need to mitigate pollution from potentially toxic elements in the Nile delta and minimize health concerns for the local population.}, }
@article {pmid41210100, year = {2024}, author = {Boyes, D and Holland, PWH and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the March moth, Alsophila aescularia (Denis &amp; Schiffermüller).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {50}, pmid = {41210100}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Alsophila aescularia (the March moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 901.6 megabases in span. Most of the assembly is scaffolded into 14 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.67 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,618 protein coding genes.}, }
@article {pmid41208809, year = {2026}, author = {Lee, K and Kummerfeld, E and McMorris, BJ and Looman, WS and Burns, MK and Delaney, CW}, title = {Causal Pathways to Risk and Protective Factors for Partial-Day School Absenteeism for Secondary School Students.}, journal = {Journal of adolescence}, volume = {98}, number = {2}, pages = {450-460}, doi = {10.1002/jad.70073}, pmid = {41208809}, issn = {1095-9254}, support = {//The authors received no specific funding for this work./ ; }, mesh = {Humans ; *Absenteeism ; Adolescent ; Male ; Female ; *Students/psychology/statistics &amp; numerical data ; Schools ; Risk Factors ; Protective Factors ; Minnesota ; Surveys and Questionnaires ; Sleep Deprivation/psychology ; Child ; }, abstract = {INTRODUCTION: Chronic absenteeism, defined as missing 10% or more school days annually, negatively impacts academic achievement and correlates with long-term risks like poverty, poor health, and criminal behavior. While prior research has focused on full-day absences, partial-day absences, missing portions of the school day, are more prevalent and may have detrimental effects on academic outcomes. Despite this significance, PDAs are underexplored, leaving gaps in understanding their prevalence, causes, and impact. This study seeks to address these gaps and provide insights to guide comprehensive absenteeism interventions.<br><br>METHODS: In this study we used the Kids and Teens at School framework and causal discovery analysis to model the factors causally associated with partial-day absences using secondary school student-level data (n&#x2009;=&#x2009;125,375) from the 2019 Minnesota Student Survey. The discovered model indicate specified factors as causes of PDAs and broader absenteeism patterns.<br><br>RESULTS AND CONCLUSIONS: The findings highlighted a pattern of partial-day absences directly affecting full-day absences. Additional factors influencing school absences were discovered including (a) a positive association of sleep deprivation with mental health difficulties, and (b) a negative association between school engagement and partial-day absences. These findings emphasize the need for targeted policies addressing the behavioral and structural factors influencing absenteeism. Implications for practice include strategies to enhance engagement and mitigate the impact of sleep deprivation on attendance.}, }
@article {pmid41207298, year = {2026}, author = {Zhai, Z and Che, X and Shen, W and Zhang, Z and Li, Y and Pan, J}, title = {HLRMDB: a comprehensive database of the human microbiome with metagenomic assembly, taxonomic classification, and functional annotation by analysis of long-read and hybrid sequencing data.}, journal = {Nucleic acids research}, volume = {54}, number = {D1}, pages = {D763-D775}, pmid = {41207298}, issn = {1362-4962}, support = {32470699//National Natural Science Foundation of China/ ; //Chongqing Medical University/ ; }, mesh = {Humans ; *Metagenomics/methods ; *Microbiota/genetics ; *Metagenome ; *Databases, Genetic ; Molecular Sequence Annotation ; Bacteria/genetics/classification ; Software ; Internet ; }, abstract = {The human microbiome harbours an immense diversity of uncultivated microbes; short-read metagenomic sequencing has elucidated much of this diversity, but fragment repeats and mobile elements constrain strain-level resolution. Fortunately, long-read metagenomic sequencing can generate reads spanning tens of kilobases with single-molecule accuracies exceeding 99%, enabling near-complete genome and gene cluster recovery in a cultivation-independent manner. However, systematic resources that aggregate and standardise long-read outputs remain limited. Here, we present HLRMDB (http://www.inbirg.com/hlrmdb/), a comprehensive database of human microbiome datasets derived from long-read and hybrid metagenomic sequencing. We curated 1672 publicly available metagenomes (1291 long reads; 381 hybrids) spanning 38 studies, 39 sampling contexts and 42 host health states. A uniform assembly and binning pipeline reconstructed >98 Gb of contigs and yielded 18 721 metagenome-assembled genomes (MAGs). These MAGs span 21 phyla and 1323 bacterial species, with 6339 classified as near-complete and 5609 as medium-quality. HLRMDB integrates these genome-resolved data with extensive gene-centric functional profiles and antimicrobial resistance annotations. An interactive web interface supports flexible access to both sample-level and genome-level results, with multiple visualisations linking raw reads to assembled genomes. Overall, HLRMDB offers a harmonised, long-read-oriented repository that supports reproducible, strain-resolved comparative genomics and context-sensitive ecological investigations of the human microbiome.}, }
@article {pmid41205483, year = {2026}, author = {Ma, X and Wang, Z and Ishida, Y and Kobayashi, H}, title = {Land-cover-based indoor gamma-ray dose after a nuclear accident: location factor mapping via Monte Carlo simulation, GIS, and remote sensing.}, journal = {Journal of environmental radioactivity}, volume = {291}, number = {}, pages = {107853}, doi = {10.1016/j.jenvrad.2025.107853}, pmid = {41205483}, issn = {1879-1700}, mesh = {*Radiation Monitoring/methods ; Monte Carlo Method ; Gamma Rays ; Geographic Information Systems ; *Air Pollutants, Radioactive/analysis ; Remote Sensing Technology ; Fukushima Nuclear Accident ; *Air Pollution, Indoor/analysis/statistics &amp; numerical data ; Cesium Radioisotopes/analysis ; *Radioactive Hazard Release ; Radiation Dosage ; }, abstract = {Long-term indoor dose prediction is critical for health risk assessment and disaster management of accidental radionuclide releases. The gamma rays emitted from the ground deposition of [137]Cs are the primary concern in this context. This deposition exhibits variations in the relative initial source strength, ecological half-life, and vertical migration depending on the ground material. The dose response is further influenced by the attenuation within the ground, air, and building structures. Therefore, evaluating indoor doses in complex urban environments is challenging, particularly when accounting for directional variations in factors such as building density and ground materials. To address this issue, this study draws on the Local Climate Zone (LCZ) concept to propose a universal urban classification method suited to areas with mixed land cover and low-rise detached wooden structures, such as Fukushima. Monte Carlo simulations are then used to identify time-dependent indoor dose location factors across various environment type combinations. A mapping approach referencing LCZ recognition is developed using geographic information systems and remote sensing.}, }
@article {pmid41203806, year = {2025}, author = {Yang, J and Li, J and Liang, B and Zhao, N and Zhang, P and Fang, C and Xie, T and Xiang, P and Liu, H}, title = {Network toxicology, transcriptomics, and cytotoxic validation reveal TDCPP-induced pterygium mechanisms.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {39077}, pmid = {41203806}, issn = {2045-2322}, support = {ZKF2024042//National Clinical Key Specialty Ophthalmology Open Foundation/ ; ZKF2024041//National Clinical Key Specialty Ophthalmology Open Foundation/ ; YNQR-QNRC-2018-049//Yunnan Xingdian Youth Talent Program/ ; XDYC-MY-2024//Yunnan Xingdian Youth Talent Program/ ; 82460201//National Natural Science Foundation of China/ ; YDYXJJ2024-0003//Yunnan University Medical Research Foundation/ ; 202205AC160016//Yunnan Young and middle-aged Academic and Technical Leader Project/ ; 2024YNLCYXZX0343//Key Project of the Provincial Clinical Medical Center of Yunnan Province/ ; }, mesh = {Humans ; *Pterygium/chemically induced/genetics/pathology/metabolism ; Matrix Metalloproteinase 3/metabolism/genetics/chemistry ; *Transcriptome/drug effects ; Molecular Docking Simulation ; Gene Expression Profiling ; Fibroblasts/drug effects/metabolism ; Gene Regulatory Networks/drug effects ; Cell Proliferation/drug effects ; *Organophosphorus Compounds/toxicity ; Computational Biology ; }, abstract = {Pterygium, a common ocular surface disorder, is associated with environmental factors such as ultraviolet exposure and air pollution. Tris(1,3-dichloro-2-propyl) phosphate (TDCPP), a widely used organophosphate flame retardant, has been detected in environmental and biological samples, yet its role in pterygium pathogenesis remains unclear. This study employed an integrative approach combining network toxicology, transcriptome sequencing, and in vitro cytotoxicity assays to elucidate the molecular mechanisms linking TDCPP exposure to pterygium development. Bioinformatics analysis identified 273 TDCPP-related targets and 1,078 pterygium-associated genes, with 43 overlapping candidates. Weighted gene co-expression network analysis (WGCNA) revealed two key modules correlated with pterygium phenotypes, highlighting MMP3 as a central regulator. Molecular docking and dynamics simulations confirmed stable interactions between TDCPP and MMP3 (binding energy: -5.9 kcal/mol), supported by RMSD, RMSF, and hydrogen bonding analyses. In vitro experiments demonstrated that low-dose TDCPP (0.5 µM) upregulated MMP3 expression in immortalized human conjunctival fibroblasts, enhancing cell proliferation, while higher concentrations (50 µM) induced cytotoxicity. These findings suggest that TDCPP promotes pterygium pathogenesis via MMP3-mediated extracellular matrix remodeling and fibroblast proliferation. This study provides novel insights into the environmental etiology of pterygium and identifies MMP3 as a potential therapeutic target for TDCPP-associated ocular surface disorders.}, }
@article {pmid41203782, year = {2025}, author = {Baghbanzadeh, M and Dawson, T and Sayoldin, B and Frazer, SA and Oakley, TH and Crandall, KA and Rahnavard, A}, title = {deepBreaks identifies and prioritizes genotype-phenotype associations using machine learning.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {39095}, pmid = {41203782}, issn = {2045-2322}, support = {2109688//National Science Foundation/ ; 2109688//National Science Foundation/ ; 1754770//National Science Foundation/ ; 1754770//National Science Foundation/ ; 2109688//National Science Foundation/ ; 2109688//National Science Foundation/ ; }, mesh = {*Machine Learning ; *Software ; Algorithms ; *Genetic Association Studies/methods ; Humans ; Genotype ; Phenotype ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; }, abstract = {Sequence data, such as nucleotides or amino acids, are crucial in advancing our understanding of biology. However, investigating and analyzing sequencing data and genotype-phenotype associations present several challenges, including noise components that arise from the sequencing, nonlinear genotype-phenotype associations, collinearity between input features, and high dimensionality of the input data. Machine learning (ML) algorithms have proven to be effective in detecting intricate and nonstructural patterns, making them a valuable tool for studies focused on genotype-phenotype associations. Yet, there needs to be more user-friendly ML implementations that leverage the unique features of high-volume DNA sequence data. Here, we introduce deepBreaks, a generic approach that detects important positions (genotypes) in sequence data that are associated with phenotypic traits. deepBreaks compares the performance of multiple ML algorithms and prioritizes positions based on the best-fit models. It is open-source software with online documentation and examples available at https://github.com/omicsEye/deepBreaks .}, }
@article {pmid41202092, year = {2025}, author = {Sundh, J and Granqvist, E and Iwaszkiewicz-Eggebrecht, E and Manoharan, L and van Dijk, LJA and Goodsell, R and Godeiro, NN and Bellini, BC and Orsholm, J and Łukasik, P and Miraldo, A and Roslin, T and Tack, AJM and Andersson, AF and Ronquist, F}, title = {HAPP: High-accuracy pipeline for processing deep metabarcoding data.}, journal = {PLoS computational biology}, volume = {21}, number = {11}, pages = {e1013558}, pmid = {41202092}, issn = {1553-7358}, mesh = {*DNA Barcoding, Taxonomic/methods ; Algorithms ; Animals ; Computational Biology/methods ; Biodiversity ; DNA, Mitochondrial/genetics ; Software ; Insecta/genetics/classification ; Sequence Analysis, DNA/methods ; }, abstract = {Deep metabarcoding offers an efficient and reproducible approach to biodiversity monitoring, but noisy data and incomplete reference databases challenge accurate diversity estimation and taxonomic annotation. Here, we introduce a novel algorithm, NEEAT, for removing spurious operational taxonomic units (OTUs) originating from nuclear-embedded mitochondrial DNA sequences (NUMTs) or sequencing errors. It integrates 'echo' signals across samples with the identification of unusual evolutionary patterns among similar DNA sequences. We also extensively benchmark current tools for chimera removal, taxonomic annotation and OTU clustering of deep metabarcoding data. The best performing tools/parameter settings are integrated into HAPP, a high-accuracy pipeline for processing deep metabarcoding data. Tests using CO1 data from BOLD and large-scale metabarcoding data on insects demonstrate that HAPP significantly outperforms existing methods, while enabling efficient analysis of extensive datasets by parallelizing computations across taxonomic groups.}, }
@article {pmid41200470, year = {2025}, author = {Maldonado, M and Pita, L and Erpenbeck, D and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and ,  and ,  and ,  and ,  and , }, title = {The chromosomal genome sequence of the sponge, Corticium candelabrum Schmidt, 1862 and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {535}, pmid = {41200470}, issn = {2398-502X}, abstract = {We present a genome assembly from a specimen of Corticium candelabrum (sponge; Porifera; Homoscleromorpha; Homosclerophorida; Plakinidae). The genome sequence has a total length of 185.49 megabases. Most of the assembly (99.4%) is scaffolded into 22 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.19 kilobases in length. Gene annotation of this assembly on Ensembl identified 26,198 protein-coding genes. The metagenome of the specimen was also assembled, and 53 binned bacterial genomes were identified, including 44 high-quality MAGs that were typical of high microbial abundance sponge and included, besides the phyla Chloroflexota (class Dehalococcoidia), Acidobacteriota (order Acidomicrobiales), Alpha- and Gammaproteobacteria, also representatives of several candidatus phyla (Candidatus Latescibacterota, Binatota, Poribacteria).}, }
@article {pmid41198702, year = {2025}, author = {Cartereau, M and Biffoni, G and Baumel, A and Bacchetta, G and Brousset, L and Calvia, G and Casazza, G and Costanzo, A and Guerrina, M and Modaffari, A and Noble, V and Peruzzi, L and Pavon, D and Porceddu, M and Šegota, V and Silva, E and Todaro, F and Vuković, N and Leriche, A}, title = {WOODIV v2, more occurrences, functional traits, and a time-calibrated phylogeny for Euro-Mediterranean trees.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1756}, pmid = {41198702}, issn = {2052-4463}, mesh = {*Phylogeny ; *Trees/classification/anatomy &amp; histology ; Biodiversity ; *Databases, Factual ; Mediterranean Region ; Europe ; }, abstract = {The WOODIV v1 database provided occurrences at 10 km spatial resolution, traits and phylogenetic data for all 210 species (and 35 subspecies, totalling 245 taxa) in the Euro-Mediterranean Basin. While this reliable and readily accessible database has been of crucial help to investigate macro-ecological and biodiversity conservation questions, important knowledge gaps remained. To fill these gaps, we present an updated and extended version of the WOODIV database. (i) Occurrence data were updated from sources already considered in v1, three additional sources and an intensive field work campaign in Italy where occurrence data were scarce in v1, allowing to highly increase spatial coverage and data completeness. (ii) Besides increasing taxonomic coverage of traits already considered in v1, the traits data set has been extended to 15 new functional traits encompassing morpho-anatomy, reproduction and phenology, using new traits measurements from the field and data compilation from botanical literature not available in other databases. (iii) Finally, a new time-calibrated phylogeny for all 210 tree species was built and made available.}, }
@article {pmid41198686, year = {2025}, author = {Adde, A and Rey, PL and Külling, N and Chauvier-Mendes, Y and Fopp, F and Popp, MR and Broennimann, O and Petitpierre, B and Strebel, N and Gross, A and Stofer, S and Lehmann, A and Zimmermann, NE and Pellissier, L and Guisan, A and Altermatt, F}, title = {SDMapCH: a Comprehensive database of &gt;7,500 modelled species habitat suitability maps for Switzerland.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1752}, pmid = {41198686}, issn = {2052-4463}, mesh = {Switzerland ; *Ecosystem ; *Biodiversity ; *Databases, Factual ; Conservation of Natural Resources ; Software ; }, abstract = {Conserving natural ecosystems requires consistent and standardized biodiversity data to advance scientific research and ecological understanding. Despite several national initiatives to develop databases of species habitat suitability maps, even well-studied countries often lack comprehensive, standardized databases that cover a wide range of taxonomic groups modelled using a consistent framework. Using Switzerland as a case study, we demonstrate how these gaps can be addressed by introducing SDMapCH (v1.3), a nationwide raster database of species habitat suitability maps at 25-meter resolution. SDMapCH provides maps for about 7,500 species under both present conditions and future climate scenarios. SDMapCH was developed using the N-SDM software, an end-to-end platform based on a spatially-nested hierarchical framework. N-SDM allows multi-level integration of species and covariate data, helping to address niche truncation. SDMapCH outputs were evaluated using a state-of-the-art cross-validation procedure, and all layers passed a systematic data integrity check. By providing standardized, high-resolution habitat suitability maps for diverse species across various taxonomic and functional groups, SDMapCH stands as a key resource for scientific research and biodiversity assessments.}, }
@article {pmid41195458, year = {2025}, author = {Davis, AJS and Dawson, W and Essl, F and Kreft, H and Lenzner, B and Pergl, J and Pyšek, P and Weigelt, P and Winter, M and van Kleunen, M}, title = {The updated Global Naturalized Alien Flora (GloNAF 2.0) database.}, journal = {Ecology}, volume = {106}, number = {11}, pages = {e70245}, doi = {10.1002/ecy.70245}, pmid = {41195458}, issn = {1939-9170}, support = {//Czech Science Foundation/ ; RVO 67985939//Czech Academy of Sciences/ ; 202548816//German Research Foundation/ ; 264740629//German Research Foundation/ ; 379417748//German Research Foundation/ ; 52112243//German Research Foundation/ ; }, mesh = {*Plants/classification ; *Introduced Species ; *Databases, Factual ; }, abstract = {GloNAF is a continuously updated, curated compilation of alien naturalized vascular plant inventories for geographic regions worldwide. Building on its predecessor, GloNAF 2.0 now contains 16,429 taxa and introduces major updates, including the standardization of taxonomic names using the World Checklist of Vascular Plants (WCVP), removal of outdated records, and the net addition of 117,229 new records. These new entries have substantially increased the size of GloNAF, resulting in a 26% increase in the number of naturalized taxa in the database and a 31% increase in the number of geographic regions compared to GloNAF 1.2. We provide an overview of GloNAF 2.0, highlighting its expanded geographic and taxonomic coverage. In addition, we have aligned GloNAF with FAIR data principles through improvements in data accessibility, metadata standards, and support for data reuse. GloNAF 2.0 represents a significant and comprehensive resource for researchers aiming to advance our understanding of the drivers and consequences of biological invasions and naturalization success. The dataset is published under a CC-BY 4.0 license; thus, when using these data, please give credit to this paper.}, }
@article {pmid41192332, year = {2025}, author = {Zhou, L and She, J and Li, Q and Zheng, Q and Yang, J and Cui, M and Chen, T and Sun, S and Tang, F and Liu, Y}, title = {Integrated multi-omics and network pharmacology reveals antioxidant-active metabolites and health benefits of Camellia oleifera seed oil.}, journal = {Food chemistry}, volume = {496}, number = {Pt 3}, pages = {146913}, doi = {10.1016/j.foodchem.2025.146913}, pmid = {41192332}, issn = {1873-7072}, mesh = {*Antioxidants/metabolism/chemistry/pharmacology ; *Plant Oils/metabolism/chemistry/pharmacology ; *Camellia/chemistry/metabolism ; Metabolomics ; *Seeds/chemistry/metabolism ; Network Pharmacology ; Fatty Acids/metabolism/chemistry ; Humans ; Multiomics ; }, abstract = {The antioxidant properties of camellia oil (CO) remain insufficiently characterized. Here, multi-omics profiling combined with ABTS, DPPH, and FRAP assays was applied to identify antioxidant-active metabolites (AAMs). Widely-targeted metabolomics detected 2110 metabolites, while fatty acid, tocopherol, and elemental analyses revealed key nutritional contributors. Oleic acid dominated the fatty acid fraction (68.2-82.7 %), α-tocopherol was the major tocopherol (139.78-337.20 mg/kg), and selenium and zinc were the most relevant trace elements. A total of 160 AAMs were defined by OPLS-DA and WGCNA, with over 42 % being non-phenolics. Antioxidant assays indicated ABTS activity was mainly phenolic-driven, whereas DPPH involved both phenolics and amino acids. Network pharmacology linked core AAMs to targets in neurological, cardiovascular, hepatic, and respiratory systems. An integrated metabolic pathway network highlighted the multi-dimensional basis of CO's antioxidant potential. These findings reveal a broader antioxidant architecture beyond phenolics and provide a mechanistic foundation for developing CO as a functional nutraceutical oil.}, }
@article {pmid41192043, year = {2026}, author = {Kumar, A and Xu, C and Dakal, TC}, title = {Microbiome based precision medicine through integrated multiomics and machine learning.}, journal = {Microbiological research}, volume = {303}, number = {}, pages = {128384}, doi = {10.1016/j.micres.2025.128384}, pmid = {41192043}, issn = {1618-0623}, mesh = {Humans ; *Machine Learning ; *Precision Medicine/methods ; *Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; Metabolomics/methods ; Proteomics/methods ; Dysbiosis/microbiology ; Inflammatory Bowel Diseases/microbiology ; Multiomics ; }, abstract = {Gut microbiome (GME) is a dynamic ecosystem composed of diverse microorganisms with extensive functional potential that influence host physiology, endocrinology, and neurology. This review explores how multiomics (m[OMICS]) and machine learning (ML) enhance understanding of the GME and its implications for human disease and therapy. Integrating metagenomics, metatranscriptomics, metaproteomics, and metabolomics with ML enables the linkage of microbial composition and function to clinical outcomes. Combined m[OMICS] approaches elucidate species and strain dynamics, metabolic pathways, and metabolite production within the gut environment. Techniques such as shotgun metagenomics, metagenome-assembled genomes, and pathway mapping reveal associations between dysbiosis and diseases including inflammatory bowel disease, colorectal cancer, cardiometabolic, and neurological disorders. Mechanistic insights highlight short-chain fatty acids in immune regulation, bile acid transformations in metabolic signaling, and trimethylamine N-oxide in cardiovascular risk. ML models trained on heterogeneous datasets identify disease-related microbial modules, improve patient stratification, and predict therapeutic responses, such as differentiating IBD subtypes and detecting cancer-linked microbial signatures. Network analyses uncover gut microbial interaction patterns influencing host physiology. Emerging integrative tools like MOFA+ , DIABLO, and MintTea strengthen cross-modal analysis and biomarker discovery. Standardized workflows addressing quality control, assembly, binning, annotation, and visualization ensure reproducibility. Together, m[OMICS] and ML establish a robust framework for translating GME ecology into clinically relevant biomarkers and precision interventions. To enhance reliability, GME studies should adopt uniform sampling protocols, correct compositional biases, employ interpretable models, and validate findings across multi-site cohorts to advance microbiome-based diagnostics and therapeutics in precision medicine.}, }
@article {pmid41190312, year = {2025}, author = {Liuzzo, M and Utevsky, S and Marrone, F}, title = {Predictive Distribution Modeling of the Medicinal Leech Hirudo verbana Carena, 1820 (Hirudinea, Hirudinidae) in Sicily: Implications for Conservation.}, journal = {Ecology and evolution}, volume = {15}, number = {11}, pages = {e72410}, pmid = {41190312}, issn = {2045-7758}, abstract = {Hirudo verbana, a medicinal leech species of conservation concern, has long been considered rare and fragmented across its distribution range due to overexploitation and habitat alteration. In this study, we present the first predictive distribution model for H. verbana in Sicily, combining field occurrence data (time: 1980-2024) with environmental variables using an ensemble species distribution modeling (SDM) framework. Unlike its typical occurrence in temperate lowland wetlands of central-eastern Europe, the species in Sicily shows a marked shift toward upper hill and montane zones. Species presence was strongly associated with high NDVI values, reflecting a preference for areas with dense and structurally complex vegetation. In contrast, presence probability declined sharply with increasing terrestrial human footprint (THF), indicating a notable sensitivity to anthropogenic disturbance. Aquatic habitat type also emerged as a key predictor: the species was most likely to occur in lentic environments such as standing water bodies, and least likely in lotic systems or areas lacking aquatic habitats. Notably, most high-suitability areas overlapped with sites in the Natura 2000 network, emphasizing the importance of existing protected areas as refugia for the species. Moreover, some previously undocumented areas of high habitat suitability were identified, providing a spatially basis for refining monitoring strategies and informing conservation planning for this ecologically sensitive freshwater invertebrate.}, }
@article {pmid41189540, year = {2026}, author = {Inoue, J and Hirai, J and Ikeba, K and Yu, Z and Ahmed, SI and Lin, Z and Lin, Y and Wong, MK and Shinzato, C and Itoh, S and Ito, SI and Saito, H and Hyodo, S}, title = {eDNAmap: A Metabarcoding Web Tool for Comparing Marine Biodiversity, With Special Reference to Teleost Fish.}, journal = {Molecular ecology resources}, volume = {26}, number = {1}, pages = {e70066}, pmid = {41189540}, issn = {1755-0998}, support = {21H04922//Japan Society for the Promotion of Science/ ; //The University of Tokyo - FSI Project &#x201b;Ocean DNA'/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Fishes/genetics/classification ; *Biodiversity ; Internet ; *DNA, Environmental/genetics ; *Computational Biology/methods ; *Aquatic Organisms/classification/genetics ; *Metagenomics/methods ; *Software ; }, abstract = {Marine environmental DNA (eDNA) metabarcoding data are beginning to accumulate, even for remote and poorly studied areas, such as marine environments. These data enable us to identify distributions of target organisms and then to compare biological compositions between different marine areas. However, there is no platform to effectively utilise and accumulate these data. In this study, we developed eDNAmap, a web-based platform designed to analyse and store marine eDNA metabarcoding data. By uploading species or sequence composition data with location information, eDNAmap users can automatically (1) plot sampling locations on a map, (2) generate a heatmap to evaluate potential batch effects arising from methodological differences and (3) perform nonmetric multidimensional scaling and cluster analyses using similarity indices. Furthermore, users can specify scientific names to display species distributions and upload species lists to assess species compositions of the target sea area. As an example, fish sequence composition data obtained from 55 stations around the Watase line-believed to exist along a geographic canyon known as the Tokara Gap-were used to verify its existence using eDNAmap. The platform includes a database primarily consisting of teleost fish data from the Northwestern Pacific, which users can analyse similarly to their own uploads. Although originally designed for fish, eDNAmap is flexible enough to handle data from other marine organisms. Analysing multiple taxa enables the detection of concordant biogeographic patterns across different groups, which can strengthen ecological interpretations and lay the groundwork for identifying environmental drivers shaping community structures. eDNAmap is available at https://github.com/jun-inoue/eDNAmap.}, }
@article {pmid41189536, year = {2025}, author = {Hagan Brown, W and Gloor, E and Fyfe, R and MacKenzie, AR and Harper, NJ and Ganderton, P and Hart, K and Curioni, G and Quick, S and Davidson, SJ and Yetton, E and Diehl, JL and Fauset, S}, title = {Elevated CO2 Increases the Canopy Temperature of Mature Quercus robur (Pedunculate Oak).}, journal = {Global change biology}, volume = {31}, number = {11}, pages = {e70565}, pmid = {41189536}, issn = {1365-2486}, support = {//John Horseman Trust/ ; //Ecological Continuity Trust, UK/ ; //Royal Forestry Society, UK/ ; NE/S015833/1//Natural Environmental Research Council/ ; NE/V008366/1//Natural Environmental Research Council/ ; //University of Birmingham/ ; //Jabbs Foundation/ ; }, mesh = {*Quercus/physiology ; *Carbon Dioxide/metabolism ; Temperature ; Climate Change ; England ; Plant Leaves/physiology ; Forests ; }, abstract = {The canopy thermal response of natural forests to elevated CO2 (eCO2) is an understudied biophysical feedback in the global climate system. We investigated the effects of eCO2 (150 μmol mol[-1] above ambient) on canopy temperature (Tcan) dynamics of mature (> 175 years) Quercus robur (oak) at the Birmingham Institute for Forest Research Free Air CO2 Enrichment (BIFoR-FACE) facility in Staffordshire, England, during the growing seasons of 2021, 2022 and 2023. We employed long-term, high-frequency thermal infrared (TIR) imaging to measure Tcan. Our results show that daily maximum oak Tcan under eCO2 was, on average, approximately 1.3°C higher than under ambient (aCO2) conditions (21.5°C ± 4.4°C for aCO2 vs. 22.8°C ± 5.2°C for eCO2 oaks). Moreover, daily maximum Tcan-air temperature (Tair) differences were significantly higher under eCO2, resulting from more frequent extreme temperature excursions. These differences appear primarily to be driven by reduced stomatal conductance under eCO2, which limits transpirational cooling and alters the surface energy balance. This effect was evident in the different relationship between Tcan-Tair and vapour pressure deficit (VPD) for eCO2 compared to aCO2, showing a reduction in transpirational cooling under high VPD. Also, CO2-induced leaf structural and anatomical modifications, such as increased leaf mass per area, may have enhanced solar radiation absorption, thereby enabling greater canopy warming under high radiation conditions. Thus, eCO2 could likely cause a reduction in leaf transpiration in oaks, reducing its contribution to processes such as humidification of the lower atmosphere and precipitation in local and regional climates. Our findings highlight how high CO2 conditions may intensify thermal stress in temperate forests, influencing water and carbon cycles and potentially impacting forest resilience. Furthermore, Tcan will be essential for refining global Earth system models, which often use Tair as a proxy for Tcan, despite the latter's direct influence on carbon and hydrological cycles.}, }
@article {pmid41187144, year = {2025}, author = {Mercan, &#xc7; and Acıbuca, V}, title = {Utilizing FUCOM and AHP methods to identify the optimal beekeeping lands: A case study from Mardin, Türkiye.}, journal = {PloS one}, volume = {20}, number = {11}, pages = {e0335784}, pmid = {41187144}, issn = {1932-6203}, mesh = {*Beekeeping/methods ; Geographic Information Systems ; Bees ; Animals ; Conservation of Natural Resources ; }, abstract = {Beekeeping plays a vital role in agricultural sustainability and biodiversity conservation, yet identifying ecologically suitable areas for apiculture remains challenging. The objective of this study is to evaluate and compare two Multi-Criteria Decision-Making (MCDM) methods-the Analytical Hierarchy Process (AHP) and the Full Consistency Method (FUCOM)-within a Geographic Information Systems (GIS) framework to identify optimal beekeeping areas in Mardin Province, Türkiye. Nine environmental, climatic, topographical, logistic, and socio-economic factors were selected through literature review, legal regulations, expert consultation, and field observations. Suitability maps were generated and validated using field-verified hive locations and Receiver Operating Characteristic-Area Under the Curve (ROC-AUC) analysis. The results show that land use/cover, proximity to water sources, and precipitation were the most influential factors. Overall, 83% of hive locations coincided with areas classified as moderately suitable or higher. AHP achieved slightly higher predictive accuracy (AUC = 0.774) than FUCOM (AUC = 0.754), while FUCOM required substantially fewer pairwise comparisons, underscoring its efficiency. These findings confirm the robustness of the framework and provide a practical tool for sustainable apicultural land-use planning, offering transferable insights for policymakers, decision-makers, and beekeepers in Türkiye and other regions with similar ecological conditions.}, }
@article {pmid41184763, year = {2025}, author = {Jiao, Y and Hu, N and Xia, H and Li, X and Li, J and Liu, Y and Wang, J}, title = {Multi-omics approaches investigate the bitter flavor in the shoot of Bambusa oldhamii Munro.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {1501}, pmid = {41184763}, issn = {1471-2229}, support = {32101606//National Natural Science Foundation of China/ ; }, mesh = {*Plant Shoots/genetics/metabolism/chemistry ; *Bambusa/genetics/metabolism ; Taste ; Genome, Plant ; Genomics ; Transcriptome ; Multiomics ; }, abstract = {BACKGROUND: Bamboo, widely distributed in Southeast Asian and East Asia, is a palatable food resource, with its nutritional and low-fat properties, and functions in economic and ecological balance. As an important food source, some bamboo shoots often synthesize bitter chemicals in a special developing period or in a particular position of the shoot, which depends on the edible bamboo species. In this research, we focus on a sympodium bamboo, Bambusa oldhamii Munro, located in Southeast China, which has special biological properties. When the shoots are harvested underground, the shoots taste tender and tasty enough, but when the shoots erupt out of the soil surface with sunlight for days, the shoot has a little bitterness in the tip portion. This research conducts multi-omics approaches to investigate the bitter flavor formation with multiple developing phases of the shoot in B. oldhamii Munro.<br><br>RESULTS: The PacBio and Hi-C technologies were used to sequence the hexaploid species, B. oldhamii Munro, for de novo genome assembly. The assembled genome size of B. oldhamii is 1,446&#xa0;Mb, with a scaffold-level N50 equal to 38,936,033&#xa0;bp. A total of 88,140 genes in the genome were acquired, and about 53.89% of the genome is occupied by repeat components. The BUSCO score is 96.59%, suggesting a relatively complete and reliable assembly. Three subgenomes (ABC) include 35 pseudo-chromosomes based on the synteny analysis with another hexaploid species, Dendrocalamus latiflorus. The technologies of transcriptome analysis on the genome level and widely targeted metabolome were used to classify the key transcription factors and key bitter metabolites that account for the bamboo shoot flavor transition of B. oldhamii from underground to above ground, especially in the multiple developing phases. We finally mined out several bitter metabolites belonging to amino acids, flavonoids, terpenoids, purines, and other families, and several related pathways of Circadian rhythm, plant hormone signal transduction, flavonoid biosynthesis, and flavone and flavonol biosynthesis. Additionally, from joint analysis between bitter metabolites and transcription factors, we found that the family of bHLH and HB- transcription factors might influence the shoot bitter flavor transition and formation via influencing the accumulation of bitter metabolites in B. oldhamii.<br><br>CONCLUSIONS: In this research, we used Multi-omics methods to investigate the bitter flavor formation and transition in the shoot of B. oldhamii and hypothesized a simple model about this biological process. In a suitable circumstance (warm temperature and sunlight), the environment signals transduction influences the expression of transcription factor (bHLH, HB-, and others) which activate or suppress the expression level of genes or enzymes in the bitter flavor metabolites related pathways (biosynthesis of secondary metabolites, amino acid metabolism, biosynthesis of flavonoid, flavone, flavonol and isoflavonoid, plant hormone signal transduction and others), then causing the contents of bitter flavor metabolites (flavonoids, amino acids, terpenoids, cyanogenic glycosides and others) increase or decrease. This phenomenon influences the bitter flavor formation or transition in the shoot of B. oldhamii.}, }
@article {pmid41184333, year = {2025}, author = {Ghosh, A and Maile, A and Nagarajaram, HA}, title = {Prokaryotic co-occurrence patterns in diverse Indian mangrove ecosystems.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {38283}, pmid = {41184333}, issn = {2045-2322}, mesh = {India ; *Wetlands ; Biodiversity ; *Bacteria/genetics/classification/isolation &amp; purification ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Ecosystem ; Phylogeny ; Soil Microbiology ; }, abstract = {Mangrove ecosystems are unique coastal zones known to harbour a rich biodiversity of flora and fauna, including microbial communities. These microorganisms play a crucial role in nutrient cycling and sustain the primary productivity driven by plants within this ecosystem. Recent advancements in microbial ecology research emphasise that microbial community structure and composition are critical for an ecosystem to thrive. Studies have focused on the microbial diversity within Indian mangrove forests; however, there is a limited understanding of the co-occurrence patterns and functional roles of microbial communities in these ecosystems. This study explores prokaryotic diversity, primarily focusing on community interactions across three major Indian mangrove forests: the Bhitarkanika mangrove forest in Odisha, the Goan mangroves, and the Sundarbans in West Bengal. By analysing the publicly available 16 S rRNA amplicon datasets of the Indian mangrove microbiomes and performing co-occurrence network analysis on these datasets, we identified positively correlated genera and their predicted functional roles. Furthermore, the findings revealed the co-occurrence of several pathogenic bacteria in two of the mangrove ecosystems. Overall, our study highlights the shared functional roles adopted by co-occurring microbes in three major Indian mangrove ecosystems and suggests the need for large-scale studies in these understudied Indian ecosystems.}, }
@article {pmid41180493, year = {2025}, author = {Choi, JM and Wu, X and Zhang, L}, title = {FastST: an efficient tool for inferring decomposition and directionality of microbial communities.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e20161}, pmid = {41180493}, issn = {2167-8359}, mesh = {*Microbiota ; Humans ; Bayes Theorem ; Computer Simulation ; *Software ; *Computational Biology/methods ; }, abstract = {Microbiomes play crucial roles in human health, disease development, and global ecosystem functioning. Understanding the origins, movements, and compositions of microbial communities is essential for unraveling the principles governing microbial ecology. Microbial source tracking (MST) approaches have emerged as valuable tools for quantifying the proportions of different microbial sources within target communities, enabling researchers to track transmissions between hosts and environments, identify similarities between microbiome samples, and determine sources of contamination in various settings. Current MST methods like SourceTracker2 and FEAST have advanced the field by employing Bayesian and expectation-maximization approaches, respectively, but are limited by computational inefficiency with high-dimensional data and inability to infer directionality in source-sink relationships. This study presents a novel computational framework for microbial source tracking called FastST. FastST infers the relative contributions of source environments to sink microbiomes while also determining directionality when source-sink relationships are not predefined. Through extensive simulation studies with varying numbers of sources and complexity, FastST demonstrates superior performance in both accuracy and computational efficiency compared to FEAST and SourceTracker2, maintaining consistent execution times even as the number of source environments increases. Furthermore, the proposed method achieved over 90% accuracy in directionality inference across all tested scenarios, even when multiple major sources are present, broadening its applicability in practical microbiome research and environmental monitoring. FastST and data simulation codes are publicly available at https://github.com/joungmin-choi/FastST.}, }
@article {pmid41178269, year = {2026}, author = {Ono, S and Takebe, K and Tosa, I and Nishiya, Y and Nakayama, M and Wada, T and Takashiba, S and Ohara, N}, title = {PGN_0298 in the Assembly and Insertion Machinery (Aim) Operon Is Essential for the Viability of Porphyromonas gingivalis.}, journal = {Microbiology and immunology}, volume = {70}, number = {1}, pages = {9-14}, pmid = {41178269}, issn = {1348-0421}, support = {//JSPS KAKENHI Grant Number JP24K02614 (NO), JP23K15970 (SO), JP21K09842 (MN), JP24K23551 (KT)./ ; }, mesh = {*Porphyromonas gingivalis/genetics/physiology ; *Operon ; Gingipain Cysteine Endopeptidases ; Virulence Factors/genetics/metabolism ; Adhesins, Bacterial/metabolism/genetics ; Cysteine Endopeptidases/metabolism/genetics ; *Microbial Viability ; *Bacterial Proteins/genetics/metabolism ; Computational Biology ; Humans ; Bacterial Secretion Systems/genetics ; }, abstract = {Porphyromonas gingivalis is a typical periodontal pathogen, and one of its key virulence factors is the powerful protease gingipains. Gingipains are secreted via the type IX secretion system (T9SS) and are associated with the assembly and insertion machinery (Aim) operon (PGN_0296 to PGN_0301), which encodes both T9SS components and non-T9SS proteins. In this study, we investigated PGN_0298, a gene of unknown function within this operon, to elucidate its role in P. gingivalis and to gain insights into its potential function through bioinformatics analyses. Our results demonstrated that PGN_0298 is essential for the viability of P. gingivalis, despite having limited direct association with T9SS. Sequence homology and structure predictions indicate that PGN_0298 encodes a putative isoprenyl transferase. The essentiality of PGN_0298 underscores its potential as a novel drug target for the treatment of periodontal disease.}, }
@article {pmid41175854, year = {2025}, author = {Schor, J and Schulze, T and Ulrich, N and Mutlu, &#x130; and Krauss, M and Brack, W and Doan, T and Bingert, S and Bumberger, J and Busch, W and Hackermüller, J}, title = {Chemical mixture risk drivers and their heterogeneity in European freshwaters.}, journal = {Environment international}, volume = {205}, number = {}, pages = {109881}, doi = {10.1016/j.envint.2025.109881}, pmid = {41175854}, issn = {1873-6750}, mesh = {Europe ; *Water Pollutants, Chemical/analysis/toxicity ; *Environmental Monitoring ; Risk Assessment ; *Fresh Water/chemistry ; }, abstract = {Chemical pollution of aquatic environments involves diverse substance combinations that can provoke combined biological and toxicological effects even when individual concentrations remain below effect thresholds. Multiple efforts are ongoing to better consider mixture effects in chemical safety regulation, but debate continues over whether a few substances drive aquatic mixture risks or whether a large heterogeneous set of drivers must be considered. We employed a data re-use strategy to investigate the heterogeneity of chemical mixture risk drivers to aquatic species in Europe. Initially, we derived 201 risk-driving chemicals from a single measurement campaign, allowing driver comparisons between sites based on consistently measured substances. We then extended our analysis to extensive chemical monitoring data of the NORMAN network, originating from different campaigns focusing on diverging substance sets measured at different times and locations. Data were aggregated quarterly and sites clustered per quarter according to measured substances. Using a robust definition of risk drivers (the most significant chemicals whose cumulative toxic units contribute ≥75% of total risk), our study concludes that at least 580 different substances drive chemical mixture risks in European freshwaters, with high heterogeneity between locations. Notably, mixture risk drivers were species-specific, exhibited temporal variability, and belonged to different chemical use groups considered in various safety regulations. We also found that monitoring data gaps prevented more precise analysis, particularly regarding temporal variability. These findings have important implications for future chemical monitoring strategies and mixture risk regulation in Europe, highlighting the complexity and heterogeneity of chemical mixture risks in aquatic environments.}, }
@article {pmid41175080, year = {2025}, author = {Carroll, RA and Ricemeyer, ES and Hillier, LW and DaCosta, JM and Osipova, E and Smith, S and Jamie, GA and Martinez, JG and Molina-Morales, M and Marques-Bonet, T and Manthey, JD and Haddad, D and Fuxjager, MJ and Lynch, KS and Wood, JMD and Jarvis, E and Masterson, P and Thibaud-Nissen, F and Hauber, M and Spottiswoode, CN and Sackton, TB and Balakrishnan, CN and Sorenson, MD and Warren, WC}, title = {Genomic resources for comparative analyses of obligate avian brood parasitism.}, journal = {The Journal of heredity}, volume = {}, number = {}, pages = {}, doi = {10.1093/jhered/esaf087}, pmid = {41175080}, issn = {1465-7333}, abstract = {Examples of convergent evolution, wherein distantly related organisms evolve similar traits, including behaviors, underscore the adaptive power of natural selection. In birds, obligate brood parasitism, and the associated loss of parental care behaviors, has evolved independently in seven different lineages, though little is known about the genetic basis of the complex suite of traits associated with this rare life history strategy. We generated genome assemblies for ten brood parasitic species plus eight species representatives of their parental/nesting outgroups. This includes nine long-read chromosome-level assemblies, with scaffold N50 sizes ranging from 38.1 to 72.6 MB, and gene representation completeness measures > 97%. Leveraging this new catalog of avian genomes, we constructed clade-level alignments that reveal variation in chromosomal synteny, provide first-time or improved annotations of protein-coding and non-coding genes, and define cross-species ortholog reference sets. We also refine estimates for the timing of the seven independent origins of brood parasitism, ranging from recent events such as 1.6 to 4.5 million years ago in Molothrus cowbirds to much earlier origins over 30 million years ago in two of the three cuckoo lineages. These genomic resources lay the foundation for investigating the genetic and genomic underpinnings of brood parasitism, including the loss of parental care, shifts in mating systems, perhaps resulting in heightened sperm competition, elevated annual fecundity, improved spatial cognition related to nest-finding, and the diverse adaptations shaped by intense coevolution with host species.}, }
@article {pmid41173371, year = {2025}, author = {Mehta, S and Allen, LH and Bailey, RL and Boushey, CJ and Duggan, CP and Crouter, SE and Engle-Stone, R and Fahim, SM and Gibbs, K and Hernandez, E and Huey, SL and Owino, VO and Prado, EL and Proaño, GV and Savage, JS and Steiber, AL and Zemel, BS and Raiten, DJ}, title = {Application of an Ecological Approach to Assessment of Nutrition in School-Aged Children-A Report from the "Biomarkers of Nutrition for Development: Knowledge Indicating Dietary Sufficiency (BOND-KIDS)" Project Working Group 3.}, journal = {The Journal of nutrition}, volume = {}, number = {}, pages = {}, pmid = {41173371}, issn = {1541-6100}, support = {T32 HD087137/HD/NICHD NIH HHS/United States ; }, abstract = {The global health community must extend its attention beyond the "first 1000 d" to include school-aged children (i.e., the "next 7000 d") given the critical windows of development during this period. An opportunity exists to leverage school settings to implement programs for supporting child health and nutrition. Historically, many school-based programs evaluate "learning" or academic achievement as a priority outcome, with less attention paid to the "learner." This has left gaps in studying the impact school nutrition programs and interventions may have on children's health and development, and how to measure these outcomes. The "Biomarkers of Nutrition for Development: Knowledge Indicating Dietary Sufficiency (BOND-KIDS)" Project primarily focused on these gaps-specifically, the need for better tools to measure the functional impact of school-based nutritional interventions on the health and development of school-aged children aged 5-19 y. Functionally, BOND-KIDS applied an ecological approach via the organization of 4 interacting thematic working groups (WG): 1) biology (internal environment), 2) environment (external; home, school, physical), 3) assessment, and 4) translation and implementation. This report represents the work of WG 3: assessment, which addresses the specific need for better assessment tools, and also includes general considerations for nutritional assessment in children. We included the evidence, relevance, and feasibility of current approaches in assessing dietary intake, nutritional status, and key functional outcomes for the developing school-aged children. The findings will help to determine context-specific approaches to assess the need for and impact of interventions designed to improve the diet, nutrition, and health of school-aged children. To increase utility and accessibility, the data contained in this report are accessible via a self-service online dashboard. The current version of this dashboard is hosted at https://www.cpnh.cornell.edu/bond-kids-1, via the Cornell Joan Klein Jacobs Center for Precision Nutrition and Health at Cornell University.}, }
@article {pmid41172900, year = {2026}, author = {Kou, X and Yang, S and Zou, J and Chen, S and Wu, J and Sun, B and Yan, Z and Liu, D and Tan, H}, title = {Rapid spectrophotometric method for the selective determination of peracetic acid in water with cobalt-mediated oxidation decolorization of rhodamine B.}, journal = {Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy}, volume = {348}, number = {Pt 1}, pages = {127082}, doi = {10.1016/j.saa.2025.127082}, pmid = {41172900}, issn = {1873-3557}, abstract = {Recently, increasing attention had been paid for using peracetic acid (PAA) as an efficient disinfectant or a strong oxidant in wastewater treatment. In this study, a rapid and simple spectrophotometric method for the selective determination of PAA in aqueous solution was established, based on the oxidative decolorization of rhodamine B (RhB) by reactive species generated from the combination of PAA and Co(II). Under the optimized conditions (20 μmol L[-1] RhB, 1.0 mmol L[-1] Co(II), pH = 5.0 buffered with 10 mM acetate acid buffer, and reaction time = 40 s), the extent of RhB decolorization at the characteristic wavelength of 552 nm was found to be proportional to the concentration of PAA in the aqueous solution. A strong linear correlation was observed between the consumption of RhB and the concentration of PAA in the range of 0.25-25 μmol L[-1] (R[2] = 0.9991), and the sensitivity for PAA was as high as 2.99 × 10[4] M[-1] cm[-1]. The RhB spectrophotometric method is effectively tolerant to interference the coexistent H2O2 in PAA solution, the common coexisting species in practical water samples (KCl, MgSO4, NaNO3, NaHCO3, DCF and humic acid) and even the added reducing substances such as hydroxylamine and ascorbic acid. As a selective colorimetric agent, RhB is resistant to interference from reducing substances and water bodies, enabling accurate determination of PAA concentration in actual water environments. Overall, the RhB spectrophotometric method could be used as an alternative method for the cheap, rapid and selective determination of PAA in water samples.}, }
@article {pmid41171142, year = {2026}, author = {Lyu, B and Wu, K and Huang, Y and Anton, M and Li, X and Viknander, S and Anwer, D and Yang, Y and Lu, D and Kerkhoven, E and Zelezniak, A and Gao, D and Chen, Y and Li, F}, title = {GotEnzymes2: expanding coverage of enzyme kinetics and thermal properties.}, journal = {Nucleic acids research}, volume = {54}, number = {D1}, pages = {D583-D592}, pmid = {41171142}, issn = {1362-4962}, support = {2024YFA0920300//National Key R&amp;D Program of China/ ; 22478223//National Natural Science Foundation of China General Project/ ; A2403013//National Natural Science Foundation of China General Project/ ; JC2024004//Tsinghua Shenzhen International Graduate School/ ; DCE-iBHE-2023-1//Tsinghua Shenzhen International Graduate School/ ; 2023-04254//Swedish Research Council/ ; 2019-05356//Swedish Research Council/ ; 2019-01403//Formas grant/ ; BB/Y000730/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Kinetics ; *Enzymes/chemistry/metabolism ; *Databases, Protein ; Temperature ; Enzyme Stability ; Humans ; }, abstract = {Enzyme kinetics are fundamental for understanding metabolism, yet experimentally measured parameters remain scarce. To address this gap, we introduce GotEnzymes2, a substantially expanded resource covering 10 765 species, 7.3 million enzymes, and 59.6 million unique entries. Compared with the first version, GotEnzymes2 now integrates both catalytic and thermal parameters, enabling unified predictions of kcat, Km,kcat/Km, optimal temperature, and melting temperature. This expansion markedly broadens species and enzyme coverage, creating the most comprehensive database of enzyme kinetic and stability parameters to date. To construct the resource, we systematically benchmarked state-of-the-art models for catalytic and thermal parameter prediction, and incorporated the best-performing strategies to ensure accuracy and generalizability. Altogether, GotEnzymes2 provides the community with a powerful resource for data-driven enzyme discovery, design, and engineering, with broad applications in systems biology, metabolic engineering, and synthetic biology. GotEnzymes2 is publicly accessible at https://metabolicatlas.org/gotenzymes.}, }
@article {pmid41171134, year = {2026}, author = {Sun, Y and Chen, Q and Fan, G and Sun, Q and Zhou, Q and Zhang, J and Nie, J and Ma, J and Wu, L}, title = {gcMeta 2025: a global repository of metagenome-assembled genomes enabling cross-ecosystem microbial discovery and function research.}, journal = {Nucleic acids research}, volume = {54}, number = {D1}, pages = {D724-D733}, pmid = {41171134}, issn = {1362-4962}, support = {2021YFA0717001//National Key R&amp;D Program of China/ ; XDB0830000//Chinese Academy of Sciences/ ; 153211KYSB201900211//Chinese Academy of Science/ ; //Chinese Academy of Sciences/ ; }, mesh = {*Metagenome/genetics ; *Metagenomics/methods ; *Databases, Genetic ; Humans ; *Ecosystem ; Animals ; Molecular Sequence Annotation ; Bacteria/genetics/classification ; }, abstract = {The rapid growth of metagenomic sequencing has generated an unprecedented wealth of metagenome-assembled genomes (MAGs), transforming opportunities for microbial discovery and functional characterization. Yet, full utilization of these resources has been constrained by heterogeneous data generation practices and inconsistent analytical pipelines. The gcMeta database addresses this gap by compiling MAGs through both public acquisition and de novo assembly. This release integrates over 2.7 million MAGs from 104 266 samples spanning various biomes, covering human, animal, plant, marine, freshwater, and extreme environments. It establishes 50 biome-specific MAG catalogues comprising 109 586 species-level clusters, of which 63% (69 248) represents previously uncharacterized taxa, and annotates >74.9 million novel genes. By linking functional traits with microbial co-occurrence networks, gcMeta identifies keystone taxa central to biogeochemical cycling and environmental adaptation. The platform further supports cross-ecosystem functional comparisons, revealing niche-specific metabolic pathways and stress-response genes. Moreover, gcMeta provides standardized, AI-ready datasets encompassing microbial enzymes, anti-phage defense systems, and other functional modules, enabling advanced machine learning applications. By bridging microbial "sequence discovery" with "functional utilization," gcMeta establishes a foundation for ecological research, industrial biotechnology, and novel gene mining. The platform is freely accessible at https://gcmeta.wdcm.org/.}, }
@article {pmid41171124, year = {2026}, author = {Lv, J and Ma, S and Ma, C and Liu, F and Duan, X and Huang, X and Geng, Q and Liu, F and Li, G and Li, Y and Wang, J and Li, C and Zheng, H and Zhang, Y and Sun, Z and Wang, J and Fan, G and Huang, S and Zhang, L and Bao, Z and Wang, S}, title = {Ocean-M: an integrated global-scale multi-omics database for marine microbial diversity, function and ecological interactions.}, journal = {Nucleic acids research}, volume = {54}, number = {D1}, pages = {D813-D825}, pmid = {41171124}, issn = {1362-4962}, support = {2024YFC2816000//National Key Research and Development Program of China/ ; LSKJ202202804//Marine S&amp;T Fund of Shandong Province for Laoshan Laboratory/ ; 2025B1111180001//Guangdong Provincial Key Areas R&amp;D Program Project/ ; SOLZSKY2025013//Hainan Province Science and Technology Special Fund/ ; 32573498//Natural Science Foundation of China/ ; 32222085//Natural Science Foundation of China/ ; QDLYY-2024011//Blue Seed Industry Science and Technology Innovation Project/ ; GZB20250215//Postdoctoral Fellowship Program of CPSF/ ; }, mesh = {Metagenome ; *Databases, Genetic ; *Microbiota/genetics ; Metagenomics/methods ; *Aquatic Organisms/genetics/classification ; Oceans and Seas ; *Seawater/microbiology ; Biodiversity ; Ecosystem ; Bacteria/genetics/classification ; Molecular Sequence Annotation ; Software ; Multiomics ; }, abstract = {Multi-omics analyses have significantly advanced the understanding of complex marine microbial communities and their interactions. Despite notable progress from recent large-scale ocean meta-analysis efforts, the effective integration and accessibility of these diverse datasets remain challenging. To address this, we introduce Ocean-M (http://om.qnlm.ac), a comprehensive and publicly accessible platform for marine microbial multi-omics data integration, analysis, and visualization. Ocean-M provides a systematic view of 54 083 high-quality metagenome-assembled genomes, including genome assembly statistics, genome clustering, gene annotation, and interactive tools for global-scale taxonomic profiling. The platform also incorporates microbial community networks, host-microbiome interactions, and environmental DNA datasets to support an integrated ecological framework for studying microbial interactions and ecosystem functions. Additionally, Ocean-M enables large-scale mining of ecologically and biotechnologically important genes, with curated catalogs of 151 798 biosynthetic gene clusters, 52 699 antibiotic resistance genes, and millions of carbohydrate-active enzymes and plastic-active enzymes. By combining multi-omics data with environmental metadata, Ocean-M serves as a valuable resource for advancing marine microbial ecology, global biogeography, and functional gene discovery.}, }
@article {pmid41168455, year = {2025}, author = {Oka, SO and Tomass, Z and Takele, S and Megaze, A and Kano, JK}, title = {Habitat suitability assessment for hippopotamus (Hippopotamus amphibius) conservation using GIS-based multi-criteria decision analysis in Ethiopia's Southern Rift Valley.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {11}, pages = {1276}, pmid = {41168455}, issn = {1573-2959}, mesh = {Ethiopia ; Geographic Information Systems ; *Conservation of Natural Resources/methods ; *Ecosystem ; Animals ; *Environmental Monitoring/methods ; *Artiodactyla/physiology ; Decision Support Techniques ; }, abstract = {The hippopotamus (Hippopotamus amphibius) is a keystone species inhabiting freshwater ecosystems across sub-Saharan Africa but is increasingly threatened by habitat loss, fragmentation, and human-wildlife conflict. This study assessed habitat suitability for hippopotamus conservation in Ethiopia's southern Rift Valley, focusing on Lakes Abaya and Chamo, using a Geographic Information System (GIS)-based multi-criteria decision analysis (MCDA). Data from October to December 2024 included satellite imagery, bathymetry, rainfall records, a digital elevation model (DEM), focus group discussions, and farmer interviews. Six socio-ecological criteria-land use/land cover (LULC), lake depth, slope, elevation, rainfall, and distance from settlements-were integrated through a weighted overlay. Results show that 26% of the study area is highly suitable, 23% suitable, 39% moderately suitable, and 12% unsuitable. Wetlands and shallow waters emerged as the most critical habitats, while croplands, settlements, and steep or upland areas were least favorable. Human-hippo conflicts were strongly linked to cropland encroachment near lakeshores, consistent with local reports and previous studies. Compared to other Ethiopian hippo ranges, the Abaya-Chamo system supports a relatively higher proportion of suitable habitat, attributed to persistent wetlands and aquatic-terrestrial connectivity. However, threats from wetland degradation, agricultural expansion, and settlement growth continue to reduce habitat quality. These findings highlight the urgent need for wetland restoration, buffer zones, and community-based conflict mitigation strategies to sustain hippopotamus populations in the region.}, }
@article {pmid41166222, year = {2025}, author = {Boot, J and van den Ende, MWJ and Wiers, RW and Lees, MH and van der Maas, HLJ}, title = {Integrating dual-process decision making and social dynamics: A formal modeling framework for addiction.}, journal = {Psychological review}, volume = {}, number = {}, pages = {}, doi = {10.1037/rev0000584}, pmid = {41166222}, issn = {1939-1471}, support = {//Horizon Europe Framework Programme/ ; }, abstract = {Currently, formal models of addiction focus either on the complex individual decision-making processes involved in addiction or on the social dynamics of addiction. They do not integrate these two levels, which has been identified as a key shortcoming of current formal models of addiction. To address this, we propose a nonlinear dynamical modeling framework of addiction integrating both the individual level and social level of addictive behavior. The individual level of our modeling framework is a formalization of a dual-process theory, where one type of process increases the consumption of addictive goods, and another type of process limits consumption. For our formalization, we build on a well-studied model from ecology, originally used to model periodic outbreaks of the spruce budworm population. To this model, we add the process of incentive sensitization at the individual level and at the social level, we incorporate the critical processes of selection homophily and peer influence. We show that our integrated modeling framework can be used to explain key phenomena identified in addiction literature: a gradual transition to heavy use, sudden relapse and sudden quitting, relatively stable use states over time (i.e., abstinence moderate use, and heavy use), social contagion and sudden outbreaks, clustering of users, and social aid in recovery. In addition, we demonstrate how our modeling framework can be extended to include mutualistic, competitive, and more complex interactions between different addictive behaviors. Finally, we show how our framework can lead to new insights and predictions and suggest avenues for future research. (PsycInfo Database Record (c) 2025 APA, all rights reserved).}, }
@article {pmid41165898, year = {2025}, author = {Doležel, M and Lískovec, R}, title = {Reference and Solution Architecture for GenAI- and GIS-Enhanced Physical Activity Interventions: Towards Implementing the AI4Motion Platform.}, journal = {Journal of medical systems}, volume = {49}, number = {1}, pages = {150}, pmid = {41165898}, issn = {1573-689X}, mesh = {Humans ; *Geographic Information Systems ; *Exercise ; *Mobile Applications ; Ecological Momentary Assessment ; }, abstract = {Digital Behaviour Change Interventions (DBCIs) aim at improving individual health by engaging various means of Information and Communication Technology (ICT), including mobile apps and wearables. Participant intervention fatigue may happen when DBCIs become too frequent, repetitive, demanding, or lack perceived relevance, and this may result in participants' reduced motivation and adherence over time. Advancing technology-supported engagement mechanisms is therefore of utmost importance. To address this problem, we present a reference and solution architecture based on open-source technologies and open Application Programming Interfaces (Open APIs). First, we integrated a Large Language Model (LLM) component into the DBCI design. Second, to support context-awareness, we enhanced this integration by adding a Geographic Information Systems (GIS) element. Our pilot implemented AI4Motion platform targets both personalization and contextualization aspects of DBCIs. Our work contributes to the emerging discussion on LLM/GIS-related system design patterns for digital platforms supporting Ecological Momentary Assessment (EMA), Experience Sampling Method (ESM), and Just-in-Time Adaptive Interventions (JITAIs).}, }
@article {pmid41163612, year = {2025}, author = {Belgaid, Y and Helal, M and Lakmeche, A and Venturino, E}, title = {A model for the interactions of wild boars and park rangers.}, journal = {Mathematical biosciences and engineering : MBE}, volume = {22}, number = {11}, pages = {2780-2806}, doi = {10.3934/mbe.2025102}, pmid = {41163612}, issn = {1551-0018}, mesh = {Animals ; *Sus scrofa/physiology ; Computer Simulation ; Population Dynamics ; Ecosystem ; Conservation of Natural Resources ; Swine ; Parks, Recreational ; Population Density ; *Models, Biological ; }, abstract = {Boars, being one of the most widely spread ungulates worldwide, have a widely recognized important role in the balance of natural environment and forests. Since large boar populations severely damage crops and cause serious traffic accidents, they are widely hunted, thereby also representing a relevant economic resource. In the model presented here, the species is at times considered ravaging, enabling it to be kept in check, while on the other hand, it must be preserved from extinction as a protected species. We considered an idealized, relatively simple situation in which rangers of the park where the boars are hosted manage this animal population size when they extrude into the surrounding areas through the woods perimeter. Modeling this situation involves considering not the whole boar population, but only those that are involved in the spillover, i.e., those living in proximity of the woods edge. The theoretical investigation and the simulations revealed the existence of a transcritical bifurcation relating the two viable equilibria, coexistence, and the ranger-free point. Also, the possible onset of persistent oscillations via a Hopf bifurcation is shown, leading to periodic recalling of rangers to contain the spillovers. On the other hand, a better regime was obtained by reducing the environment's resources for the wild boars, which stabilized the the boar population at constant level, with a reduced presence of the rangers, reducing the costs of their periodic recalling.}, }
@article {pmid41163577, year = {2025}, author = {Fujiwara, K and Toyoda, A and Katsuki, T and Sato, Y and Biswa, BB and Kishida, T and Tsuruta, M and Nakamura, Y and Mochizuki, T and Kimura, N and Kawamoto, S and Ohta, T and Nonomura, KI and Niki, H and Yano, H and Umehara, K and Suzuki, C and Koide, T}, title = {Chromosome-scale genomes of two wild flowering cherries (Cerasus itosakura and Cerasus jamasakura) provide insights into structural evolution in Cerasus.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {32}, number = {6}, pages = {}, pmid = {41163577}, issn = {1756-1663}, support = {//ROIS/ ; }, mesh = {*Genome, Plant ; *Chromosomes, Plant/genetics ; *Evolution, Molecular ; Japan ; }, abstract = {Flowering cherries (genus Cerasus) are iconic trees in Japan, celebrated for their cultural and ecological significance. Despite their prominence, high-quality genomic resources for wild Cerasus species have been limited. Here, we report chromosome-level genome assemblies of two representative Japanese cherries: Cerasus itosakura, a progenitor of the widely cultivated C. ×yedoensis "Somei-yoshino," and Cerasus jamasakura, a traditional popular wild species endemic to Japan. Using deep PacBio long-read and Illumina short-read sequencing, combined with reference-guided scaffolding based on near-complete C. speciosa genome, we generated assemblies of 259.1 Mbp (C. itosakura) and 312.6 Mbp (C. jamasakura), with both >98% BUSCO completeness. Consistent with their natural histories, C. itosakura showed low heterozygosity, while C. jamasakura displayed high genomic diversity. Comparative genomic analyses revealed structural variations, including large chromosomal inversions. Notably, the availability of both the previously published C. speciosa genome and our new C. itosakura genome enabled the reconstruction of proxy haplotypes for both parental lineages of "Somei-yoshino." Comparison with the phased genome of "Somei-yoshino" revealed genomic discrepancies, suggesting that the cultivar may have arisen from genetically distinct or admixed individuals, and may also reflect intraspecific diversity. Our results offer genomic foundations for evolutionary and breeding studies in Cerasus and Prunus.}, }
@article {pmid41162447, year = {2025}, author = {Sayed, E and Ali, AM and Alrashdi, I and Sallam, KM and Abdel-Basset, M and Ismail, MM}, title = {A robust framework for evaluating green mines towards sustainable development.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {37739}, pmid = {41162447}, issn = {2045-2322}, abstract = {The development of green mines is essential for promoting sustainability in the mining sector due to the significant ecological impacts of resource extraction. This study proposes a novel hybrid multi-criteria decision-making (MCDM) framework that integrates Spherical Fuzzy Sets (SFSs) with SWOT analysis, the CRITIC method, and Grey Relational Analysis (GRA). The framework introduces several innovations: it applies SFS-based MCDM for the first time to green mine evaluation in Egypt, structures 37 sustainability-related criteria under SWOT dimensions, and employs SF-CRITIC for objective weighting without subjective comparisons. The model is applied to assess 20 gold mines, where the SF-GRA method is used to rank alternatives based on proximity to an ideal solution. The results show that GME20 consistently ranks highest, while GME5 ranks lowest. A sensitivity analysis is conducted by varying the Grey relational coefficient and simulating 37 weight scenarios, demonstrating stable rankings and strong model resilience. Comparative analysis against ten SFS-based MCDM methods confirms the consistency of results, with Spearman correlation coefficients exceeding 0.77. In addition to its methodological novelty, the framework supports interpretable decision outcomes by identifying key sustainability drivers such as renewable energy adoption and land reclamation. This contributes actionable insights for policymakers and stakeholders, enabling informed green investment and regulatory decisions. The study offers a transparent, reproducible, and scalable tool for sustainability evaluation in resource-intensive industries. The proposed model introduces a structured integration of SWOT-based criteria classification, objective weight computation via SF-CRITIC, and robust alternative ranking using SF-GRA. Furthermore, it contributes uniquely by applying the methodology to the underexplored context of green mine evaluation in Egypt. These distinctions articulate the methodological and application-based novelties of the proposed framework.}, }
@article {pmid41162384, year = {2025}, author = {Outhwaite, CL and Cocker, L and Comont, RF and White, HJ and Powney, GD and Turvey, K and Roy, HE and Brown, PMJ}, title = {A database of traits for the ladybird species of the United Kingdom.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1708}, pmid = {41162384}, issn = {2052-4463}, support = {Open Access Fund//Anglia Ruskin University/ ; NE/V006533/1//RCUK | Natural Environment Research Council (NERC)/ ; Algorithm studentship//RCUK | Natural Environment Research Council (NERC)/ ; NE/V006878/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/V006878/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/R016429/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/Y006208/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/V007548/1//RCUK | Natural Environment Research Council (NERC)/ ; }, mesh = {Animals ; United Kingdom ; *Coleoptera ; Ecosystem ; Databases, Factual ; }, abstract = {Trait-based approaches have become common in ecological research as they can contribute to an understanding of ecosystem functioning and how species, communities and systems may respond to environmental change. However, trait datasets are difficult and time-consuming to compile and consequently not commonly available, particularly for insects. Ladybirds, beetles in the family Coccinellidae, are an important insect group that provide key ecosystem services, primarily through predation of pest insects such as aphids and coccids. Here, we have compiled information on species traits, ecological preferences and distribution metrics for 48 species considered resident in the United Kingdom (UK) (including the harlequin ladybird) using published sources, a recently published field guide, and biological records. Species traits may inform analyses useful for conservation purposes. This database provides researchers with access to the most up-to-date assessment of UK ladybird species, promoting research into this important insect group.}, }
@article {pmid41161774, year = {2025}, author = {Khaing, PT and Han, YMZ and Zaww, K and Kyaw, MS and Thwin, KM and Orui, M and Kunii, Y and Hamaie, Y and Kyaw, SS and Tsuboi, M and Egawa, S}, title = {A Remote Access Qualitative Study Protocol to Investigate the Coping Strategies in the Mindset of the Affected Adults after the 2025 Myanmar Earthquake.}, journal = {The Tohoku journal of experimental medicine}, volume = {267}, number = {3}, pages = {263-272}, doi = {10.1620/tjem.2025.J130}, pmid = {41161774}, issn = {1349-3329}, mesh = {Humans ; Myanmar ; *Adaptation, Psychological ; *Earthquakes ; Qualitative Research ; Adult ; Middle Aged ; Female ; Male ; Young Adult ; Adolescent ; Social Support ; Coping Skills ; }, abstract = {On March 28, 2025, a 7.7-magnitude earthquake struck central Myanmar (GLIDE #EQ-2025-000043-MMR), compounding the country's existing political instability, economic fragility, and infrastructural weaknesses. Although seismic events have recurred throughout history, limited knowledge exists regarding how working-age adults (18-60), who play a central role in recovery, mobilize personal, cultural, and community resources to cope with adversity and reconstruct their lives. This is a protocol clarification for a remote access qualitative study using semi-structured interviews with 30 purposively sampled participants, half from heavily impacted zones (Sagaing, Mandalay) and half from nearby regions experiencing secondary disruption (Yangon). Using a remote system, interviews will be audio-recorded, transcribed verbatim, and analyzed thematically following Graneheim and Lundman's approach. This study aims to identify key coping strategies, including social support networks, spiritual practices, and local initiatives of working-age adults in Myanmar, and to compare how exposure severity shapes adaptive responses. Anticipated themes based on existing disaster and resilience literature include community-led resilience, hope through faith, and resource-sharing practices. Findings are expected to offer in-depth, culturally grounded insights that can inform disaster recovery programs, psychosocial support services, and policy frameworks aimed at strengthening resilience in Myanmar and similar low-resource, low-accessibility, crisis-affected settings.}, }
@article {pmid41160887, year = {2026}, author = {Guo, S and Jiang, Y and Zou, J and Lu, M and Li, D and Zhang, Q and Li, W and Mao, L and Xu, Z and Liu, S}, title = {GPSAdb 2.0: an expanded atlas of gene-perturbation transcriptomes with enhanced tools for regulatory gene discovery.}, journal = {Nucleic acids research}, volume = {54}, number = {D1}, pages = {D1082-D1086}, pmid = {41160887}, issn = {1362-4962}, support = {82403086//National Natural Science Foundation of China/ ; CSTB2022NSCQ-BHX0698//Natural Science Foundation of Chongqing/ ; //Chongqing Medical Scientific Research Project/ ; 2025DBXM005//Chongqing Health Commission and Science and Technology Bureau/ ; CYYY-DSTDXM202502//Chongqing Medical University/ ; }, mesh = {Humans ; *Transcriptome ; *Software ; *Gene Expression Profiling/methods ; Gene Knockdown Techniques ; *Gene Expression Regulation ; Cell Line ; *Databases, Genetic ; }, abstract = {Gene perturbation is essential for uncovering gene function and its involvement in various biological processes and diseases. GPSAdb 2.0 (https://www.gpsadb.com/) presents a significantly expanded and improved platform for exploring gene expression changes following gene knockdown across diverse cell lines. Compared to GPSAdb 1.0, this new version offers several key upgrades: (i) a substantial increase in data coverage, now featuring 7665 gene knockdown groups, 42 235 samples, and 2810 perturbation genes across a broader array of cell lines and biological conditions; (ii) the introduction of new tools, including "BioTrigger" for flexible gene set enrichment analysis and "fastGPSA" for rapid, advanced differential expression analysis. With these enhancements, GPSAdb 2.0 provides researchers with a powerful resource for investigating gene perturbation effects and gaining deeper insights into transcriptional regulation, making it an invaluable resource for studies on gene regulation, disease mechanisms, and potential therapeutic targets.}, }
@article {pmid41156942, year = {2025}, author = {Gao, L and Zhao, H and Guo, N and Jiang, X and Zhang, Y}, title = {Mechanical and Environmental Properties of Cemented Paste Backfill Prepared with Bayer Red Mud as an Alkali-Activator Substitute.}, journal = {Materials (Basel, Switzerland)}, volume = {18}, number = {20}, pages = {}, pmid = {41156942}, issn = {1996-1944}, abstract = {This study developed a sustainable high-strength coal gangue backfill material for underground mining applications using coal gangue, fly ash, and cement as primary raw materials, with red mud (RM) as an alternative alkali activator. The mechanical properties of the backfill material were systematically optimized by adjusting coal gangue particle size and alkali activator dosage. The optimized formulation (coal gangue/fly ash/cement = 5:4:1, 3-6 mm coal gangue particle size, 5% RM, which named BF-6-5RM) achieved superior compressive strengths of 8.23 MPa (7 days) and 10.5 MPa (28 days), significantly exceeding conventional backfill requirements and outperforming a CaO-activated reference system (coal gangue/fly ash/cement = 5:4:1, 3-6 mm coal gangue particle size, 2% CaO, which named BF-6-2CaO). Microstructural and physicochemical analyses revealed that both formulations produced calcium silicate hydrate gels (C-S-H gels) and ettringite (AFt) as key hydration products, though BF-6-5RM exhibited a denser microstructure with well-developed ettringite networks and no detectable portlandite (CH), explaining its enhanced early-age strength. Environmental assessments confirmed effective heavy metal immobilization via encapsulation, adsorption, precipitation and substitution, except for arsenic (As), which exceeded Class III groundwater thresholds (DZ/T 0290-2015) due to elevated raw material content, displaying "surface wash-off, diffusion and depletion" leaching behavior. The findings confirm that red mud-based alkali activation is a viable technology for underground backfilling, provided it is coupled with arsenic control strategies like chemical stabilization or the selection of low-arsenic raw materials. This approach not only enables the resource utilization of hazardous industrial waste but also facilitates the production of backfill materials that combine both mechanical strength and environmental compatibility, thereby delivering dual economic and ecological benefits for sustainable mining practices.}, }
@article {pmid41154259, year = {2025}, author = {Dabic, M and Djordjevic, G and Radovanovic, S and Mihaljevic, O and Stepovic, M and Zdravkovic, M and Zdravkovic, N and Stojic, V and Milojevic, S and Zdravkovic, D and Djonovic, N and Knezevic, D and Popovic, S and Janicijevic, K and Selakovic, V and Radovanovic, J}, title = {Disparities in Healthcare Utilization by Settlement Type in Serbia.}, journal = {Healthcare (Basel, Switzerland)}, volume = {13}, number = {20}, pages = {}, pmid = {41154259}, issn = {2227-9032}, abstract = {Background and Objectives: Urban-rural health disparities reflect differences in health outcomes, healthcare access, and socio-economic conditions between populations. In Serbia, limited research has quantified how socio-demographic and socio-economic characteristics influence settlement type and healthcare utilization. The aim of this study was to examine the relationship between settlement type and socio-demographic/socio-economic factors, and to assess whether these differences are reflected in patterns of healthcare utilization. Materials and Methods: Data were drawn from the 2019 Serbian National Health Survey, a nationally representative, stratified, two-stage random sample including 12,439 adults aged ≥20 years. Settlement type (urban vs. rural) was the primary dependent variable. Descriptive statistics, Chi-square and t-tests, and bivariate and multivariate logistic regression models were used to assess associations. Odds ratios (ORs) with 95% confidence intervals (CIs) were calculated, with significance set at p < 0.05. Results: Urban residence was more likely among unmarried individuals, those living in Šumadija/Central Serbia, and those with higher education. Primary or lower education reduced the odds of urban residence, and middle-income groups were less likely to live in urban areas compared to the richest. Settlement type was not significantly associated with hospital or day hospital use. However, rural residents had lower use of prescribed medicines, higher use of non-prescribed medicines, and more frequent physiotherapy visits. Private practice use was over twice as likely in urban settlements. Conclusions: To address urban-rural healthcare disparities in Serbia, targeted strategies could include enhancing health literacy in rural areas, incentivizing physicians to work in underserved regions, expanding telemedicine and mobile health services, improving access to prescribed medications, and strengthening public-private healthcare integration to ensure equitable access across all settlement types.}, }
@article {pmid41150182, year = {2025}, author = {Jones, L and Lay, M and Seneci, L and Hodgson, WC and Koludarov, I and Senoner, T and Soria, R and Fry, BG}, title = {Neurotoxic Sleight of Fang: Differential Antivenom Efficacy Against Mamba (Dendroaspis spp.) Venom Spastic-Paralysis Presynaptic/Synaptic vs. Flaccid-Paralysis Postsynaptic Effects.}, journal = {Toxins}, volume = {17}, number = {10}, pages = {}, pmid = {41150182}, issn = {2072-6651}, support = {DP210102406//Australian Research Council/ ; }, mesh = {Animals ; *Antivenins/pharmacology ; *Elapid Venoms/toxicity/genetics/chemistry ; *Dendroaspis ; Chickens ; *Paralysis/chemically induced/drug therapy ; *Neurotoxins/toxicity ; }, abstract = {Mamba (Dendroaspis species) snakebites are critical medical emergencies across sub-Saharan Africa. Envenomings can result in the rapid onset of complex neurotoxic symptoms, often leading to high rates of mortality without timely intervention with antivenom. The ancestral state of mambas is the green coloured, forest dwelling type, with the tan/grey coloured, savannah dwelling D. polylepis (Black Mamba) representing a derived state both ecologically and morphologically. However, it has not been tested whether these changes are paralleled by changes in venom biochemistry or if there are differential molecular evolutionary patterns. To fill these knowledge gaps, this study evaluated the neurotoxic effects of all Dendroaspis species venoms using the chick biventer cervicis nerve-muscle preparation, assessed the neutralizing efficacy of three antivenoms commercially available in Africa, and reconstructed the molecular evolutionary history of the toxin types to ascertain whether some were unique to particular species. All Dendroaspis venoms demonstrated potent flaccid-paralysis due to postsynaptic neurotoxicity. The only exception was D. angusticeps venom, which conversely exhibited spastic-paralysis due to presynaptic/synaptic neurotoxicity characterised by potentiation of acetylcholine presynaptic release and sustained synaptic activity of this neurotransmitter. Antivenom efficacy varied significantly. All three antivenoms neutralized to some degree the flaccid-paralysis postsynaptic effects for all species, with D. viridis venom being the best neutralized, and this pattern extended to all the antivenoms. However, neutralisation of flaccid-paralysis postsynaptic effects unmasked spastic-paralysis presynaptic/synaptic neurotoxicity within non-angusticeps venoms. Spastic-paralysis presynaptic effects were poorly neutralized for all species by all antivenoms, consistent with prior clinical reports of poor neutralisation of spastic-paralytic effects. Geographic variation in D. polylepis venom was evident for the relative neutralisation of both spastic-paralysis presynaptic/synaptic and flaccid-paralysis postsynaptic/synaptic neurotoxic pathophysiological effects, with differential neutralization capabilities noted between the Kenyan and South African populations studied. Molecular phylogenetic analyses confirmed spastic-paralysis and flaccid- paralysis toxins to be a trait that emerged in the Dendroaspis last common ancestor, with all species sharing all toxin types. Therefore, differences in venoms' pathophysiological actions between species are due to differential expression of toxin isoforms rather than the evolution of species-specific novel toxins. Our findings highlight the synergistic nature of flaccid-paralysis postsynaptic and spastic-paralysis presynaptic/synaptic toxins, while contributing significant clinical and evolutionary knowledge of Dendroaspis venoms. These data are crucial for the continued development of more effective therapeutic interventions to improve clinical outcomes and for evidence-based design of clinical management strategies for the envenomed patient.}, }
@article {pmid41148369, year = {2025}, author = {Kuannaxiaer, A and Liu, J and Kasthuri, N}, title = {Integrating machine learning and geospatial approaches for multi-hazard vulnerability mapping: implications for environmental health and contaminant risk in fragile ecosystems.}, journal = {Environmental geochemistry and health}, volume = {47}, number = {12}, pages = {526}, pmid = {41148369}, issn = {1573-2983}, mesh = {*Machine Learning ; *Ecosystem ; Geographic Information Systems ; India ; *Environmental Monitoring/methods ; *Environmental Health ; Humans ; Risk Assessment ; }, abstract = {High-altitude ecosystems face growing threats from natural hazards and human activities, intensifying socio-economic and environmental risks. The Nilgiris District, Tamil Nadu, is a hotspot where steep terrain, fragile ecosystems, climate variability, and anthropogenic pressures converge. This study integrates geospatial technologies and machine learning (XGBoost) to map multi-hazard risk zones and assess their implications for ecosystem stability and contaminant susceptibility. The GIS-based multi-moderated evaluation was applied using slope, elevation, land use/land cover (LULC), drainage density and proximity to roads and settlements. Improved the accuracy of the XGBoost classification by capturing complex spatial relationships. The multi-hazard risk zone map identified five classes with very low-risk zones with high-risk zones cantered near Coonoor and Kotagiri, which are associated for landslides and contaminated mobility, while in the lower-way areas cluster around AU. Combining crisis weakness with environmental fragility, this structure supports durable land-use management, ecosystem conservation and reducing pollution. The integration of geospatial analytics and machine learning provides a strong tool for disaster preparedness, risk reducing and elasticity in ecological sensitive hill districts.}, }
@article {pmid41145216, year = {2025}, author = {Peel, N and Martin, S and Heavens, D and Yu, DW and Clark, MD and Leggett, RM}, title = {Real-time analysis and visualization of nanopore metagenomic samples with MARTi.}, journal = {Genome research}, volume = {35}, number = {11}, pages = {2488-2500}, pmid = {41145216}, issn = {1549-5469}, mesh = {*Metagenomics/methods ; *Software ; *Nanopore Sequencing/methods ; *Nanopores ; Metagenome ; Humans ; Computational Biology/methods ; }, abstract = {The emergence of nanopore sequencing technology has the potential to transform metagenomics by offering low-cost, portable, and long-read sequencing capabilities. Furthermore, these platforms enable real-time data generation, which could significantly reduce the time from sample collection to result, a crucial factor for point-of-care diagnostics and biosurveillance. However, the full potential of real-time metagenomics remains largely unfulfilled due to a lack of accessible, open-source bioinformatic tools. We present Metagenomic Analysis in Real-Time (MARTi), an innovative open-source software designed for the real-time analysis, visualization, and exploration of metagenomic data. MARTi supports various classification methods, including BLAST, Centrifuge, and Kraken2, letting users customize parameters and utilize their own databases for taxonomic classification and antimicrobial resistance analysis. With a user-friendly, browser-based graphical interface, MARTi provides dynamic, real-time updates on community composition and AMR gene identification. MARTi's architecture and operational flexibility make it suitable for diverse research applications, ranging from in-field analysis to large-scale metagenomic studies. Using both simulated and real-world data, we demonstrate MARTi's performance in read classification, taxon detection, and relative abundance estimation. By bridging the gap between sequencing and actionable insights, MARTi marks a significant advance in the accessibility and functionality of real-time metagenomic analysis.}, }
@article {pmid41143093, year = {2025}, author = {Liu, J and Liu, S}, title = {HealthBench: Advancing AI evaluation in healthcare, but not yet clinically ready.}, journal = {Digital health}, volume = {11}, number = {}, pages = {20552076251390447}, pmid = {41143093}, issn = {2055-2076}, abstract = {Large language models (LLMs) are increasingly applied in healthcare, yet their evaluation remains inconsistent and often disconnected from clinical practice. OpenAI's HealthBench represents an important advancement, encompassing 5000 multiturn synthetic clinical conversations benchmarked against 48,562 clinician-developed criteria across accuracy, completeness, context awareness, communication, and instruction-following. Key strengths include broad scenario coverage, contributions from 262 clinicians across 60 countries, and automated grading methods that show high concordance with physician ratings. HealthBench provides a scalable and globally relevant framework. Nevertheless, important limitations constrain its clinical applicability. Exclusive reliance on synthetic dialogs limits ecological validity, and model-based graders may reinforce shared blind spots. Moreover, HealthBench assesses static, offline interactions while omitting multimodal inputs, longitudinal care, and patient outcomes-factors critical to real-world decision-making. Without external validation, strong benchmark performance may not translate into improved diagnostic accuracy, workflow efficiency, or patient safety. To ensure safe and effective integration of LLMs into practice, future benchmarks must incorporate authentic clinical data, longitudinal outcomes, and system-level considerations. HealthBench is a valuable step, but evaluation strategies must evolve to capture the complexity and demands of frontline care.}, }
@article {pmid41141935, year = {2025}, author = {Montecino-Latorre, D and Pruvot, M and Shimabukuro, PHF and Barker, CM and Gallo, S and Palmer, J and Kutz, SJ and Cayol, C and Dórea, F and Noguera, LP and Joly, DO and Walzer, C and Keatts, L and Fine, AE and Olson, SH}, title = {A community-of-practice-built database to support the implementation and operation of national and subnational wildlife health surveillance systems.}, journal = {One health (Amsterdam, Netherlands)}, volume = {21}, number = {}, pages = {101227}, pmid = {41141935}, issn = {2352-7714}, abstract = {Historically, poor data management has hampered the establishment and operation of wildlife health surveillance (WHS) systems and limited the integration of environmental data into One Health frameworks. Effective WHS purpose-built databases are key to solve this problem, yet the few options available remain inaccessible or narrow in scope. To address this gap, an international partnership is developing the Health and Wildlife Knowledge (HAWK) database. HAWK supports the management of diverse data generated by multiple actors and methodologies, all within a harmonized structure and vocabulary facilitating data access, analysis, communication, and reuse. Data are secured through compartmentalization across organizations and users, while supporting compliance of FAIR and CARE data principles. Slated for release in late 2025, HAWK is envisioned as a global public good to encourage data compatibility and best practices in the wildlife conservation and One Health communities, independent of languages and location, with minimal to no cost for users.}, }
@article {pmid41140638, year = {2025}, author = {Boyes, D and Boyes, C and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Shy Cosmet Moth, Limnaecia phragmitella Stainton, 1851 (Lepidoptera: Cosmopterigidae).}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {509}, pmid = {41140638}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Limnaecia phragmitella (Shy Cosmet Moth; Arthropoda; Insecta; Lepidoptera; Cosmopterigidae). The assembly contains two haplotypes with total lengths of 539.22 megabases and 553.78 megabases. Most of haplotype 1 (98.9%) is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 15.26 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.}, }
@article {pmid41140115, year = {2025}, author = {Symonová, R and Jůza, T and Tesfaye, M and Brabec, M and Sajdlová, Z and Brabec, J and Kubečka, J}, title = {Differential activity of transcription factors and neuronal effectors during the development of pikeperch brain.}, journal = {Biology open}, volume = {14}, number = {11}, pages = {}, pmid = {41140115}, issn = {2046-6390}, support = {LM2023055//ELIXIR CZ/ ; MEYS CR//ELIXIR CZ/ ; RVO 67985807//Akademie V&#x11b;d &#x10c;esk&#xe9; Republiky/ ; }, mesh = {Animals ; *Brain/metabolism/growth &amp; development ; *Transcription Factors/metabolism/genetics ; *Perches/growth &amp; development/genetics/metabolism ; Transcriptome ; *Neurons/metabolism ; Gene Expression Profiling ; *Gene Expression Regulation, Developmental ; Computational Biology/methods ; Body Size ; }, abstract = {Juvenile pikeperch (Sander lucioperca) undergo several ontogenetic shifts, the timing of which determines the survival of their first winter. The shift from planktivory to a more active piscivorous phenotype involves moving from pelagic to demersal habitat with more stimuli and hence potential brain functional reorganizations. During two consecutive years, we collected planktivores and piscivores with different body sizes between the years, recording distinct stages relative to the shift, and analyzed their whole-brain transcriptomes in an ecological context. We identified a distinct non-overlapping group of transcription factors (TFs) significantly upregulated in each phenotype: TFs upregulated in planktivores correspond to initial establishment of brain regions and overall architecture; TFs upregulated in piscivores correspond to the refinement of neurons and the formation of specific neuronal circuits. The planktivores independently of body size were characterized by interconnected activity of two TFs, fosab and junba. Gene set enrichment revealed extracellular matrix and collagen-related transcripts in piscivores from both years. A high activity of solute carrier (Slc) transporters was identified in the smaller-bodied piscivores. The neurotranscriptomics results reflected differences in body size and matched with ecological data and survival rates. The brain regulome indicated that body size differences translate into the specific gene activity of juvenile pikeperch.}, }
@article {pmid41138856, year = {2026}, author = {Krutikov, M and Price, JR and Fry, Z and Longstaff, V and Meacock, K and Stephenson, C and O'Reilly, K and Singer, A and Shallcross, L}, title = {The hidden iceberg: can wastewater transform infection surveillance and prevention in care homes?.}, journal = {The Journal of hospital infection}, volume = {167}, number = {}, pages = {187-191}, doi = {10.1016/j.jhin.2025.09.022}, pmid = {41138856}, issn = {1532-2939}, }
@article {pmid41138377, year = {2025}, author = {You, W and Xu, H and Duan, J and Zhou, Y and Li, J and He, D and Kizos, T}, title = {Assessing spatial differences of perceptions of cultural ecosystem services for coastal cultural landscape management: A case study from rural and urban areas in Quanzhou, China.}, journal = {Journal of environmental management}, volume = {395}, number = {}, pages = {127674}, doi = {10.1016/j.jenvman.2025.127674}, pmid = {41138377}, issn = {1095-8630}, mesh = {China ; *Ecosystem ; *Conservation of Natural Resources ; Humans ; Surveys and Questionnaires ; Rural Population ; Urbanization ; Perception ; Culture ; Geographic Information Systems ; }, abstract = {Coastal cultural landscapes are critical ecosystems that provide essential cultural, social, and ecological services, supporting dense populations and contributing to global ecosystem functions. However, rapid urbanization and environmental degradation are transforming these landscapes, posing significant challenges for sustainable management. This study examines the spatial distribution of Cultural Ecosystem Services (CES) in urban and rural context of coastal cultural landscapes of Quanzhou. Using questionnaire surveys and Participatory Geographic Information Systems (PPGIS), we analyzed public perceptions of CES across different infrastructure types, including grey, blue, and green infrastructure. Results show that urban areas, especially the historic areas are hotspots for CES such as cultural heritage, religious values, and sense of place. In contrast, rural areas emphasize landscape appreciation and recreation. Grey infrastructure, particularly historic buildings, and blue-green infrastructure, such as urban parks and historic villages, are major contributors to CES perceptions. Significant differences in CES perceptions were observed between urban and rural contexts, shaped by socio-economic factors and local multiple landscape features and infrastructures. This study highlights the importance of integrating urban and rural perspectives in the sustainable management of coastal cultural landscapes and offers recommendations for enhancing the protection and utilization of cultural and natural heritage to foster socio-ecological sustainability in coastal regions.}, }
@article {pmid41131611, year = {2025}, author = {Zhong, F and Zhou, W and Gao, X and Li, D and Zeng, J and Xiong, X and Lu, T and Gong, X and Xiao, Y and Li, J}, title = {Development and validation of a machine learning-based model for predicting radiation-induced hypothyroidism in nasopharyngeal carcinoma.}, journal = {Radiation oncology (London, England)}, volume = {20}, number = {1}, pages = {158}, pmid = {41131611}, issn = {1748-717X}, support = {20212BAB216064//Natural Science Foundation of Jiangxi Province/ ; 20224BAB206065//Natural Science Foundation of Jiangxi Province/ ; 82103478//National Natural Science Foundation of China/ ; 2021K01//Open Fund for Scientific Research of Jiangxi Cancer Hospital/ ; 2021&#x2009;J13//Open Fund for Scientific Research of Jiangxi Cancer Hospital/ ; 20232BBG70025//Jiangxi Province Key R&amp;D Program (Key Program)/ ; WCDJ2024YQ01//"Five-level Progressive" talent cultivation project of Jiangxi Cancer Hospital &amp; Institute/ ; }, mesh = {Humans ; *Machine Learning ; *Nasopharyngeal Carcinoma/radiotherapy ; *Hypothyroidism/etiology/diagnosis ; Male ; Female ; Middle Aged ; *Nasopharyngeal Neoplasms/radiotherapy ; *Radiotherapy, Intensity-Modulated/adverse effects ; Adult ; Nomograms ; Aged ; *Radiation Injuries/etiology ; }, abstract = {BACKGROUND AND PURPOSE: This study aims to develop a robust and user-friendly prediction model for radiation-induced hypothyroidism (RIHT) in nasopharyngeal carcinoma (NPC) patients.<br><br>MATERIALS AND METHODS: NPC patients treated with IMRT between Jan. 2019 and Dec. 2021 were randomly assigned to a training cohort (n&#x2009;=&#x2009;328) and a validation cohort (n&#x2009;=&#x2009;141) at a ratio of 7:3. A total of 33 clinical and dose-volume variables were collected. Significant variables (p&#x2009;<&#x2009;0.05) were identified through univariate Cox analysis and further refined using a 101-combination machine learning (ML) framework to develop a robust predictive model. The model was subsequently simplified through multivariate Cox analysis and a nomogram. Finally, the performance of the model was evaluated using the C-index, calibration plots, and decision curve analysis.<br><br>RESULTS: Using a 101-combination ML framework, we developed a predictive model for RIHT in NPC. The Coxboost&#x2009;+&#x2009;RSF method with 11 predictors achieved the best performance (C-index: 0.91 [training], 0.71 [validation]). A simplified five-variable model (pre-treatment TSH, TSH-to-thyroid-volume ratio, age, V45, V20) was created via multi-cox regression, with a C-index of 0.80 [training] and 0.71 [validation]. High-risk patients had significantly higher three-year RIHT incidences (72.3% vs. 18.6%, p&#x2009;<&#x2009;0.0001) in the training cohort, and 67.9% versus 24.4% (p&#x2009;<&#x2009;0.0001) in the validation cohort. The model showed strong calibration and confirmed clinical utility through decision curve analysis, supporting its use in personalized treatment planning.<br><br>CONCLUSION: We developed a ML framework to identify key predictive factors for RIHT, which was simplified into a five-variable model for clinical use, offering a robust tool for predicting RIHT risk in decision-making.}, }
@article {pmid41130983, year = {2025}, author = {Tang, C and Chen, X and Ke, S and Han, W and Chang, X and Li, X and Wang, Z and Chen, K and Bao, L and Hu, J and Wang, S and Bao, Z}, title = {A draft genome assembly of the mushroom coral Podabacia crustacea (Pallas, 1766).}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1677}, pmid = {41130983}, issn = {2052-4463}, support = {2024M763096//China Postdoctoral Science Foundation/ ; }, mesh = {Animals ; *Anthozoa/genetics ; Coral Reefs ; *Genome ; Phylogeny ; Datasets as Topic ; }, abstract = {Coral reefs are facing significant environmental changes that greatly impact biodiversity, including species such as the widely distributed coral Podabacia. In particular, Podabacia crustacea is notable for its high abundance and broad distribution. Despite its ecological importance, comprehensive genomic studies of this species have been limited, even though such data are crucial for the conservation of coral ecosystems. In this study, we generated a high-quality genome assembly of P. crustacea, the type species of the genus Podabacia, to provide a foundation for further genomic research on the genus. Using PacBio HiFi long reads, we assembled a genome of 853.9 Mb with a contig N50 of 2.9 Mb. BUSCO analysis revealed a completeness score of 97.0%. Additionally, we identified 29,342 protein-coding genes, 95.6% of which were functionally annotated through comparisons with established protein databases. This genomic resource advances our understanding of coral phylogeny and serves as an important reference for coral conservation studies.}, }
@article {pmid41130938, year = {2025}, author = {Li, L and Simopoulos, CMA and Mayne, J and Ning, Z and Zhang, X and Hamada, M and Butcher, J and Serrana, JM and Wang, L and Cheng, K and Qin, H and Walker, K and Zhang, X and Stintzi, A and Figeys, D}, title = {Systematic metaproteomics mapping reveals functional and ecological landscapes of Ex vivo human gut microbiota responses to therapeutic drugs.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {9383}, pmid = {41130938}, issn = {2041-1723}, support = {32370050//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Gastrointestinal Microbiome/drug effects/genetics ; Humans ; *Proteomics/methods ; Bacteria/drug effects/metabolism/genetics/classification ; *Proteome/metabolism/drug effects ; Bacterial Proteins/metabolism ; }, abstract = {Therapeutic compounds exert impacts on gut microbiota; however, how they affect the community functional ecology, especially as reflected at the protein level, remains largely unexplored. In this study, we systematically map metaproteomic responses of ex vivo human gut microbiota to 312 compounds, generating 4.6 million microbial protein responses, available as an interactive resource (https://shiny.imetalab.ca/MPR_Viz/). Protein-level analyses identify significant metaproteomic shifts induced by 47 compounds, with neuropharmaceuticals as the sole drug class significantly enriched among these hits. Further analyses on the community level reveal a tri-stability pattern in microbial composition and the emergence of three distinct functional states, based on a functional beta-diversity metric. Notably, neuropharmaceuticals cause particularly strong effects on the microbiomes, lowering the proteome-level functional redundancy and raising the level of antimicrobial resistance proteins, ultimately pushing the microbiome into an alternative functional state. Preliminary validation suggests that enhancing functional redundancy may contribute to maintaining microbiota resilience against neuropharmaceutical-induced antimicrobial resistance. Overall, this work establishes a comprehensive view of how drugs influence gut microbiome function and ecology at the protein level, proposes a landscape-based framework for interpreting community resilience, and highlights the need to consider protein-level and ecological responses in the evaluation of therapeutic interventions.}, }
@article {pmid41129719, year = {2025}, author = {Astill Wright, L and Monk-Cunliffe, J and Guo, B and Morriss, R}, title = {Adverse Events of Mood Monitoring and Ambulatory Assessment in Depression and Bipolar Disorder: Systematic Review and Meta-Analysis.}, journal = {JMIR mental health}, volume = {12}, number = {}, pages = {e79500}, pmid = {41129719}, issn = {2368-7959}, mesh = {Humans ; *Bipolar Disorder/diagnosis/psychology ; *Monitoring, Ambulatory/adverse effects ; *Affect ; *Depression/diagnosis ; *Depressive Disorder/diagnosis ; }, abstract = {BACKGROUND: Mood monitoring and ambulatory assessment offer improvements in measuring mood and behavior for mental health research and clinical practice. However, concerns about adverse effects and usability may hinder their implementation.<br><br>OBJECTIVE: This systematic review and meta-analysis assessed the prevalence of adverse events, barriers and facilitators to use, and suggestions for improvement in quantitative mood monitoring studies involving people with depression and bipolar disorder.<br><br>METHODS: We conducted a systematic review and meta-analysis of 77 quantitative studies that used mood monitoring or ambulatory assessment in depression and bipolar disorder, assessing adverse events, barriers and facilitators to use, and suggestions for improvement. Adverse events data were pooled to identify prevalence.<br><br>RESULTS: Of the 77 studies, 15 (19%) reported adverse events, and 20 (26%) reported usability issues. Pooled prevalence of adverse events was 0.04 (95% CI 0.03-0.06; P<.001). Specific adverse effects included increased burden or stress (0.04, 95% CI 0.02-0.07; P<.001), mood worsening (0.02, 95% CI 0.01-0.02; P=.001), self-harm (0.05, 95% CI-0.02 to 0.10; P=.007), and hospitalization (0.06, 95% CI 0.04-0.09; P=.26). The top facilitators were perceived helpfulness and ease of use, the top barriers included technical challenges and the time-consuming nature of the interventions, and the top suggested improvement was personalization.<br><br>CONCLUSIONS: A small number of mood monitoring or ambulatory assessment users experienced negative psychological effects; however, we were unable to infer causality. Due to the severe underreporting of adverse events as well as heterogeneity and publication bias in the included studies, there was limited certainty in the prevalence, duration, and severity of these adverse events. More systematic monitoring of adverse events is needed to optimize safety and usability. Many mood monitoring protocols may require additional development to decrease adverse events and improve acceptability.}, }
@article {pmid41128166, year = {2025}, author = {Campbell, C and Wang, T and Stockdale, AJ and Todd, S and Jaworski, J and Glampson, B and Papadimitriou, D and Mayer, E and Salih, H and Roadknight, G and Little, S and Noble, T and Várnai, KA and Davis, C and Heinson, AI and George, M and Borca, F and Roberts, T and Ribeyre, BB and English, L and Zhu, L and ,  and Woods, K and Davies, J and Cooke, GS and Nastouli, E and Khakoo, SI and Gelson, W and Elsharkawy, AM and Barnes, E and Matthews, PC}, title = {Hepatitis B Virus (HBV) Treatment Eligibility in the UK: Retrospective Longitudinal Cohort Data to Explore the Impact of Changes in Clinical Guidelines.}, journal = {Journal of viral hepatitis}, volume = {32}, number = {11}, pages = {e70098}, pmid = {41128166}, issn = {1365-2893}, support = {//National Institute for Health Research (NIHR) Health Informatics Collaborative (HIC)/ ; //National Institute for Health and Care Research/ ; //University College London/ ; }, mesh = {Humans ; Male ; Female ; Middle Aged ; Adult ; *Antiviral Agents/therapeutic use ; *Hepatitis B, Chronic/drug therapy ; Longitudinal Studies ; Retrospective Studies ; United Kingdom/epidemiology ; Aged ; Practice Guidelines as Topic ; Young Adult ; Hepatitis B virus/drug effects ; Hepatitis B e Antigens/blood ; Alanine Transaminase/blood ; Adolescent ; }, abstract = {Nucleos/tide analogue (NA) drugs are used for long-term treatment of chronic hepatitis B virus (HBV) infection, with treatment eligibility criteria changing rapidly amidst globally evolving clinical guidelines. We aimed to quantify the prescription of NA drugs to date, and to undertake a preliminary assessment of the impact of relaxing treatment eligibility thresholds, leveraging a unique large real-world secondary care dataset. We assimilated longitudinal clinical data, collected between February 1997 and April 2023 from adults with chronic HBV infection from six centres in England through the UK NIHR Health Informatics Collaborative (HIC) Viral Hepatitis and Liver Disease theme. We describe factors currently associated with the receipt of NA treatment and determine the proportion of the population who would become treatment eligible as thresholds change. Across 7558 adults with a mean follow-up of 4.0 years (SD 3.9), NA treatment was prescribed in 2014/7558 (26.6%), and as expected according to guidelines at the time, was associated with HBV e-antigen (HBeAg) positivity and alanine transferase (ALT) above the upper limit of normal (> ULN). Treatment was more likely in males, older adults, in Asian and Other ethnicities (compared to White), and less likely in socioeconomically deprived individuals. The proportion of treatment-eligible individuals was 32.3% based on 2 records of ALT > ULN over 6-12 months, 41.7% based on ALT > ULN and viral load (VL) > 2000 IU/mL, and 95.1% based on detectable VL and either ALT > ULN or age > 30 years. Evolving clinical guidelines will lead to substantial increases in the proportion of individuals living with HBV who are eligible for treatment, underlining the need for services to adapt rapidly to the changing clinical environment.}, }
@article {pmid41128050, year = {2025}, author = {Ben Mocha, Y and Woith, M and Scemama de Gialluly, S and Bruscagnin, L and Kestel, N and Markman, S and Drobniak, SM and Baglione, V and Boersma, J and Cousseau, L and Covas, R and Braga de Miranda, GH and Dey, CJ and Doutrelant, C and Gula, R and Heinsohn, R and Keynan, O and Kingma, SA and Leitão, AV and Li, J and Makuya, L and Middleton, KM and Pruett-Jones, S and Radford, AN and Restrepo, C and Rubenstein, DR and Schradin, C and Theuerkauf, J and Warrington, MH and Williams, DA and Woxvold, IA and Griesser, M}, title = {An integrative, peer-reviewed and open-source cooperative-breeding database (Co-BreeD).}, journal = {The Journal of animal ecology}, volume = {94}, number = {12}, pages = {2597-2614}, pmid = {41128050}, issn = {1365-2656}, support = {//Zukunftskolleg, Universit&#xe4;t Konstanz/ ; //Oxford Brookes Emerging Leaders Research Fellowship/ ; //SAVE Wildlife Conservation Fund/ ; 2018/29/B/NZ8/023123//Polska Akademia Nauk/ ; 4650/2-1//Deutsche Forschungsgemeinschaft/ ; EXC 2117-422037984//Deutsche Forschungsgemeinschaft/ ; //Ministerium f&#xfc;r Wissenschaft, Forschung und Kunst Baden-W&#xfc;rttemberg/ ; //Klaus Tschira Stiftung gGmbH/ ; }, mesh = {Animals ; *Mammals/physiology ; *Birds/physiology ; *Databases, Factual ; *Cooperative Behavior ; *Reproduction ; *Breeding ; }, abstract = {Large-scale, cross-species comparative analyses on cooperative breeding-where individuals care for the offspring of other group members-are important for understanding sociality and cooperation. However, the datasets that facilitate these analyses are often limited in precision. To advance comparative research on cooperative breeding, we hereby introduce the Cooperative-Breeding Database (Co-BreeD) for birds and mammals. We describe key features of Co-BreeD's structure: (i) integration of complementary datasets, each presenting a biological parameter relevant to cooperative-breeding research; (ii) sample-based (i.e. multiple samples per species linked to an exact sampling location and period); and (iii) open-source. Respectively, these features enable: (a) comprehensive identification of cooperative-breeding species according to the user's chosen definition, (b) linking intra- and inter-specific variation in traits with fine-scale environmental parameters and (c) enabling the research community to correct and expand this database. We present the initial Co-BreeD dataset, which estimates the prevalence of breeding events involving potential alloparents in 460 populations of 324 species, including 6 human populations (No. total = 43,247 breeding events). We conclude by demonstrating: (i) how Co-BreeD can improve comparative research (e.g. by enabling the study of cooperative breeding as a continuous rather than a binary trait); and (ii) that cooperative breeding is probably more prevalent than previously estimated in birds and mammals.}, }
@article {pmid41127944, year = {2026}, author = {Misono, S and Kummerfeld, E and Lim, KO}, title = {In Response to Ecological Momentary Assessment of Voice and Psychological Factors: Group and Individual Mechanisms.}, journal = {The Laryngoscope}, volume = {136}, number = {3}, pages = {E46}, doi = {10.1002/lary.70204}, pmid = {41127944}, issn = {1531-4995}, }
@article {pmid41121164, year = {2025}, author = {Yang, YA and Huang, YH and Weng, YH and Chiu, YW}, title = {Socioeconomic factors in relation to dental caries among children aged 5-14 years: a cross-national comparative study using secondary data analyses.}, journal = {BMC oral health}, volume = {25}, number = {1}, pages = {1640}, pmid = {41121164}, issn = {1472-6831}, support = {CMRPG1N0032//Chang Gung Memorial Hospital, Linkou/ ; NSTC 112-2314-B-037-098-MY3, NSTC 112-2314-B-182A-106 -MY3//National Science and Technology Council/ ; NSTC 112-2314-B-037-098-MY3, NSTC 112-2314-B-182A-106 -MY3//National Science and Technology Council/ ; }, mesh = {Humans ; *Dental Caries/epidemiology ; Child ; Child, Preschool ; Adolescent ; *Socioeconomic Factors ; Fluoridation/statistics &amp; numerical data ; Male ; Female ; Risk Factors ; Prevalence ; Global Health ; Tooth, Deciduous ; Income ; Cross-Sectional Studies ; Secondary Data Analysis ; }, abstract = {BACKGROUND: Dental caries is a preventable non-communicable disease. Untreated caries in deciduous teeth may contribute to the development of caries in permanent teeth. Nevertheless, limited research has focused specifically on the risk factors in children. The current study examined the association between dental caries and socioeconomic risk factors among children aged 5-14 years across countries worldwide.<br><br>METHODS: An ecological survey was conducted using nation-based, publicly available online databases from six reputable organizations: the World Health Organization, the Food and Agriculture Organization of the United Nations, the World Bank, the British Fluoridation Society, the United Nations Development Programme, and the Global Burden of Disease Project. Data were collected from these sources between 2014 and 2017. Independent variables included density of dental personnel, parental education, family income, water fluoridation, and sugar consumption. The dependent variables were the prevalence of caries in deciduous and permanent teeth. Data were analyzed using descriptive statistics, univariate analysis, and multinomial logistic regression.<br><br>RESULTS: After eliminating countries without complete information, this study enrolled 120 countries with complete data for both dependent and independent variables. Univariate analysis revealed significant differences by parental education, income level, and water fluoridation. We further conducted multivariate logistic regression analysis, indicating that countries with low fluoridation (<&#x2009;50%) had significantly higher odds of caries in permanent teeth (OR: 13.23; 95% CI: 1.22-143.53; p&#x2009;=&#x2009;0.03); shorter years of parental schooling was associated with lower prevalence of caries in permanent teeth (OR: 0.12; 95% CI: 0.03-0.47; p&#x2009;=&#x2009;0.002); and middle-income countries showed increased risk in both deciduous teeth (OR: 3.44; 95% CI: 1.26-9.43; p&#x2009;=&#x2009;0.02) and permanent teeth (OR: 6.93; 95% CI: 1.75-27.38; p&#x2009;=&#x2009;0.01) than high-income countries. Sugar consumption and density of dental personnel were not significantly associated.<br><br>CONCLUSION: This ecological study provides valuable insights into the global patterns of dental caries in children aged 5-14 years and their associations with selected socioeconomic indicators. Our results reveal significant correlations of dental caries with income level, water fluoridation coverage, and parental education. However, these associations should be interpreted with caution due to the ecological nature of the data and several important limitations.}, }
@article {pmid41120627, year = {2025}, author = {Zhong, X and Zheng, R and Chen, W and Lv, L and Wei, Z}, title = {Regional differences, dynamic evolution, and driving factors of ecological resilience in China's urban agglomerations.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {36791}, pmid = {41120627}, issn = {2045-2322}, support = {Grant No. 22XTY006//Western Program of the National Social Science Foundation of China/ ; Grant No. 23FYJ024//Philosophy and Social Science Planning Project of Guangxi, China/ ; Grant No. XYCSR2024025//Graduate Innovation Project of School of Economics and Management, Guangxi Normal University/ ; }, abstract = {With the ongoing progress of urbanization, the urban ecosystem is becoming increasingly fragile, exacerbated further by the emergence of urban agglomerations. Based on the 'Pressure-State-Response' model and panel data covering the period from 2010 to 2021, the step-by-step vertical and horizontal tiered evaluation method is employed to calculate the scores of ecological resilience in China's urban agglomerations. The Dagum's Gini coefficient, global and local Moran's index, unite strength and unite threshold, Markov chain, and geographic detector are utilized to reveal regional disparities, dynamic evolution, and driving factors of ecological resilience in China's urban agglomerations. The results reveal several significant findings: (1) The ecological resilience in Chinese urban agglomerations exhibited a fluctuating yet upward trend. (2) Although disparities in the ecological resilience of China's urban agglomerations are decreasing, differences between them remain significant. (3) Spatial correlation is evident in the ecological resilience of China's urban agglomerations. High-high clusters are primarily found in the eastern and upgrading urban agglomerations, while low-low clusters are concentrated in the western and fostering urban agglomerations. (4) The number of cities exceeding the ecological resilience threshold is gradually increasing, with core cities playing a pivotal role. (5) The probability of transition in a city is affected by the ecological resilience states of adjacent cities. (6) Driving factors such as Internet penetration rate, informatization level, and innovation capacity have significant but heterogeneous effects on ecological resilience. This paper enlightens that spatial co-governance and zoning management of ecological resilience are crucial for achieving regional ecological security.}, }
@article {pmid41115518, year = {2026}, author = {Seneci, L and Suranse, V and Mancuso, M and Senoner, T and Xie, B and Koludarov, I and Sunagar, K and Fry, BG}, title = {Deadly innovations: Molecular phylogenetics and evolution of phospholipase A2 toxins in viperid snake venoms.}, journal = {Biochimie}, volume = {240}, number = {}, pages = {137-152}, doi = {10.1016/j.biochi.2025.10.010}, pmid = {41115518}, issn = {1638-6183}, mesh = {*Viperidae/genetics ; Animals ; *Phospholipases A2/chemistry/genetics ; Evolution, Molecular ; *Viper Venoms/chemistry/genetics ; Phylogeny ; Bayes Theorem ; Cluster Analysis ; Mutation ; Aspartic Acid/analysis/genetics ; Lysine/analysis/genetics ; }, abstract = {Snake venoms have surged as model systems in evolutionary biology thanks to the dynamic diversification and accelerated evolution of many toxin families. Among these, phospholipase A2 (PLA2) constitute a prime example as they are ubiquitous across the venomous snake radiation and have evolved a wide variety of pathophysiological activities. This is especially true in vipers (family Viperidae), one of the most successful and medically significant venomous snake lineages worldwide. In this study, we gathered publicly available sequences of viper venom PLA2s to recreate the molecular phylogeny and toxicological evolution of this toxin family to date. Furthermore, we determined the selection regimes regulating the evolution of these toxins with a comparative approach that combines multiple methodologies of phylogenetic reconstruction and analysis of selection signatures. Our phylogeny confirms the basal position of Asp49 PLA2s (proteins with Asp at position 49), while derived clades, such as the non-enzymatic Lys49 myotoxins and the poorly characterised Ser49 type, are nested within. Neurotoxicity arose on multiple independent occasions (all within the Asp49 clade), with monomeric and dimeric forms only distantly related to each other. Positive Darwinian selection was widespread across the viper PLA2 tree, in line with previous research. However, purifying selection was also preponderant (perhaps due to structural constraints imposed by the pathophysiological targets of these toxins) and relatively neutral substitutions were observed in certain clades. Overall, this study provides novel insights into the evolutionary history of viper venom PLA2s through a comprehensive phylogenetic framework and highlights the need for complementary genomic and functional research into these toxins.}, }
@article {pmid41106617, year = {2026}, author = {Losiewicz, OM and Cohen, ZD and Akre, S and Welborn, A and Craske, MG}, title = {Daily spread of positive affect is associated with subsequent well-being: A study of idiographic network analysis and emotional inertia.}, journal = {Journal of affective disorders}, volume = {393}, number = {Pt B}, pages = {120461}, doi = {10.1016/j.jad.2025.120461}, pmid = {41106617}, issn = {1573-2517}, mesh = {Humans ; Female ; Male ; Adult ; Ecological Momentary Assessment ; *Affect ; Middle Aged ; Cross-Sectional Studies ; *Emotions ; Longitudinal Studies ; Young Adult ; *Personal Satisfaction ; }, abstract = {Emotional inertia, or the persistence of affect over time, and emotion network density, a measurement of the interconnected or relatedness of one's emotions, both capture dynamics of emotional experiences. Previous research has found that higher levels of negative emotional inertia and network density are associated with anxiety and depression. However, there is a dearth of research examining inertia and density of positive emotions and prospective associations between emotion dynamics and subsequent wellbeing. This study sought to address these limitations by examining both cross-sectional and longitudinal associations between emotional inertia and network density and well-being. We examined inertia and density of both positive and negative emotions. Adults with moderate-to-severe depression (N = 333) completed two 8-day epochs of ecological momentary assessment (EMA) five times daily. Emotional inertia and idiographic networks were calculated separately for EMA measures of negative and positive affect, and associations with self-reported well-being were examined using nested comparison tests and Bayesian multilevel models. In partial support of hypotheses, contemporaneous network density of positive emotions was positively associated with self-reported well-being six months later. Conversely, inertia of positive affect was inversely associated with well-being six months later. Neither inertia nor network density of negative affect was associated with subsequent well-being. These results suggest that inertia and network density of positive affect may indicate likelihood of experiencing changes in well-being in the future. Future research should investigate the underlying mechanisms, discern differences between emotional inertia and emotion network density, and explore potential implications for treatment.}, }
@article {pmid41106353, year = {2026}, author = {Asteraye, GB and Jobling, R and Jemberu, WT and Pinchbeck, G and Knight-Jones, TJD and Critchlow, R and Rushton, J and Chaters, GL}, title = {Classification of donkey systems in Ethiopia.}, journal = {Preventive veterinary medicine}, volume = {246}, number = {}, pages = {106719}, doi = {10.1016/j.prevetmed.2025.106719}, pmid = {41106353}, issn = {1873-1716}, mesh = {Animals ; Ethiopia ; *Equidae ; *Animal Husbandry/classification/methods/statistics &amp; numerical data ; Ownership/statistics &amp; numerical data ; Surveys and Questionnaires ; Animal Welfare ; Female ; }, abstract = {Working donkeys play a critical role in transportation, agriculture and household resilience in low- and middle-income countries. Other animals that are kept for production purposes, such as cattle, are often grouped into broad production system classes, such as dairy or pastoral, for comparison between and better understanding of the needs and outputs of animals within specific sectors. Despite the importance of working donkeys for sustaining livelihoods there are no systematic classifications of these populations. The aim of this study was to classify and characterise donkey systems in Ethiopia using household-level questionnaire data which included donkey ownership, husbandry, use and local environment data, through multiple factor and hierarchical cluster analysis. Household questionnaire data from 241 donkey-owning households in three districts of Ethiopia were used. Three distinct clusters of donkey ownership were identified: 'Domestic-Pastoral'; 'Domestic-Agricultural' and 'Commercial'. Differences between systems are primarily influenced by donkey purpose, environmental (agro-ecological) factors, and husbandry practices. Constraints associated with donkey ownership varied across clusters: households in the commercial system reported higher incidence of injuries and welfare concerns, in the pastoral system the main constraints were drought and feed shortage, and domestic-agricultural households reported infectious diseases as the main challenge. This new classification of donkey systems provides a framework for analysing donkey health and welfare data, enabling more context-specific needs assessments and facilitating the design of targeted interventions to improve equid health and household livelihoods.}, }
@article {pmid41106000, year = {2025}, author = {Kang, X and Wang, X and Zhang, Y and Ju, F}, title = {Multi-omics-guided discovery of broad-spectrum plasticizer degrader Rhodococcus sp. SPR1 and key enzymes driving tris(2-ethylhexyl) trimellitate (TOTM) degradation.}, journal = {Journal of hazardous materials}, volume = {499}, number = {}, pages = {140086}, doi = {10.1016/j.jhazmat.2025.140086}, pmid = {41106000}, issn = {1873-3336}, mesh = {*Plasticizers/metabolism ; *Rhodococcus/metabolism/enzymology/genetics ; Biodegradation, Environmental ; Animals ; Bacterial Proteins/metabolism ; *Environmental Pollutants/metabolism ; Larva/microbiology ; Multiomics ; }, abstract = {Plastic pollution has garnered global attention, yet the environmental threats posed by plasticizers remain largely understudied. Emerging plasticizers, such as tris(2-ethylhexyl) trimellitate (TOTM), are increasingly prevalent in anthropogenically impacted environmental reserviros, but their biodegradation mechanism and associated strains and enzymes are poorly understood. Here, we discovered Rhodococcus strain SPR1 from the gut of polyvinyl chloride (PVC)-consuming insect larvae, which exhibits broad-spectrum degradation capabilities across five representative plasticizers, including both traditional and emerging types. SPR1 achieved up to 63.07 % degradation of TOTM in 120 h, with two enzymes TOTMaseA (linear primary-alkylsulfatase) and TOTMaseB (α/β hydrolase), validated as key contributors. Enzyme kinetics revealed that TOTMaseA exhibited a Vmax of 2.655 mM and Km of 0.3821 µM/min, while TOTMaseB showed a Vmax of 0.9664 mM and Km of 0.2245 µM/min, confirming that TOTMaseA has superior catalytic throughput and serves as the dominant contributor to TOTM degradation. Notably, TOTMaseA also displayed consistently greater abundance compared to TOTMaseB under TOTM exposure. The widespread presence of homologous strains and enzymes of TOTM-degrading SPR1 in environmental samples underscores the ecological relevance and bioremediation potential. This study provides quantitative and mechanistic insights into the microbial degradation of TOTM and advances our understanding of enzymatic strategies that enable the breakdown of emerging plasticizers.}, }
@article {pmid41105870, year = {2025}, author = {Astill Wright, L and Majid, M and Moore, M and Momoh, G and Patil, R and Shajan, G and Purewal, D and Patel, S and Morriss, R}, title = {The User Experience of Ambulatory Assessment and Mood Monitoring in Bipolar Disorder: Systematic Review and Meta-Synthesis of Qualitative Studies.}, journal = {Journal of medical Internet research}, volume = {27}, number = {}, pages = {e71525}, pmid = {41105870}, issn = {1438-8871}, mesh = {*Bipolar Disorder/psychology/diagnosis ; Humans ; Qualitative Research ; *Affect ; *Monitoring, Ambulatory ; }, abstract = {BACKGROUND: Mood monitoring and ambulatory assessment hold promise for supporting self-management and data collection in bipolar disorder (BD), but the effectiveness of these depends crucially on the preferences and perspectives of those who use them. To date, these user experiences have not been systematically synthesized.<br><br>OBJECTIVE: This study aimed to explore and synthesize qualitative evidence on the user experience of mood monitoring and ambulatory assessment in BD, with a focus on identifying barriers and facilitators for both individuals with BD and clinicians, as well as the intended purposes of these tools.<br><br>METHODS: We conducted a systematic review and meta-synthesis of qualitative and mixed-methods studies reporting on ambulatory assessment and mood monitoring in BD (PROSPERO CRD42023396473). A total of 8 electronic databases were searched. Studies were appraised using established criteria for qualitative research. First- and second-order constructs were extracted, and a third-order synthesis was developed using the Noblit and Hare meta-ethnographic approach.<br><br>RESULTS: A total of 20 studies comprising 2365 participants met inclusion criteria. We identified 9 overarching themes: adverse effects, barriers to use, facilitators to use, perceived purpose, sharing with others (positive and negative), clinician concerns, clinician suggestions, and desired features. Users reported both benefits and harms. Some experienced increased insight, behavioral change, and relapse prevention skills, while others reported emotional burden, repetitive content, and worsened mood or anxiety. Preferences varied widely, but a strong, consistent emphasis was placed on personalization, including the ability to control what is tracked, when and how it is shared, and the level of engagement with health care providers. Passive data collection was often seen as less intrusive and more sustainable. Sharing data was sometimes seen as empowering, especially when it enabled communication with trusted individuals or clinicians, but also raised concerns around autonomy, misinterpretation, and privacy. Clinicians echoed many user views but raised additional concerns about liability and interpretability of data. Participants also highlighted the need for onboarding or support to aid comprehension and effective use.<br><br>CONCLUSIONS: This review highlights the complexity and diversity of user experiences with ambulatory assessment and mood monitoring in BD. While many found these tools valuable for fostering insight, self-management, and relapse prevention, others found them burdensome or confronting. User engagement appears closely tied to perceived control, relevance, and personal fit. These findings underscore the need for flexible, user-centered design in future interventions. Customizability should be prioritized-including what is monitored, how feedback is delivered, and whether data is shared externally. Incorporating onboarding and adaptive feedback could help users better understand and apply their data to better self-manage. By aligning interventions more closely with user preferences and lived experience, ambulatory assessment and mood monitoring protocols may achieve greater uptake, engagement, and ultimately, a more effective intervention.}, }
@article {pmid41103550, year = {2025}, author = {McLean, BS and Bloom, D and Davis, EB and Guralnick, RP and Santana, SE and Allen, JM and Amarilla-Stevens, H and Bell, KC and Blackburn, DC and Bradley, JE and Bradley, RD and Carling, MD and Coconis, A and Colella, JP and Conroy, CJ and Cook, JA and de Bastos Cruz Machado, H and Demboski, JR and Derieg, KM and Doll, A and Dumbacher, JP and Duncan, WD and Dunnum, JL and Feldman, C and Ferguson, AW and Fitzgerald, KE and Flannery, ME and Hood, K and Hornsby, AD and Krejsa, D and LaFrance, R and Light, JE and Pavan, SE and Peterson, S and Raniszewski, A and Rickart, EA and Robson, S and Rowe, RJ and Rowsey, DM and Semerdjian, A and Stankowich, T and Steger, L and Stevens, R and Thibault, KM and Thompson, CW and Upham, NS and Wilkins, A and Wommack, EA}, title = {Extending mammal specimens with their essential phenotypic traits.}, journal = {Journal of mammalogy}, volume = {106}, number = {5}, pages = {1282-1291}, pmid = {41103550}, issn = {0022-2372}, abstract = {Natural history collections are repositories of biodiversity specimens that provide critical infrastructure for studies of mammals. Over the past 3 decades, digitization of collections has opened up the temporal and spatial properties of specimens, stimulating new data sharing, use, and training across the biodiversity sciences. These digital records are the cornerstones of an "extended specimen network," in which the diverse data derived from specimens become digital, linked, and openly accessible for science and policy. However, still missing from most digital occurrences of mammals are their morphological, reproductive, and life-history traits. Unlocking this information will advance mammalogy, establish richer faunal baselines in an era of rapid environmental change, and contextualize other types of specimen-derived information toward new knowledge and discovery. Here, we present the Ranges Digitization Network (Ranges), a community effort to digitize specimen-level traits from all terrestrial mammals of western North America, append them to digital records, publish them openly in community repositories, and make them interoperable with complimentary data streams. Ranges is a consortium of 23 institutions with an initial focus on non-marine mammal species (both native and introduced) occurring in western Canada, the western United States, and Mexico. The project will establish trait data standards and informatics workflows that can be extended to other regions, taxa, and traits. Reconnecting mammalogists, museum professionals, and researchers for a new era of collections digitization will catalyze advances in mammalogy and create a community-curated trait resource for training and engagement with global conservation initiatives.}, }
@article {pmid41102527, year = {2025}, author = {Pei, Y and Forstmeier, W and Suh, A and Bambach, L and Borges, I and Low, GW and Dion-Côté, AM and Knief, U and Wolf, J and Kempenaers, B}, title = {Evolution of Large Polymorphic Inversions in a Panmictic Songbird.}, journal = {Molecular biology and evolution}, volume = {42}, number = {11}, pages = {}, pmid = {41102527}, issn = {1537-1719}, support = {//Max Planck Society/ ; //Lillawski/ ; RGPIN-2019-05744//NSERC Discovery/ ; //New Brunswick Innovation Foundation/ ; }, mesh = {Animals ; *Chromosome Inversion ; *Finches/genetics ; *Evolution, Molecular ; Polymorphism, Single Nucleotide ; *Songbirds/genetics ; Polymorphism, Genetic ; Male ; }, abstract = {Chromosomal inversions have long been appreciated as an important source of genetic diversity, local adaptation, and speciation. However, selection pressures maintaining ancestral and derived alleles at high frequency over extended periods of time remain poorly characterized. Using genome-wide single-nucleotide polymorphism markers and shared barcodes of linked-read sequences from 20 wild and 7 captive zebra finches Taeniopygia guttata, we systematically scanned a high-quality zebra finch reference genome and identified all large polymorphic inversions that segregate at high minor allele frequencies. Apart from the known polymorphic inversions on chromosomes Tgu5, Tug11, Tgu13, and TguZ, we characterized two inversions on microchromosomes Tgu26 and Tgu27 and identified another eight putative inversions, located mostly on microchromosomes and ranging in size from 0.42 to 65.22 Mb. Population genomic analyses show that most of the six bona fide inversions are complex, containing short nested inversions. The early inversions emerged an estimated 0.6 to 2.2 million years ago and segregate at relatively high frequencies in the wild (minor haplotype frequency range: 0.289 to 0.429). Based on fitness-related measures of about 5,000 captive zebra finches, we conclude that three of the inversion polymorphisms (Tgu11, Tgu27, and TguZ) may be maintained by net heterosis. In the youngest of the six inversions (Tgu13), the derived haplotype showed weak positive additive effects on various fitness components. In combination with previous discoveries, we provide a comprehensive overview of the genomic distribution and evolutionary dynamics of large polymorphic inversions in the panmictic zebra finch. Our findings highlight (i) that microchromosomes may harbor quite a few additional inversion polymorphisms, (ii) that most of the inversions contain smaller nested or overlapping inversions, and (iii) that inversions were most likely maintained by weak heterosis with small fitness effects requiring large sample sizes to be detected.}, }
@article {pmid41102232, year = {2025}, author = {Fassoni, AC and Yong, ASM and Clark, RE and Roeder, I and Glauche, I}, title = {Predicting treatment-free remission in chronic myeloid leukemia patients using an integrated model of tumor-immune dynamics.}, journal = {NPJ systems biology and applications}, volume = {11}, number = {1}, pages = {115}, pmid = {41102232}, issn = {2056-7189}, mesh = {Humans ; *Leukemia, Myelogenous, Chronic, BCR-ABL Positive/immunology/drug therapy/therapy ; Killer Cells, Natural/immunology ; Remission Induction ; Treatment Outcome ; Models, Biological ; }, abstract = {The interactions between tumor and the immune system are main factors in determining cancer treatment outcomes. In Chronic Myeloid Leukemia (CML), considerable evidence shows that the dynamics between residual leukemia and the patient's immune system can result in either sustained disease control, leading to treatment-free remission (TFR), or disease recurrence. The question remains how to integrate mechanistic and data-driven models to support prediction of treatment outcomes. Starting from classical ecological modeling concepts, which allow to explicitly account for immune interactions at the cellular level, we incorporate time-course data on natural killer (NK) cell number, function, and their tumor-induced suppression into our general model of CML treatment. We identify relevant time scales governing treatment and immune response, enabling refined model calibration using tumor and NK cell time courses from different datasets. While the model successfully describes patient-specific response dynamics, critical parameters for predicting treatment outcome remain uncertain. However, by explicitly incorporating tumor load changes in response to TKI dose alterations, these parameters can be estimated and used to derive model predictions for treatment cessation. Further exploring dynamic changes in the number of functional immune cells, we suggest specific measurement strategies of immune effector cell populations to enhance prediction accuracy for CML recurrence following treatment cessation. The generalizability and flexibility of our approach represent a significant step towards quantitative, personalized medicine that integrates tumor-immune dynamics to guide clinical decisions and optimize dynamic cancer therapies.}, }
@article {pmid41098171, year = {2025}, author = {Boyes, D and Boyes, C and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Yellow-barred Brindle, Acasis viretata (Hübner, 1799) (Lepidoptera: Geometridae).}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {516}, pmid = {41098171}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Acasis viretata (Yellow-barred Brindle; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 297.68 megabases. Most of the assembly (99.98%) is scaffolded into 17 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled, with a length of 16.01 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.}, }
@article {pmid41096595, year = {2025}, author = {Sakaguchi, T and Irifune, Y and Kamada, R and Sakaguchi, K}, title = {Bacterial Systematic Genetics and Integrated Multi-Omics: Beyond Static Genomics Toward Predictive Models.}, journal = {International journal of molecular sciences}, volume = {26}, number = {19}, pages = {}, pmid = {41096595}, issn = {1422-0067}, support = {25K00273//Japan Society for the Promotion of Science/ ; 24K01633//Japan Society for the Promotion of Science/ ; 23K17966//Japan Society for the Promotion of Science/ ; 23H02098//Japan Society for the Promotion of Science/ ; JPMJSP2119//Japan Science and Technology Agency/ ; none//the Photo-excitonix Project at Hokkaido University/ ; }, mesh = {*Bacteria/genetics/metabolism ; *Genomics/methods ; Proteomics/methods ; Genome-Wide Association Study ; Systems Biology/methods ; Quantitative Trait Loci ; *Genome, Bacterial ; Polymorphism, Single Nucleotide ; Transcriptome ; Multiomics ; }, abstract = {The field of bacterial systems biology is rapidly advancing beyond static genomic analyses, and moving toward dynamic, integrative approaches that connect genetic variation with cellular function. This review traces the progression from genome-wide association studies (GWAS) to multi-omics frameworks that incorporate transcriptomics, proteomics, and interactome mapping. We emphasize recent breakthroughs in high-resolution transcriptomics, including single-cell, spatial, and epitranscriptomic technologies, which uncover functional heterogeneity and regulatory complexity in bacterial populations. At the same time, innovations in proteomics, such as data-independent acquisition (DIA) and single-bacterium proteomics, provide quantitative insights into protein-level mechanisms. Experimental and AI-assisted strategies for mapping protein-protein interactions help to clarify the architecture of bacterial molecular networks. The integration of these omics layers through quantitative trait locus (QTL) analysis establishes mechanistic links between single-nucleotide polymorphisms and systems-level phenotypes. Despite persistent challenges such as bacterial clonality and genomic plasticity, emerging tools, including deep mutational scanning, microfluidics, high-throughput genome editing, and machine-learning approaches, are enhancing the resolution and scope of bacterial genetics. By synthesizing these advances, we describe a transformative trajectory toward predictive, systems-level models of bacterial life. This perspective opens new opportunities in antimicrobial discovery, microbial engineering, and ecological research.}, }
@article {pmid41094481, year = {2025}, author = {Karami, H and Bleichrodt, A and Luo, R and Chowell, G}, title = {BayesianFitForecast: a user-friendly R toolbox for parameter estimation and forecasting with ordinary differential equations.}, journal = {BMC medical informatics and decision making}, volume = {25}, number = {1}, pages = {385}, pmid = {41094481}, issn = {1472-6947}, mesh = {Bayes Theorem ; Humans ; Forecasting/methods ; *Software ; *Models, Theoretical ; }, abstract = {BACKGROUND: Mathematical models based on ordinary differential equations (ODEs) are essential tools across various scientific disciplines, including biology, ecology, epidemic modeling, and healthcare informatics, where they are used to simulate complex dynamic systems and inform decision-making. However, implementing Bayesian calibration and forecasting typically requires substantial coding in Stan or similar tools. To support Bayesian parameter estimation and forecasting for such systems, we introduce BayesianFitForecast, a user-friendly R toolbox specifically developed to streamline Bayesian parameter estimation and forecasting in ODE models, making it particularly relevant to health informatics and public health decision-making (https://github.com/gchowell/BayesianFitForecast/).<br><br>RESULTS: This toolbox enables automatic generation of Stan files, allowing users to configure models, define priors, and analyze results with minimal programming expertise. By eliminating manual coding, BayesianFitForecast significantly lowers the technical barrier to Bayesian inference with dynamical systems. We demonstrate its flexibility and usability through applications to historical epidemic datasets (e.g., the 1918 influenza pandemic in San Francisco and the 1896-1897 Bombay plague) and simulated data, showing robust parameter estimation and forecasting performance under Poisson and negative binomial observation error structures. The toolbox also provides robust tools for evaluating model performance, including convergence diagnostics, posterior distributions, credible intervals, and performance metrics.<br><br>CONCLUSION: By improving the accessibility of advanced Bayesian methods, BayesianFitForecast broadens the application of Bayesian inference in time-series modeling, healthcare forecasting, and epidemiological applications. In addition to the R scripting interface, a built-in Shiny web application is included, enabling interactive model configuration, visualization, and forecasting. A tutorial video demonstrating the toolbox's functionality is also available (https://youtu.be/jnxMjz3V3n8).}, }
@article {pmid41093425, year = {2025}, author = {Guo, JX and Xie, Y and Qi, WX and Liao, YJ and Cao, XF and Peng, JF}, title = {[Pollution Characteristics and Identification of Risk Zones of Polycyclic Aromatic Hydrocarbons and Their Derivatives in Sediments and Soils of Chagan Lake].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {46}, number = {10}, pages = {6593-6602}, doi = {10.13227/j.hjkx.202409321}, pmid = {41093425}, issn = {0250-3301}, abstract = {Sediments and soils are primary reservoirs and potential secondary sources of polycyclic aromatic hydrocarbons （PAHs）. Investigating the pollution characteristics of PAHs and their derivatives in these environments is of significant environmental， health， and ecological relevance. In this study， Chagan Lake， a typical lake in the agricultural region of northeast China， was selected as the research area. Thirteen surface sediment and soil samples were collected in July 2021 to analyze the pollution characteristics， influencing factors， and ecological risks of 19 PAHs and 11 derivatives. The results showed that the contents of 19 PAHs in sediments ranged from 106.7 to 915.0 ng·g[-1]， higher values than those in soils， which ranged from 251.7 to 718.1 ng·g[-1]. The average contents of parent PAHs （PPAHs）， methylated PAHs （MPAHs）， oxygenated PAHs （OPAHs）， and nitro PAHs （NPAHs） in sediments and soils were 327.6， 57.7， 59.7， and 21.1 ng·g[-1]， respectively. The dominant congeners were primarily 3-ring （38%）， 2-ring （91%）， 3-ring （72%） and 2-ring （81%）， PAHs. An examination of derivatives of Nap， Flu， Ant， and BaA revealed that 2-MN and BA-7，12-D were the main derivatives of Nap and BaA， respectively， with contents lower than their parent compounds. In contrast， the contents of derivatives such as 9-FL， 2-NF， AQ， and 2-MAQ were higher than those of their parent compounds Flu and Ant. Quantitative results from the linear mixing model indicated that the sand ratio had a greater influence on the contents of PPAHs and MPAHs than TOC， particularly for 2-3 ring PPAHs， whereas the effect on 4-6 rings was opposite. Ecological risk assessments indicated that the contents of Nap and Phe in sediments and surrounding soils exceeded the threshold for adverse ecological effects， with 28% of the Chagan Lake area classified as a high-risk zone for overlapping Nap and Phe contamination.}, }
@article {pmid41093395, year = {2025}, author = {Men, C and Cai, HJ and Fu, H and Zuo, JE}, title = {[Occurrence Characteristics， Ecological Risks， and Main Sources of Antibiotics in Rivers in Tongzhou District， Beijing].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {46}, number = {10}, pages = {6264-6273}, doi = {10.13227/j.hjkx.202408216}, pmid = {41093395}, issn = {0250-3301}, mesh = {Rivers/chemistry ; *Water Pollutants, Chemical/analysis ; *Anti-Bacterial Agents/analysis ; *Environmental Monitoring ; China ; Beijing ; Risk Assessment ; Ecosystem ; Geographic Information Systems ; Wastewater/chemistry ; }, abstract = {China is a major producer and consumer of antibiotics. Because humans and animals have difficulty fully metabolizing antibiotics and the limited degradation efficiency of antibiotics in current wastewater treatment plants， antibiotic pollution is common in rivers in China， threatening the health of river ecosystems. Tongzhou District， Beijing， is the sub-center of Beijing， and all of the rivers flowing through the main urban area of Beijing converge in this district. A total of 16 antibiotics in the rivers of Tongzhou District， Beijing， were used as research objects， an analysis of the antibiotic concentration and spatial distribution characteristics was performed based on the geographic information system （GIS）， the ecological risk of the antibiotics and its uncertainty were evaluated by the coupling risk quotient method and Monte Carlo method， and the main sources of antibiotics were identified using the principal component analysis method. The results showed that the total concentrations of the 16 target antibiotics ranged from 69.52 to 1 913.05 ng·L[-1]. Ofloxacin （OFL） had the highest concentration among all antibiotics， with an average concentration of 279.95 ng·L[-1]， accounting for 50.07% of the total antibiotic concentration. Spatially， the concentrations of most of the antibiotics were relatively high in the Beiyun River and relatively low in the Wenyu River and Yunchaojian River. Compared to the Hai， Yangtze， Yellow， Pearl， Huai， and Liao Rivers， the concentrations of antibiotics in the rivers in Tongzhou District were low. The results of the ecological risk assessment showed that the ecological risk levels of sulfadimethoxine （SDM） and OFL were higher than those of the other antibiotics. The upper limits of the 90% confidence interval of the probability distribution of ecological risk for these antibiotics were 132.04 and 86.58 times the threshold of the high-risk class， respectively， and the probability of SDM leading to high ecological risk was higher than 95%. The results of source identification showed that the main sources of antibiotics were effluents of wastewater treatment plants， aquaculture， and livestock farming. Among these， effluent of wastewater treatment plants was the most dominant source， explaining 41.38% of the antibiotics. This study comprehensively explored the occurrence， ecological risks， and major sources of antibiotics in the rivers in Tongzhou District， Beijing， which is of great significance for targeted antibiotic pollution control and ecosystem health protection.}, }
@article {pmid41093232, year = {2025}, author = {Lei, W and Guo, J and Liang, X and Wang, H and Qi, W and Mao, Z and He, S}, title = {Occurrence characteristics and environmental fate of neonicotinoid insecticides in mountain agricultural soils and river waters.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {386}, number = {}, pages = {127269}, doi = {10.1016/j.envpol.2025.127269}, pmid = {41093232}, issn = {1873-6424}, abstract = {Neonicotinoid insecticides (NNIs) have been widely detected in terrestrial ecosystems and may pose potential threats to ecosystem functions. Yet comprehensive evaluation of their occurrence characteristics, influencing factors, and soil-water connections remains limited. This study investigated NNIs occurrence patterns, transport dynamics, and ecological risks in soils and river waters of mountainous agricultural areas. The results revealed that NNIs were detected in soils and waters with a 100 % detection rate. Imidacloprid (IMI) was the predominant compound in soils (84.8 %), whereas river waters exhibited multi-component coexistence, with IMI, thiamethoxam (THIA), dinotefuran (DIN), and clothianidin (CLO) accounting for 30.9 %, 14.3 %, 12.9 %, and 11.8 % of NNIs, respectively. The mean concentration of eight NNIs (∑8NNIs) in stem mustard fields (11.45 ng/g) was higher than in forest soils (0.17 ng/g). The ∑8NNIs in water bodies near towns (102.65 ng/L) was 3.4 times higher than that in forest background areas. Additionally, A significant negative correlation between soil and water NNIs concentrations suggests that soil NNIs influence water NNIs levels. SEM and SHAP analyses identified soil NNIs concentration, bulk density, and elevation as primary factors regulating NNIs in adjacent waters. Ecological risk assessment outcomes indicate that the overall ecological risk in the study area was low. There were 13 % of soil sites with an α (risk entropy) exceeding 1, and 28 % of water sites with a risk coefficient surpassing the chronic HC5. These results provide theoretical support for understanding the occurrence characteristics and transfer trends of NNIs in soils and waters of agricultural areas.}, }
@article {pmid41093042, year = {2025}, author = {Noordzij, HT and Wortel, MT and Heintz-Buschart, A and Petrikonyte, P and de Muinck, EJ and Trosvik, P}, title = {Assembly-based analysis of the infant gut microbiome reveals novel ubiquitous plasmids.}, journal = {Plasmid}, volume = {134}, number = {}, pages = {102761}, doi = {10.1016/j.plasmid.2025.102761}, pmid = {41093042}, issn = {1095-9890}, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Plasmids/genetics ; Infant ; Feces/microbiology ; Infant, Newborn ; Bacteroides/genetics ; Longitudinal Studies ; Female ; Computational Biology/methods ; Male ; Clostridium/genetics ; }, abstract = {Little is known about the role of mobile genetic elements in natural ecosystems such as the infant gut microbiome. Here, we conduct the most comprehensive longitudinal study of the infant plasmidome to date by analyzing monthly fecal samples from 12 infants from birth to one year of age. We employ an assembly-based bioinformatic pipeline for the reconstruction and identification of full-length plasmids, including a novel approach for assigning putative plasmid hosts. We then investigated plasmid content and dynamics in the infant gut microbiome. After assembly and identification, we identified 620 unique circular plasmids in the infant cohort, including a number of novel sequences. Independent assembly of the same plasmids in several samples and infants helped corroborate the authenticity of the plasmids. Among the observed plasmids was the recently described ubiquitous and abundant Bacteroides plasmid pBI143. Overall, the genus Bacteroides had the highest plasmid carriage, while the highest plasmid diversity was observed in Clostridium, including 5 previously unknown widespread plasmids. Lastly, we leveraged the longitudinal nature of our dataset to investigate contemporaneous correlations between temporal variations in plasmid abundances and species dynamics. This enabled us to link co-residing plasmids and tightly linked plasmid-taxon pairs within each infant. These insights into plasmid ecology help us understand determinants driving plasmid distribution in complex microbial communities.}, }
@article {pmid41092928, year = {2025}, author = {, }, title = {Global burden of 292 causes of death in 204 countries and territories and 660 subnational locations, 1990-2023: a systematic analysis for the Global Burden of Disease Study 2023.}, journal = {Lancet (London, England)}, volume = {406}, number = {10513}, pages = {1811-1872}, pmid = {41092928}, issn = {1474-547X}, support = {P01 HD031921/HD/NICHD NIH HHS/United States ; R01 AG044917/AG/NIA NIH HHS/United States ; R01 AG030153/AG/NIA NIH HHS/United States ; HHSN271201300071C/AG/NIA NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; R03 AG043052/AG/NIA NIH HHS/United States ; R01 AG034479/AG/NIA NIH HHS/United States ; R01 AG018016/AG/NIA NIH HHS/United States ; R21 AG032572/AG/NIA NIH HHS/United States ; U01 AG009740/AG/NIA NIH HHS/United States ; R01 AG031716/AG/NIA NIH HHS/United States ; R21 AG034263/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; *Global Burden of Disease/trends ; Cause of Death/trends ; Male ; Female ; Aged ; Middle Aged ; Adult ; Infant ; Child ; Child, Preschool ; Adolescent ; Life Expectancy/trends ; Global Health/statistics &amp; numerical data ; Young Adult ; Infant, Newborn ; Aged, 80 and over ; Risk Factors ; Mortality/trends ; }, abstract = {BACKGROUND: Timely and comprehensive analyses of causes of death stratified by age, sex, and location are essential for shaping effective health policies aimed at reducing global mortality. The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2023 provides cause-specific mortality estimates measured in counts, rates, and years of life lost (YLLs). GBD 2023 aimed to enhance our understanding of the relationship between age and cause of death by quantifying the probability of dying before age 70 years (70q0) and the mean age at death by cause and sex. This study enables comparisons of the impact of causes of death over time, offering a deeper understanding of how these causes affect global populations.<br><br>METHODS: GBD 2023 produced estimates for 292 causes of death disaggregated by age-sex-location-year in 204 countries and territories and 660 subnational locations for each year from 1990 until 2023. We used a modelling tool developed for GBD, the Cause of Death Ensemble model (CODEm), to estimate cause-specific death rates for most causes. We computed YLLs as the product of the number of deaths for each cause-age-sex-location-year and the standard life expectancy at each age. Probability of death was calculated as the chance of dying from a given cause in a specific age period, for a specific population. Mean age at death was calculated by first assigning the midpoint age of each age group for every death, followed by computing the mean of all midpoint ages across all deaths attributed to a given cause. We used GBD death estimates to calculate the observed mean age at death and to model the expected mean age across causes, sexes, years, and locations. The expected mean age reflects the expected mean age at death for individuals within a population, based on global mortality rates and the population's age structure. Comparatively, the observed mean age represents the actual mean age at death, influenced by all factors unique to a location-specific population, including its age structure. As part of the modelling process, uncertainty intervals (UIs) were generated using the 2&#xb7;5th and 97&#xb7;5th percentiles from a 250-draw distribution for each metric. Findings are reported as counts and age-standardised rates. Methodological improvements for cause-of-death estimates in GBD 2023 include a correction for the misclassification of deaths due to COVID-19, updates to the method used to estimate COVID-19, and updates to the CODEm modelling framework. This analysis used 55&#x2008;761 data sources, including vital registration and verbal autopsy data as well as data from surveys, censuses, surveillance systems, and cancer registries, among others. For GBD 2023, there were 312 new country-years of vital registration cause-of-death data, 3 country-years of surveillance data, 51 country-years of verbal autopsy data, and 144 country-years of other data types that were added to those used in previous GBD rounds.<br><br>FINDINGS: The initial years of the COVID-19 pandemic caused shifts in long-standing rankings of the leading causes of global deaths: it ranked as the number one age-standardised cause of death at Level 3 of the GBD cause classification hierarchy in 2021. By 2023, COVID-19 dropped to the 20th place among the leading global causes, returning the rankings of the leading two causes to those typical across the time series (ie, ischaemic heart disease and stroke). While ischaemic heart disease and stroke persist as leading causes of death, there has been progress in reducing their age-standardised mortality rates globally. Four other leading causes have also shown large declines in global age-standardised mortality rates across the study period: diarrhoeal diseases, tuberculosis, stomach cancer, and measles. Other causes of death showed disparate patterns between sexes, notably for deaths from conflict and terrorism in some locations. A large reduction in age-standardised rates of YLLs occurred for neonatal disorders. Despite this, neonatal disorders remained the leading cause of global YLLs over the period studied, except in 2021, when COVID-19 was temporarily the leading cause. Compared to 1990, there has been a considerable reduction in total YLLs in many vaccine-preventable diseases, most notably diphtheria, pertussis, tetanus, and measles. In addition, this study quantified the mean age at death for all-cause mortality and cause-specific mortality and found noticeable variation by sex and location. The global all-cause mean age at death increased from 46&#xb7;8 years (95% UI 46&#xb7;6-47&#xb7;0) in 1990 to 63&#xb7;4 years (63&#xb7;1-63&#xb7;7) in 2023. For males, mean age increased from 45&#xb7;4 years (45&#xb7;1-45&#xb7;7) to 61&#xb7;2 years (60&#xb7;7-61&#xb7;6), and for females it increased from 48&#xb7;5 years (48&#xb7;1-48&#xb7;8) to 65&#xb7;9 years (65&#xb7;5-66&#xb7;3), from 1990 to 2023. The highest all-cause mean age at death in 2023 was found in the high-income super-region, where the mean age for females reached 80&#xb7;9 years (80&#xb7;9-81&#xb7;0) and for males 74&#xb7;8 years (74&#xb7;8-74&#xb7;9). By comparison, the lowest all-cause mean age at death occurred in sub-Saharan Africa, where it was 38&#xb7;0 years (37&#xb7;5-38&#xb7;4) for females and 35&#xb7;6 years (35&#xb7;2-35&#xb7;9) for males in 2023. Lastly, our study found that all-cause 70q0 decreased across each GBD super-region and region from 2000 to 2023, although with large variability between them. For females, we found that 70q0 notably increased from drug use disorders and conflict and terrorism. Leading causes that increased 70q0 for males also included drug use disorders, as well as diabetes. In sub-Saharan Africa, there was an increase in 70q0 for many non-communicable diseases (NCDs). Additionally, the mean age at death from NCDs was lower than the expected mean age at death for this super-region. By comparison, there was an increase in 70q0 for drug use disorders in the high-income super-region, which also had an observed mean age at death lower than the expected value.<br><br>INTERPRETATION: We examined global mortality patterns over the past three decades, highlighting-with enhanced estimation methods-the impacts of major events such as the COVID-19 pandemic, in addition to broader trends such as increasing NCDs in low-income regions that reflect ongoing shifts in the global epidemiological transition. This study also delves into premature mortality patterns, exploring the interplay between age and causes of death and deepening our understanding of where targeted resources could be applied to further reduce preventable sources of mortality. We provide essential insights into global and regional health disparities, identifying locations in need of targeted interventions to address both communicable and non-communicable diseases. There is an ever-present need for strengthened health-care systems that are resilient to future pandemics and the shifting burden of disease, particularly among ageing populations in regions with high mortality rates. Robust estimates of causes of death are increasingly essential to inform health priorities and guide efforts toward achieving global health equity. The need for global collaboration to reduce preventable mortality is more important than ever, as shifting burdens of disease are affecting all nations, albeit at different paces and scales.<br><br>FUNDING: Gates Foundation.}, }
@article {pmid41092926, year = {2025}, author = {, }, title = {Burden of 375 diseases and injuries, risk-attributable burden of 88 risk factors, and healthy life expectancy in 204 countries and territories, including 660 subnational locations, 1990-2023: a systematic analysis for the Global Burden of Disease Study 2023.}, journal = {Lancet (London, England)}, volume = {406}, number = {10513}, pages = {1873-1922}, pmid = {41092926}, issn = {1474-547X}, support = {P01 HD031921/HD/NICHD NIH HHS/United States ; R01 AG044917/AG/NIA NIH HHS/United States ; R01 AG030153/AG/NIA NIH HHS/United States ; HHSN271201300071C/AG/NIA NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; R03 AG043052/AG/NIA NIH HHS/United States ; R01 AG034479/AG/NIA NIH HHS/United States ; R01 AG018016/AG/NIA NIH HHS/United States ; R21 AG032572/AG/NIA NIH HHS/United States ; U01 AG009740/AG/NIA NIH HHS/United States ; R01 AG031716/AG/NIA NIH HHS/United States ; R21 AG034263/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; *Global Burden of Disease/trends ; *Life Expectancy/trends ; Risk Factors ; Male ; Female ; Disability-Adjusted Life Years ; *Wounds and Injuries/epidemiology ; Middle Aged ; Adult ; Global Health/statistics &amp; numerical data ; Child ; Aged ; Adolescent ; Infant ; Child, Preschool ; Young Adult ; Infant, Newborn ; COVID-19/epidemiology ; Persons with Disabilities/statistics &amp; numerical data ; Quality-Adjusted Life Years ; Aged, 80 and over ; }, abstract = {BACKGROUND: For more than three decades, the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) has provided a framework to quantify health loss due to diseases, injuries, and associated risk factors. This paper presents GBD 2023 findings on disease and injury burden and risk-attributable health loss, offering a global audit of the state of world health to inform public health priorities. This work captures the evolving landscape of health metrics across age groups, sexes, and locations, while reflecting on the remaining post-COVID-19 challenges to achieving our collective global health ambitions.<br><br>METHODS: The GBD 2023 combined analysis estimated years lived with disability (YLDs), years of life lost (YLLs), and disability-adjusted life-years (DALYs) for 375 diseases and injuries, and risk-attributable burden associated with 88 modifiable risk factors. Of the more than 310&#x2008;000 total data sources used for all GBD 2023 (about 30% of which were new to this estimation round), more than 120&#x2008;000 sources were used for estimation of disease and injury burden and 59&#x2008;000 for risk factor estimation, and included vital registration systems, surveys, disease registries, and published scientific literature. Data were analysed using previously established modelling approaches, such as disease modelling meta-regression version 2.1 (DisMod-MR 2.1) and comparative risk assessment methods. Diseases and injuries were categorised into four levels on the basis of the established GBD cause hierarchy, as were risk factors using the GBD risk hierarchy. Estimates stratified by age, sex, location, and year from 1990 to 2023 were focused on disease-specific time trends over the 2010-23 period and presented as counts (to three significant figures) and age-standardised rates per 100&#x2008;000 person-years (to one decimal place). For each measure, 95% uncertainty intervals [UIs] were calculated with the 2&#xb7;5th and 97&#xb7;5th percentile ordered values from a 250-draw distribution.<br><br>FINDINGS: Total numbers of global DALYs grew 6&#xb7;1% (95% UI 4&#xb7;0-8&#xb7;1), from 2&#xb7;64 billion (2&#xb7;46-2&#xb7;86) in 2010 to 2&#xb7;80 billion (2&#xb7;57-3&#xb7;08) in 2023, but age-standardised DALY rates, which account for population growth and ageing, decreased by 12&#xb7;6% (11&#xb7;0-14&#xb7;1), revealing large long-term health improvements. Non-communicable diseases (NCDs) contributed 1&#xb7;45 billion (1&#xb7;31-1&#xb7;61) global DALYs in 2010, increasing to 1&#xb7;80 billion (1&#xb7;63-2&#xb7;03) in 2023, alongside a concurrent 4&#xb7;1% (1&#xb7;9-6&#xb7;3) reduction in age-standardised rates. Based on DALY counts, the leading level 3 NCDs in 2023 were ischaemic heart disease (193 million [176-209] DALYs), stroke (157 million [141-172]), and diabetes (90&#xb7;2 million [75&#xb7;2-107]), with the largest increases in age-standardised rates since 2010 occurring for anxiety disorders (62&#xb7;8% [34&#xb7;0-107&#xb7;5]), depressive disorders (26&#xb7;3% [11&#xb7;6-42&#xb7;9]), and diabetes (14&#xb7;9% [7&#xb7;5-25&#xb7;6]). Remarkable health gains were made for communicable, maternal, neonatal, and nutritional (CMNN) diseases, with DALYs falling from 874 million (837-917) in 2010 to 681 million (642-736) in 2023, and a 25&#xb7;8% (22&#xb7;6-28&#xb7;7) reduction in age-standardised DALY rates. During the COVID-19 pandemic, DALYs due to CMNN diseases rose but returned to pre-pandemic levels by 2023. From 2010 to 2023, decreases in age-standardised rates for CMNN diseases were led by rate decreases of 49&#xb7;1% (32&#xb7;7-61&#xb7;0) for diarrhoeal diseases, 42&#xb7;9% (38&#xb7;0-48&#xb7;0) for HIV/AIDS, and 42&#xb7;2% (23&#xb7;6-56&#xb7;6) for tuberculosis. Neonatal disorders and lower respiratory infections remained the leading level 3 CMNN causes globally in 2023, although both showed notable rate decreases from 2010, declining by 16&#xb7;5% (10&#xb7;6-22&#xb7;0) and 24&#xb7;8% (7&#xb7;4-36&#xb7;7), respectively. Injury-related age-standardised DALY rates decreased by 15&#xb7;6% (10&#xb7;7-19&#xb7;8) over the same period. Differences in burden due to NCDs, CMNN diseases, and injuries persisted across age, sex, time, and location. Based on our risk analysis, nearly 50% (1&#xb7;27 billion [1&#xb7;18-1&#xb7;38]) of the roughly 2&#xb7;80 billion total global DALYs in 2023 were attributable to the 88 risk factors analysed in GBD. Globally, the five level 3 risk factors contributing the highest proportion of risk-attributable DALYs were high systolic blood pressure (SBP), particulate matter pollution, high fasting plasma glucose (FPG), smoking, and low birthweight and short gestation-with high SBP accounting for 8&#xb7;4% (6&#xb7;9-10&#xb7;0) of total DALYs. Of the three overarching level 1 GBD risk factor categories-behavioural, metabolic, and environmental and occupational-risk-attributable DALYs rose between 2010 and 2023 only for metabolic risks, increasing by 30&#xb7;7% (24&#xb7;8-37&#xb7;3); however, age-standardised DALY rates attributable to metabolic risks decreased by 6&#xb7;7% (2&#xb7;0-11&#xb7;0) over the same period. For all but three of the 25 leading level 3 risk factors, age-standardised rates dropped between 2010 and 2023-eg, declining by 54&#xb7;4% (38&#xb7;7-65&#xb7;3) for unsafe sanitation, 50&#xb7;5% (33&#xb7;3-63&#xb7;1) for unsafe water source, and 45&#xb7;2% (25&#xb7;6-72&#xb7;0) for no access to handwashing facility, and by 44&#xb7;9% (37&#xb7;3-53&#xb7;5) for child growth failure. The three leading level 3 risk factors for which age-standardised attributable DALY rates rose were high BMI (10&#xb7;5% [0&#xb7;1 to 20&#xb7;9]), drug use (8&#xb7;4% [2&#xb7;6 to 15&#xb7;3]), and high FPG (6&#xb7;2% [-2&#xb7;7 to 15&#xb7;6]; non-significant).<br><br>INTERPRETATION: Our findings underscore the complex and dynamic nature of global health challenges. Since 2010, there have been large decreases in burden due to CMNN diseases and many environmental and behavioural risk factors, juxtaposed with sizeable increases in DALYs attributable to metabolic risk factors and NCDs in growing and ageing populations. This long-observed consequence of the global epidemiological transition was only temporarily interrupted by the COVID-19 pandemic. The substantially decreasing CMNN disease burden, despite the 2008 global financial crisis and pandemic-related disruptions, is one of the greatest collective public health successes known. However, these achievements are at risk of being reversed due to major cuts to development assistance for health globally, the effects of which will hit low-income countries with high burden the hardest. Without sustained investment in evidence-based interventions and policies, progress could stall or reverse, leading to widespread human costs and geopolitical instability. Moreover, the rising NCD burden necessitates intensified efforts to mitigate exposure to leading risk factors-eg, air pollution, smoking, and metabolic risks, such as high SBP, BMI, and FPG-including policies that promote food security, healthier diets, physical activity, and equitable and expanded access to potential treatments, such as GLP-1 receptor agonists. Decisive, coordinated action is needed to address long-standing yet growing health challenges, including depressive and anxiety disorders. Yet this can be only part of the solution. Our response to the NCD syndemic-the complex interaction of multiple health risks, social determinants, and systemic challenges-will define the future landscape of global health. To ensure human wellbeing, economic stability, and social equity, global action to sustain and advance health gains must prioritise reducing disparities by addressing socioeconomic and demographic determinants, ensuring equitable health-care access, tackling malnutrition, strengthening health systems, and improving vaccination coverage. We live in times of great opportunity.<br><br>FUNDING: Gates Foundation and Bloomberg Philanthropies.}, }
@article {pmid41087423, year = {2025}, author = {Li, Z and Liu, J and Li, J and Zhou, Z and Huang, X and Gopinath, D and Luo, P and Wang, Q and Shan, D}, title = {Fusobacterium in the microbiome: from health to disease across the oral-gut axis and beyond.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {200}, pmid = {41087423}, issn = {2055-5008}, mesh = {Humans ; *Fusobacterium/physiology/pathogenicity/genetics ; *Mouth/microbiology ; Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; *Microbiota ; Animals ; Neoplasms/microbiology ; *Fusobacterium Infections/microbiology ; }, abstract = {Fusobacterium functions as both commensal and pathogen, linking the oral-gut axis to diverse diseases, including cancer. Evidence shows it modulates microbial balance, promotes dysbiosis, and contributes to carcinogenesis by driving inflammation, proliferation, invasion, and immune evasion. This review integrates ecological, molecular, and clinical insights, highlighting its roles in oral and systemic disease and discussing therapeutic potential, underscoring Fusobacterium's dualistic nature and implications for microbiome-targeted interventions.}, }
@article {pmid41087389, year = {2025}, author = {Jiang, C and Wu, Q and Su, F and Cui, W and Chen, T and Sun, L}, title = {Chromosome-level genome assembly of the sea cucumber, Colochirus anceps.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1643}, pmid = {41087389}, issn = {2052-4463}, mesh = {Animals ; *Chromosomes ; *Genome ; Molecular Sequence Annotation ; *Sea Cucumbers/genetics ; Datasets as Topic ; }, abstract = {Colochirus anceps is a benthic sea cucumber recognized for its striking aposematic coloration, ecological role in nutrient recycling, and biomedical potential. In this study, we utilized Illumina short-read, PacBio HiFi long-read, and Hi-C sequencing technologies to assemble the chromosome-level genome of C. anceps. This represents the first genome assembly for the order Dendrochirotida within the class Holothuroidea. The assembled genome has a total size of 2,238.33 Mb, with a contig N50 of 15.09 Mb, and 95.09% of the assembly sequences have been anchored to 23 chromosomes. Annotation identified 24,102 protein-coding genes and revealed a high repeat content of 70.95%. The genome achieved a completeness score of 94.3%, as evaluated through BUSCO analysis. This genome assembly provides valuable insights into the genomic architecture and evolutionary dynamics of sea cucumbers, laying a foundation for exploring their unique biological traits, adaptability, and diversity.}, }
@article {pmid41087306, year = {2025}, author = {Tang, Y and Qiu, S and Li, B and Sui, D and Jiang, K and Zheng, J and Zou, J and Lian, J and Wang, L and Yuan, Y}, title = {Integrative Physiological and Multi-Omics Insights: Salt Stress Adaptation and Functional Specialization in Suaeda salsa L.}, journal = {Physiologia plantarum}, volume = {177}, number = {5}, pages = {e70581}, doi = {10.1111/ppl.70581}, pmid = {41087306}, issn = {1399-3054}, support = {LYKJ[2023]01//Research on Breeding of Native Tree Species for Carbon Sequestration Afforestation in Jiangsu Coast/ ; Su[2024]TG14//Central Finance Forestry Science and Technology Extension Project/ ; JAF-2025-01//Youth Fund of Jiangsu Academy of Forestry Sciences/ ; LYKJ[2021]08//Long-Term Scientific Research Base for Cultivation of Salt-Tolerant Native Tree Species in Jiangsu/ ; }, mesh = {*Chenopodiaceae/physiology/genetics/metabolism ; Plant Leaves/physiology/metabolism/genetics ; Plant Roots/physiology/metabolism/genetics ; *Salt Stress/physiology ; Gene Expression Regulation, Plant ; Salt Tolerance/physiology ; Salt-Tolerant Plants/physiology/genetics ; Transcriptome ; Adaptation, Physiological ; Gene Expression Profiling ; Metabolomics ; Multiomics ; }, abstract = {Soil salinization, a major abiotic stress, severely limits plant growth and reduces crop yields. Understanding the salt tolerance mechanisms of halophytes is essential for the effective utilization of saline soils and improving crop resilience. Suaeda salsa L., a saline-alkali pioneer species with significant ecological and economic value, was investigated using physiological, metabolomic, and transcriptomic approaches under low, medium, and high soil electrical conductivities to elucidate its salt adaptation mechanisms. Physiological assays demonstrated that the responses were predominantly leaf-centered, with measurements of antioxidant enzymes, oxidative stress indicators, and osmolytes indicating that leaves play a key role in salt stress responses. Transcriptomic analysis revealed that the metabolic pathways were the most enriched across all conductivity comparisons. Metabolomic profiling showed that differential metabolites in the roots and leaves were enriched in starch and sucrose metabolism, whereas phenylpropanoid biosynthesis exhibited contrasting enrichment patterns in the roots and leaves under low- and high conductivity conditions. Based on these pathways, tissue-specific regulatory networks were constructed, revealing coordinated carbon allocation and the establishment of an efficient salt-tolerance network. Most genes exhibited divergent expression patterns between roots and leaves as conductivity increased, reflecting functional specialization. This study proposed that S. salsa uses a metabolic regulatory network characterized by gradient responses, functional differentiation, and energy optimization, providing a theoretical foundation for enhancing halophyte adaptation and improving crop salt tolerance.}, }
@article {pmid41085718, year = {2025}, author = {Karaarslan, F and Güneri, FD and Özen, H and Odabaşı, E}, title = {The evaluation of medical mud pack treatment from the patient's perspective in different musculoskeletal disorders- A prospective study.}, journal = {International journal of biometeorology}, volume = {69}, number = {12}, pages = {3587-3596}, pmid = {41085718}, issn = {1432-1254}, mesh = {Humans ; Male ; Female ; Middle Aged ; Patient Satisfaction ; Prospective Studies ; Adult ; *Mud Therapy ; Aged ; *Musculoskeletal Diseases/therapy ; Low Back Pain/therapy ; *Osteoarthritis, Knee/therapy ; *Myofascial Pain Syndromes/therapy ; Pain Measurement ; }, abstract = {This study evaluated patient satisfaction and expectation levels in individuals with chronic low back pain (LBP), myofascial pain syndrome (MPS), and knee osteoarthritis (KOA) who received mud pack therapy (MPT). It also investigated the relationship between these conditions and pain levels, global assessment results, and side effects. We assessed 250 patients (n = 74 for LBP, n = 75 for MPS, n = 101 for KOA) who underwent twelve sessions of MPT at 43 °C, lasting 30 min each. Patients continued their routine care and completed surveys on satisfaction and expectations, as well as measures of pain (VAS-pain), global assessment (VAS-PGA), and acceptable symptom state (PASS). Satisfaction levels were reported as "satisfied" or "definitely satisfied" by 93.1% to 96% of patients. Expectations were met by 86.7% to 89.2% of patients. Both VAS-pain and VAS-PGA showed statistically significant improvements after treatment (p < 0.001), though there were no differences between groups (p = 0.794 for VAS-pain, p = 0.234 for VAS-PGA). The PASS evaluation showed no significant group differences (p = 0.274). No serious side effects were reported, except for mild, short-term increases in pain. MPT is an effective treatment providing significant pain relief for LBP, MPS, and KOA patients, with high satisfaction and expectation fulfillment among participants.}, }
@article {pmid41082884, year = {2025}, author = {, }, title = {The burden of bacterial antimicrobial resistance in the WHO Eastern Mediterranean Region 1990-2021: a cross-country systematic analysis with forecasts to 2050.}, journal = {The Lancet. Public health}, volume = {10}, number = {11}, pages = {e955-e970}, doi = {10.1016/S2468-2667(25)00201-4}, pmid = {41082884}, issn = {2468-2667}, support = {001/WHO_/World Health Organization/International ; }, mesh = {Humans ; World Health Organization ; *Drug Resistance, Bacterial ; Mediterranean Region/epidemiology ; Disability-Adjusted Life Years ; Forecasting ; *Bacterial Infections/mortality/drug therapy/epidemiology ; *Anti-Bacterial Agents/therapeutic use ; }, abstract = {BACKGROUND: Antimicrobial resistance (AMR) is an urgent global crisis and one of the world's most complex challenges. Although there is increasing evidence of its impact on human mortality and morbidity, precise burden estimation has many challenges, and thus far has been elusive for the Eastern Mediterranean Region. Here, we present a comprehensive time-trend analysis of regional and country-level AMR burden estimates in the WHO Eastern Mediterranean Region (EMR), between 1990 and 2021, with forecasts up to 2050.<br><br>METHODS: We estimated deaths and disability-adjusted life-years (DALYs) attributable to and associated with AMR for 11 infectious syndromes, 22 bacterial pathogens, and 84 pathogen-drug combinations for the WHO EMR and each of its countries from 1990 to 2021. Data were obtained from mortality registries, surveillance systems, hospital records, systematic literature reviews, and other sources. We based our modelling approach on five broad components: the number of deaths in which infection had a role, the proportion of infectious deaths attributable to a given infectious syndrome, the proportion of infectious syndrome deaths attributable to a given pathogen, the percentage of a given pathogen resistant to an antimicrobial drug of interest, and the excess risk of mortality (or duration of an infection) associated with this resistance. These components were then used to estimate the disease burden by using two counterfactual scenarios: deaths and DALYs attributable to AMR (considering an alternative scenario where drug-resistant infections are replaced with susceptible infections), and deaths and DALYs associated with AMR (considering an alternative scenario where infections would not occur at all). Predictive statistical modelling was applied to generate estimates of AMR burden for each country. We also generated AMR burden forecasts up to 2050. We generated 95% uncertainty intervals (UIs) for the final estimates by taking the 2&#xb7;5th and 97&#xb7;5th percentiles across 500 draws through the multistage computational pipeline, and models were cross-validated for out-of-sample predictive validity.<br><br>FINDINGS: We estimated 380&#x2009;000 deaths (95% UI 332&#x2009;000-426&#x2009;000) associated with bacterial AMR and 92&#x2009;800 deaths (78&#x2009;300-111&#x2009;000) attributable to bacterial AMR in the EMR in 2021. In the past 31 years, there was considerable variation in AMR mortality trends across countries of the region and different age groups. Between 1990 and 2021, associated deaths among children younger than 5 years decreased by 50&#xb7;0% (38&#xb7;2-62&#xb7;0), while those among adults aged 70 and older rose by over 85&#xb7;7% (95% UI 57&#xb7;0-115&#xb7;7). Six pathogens were identified as the primary generators of burden: Streptococcus pneumoniae, Klebsiella pneumoniae, Escherichia coli, Staphylococcus aureus, Acinetobacter baumannii, and Pseudomonas aeruginosa. A substantial increase in the AMR burden due to S aureus was observed between 1990 (28&#x2009;200 deaths [21&#x2009;600-34&#x2009;000]) and 2021 (49&#x2009;500 deaths [43&#x2009;100-56&#x2009;200]); consequently, in 2021, methicillin-resistant S aureus was a leading pathogen-drug combination for most countries in the region for deaths and DALYs attributable to, and associated with AMR. Somalia had the highest age-standardised mortality rates in the region: for deaths attributable to and associated with AMR per 100&#x2009;000 population in both 1990 and 2021; conversely, the country with the lowest burden in the EMR was Qatar. By 2050, the number of deaths attributable to AMR in region is forecasted to reach 187&#x2009;000 (157&#x2009;000-223&#x2009;000) and deaths associated with AMR were projected to reach 752&#x2009;000 (629&#x2009;000-879&#x2009;000).<br><br>INTERPRETATION: Our study shows that bacterial AMR has been a serious public health threat in the EMR for more than 30 years, with a substantial fatal and non-fatal burden for priority bacterial pathogens and pathogen-drug combinations. The magnitude of this issue, future projects, and the inadequate response capacity in many countries underscore the need for more stringent regional leadership in this field. The insights gained from this study can direct targeted mitigation strategies for individual countries within the region, aiding in resource allocation and funding decisions, and emphasising the need for collaborative multisectoral endeavours among nations to address this issue.<br><br>FUNDING: Wellcome Trust, and the UK Department of Health and Social Care using aid funding managed by the Fleming Fund.}, }
@article {pmid41081996, year = {2025}, author = {Yetişgin, SO and Bagci, HR and Coban, HO and Goktepe, S}, title = {From grazing to green: unraveling the ecological consequences of transhumance decline in Turkey's Mediterranean mountains.}, journal = {Tropical animal health and production}, volume = {57}, number = {8}, pages = {435}, pmid = {41081996}, issn = {1573-7438}, mesh = {Animals ; Turkey ; *Goats/physiology ; Geographic Information Systems ; *Animal Husbandry/methods ; *Ecosystem ; *Conservation of Natural Resources ; *Animal Migration ; }, abstract = {Transhumance, a millennia-old pastoral practice, has been instrumental in shaping the cultural, ecological and socio-economic fabric of Turkey's Mediterranean mountains while providing a range of ecosystem services. However, profound socio-economic shifts, policy constraints, and land-use changes have led to its rapid decline, triggering cascading environmental consequences. This study investigates the spatial and temporal associations between transhumance decline and land use/cover changes (LULC) along four transhumance migration routes in Turkey's Mediterranean Mountains over the past three decades. The migration routes of transhumant goat flocks were recorded using GPS collars. Digital Elevation Model data were sourced from the U.S. Geological Survey and analyzed using ArcGIS software to produce comprehensive maps illustrating the geographical and elevational characteristics of the study area. Furthermore, CORINE (Coordination of Information on the Environment) land cover maps derived from satellite imagery were employed to assess existing land cover and temporal shifts within the region. Through Geographic Information Systems (GIS), we conducted an in-depth analysis of land use/cover changes across the years 1990 and 2018, employing the Dynamic Degree Index to quantify the rate and extent of spatial transformations. Using Geographic Information Systems (GIS) and remote sensing, the findings reveal a loss of grasslands (- 9.96%) and shrublands (- 13.19%), while forests (+ 23.81%), agricultural land (+ 13.11%), and urban areas (+ 37.03%) expanded. Although direct causality cannot be confirmed, the spatial overlap between declining grazing areas and vegetation transitions suggests a strong association. Informal conversations with herders supported the observation that reduced grazing pressure contributed to shrub encroachment and forest expansion. These findings underscore the necessity of holistic rangeland governance strategies that reconcile conservation imperatives with the cultural and economic sustainability of pastoral communities. Ensuring the resilience of these landscapes requires a nuanced approach that acknowledges transhumance as a dynamic socio-ecological system rather than a relic of the past.}, }
@article {pmid41079487, year = {2025}, author = {Owens, JBB and Wüster, W and Mulley, J and Graham, S and Morgan, R and Barlow, A and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the common adder, Vipera berus (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {11}, pmid = {41079487}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Vipera berus (common adder; Chordata; Lepidosauria; Squamata; Viperidae). The haplotype-resolved assembly contains two haplotypes with total lengths of 1,695.0 megabases and 1,476.7 megabases, respectively. Most of haplotype 1 (98.45%) is scaffolded into 19 chromosomal pseudomolecules, while haplotype 2 is assembled to scaffold level. Haplotype 1 achieves the Earth Biogenome Project reference standard of 6.C.Q52. The mitochondrial genome has also been assembled and is 17.35 kilobases in length.}, }
@article {pmid41077897, year = {2025}, author = {Rachtman, E and Jiang, Y and Mirarab, S}, title = {Machine Learning Enables Alignment-Free Distance Calculation and Phylogenetic Placement Using k-Mer Frequencies.}, journal = {Molecular ecology resources}, volume = {25}, number = {8}, pages = {e70055}, pmid = {41077897}, issn = {1755-0998}, support = {2137603//National Science Foundation (ACCESS Program)/ ; 2138259//National Science Foundation (ACCESS Program)/ ; 2138286//National Science Foundation (ACCESS Program)/ ; 2138296//National Science Foundation (ACCESS Program)/ ; 2138307//National Science Foundation (ACCESS Program)/ ; ACI-1540112//National Science Foundation (NRP/Natulius Program)/ ; CNS-2100237//National Science Foundation (NRP/Natulius Program)/ ; ACI-1541349//National Science Foundation (NRP/Natulius Program)/ ; CNS-1730158//National Science Foundation (NRP/Natulius Program)/ ; CNS-2120019//National Science Foundation (NRP/Natulius Program)/ ; OAC-1826967//National Science Foundation (NRP/Natulius Program)/ ; OAC-2112167//National Science Foundation (NRP/Natulius Program)/ ; 1R35GM142725/NH/NIH HHS/United States ; //Minderoo Foundation/ ; //Schmidt Foundation/ ; 1R35GM142725/NH/NIH HHS/United States ; }, mesh = {*Phylogeny ; *Machine Learning ; *Computational Biology/methods ; Sequence Analysis, DNA/methods ; }, abstract = {A key application of phylogenetics in ecological studies is identifying unknown sequences with respect to known ones. This goal can be formalised as assigning taxonomic labels or inserting sequences into a reference phylogenetic tree (phylogenetic placement). Much attention has been paid to the phylogenetic placement of short fragments used in amplicon sequencing or metagenomics. However, placing longer pieces of DNA, such as assembled genomes, contigs, or long reads, is less studied. Placing long sequences should be easier than short reads due to their increased signal. However, handling larger inputs poses its own challenges including finding homologues and the computational burden. Here, we explore a phylogenetic placement method that uses k-mer frequencies to measure distances between long query sequences and reference genomes. Our proposed method, kf2vec, requires no alignment and can work on any region of the genome (needs no marker genes), thus simplifying analysis pipelines. A rich literature exists on using short k-mers frequencies to measure distances that correlate with phylogeny. Existing methods, however, have had moderate practical success despite enjoying strong theory. Instead of using predefined metrics, we train a deep neural network to estimate a distance from k-mer frequency vectors such that those distances match the path lengths on the reference phylogeny. The trained model is then used to characterise new samples. We demonstrate that kf2vec outperforms existing k-mer-based approaches in distance calculation and allows accurate phylogenetic placement and taxonomic identification of new samples from various types of long sequences.}, }
@article {pmid41074313, year = {2025}, author = {Lv, J and Wang, Y and Zhou, L and Zhang, S and Song, W and Dong, R and Liu, T and Wang, G and Shi, L}, title = {Multi-omics investigation unveils the role of Eurotium cristatum fermentation in potentiating thinned young apple pomace for colitis-induced liver disorders amelioration.}, journal = {Food research international (Ottawa, Ont.)}, volume = {220}, number = {}, pages = {117095}, doi = {10.1016/j.foodres.2025.117095}, pmid = {41074313}, issn = {1873-7145}, mesh = {*Malus/microbiology ; *Fermentation ; Animals ; *Liver Diseases/etiology/prevention &amp; control ; Gastrointestinal Microbiome ; Oxidative Stress ; *Fermented Foods ; Humans ; Male ; Mice ; Liver/metabolism ; *Colitis/complications ; Multiomics ; }, abstract = {Liver disorders are the most prevalent extraintestinal manifestations observed in patients with ulcerative colitis, impacting millions of individuals worldwide. The present study elucidated the novel role of Eurotium cristatum (E. cristatum) -fermented thinned young apples (E.YAP) in preventing colitis associated liver disorders and dissected potential mechanisms through multi-omics integration. Specifically, E.YAP exhibited superior efficacy in alleviating colitis symptoms, liver damage, lipid accumulation, inflammation cytokines and oxidative stress, compared to the unfermented sample and the anti-colitis drug mesalazine. Hepatic transcriptomics demonstrated that E.YAP suppressed genes belonging to the cytochrome P450 family, CXC chemokine ligands and pro-inflammatory cytokines while enhancing PPAR signaling and oxidative phosphorylation. E.YAP exclusively elevated hepatic levels of metabolites involved in glycerophospholipid metabolism, linoleic acid metabolism, biosynthesis of unsaturated fatty acids and glutathione metabolism, whereas suppressing urobilin, a microbial metabolite implicated in fatty liver disease. Moreover, E.YAP increased α-diversity and relative abundances of Lactobacillus, Akkermansia, Muribaculum, Blautia and Faecalibaculum, concurrently increasing short-chain fatty acids. Multi-omics integration revealed robust links between E.YAP- affected hepatic genes, metabolites and gut bacteria that were associated with liver health. Furthermore, E.YAP outperformed unfermented samples in mitigating palmitic acid-induced inflammation, dyslipidemia and ROS overproduction in HepG2 cells. Additionally, network pharmacology identified key metabolites enriched by E. cristatum fermentation, particularly flavonoids, polyphenols and indole derivatives, which may synergistically inhibit hepatic inflammation and oxidative stress. Collectively, our study establishes the novel function of E.YAP in preventing colitis associated liver disorders, providing a sustainable strategy to valorize apple thinning waste into functional foods.}, }
@article {pmid41072345, year = {2026}, author = {Liu, D and Yuan, J and Ren, P and Shi, L and Zhu, Z and Zhang, C and Dong, H and Liu, D}, title = {Electrochemical ammonia recovery from wastewater: The critical roles of electrode engineering toward scale-up.}, journal = {Water research}, volume = {288}, number = {Pt B}, pages = {124708}, doi = {10.1016/j.watres.2025.124708}, pmid = {41072345}, issn = {1879-2448}, mesh = {*Ammonia ; *Wastewater/chemistry ; Electrodes ; *Electrochemical Techniques ; Waste Disposal, Fluid/methods ; Water Purification/methods ; }, abstract = {Ammonia is indispensable for producing fertilizers that sustain the global population, yet its agricultural application contributes significantly to water pollution. Electrochemical technologies offer a renewable-energy-driven and chemical-free pathway for recovering ammonia directly from wastewater, representing a critical step toward a circular nitrogen economy and net-zero emissions in the wastewater sector. Nevertheless, translating lab-scale advances to industrialization remains constrained by technological hurdles. Emerging electrode-engineering strategies promise scalable, membrane-less electrochemical systems, but a systematic and comparative assessment is lacking. In this review, we first present the electrochemical ammonia recovery pathway and elucidate the mechanisms of various electrode materials in this process. Secondly, we critically evaluate state-of-the-art scalable electrode systems for electrochemical ammonia recovery. Thirdly, we comparatively analyze the ammonia recovery performance at both the electrode-material and electrode-system levels, comprehensively discussing the current challenges and future research opportunities toward technological scale-up. Finally, we outline key research targets toward next-generation electrochemical engineering for sustainable ammonia recovery and wastewater treatment.}, }
@article {pmid41070750, year = {2025}, author = {Seah, BKB}, title = {Database Release: PPSDB, a Linked Open Data Knowledge Base for Protist-Prokaryote Symbioses.}, journal = {The Journal of eukaryotic microbiology}, volume = {72}, number = {6}, pages = {e70049}, pmid = {41070750}, issn = {1550-7408}, mesh = {*Symbiosis ; *Eukaryota/physiology/classification/genetics ; *Knowledge Bases ; *Archaea/physiology/genetics ; *Databases, Factual ; *Prokaryotic Cells/physiology ; *Bacteria/genetics/classification ; Software ; }, abstract = {As the ecological and evolutionary importance of symbiotic interactions between protists (microbial eukaryotes) and prokaryotes (bacteria and archaea) is better appreciated, keeping an overview of their diversity and the literature becomes a growing and ongoing challenge. Here I present the Protist-Prokaryote Symbiosis Database (PPSDB), comprising 1146 manually curated interaction statements sourced from 443 publications, where biological taxonomy, anatomical localization, and analytical methods applied have been annotated and mapped to external databases and ontologies, such as Wikidata, NCBI Taxonomy, and Gene Ontology. I describe how its data model deals practically with challenges such as incomplete information and inconsistent taxon concepts, which will be applicable to similar projects. Both the model and underlying Wikibase software platform are highly extensible, so new items and properties can easily be added. Unlike a static table or list of citations, PPSDB is a structured knowledge base that enables programmatic access and powerful, integrated semantic queries. The database is available at https://ppsdb.wikibase.cloud/.}, }
@article {pmid41070261, year = {2025}, author = {Câmara, J and de Aguiar, SC and Paulino, T and Faria, AL and Bermúdez I Badia, S and Vilar, M and Fermé, E}, title = {Comparing adaptive tablet-based cognitive training and paper-and-pencil cognitive training: a pilot randomized controlled trial with community-dwelling stroke survivors.}, journal = {International journal of clinical and health psychology : IJCHP}, volume = {25}, number = {3}, pages = {100627}, pmid = {41070261}, issn = {2174-0852}, abstract = {INTRODUCTION: This study explored the feasibility and the preliminary efficacy of adaptive tablet-based cognitive training (CT) and paper-and-pencil CT approaches for mitigating multidomain post-stroke cognitive and noncognitive deficits.<br><br>METHODS: In this two-arm pilot randomized controlled trial, participants were randomly assigned to the NeuroAIreh@b (NAIr; adaptive tablet-based CT inspired by activities of daily living) and the Task Generator (TG; adaptive paper-and-pencil CT). A non-randomized passive control group was recruited for comparative purposes. Interventions comprised 12 bi-weekly 30-minute sessions. Primary outcomes explored training effects on several cognitive (e.g., global cognition, episodic memory), and noncognitive domains (e.g., quality of life, functional abilities).<br><br>RESULTS: A total of 20 participants were randomized (NAIr: n = 10; TG = 10). Within-group analysis revealed that the NAIr group presented significant improvements in more cognitive domains than the TG, and reported less functional disability, increased quality of life and greater motivation for rehabilitation at post-intervention. At follow-up, the NAIr group further improved in several cognitive domains and reported greater quality of life, while TG only improved in global cognition. Between-group analysis exhibited a pattern of superior performance in the adaptive CT groups over passive controls.<br><br>CONCLUSIONS: Findings suggest that adaptive CT interventions are feasible to implement and lead to cognitive and noncognitive improvements in community-dwelling stroke survivors. However, while both training approaches yield different short and medium/long-term benefits, the NAIr - a more ecologically valid method - was the only to promote generalization of training effects to functionality and quality of life at post-intervention and three-month follow-up, respectively.<br><br>TRIAL REGISTRATION: The trial is registered at ClinicalTrials.gov, number NCT05929287. Registered July 3rd, 2023 (cf. https://classic.clinicaltrials.gov/ct2/show/NCT05929287).}, }
@article {pmid41066464, year = {2025}, author = {O'Neill, X and White, A and Northrup, GR and Saad-Roy, CM and White, PS and Boots, M}, title = {Superspreading and the evolution of virulence.}, journal = {PLoS computational biology}, volume = {21}, number = {10}, pages = {e1013517}, pmid = {41066464}, issn = {1553-7358}, mesh = {Virulence/genetics ; Humans ; *COVID-19/transmission/epidemiology/virology ; *SARS-CoV-2/pathogenicity/genetics ; Animals ; *Biological Evolution ; Computer Simulation ; Computational Biology ; Host-Pathogen Interactions ; Models, Biological ; }, abstract = {Superspreading, where a small proportion of a population can cause a high proportion of infection transmission, is well known to be important to the epidemiology of a wide range of pathogens, including SARS-CoV-2. However, despite its ubiquity in important human and animal pathogens, the impact of superspreading on the evolution of pathogen virulence is not well understood. Using theory and both deterministic and stochastic simulations we examine the evolution of pathogen virulence under a range of different distributions of infection transmission for the host. Importantly, for many pathogens, superpreader events may be associated with increased tolerance to infection or asymptomatic infection and when we account for this superspreading selects for higher virulence. In contrast, in animal populations where highly connected individuals, that are linked to superspreader events, also have fitness benefits, superspreading may select for milder pathogens. In isolation, the transmission distribution of the host does not impact selection for pathogen virulence. However, superspreading reduces the rate of pathogen evolution and generates considerable variation in pathogen virulence. Therefore, the adaptation of an emerging infectious disease, that exhibits superspreading, is likely to be slowed and characterised by the maintenance of maladaptive variants. Taken as a whole, our results show that superspreading can have important impacts on the evolution of pathogens.}, }
@article {pmid41064473, year = {2024}, author = {Boyes, D and Boyes, C and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Pale Oak Beauty, Hypomecis punctinalis (Scopoli, 1763).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {531}, pmid = {41064473}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Hypomecis punctinalis (the Pale Oak Beauty; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 741.20 megabases. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.64 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,897 protein-coding genes.}, }
@article {pmid41063758, year = {2025}, author = {Sivell, O and Sivell, D and Mitchell, R and Webb, JA and Falk, S and ,  and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of a snipefly, Rhagio lineola Fabricius, 1794.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {154}, pmid = {41063758}, issn = {2398-502X}, abstract = {We present a genome assembly from a male specimen of Rhagio lineola (snipefly; Arthropoda; Insecta; Diptera; Rhagionidae). The genome sequence has a total length of 1,654.96 megabases. Most of the assembly (97.13%) is scaffolded into 5 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled, with a length of 16.64 kilobases.}, }
@article {pmid41063755, year = {2025}, author = {Boyes, D and Boyes, C and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Treble Lines, Charanyca trigrammica (Hufnagel, 1766) (Lepidoptera: Noctuidae).}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {520}, pmid = {41063755}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Charanyca trigrammica (Treble Lines; Arthropoda; Insecta; Lepidoptera; Noctuidae). The assembly contains two haplotypes with total lengths of 546.43 megabases and 546.58 megabases. Most of haplotype 1 (99.97%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 15.44 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.}, }
@article {pmid41061883, year = {2025}, author = {de Oliveira, FG and Palmeiro, AS and Brito, PEM and Motta, WG and Cestari, MM and de Assis, HCDS and Dos Santos, LD}, title = {Environmental assessment of three southern Brazilian rivers using an integrated biomarker response index in Hypostomus ancistroides applied to GIS.}, journal = {Environmental research}, volume = {286}, number = {Pt 3}, pages = {123028}, doi = {10.1016/j.envres.2025.123028}, pmid = {41061883}, issn = {1096-0953}, mesh = {Animals ; Brazil ; Rivers/chemistry ; *Environmental Monitoring/methods ; *Catfishes/metabolism ; *Water Pollutants, Chemical/analysis/toxicity ; Biomarkers/metabolism/analysis ; Geographic Information Systems ; Oxidative Stress ; }, abstract = {This study evaluated the effects of contaminants, particularly metals and pesticides, in three rivers in Southern Brazil - São Camilo, Santa Fé, and Pioneiro - using the catfish Hypostomus ancistroides as a bioindicator. Biomarkers of oxidative stress, neurotoxicity, and genotoxicity were employed and integrated into an Integrated Biomarker Response (IBR) index, spatial analysis conducted using Geographic Information Systems (GIS). Sampling occurred during two seasons, winter (2022) and summer (2023), with sediments and fish collected from three sites per river. Detected concentrations of metals, including Cu, Zn, K, and Mn, were below Brazilian regulatory thresholds. Biomarker responses revealed significant biological effects associated with oxidative stress, particularly at intermediate and downstream sites. These included acetylcholinesterase inhibition, increased activity of superoxide dismutase (SOD) and catalase (CAT), elevated levels of metallothionein's (MET) and lipid peroxidation (LPO), indicating neurotoxicity and oxidative damage. Site SF2 (Santa Fé River) exhibited the greatest impact, likely due to the urban and industrial influences. Nuclear morphological alterations revealed localized genotoxic effects. Despite the low contaminant levels, the results highlight notable sublethal effects on fish health and ecological integrity. The integration of biomarkers proved effective in identifying critical areas and informing environmental management strategies.}, }
@article {pmid41061878, year = {2025}, author = {William, G and Qadir, A and Saqib, Z}, title = {Urbanization and pollution pressures drive functional homogenization in bird feeding guilds.}, journal = {Environmental research}, volume = {286}, number = {Pt 3}, pages = {123029}, doi = {10.1016/j.envres.2025.123029}, pmid = {41061878}, issn = {1096-0953}, mesh = {*Urbanization ; *Environmental Pollution/statistics &amp; numerical data ; Ecosystem ; Animals ; *Birds/physiology ; Pakistan ; Feeding Behavior/physiology ; Biodiversity ; }, abstract = {Urbanization and pollution are rapidly transforming ecosystems across the Global South, yet their impacts on functional biodiversity remain underexplored. Birds, as ecologically diverse and responsive taxa, are valuable indicators of environmental change and functional simplification. We examined how urbanization and pollution jointly influence the functional structure of avian communities across an urban-rural gradient in Sialkot District, a rapidly industrializing region of northeastern Pakistan. Using standardized point counts across 18 sites stratified by urban intensity and pollution levels, we quantified bird community composition and feeding guilds. We applied multidimensional indices of functional diversity (FRic, FEve, FDis, RaoQ) and ordination methods to assess trait-based filtering. Functional richness and divergence contracted markedly with increasing pollution and urbanization. Functionally specialized guilds particularly insectivores, piscivores, and carnivores were absent from the most polluted urban sites, which were dominated by ecological generalists such as omnivores and scavengers. Trait dissimilarity and redundancy declined sharply with pollution, and ordination revealed clear guild turnover along the pollution gradient, indicating homogenization of trophic roles. Functional evenness and dispersion showed weaker responses, suggesting selective persistence of a few tolerant guilds in urban cores. Feeding guild richness also declined with pollution, reflecting a strong loss of trophic diversity under anthropogenic stress. These findings provide rare empirical evidence from South Asia linking environmental contamination to multidimensional losses of avian functional diversity. By integrating trait-based metrics with ecological gradients, this study highlights the need to incorporate functional indicators into conservation planning, particularly in rapidly urbanizing regions where ecological data remain limited.}, }
@article {pmid41057836, year = {2025}, author = {Rangachari, P and Al Arkoubi, K and Shindi, R}, title = {A multi-level framework for advancing digital health equity in learning health systems: aligning practice and theory with the Quintuple Aim.}, journal = {International journal for equity in health}, volume = {24}, number = {1}, pages = {253}, pmid = {41057836}, issn = {1475-9276}, mesh = {Humans ; *Health Equity/standards ; *Learning Health System/organization &amp; administration ; Social Determinants of Health ; Electronic Health Records ; Digital Health ; }, abstract = {Achieving digital health equity is essential to realizing the transformative goals of the Quintuple. Aim: optimizing patient experience, improving population health, supporting provider well-being, reducing costs, and advancing health equity. Yet significant disparities persist in access to digital tools, driven by both traditional and digital social determinants of health (SDOH), such as housing instability and limited broadband access. Health system responses often focus on downstream interventions to meet immediate needs, such as referrals for housing assistance or smartphone distribution, while upstream strategies, like partnerships to expand access to affordable housing or advocacy to improve broadband access, remain underutilized. Similarly, targeted tools for specific populations often lack corresponding universal strategies like digital literacy campaigns. The absence of systematic Electronic Health Record (EHR) integration of SDOH data further limits health systems' ability to identify disparities, tailor interventions, and support structural change. This paper introduces a theoretically grounded, multi-level framework for advancing digital health equity within Learning Health Systems (LHS). Drawing on insights from information systems theories, socio-ecological models, organizational learning, implementation science, and systems thinking, the framework supports alignment of equity-centered strategies across micro- (individual), meso- (organizational), and macro- (policy) levels. The framework is organized around three strategic domains: (1) building equity-driven data infrastructure through SDOH-EHR integration, (2) designing scalable, equity-centered interventions that balance targeted and universal approaches, and (3) leveraging strategic starting points to transition from downstream efforts to upstream reforms. Grounded in the U.S. context yet informed by international evidence, this framework offers a roadmap for aligning theory and practice to advance digital health equity in LHS. It is both actionable and adaptable, translating evidence and theory into a structured approach that healthcare systems can use to guide health equity initiatives. It illustrates how SDOH data can inform person-centered care, how targeted tools like multilingual telehealth apps can be integrated with universal strategies such as digital literacy campaigns, and how enabling services, community partnerships, and policy advocacy can catalyze longer-term structural reforms. Emphasizing continuous learning through feedback loops and multi-level alignment, the framework equips stakeholders to embed equity into LHS design and function, ultimately advancing sustainable progress toward the Quintuple Aim.}, }
@article {pmid41056132, year = {2025}, author = {Kourtesis, P and Lizarraga, A and MacPherson, SE}, title = {Immersive virtual reality assessments of working memory and psychomotor skills: A comparison between immersive and non-immersive assessments.}, journal = {Journal of neuropsychology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jnp.70014}, pmid = {41056132}, issn = {1748-6653}, abstract = {OBJECTIVE: Immersive virtual reality (VR) enhances ecological validity and facilitates intuitive and ergonomic hand interactions for performing neuropsychological assessments. However, its comparability to traditional computerized methods remains unclear. This study investigates the convergent validity, user experience and usability of VR-based versus PC-based assessments of short-term and working memory, as well as psychomotor skills, while also examining how demographic and IT-related skills influence performance in both modalities.<br><br>METHODS: Sixty-six participants performed the Digit Span Task (DST), Corsi Block Task (CBT) and Deary-Liewald Reaction Time Task (DLRTT) in both VR- and PC-based formats. Participants' experience in using computers and smartphones, and playing videogames, was considered. User experience and system usability of the formats were also evaluated.<br><br>RESULTS: While performance on DST was similar across modalities, PC assessments enabled better performance on CBT and faster reaction times in DLRTT. Significant correlations between VR and PC versions supported convergent validity. Regression analyses revealed that performance on PC versions was influenced by computing and gaming experience, whereas performance on VR versions was largely independent of these factors, except for gaming experience predicting performance on CBT backward recall. Moreover, VR assessments received higher ratings for user experience and usability than PC-based assessments.<br><br>CONCLUSION: Immersive VR assessments provide an engaging alternative to traditional computerized methods, with minimal reliance on prior IT experience and demographic factors. This resilience to individual differences suggests that VR may offer a more equitable and accessible platform for automated cognitive assessment. Future research should explore the long-term reliability of VR-based assessments.}, }
@article {pmid41053825, year = {2025}, author = {Villette, R and Ortís Sunyer, J and Novikova, PV and Aho, VTE and Petrov, VA and Hickl, O and Busi, SB and De Rudder, C and Kunath, BJ and Heintz-Buschart, A and Trezzi, JP and Halder, R and Jäger, C and Lebrun, LA and Daujeumont, A and Schade, S and Janzen, A and Jehmlich, N and von Bergen, M and Laczny, CC and May, P and Trenkwalder, C and Oertel, W and Mollenhauer, B and Wilmes, P}, title = {Integrated multi-omics highlights alterations of gut microbiome functions in prodromal and idiopathic Parkinson's disease.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {200}, pmid = {41053825}, issn = {2049-2618}, support = {863664//HORIZON EUROPE European Research Council/ ; PRIDE/11823097//Fonds National de la Recherche Luxembourg/ ; CORE/16/BM/11333923//Fonds National de la Recherche Luxembourg/ ; CORE/15/BM/10404093//Fonds National de la Recherche Luxembourg/ ; FNR11264123//Fonds National de la Recherche Luxembourg/ ; MJFF-019228//Michael J. Fox Foundation for Parkinson's Research/ ; MCI-BIOME_2019//Institute for Advanced Studies, Universit&#xe9; of Luxembourg/ ; 101038088//European Union's Horizon 2020 Widening Fellowships/ ; INTER/DFG/19/14429377//DFG Research Unit FOR2488/ ; }, mesh = {*Parkinson Disease/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; *Metabolomics/methods ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Male ; Female ; Middle Aged ; Aged ; Feces/microbiology ; Metabolome ; Prodromal Symptoms ; Multiomics ; }, abstract = {BACKGROUND: Parkinson's disease (PD) is associated with gut microbiome shifts. These shifts are mainly described at taxonomic level, but the functional consequences remain unclear. To obtain insight into the functional disruptions of the gut microbiome in PD, we used an integrated multi-omics approach, comparing gut microbiomes of individuals with PD, prodromal PD, and healthy controls.<br><br>RESULTS: Meta-metabolomics, the most discriminatory and robust omics&#xa0;level, was selected to Guide the analysis. We identified 11 metabolites that were differentially abundant between the groups, among which &#x3b2;-glutamate was increased in PD and prodromal PD, and correlated with the transcriptional activities of Methanobrevibacter smithii and Clostridium spp. We identified decreases in transcripts, but not in gene abundances, related to glutamate metabolism, bile acids biosynthesis, chemotaxis, and flagellar assembly in PD, particularly in keystone genera such as Roseburia, Agathobacter, and Blautia. Our findings, integrated into the Expobiome map, reveal multifactorial microbiome alterations which converge with PD pathways.<br><br>CONCLUSION: Our study highlights the apparent disruption of microbial gene expression in PD, particularly in genes associated to mobility. Moreover, we showcase the importance of investigating the gut microbiome's functional dimensions to better resolve microbiome-host interactions in health and disease.}, }
@article {pmid41053814, year = {2025}, author = {Huebner, C and Huebner, NO and Goerig, T and Flessa, S}, title = {A regional One Health approach to mapping antimicrobial resistance interactions via systems thinking.}, journal = {One health outlook}, volume = {7}, number = {1}, pages = {46}, pmid = {41053814}, issn = {2524-4655}, abstract = {BACKGROUND: Antimicrobial resistance (AMR), as an original One Health problem, combines inextricable interactions between the human, animal and environmental dimensions. Addressing this challenge requires systemic thinking and coordinated networking between different levels of society and regional institutions. Knowledge of causal relationships, their mutual influence and the ability to assess the impact of possible interventions are prerequisites for coherent action to combat the further spread of antimicrobial resistance in a region. An integrated regional approach has not yet been addressed in One Health research on antimicrobial resistance.<br><br>METHODS: This study is based on a systems thinking approach and uses a causal loop diagram to visualise the relationships between human, animal and ecological components in a circular AMR system map for a One Health model region. The participatory approach actively involved regional stakeholders in the data collection and modelling process through surveys, semi structured interviews and interactive workshops. Based on the developed causal loop diagram, leverage point analysis is applied to estimate which types of interventions would have the greatest ability to address antimicrobial resistance in the One Health region.<br><br>RESULTS: Our results show that the system mapping tool is suitable for demonstrating the relationships regarding AMR in the One Health context for a defined region. It provides an opportunity to identify and visualise important risk factors that are direct or indirect drivers of AMR. Specifically, two amplifying and two balancing loops have been constructed in the model, covering antibiotic stewardship, public awareness, regional data management and environmental impact. Interdisciplinary and intersectoral collaboration, homogeneity of data and public awareness were identified as important leverage points. The graphical illustration of the causal loop diagram enables political and economic decision-makers to develop a deeper understanding of regional resistance patterns and the rational use of antibiotics from a One Health perspective.<br><br>CONCLUSION: This study is one of the first applications of a participatory systems thinking approach to the topic of AMR in the context of a One Health region.<br><br>TRAIL REGISTRATION: Not applicable.}, }
@article {pmid41052276, year = {2025}, author = {Sherwani, MK and Ruuskanen, MO and Feldner-Busztin, D and Nisantzis Firbas, P and Boza, G and Móréh, &#xc1; and Borman, T and Putu Erawijantari, P and Scheuring, I and Gopalakrishnan, S and Lahti, L}, title = {Multi-omics time-series analysis in microbiome research: a systematic review.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {5}, pages = {}, pmid = {41052276}, issn = {1477-4054}, support = {952914//European Union's Horizon 2020 research and innovation programme/ ; }, mesh = {*Microbiota ; Humans ; *Computational Biology/methods ; Machine Learning ; *Genomics/methods ; Multiomics ; }, abstract = {Recent developments in data generation have opened up unprecedented insights into living systems. It has been recognized that integrating and characterizing temporal variation simultaneously across multiple scales, from specific molecular interactions to entire ecosystems, is crucial for uncovering biological mechanisms and understanding the emergence of complex phenotypes. With the increasing number of studies incorporating multi-omics data sampled over time, it has become clear that integrated approaches are pivotal for these efforts. However, standard data analytical practices in longitudinal multi-omics are still shaping up and many of the available methods have not yet been widely evaluated and adopted. To address this gap, we performed the first systematic literature review that comprehensively categorizes, compares, and evaluates computational methods for longitudinal multi-omics integration, with a particular emphasis on four categories of the studies: (i) host and host-associated microbiome studies, (ii) microbiome-free host studies, (iii) host-free microbiome studies, and (iv) methodological framework studies. Our review highlights current methodological trends, identifies widely used and high-performing frameworks, and assesses each method across performance, interpretability, and ease of use. We further organize these methods into thematic groups-such as statistical modeling, machine learning, dimensionality reduction, and latent factor approaches-to provide a clear roadmap for future research and application. This work offers a critical foundation for advancing integrative longitudinal data science and supporting reproducible, scalable analysis in this rapidly evolving field.}, }
@article {pmid41052097, year = {2025}, author = {Teitelbaum, CS and Casazza, ML and Overton, CT and Matchett, EL and Prosser, DJ}, title = {Host responses and viral traits interact to shape the impacts of climate warming on highly pathogenic avian influenza in migratory waterfowl.}, journal = {PLoS computational biology}, volume = {21}, number = {10}, pages = {e1013451}, pmid = {41052097}, issn = {1553-7358}, mesh = {Animals ; *Influenza in Birds/virology/epidemiology/transmission ; *Animal Migration ; *Climate Change ; Disease Outbreaks ; *Influenza A virus/pathogenicity ; Birds/virology ; Models, Biological ; Computational Biology ; Computer Simulation ; Host-Pathogen Interactions ; Animals, Wild/virology ; }, abstract = {Emerging infectious diseases pose threats to wildlife populations, as exemplified by recent outbreaks of avian influenza viruses in wild birds. Climate change can affect infection dynamics in wildlife through direct effects on pathogens (e.g., environmental decay rates) and changes to host ecology, including shifting migration patterns. Here, we adapt an existing mechanistic model that couples migration and infection to study how traits of highly pathogenic avian influenza (HPAI) viruses contribute to HPAI outcomes in migratory waterfowl, then apply this model to explore potential impacts of climate change on HPAI dynamics. We find that the simulated impacts of HPAI on the host population under baseline climate conditions varied from no impact to 100% mortality, depending on viral traits. In most cases, traits related to transmission (i.e., contact rates, shedding rates) were more important for HPAI establishment probability, infection prevalence, and mortality than were other viral traits (e.g., environmental temperature sensitivity, cross-protective immunity). We then simulated the effects of climate change (i.e., altered temperature regimes) on HPAI dynamics both via viral environmental decay and via changes in bird migration phenology. In these simulations, we found that a 9-day advancement in spring migration timing increased the duration of HPAI outbreaks by increasing time birds spent at their breeding grounds, leading to higher mortality and fewer infections. In contrast, increased viral decay in warmer years had a smaller, but opposite impact. These patterns depended on the primary transmission mode of HPAI (i.e., direct vs. environmental) and its sensitivity to environmental temperatures. Together, these results suggest that climate change is likely to increase the impacts of HPAI on waterfowl populations if HPAI relies strongly on direct transmission and birds advance their spring migration. Further integrating host-viral co-evolution and other climatic changes (e.g., salinity, humidity) could provide more precise predictions of how HPAI dynamics could change in the future.}, }
@article {pmid41047667, year = {2025}, author = {Liang, S and Wang, W and Tan, C and Zhou, L and Ou, Z and Qu, Y}, title = {Multi-omics analysis reveals the potential role of MbDDC in tissue-specific alkaloid biosynthesis and distribution in Meconopsis betonicifolia.}, journal = {The Plant journal : for cell and molecular biology}, volume = {124}, number = {1}, pages = {e70515}, doi = {10.1111/tpj.70515}, pmid = {41047667}, issn = {1365-313X}, support = {32160404//National Natural Science Foundation of China/ ; 31460218//National Natural Science Foundation of China/ ; 202501BD070001-084//Yunnan Fundamental Research Projects- the General Program of the Agriculture Joint Special Project/ ; YNWR-QNBJ-2019-211//Ten Thousand Talent Plans for Young Top-notch Talents of Yunnan Province/ ; 2025Y0844//Scientific Research Fund Project of Yunnan Provincial Department of Education/ ; }, mesh = {*Alkaloids/biosynthesis/metabolism ; *Plant Proteins/metabolism/genetics ; Plant Roots/metabolism ; Plant Leaves/metabolism ; Gene Expression Regulation, Plant ; Nicotiana/metabolism/genetics ; Flowers/metabolism ; Plant Stems/metabolism ; Metabolomics ; Transcriptome ; Multiomics ; Papaveraceae ; }, abstract = {Plants of the Meconopsis (Meconopsis spp.), endemic to the Qinghai-Tibet Plateau, are prized in traditional Tibetan medicinal herbs for their bioactive alkaloids, particularly their antispasmodic and analgesic properties. To elucidate the mechanisms underlying tissue-specific alkaloid accumulation in Meconopsis betonicifolia, we integrated metabolomic and transcriptomic analyses across four organs (roots, stems, leaves, and flowers) and functionally characterized the rate-limiting enzyme MbDDC-3. Our results demonstrate that roots are the primary site of alkaloid accumulation, with codeinone and salutaridine identified as key intermediates in the isoquinoline pathway. Eleven differentially expressed genes (DEGs) were strongly correlated with these metabolites. Heterologous overexpression of MbDDC-3 in tobacco (Nicotiana tabacum) significantly increased total alkaloid by 274% in roots (P < 0.05), with (S)-cis-N-methylstylopine and its precursors (tyramine/dopamine) significantly enriched. Notably, MbDDC-3 protein contains a non-classical nuclear localization signal (NLS)-RLKPAAIFNRKLG-located near its C-terminal region and exhibits key residue substitutions compared to lowland species, suggesting adaptive evolution under high-altitude stress. Collectively, this study reveals how M. betonicifolia optimizes alkaloid distribution for ecological fitness, while offering a genetic tool for metabolic engineering of medicinal alkaloids.}, }
@article {pmid41047562, year = {2025}, author = {Takata, K and Ogawa, M and Takahashi, T}, title = {Temporal Trends and Determinants of Low-Dose Estrogen-Progestin Prescription in Japan During 2014-2022: An Ecological Study Using a Nationwide Claims Database.}, journal = {The journal of obstetrics and gynaecology research}, volume = {51}, number = {10}, pages = {e70093}, doi = {10.1111/jog.70093}, pmid = {41047562}, issn = {1447-0756}, support = {24K13368//Japan Society for the Promotion of Science/ ; }, mesh = {Female ; Humans ; Adult ; Middle Aged ; Adolescent ; Japan ; Young Adult ; Child ; *Estrogens/administration &amp; dosage ; *Progestins/administration &amp; dosage ; Databases, Factual ; *Drug Prescriptions/statistics &amp; numerical data ; *Practice Patterns, Physicians'/statistics &amp; numerical data/trends ; *Estrogen Replacement Therapy/trends/statistics &amp; numerical data ; }, abstract = {AIM: This study aimed to evaluate the trends and regional disparities in low-dose estrogen-progestin (LEP) prescription in Japan from 2014 to 2022 and the factors contributing to these disparities.<br><br>METHODS: LEP prescription data were obtained from the National Health Insurance Claims and Specific Health Examination Database; the prescriptions per 1000 women aged 10-54&#x2009;years were calculated. Trends were analyzed in terms of the overall volume, age group distribution, and formulation type. The regional distribution in 2022 was also examined; the factors influencing regional differences were identified using multiple regression analysis.<br><br>RESULTS: LEP prescriptions showed a significant annual increase (p&#x2009;<&#x2009;0.05), rising approximately five-fold over 9&#x2009;years. A significant increase was observed in all age groups, except for those in their 50s (p&#x2009;<&#x2009;0.05). Ethinylestradiol 0.035&#x2009;mg/norethisterone 1&#x2009;mg (p&#x2009;<&#x2009;0.005) and ethinylestradiol 0.02&#x2009;mg/drospirenone 3&#x2009;mg (cyclic dosing regimen) (p&#x2009;<&#x2009;0.001) usage declined. Conversely, ethinylestradiol 0.02&#x2009;mg/drospirenone 3&#x2009;mg (continuous dosing regimen) and ethinylestradiol 0.02&#x2009;mg/levonorgestrel 0.09&#x2009;mg usage increased significantly (p&#x2009;<&#x2009;0.05). In 2022, regional disparities in LEP prescriptions reached a maximum of 2.7-fold. These disparities were not associated with the number of obstetricians and gynecologists and women's health specialists. However, the prescription of EE 0.02&#x2009;mg/drospirenone 3&#x2009;mg (continuous dosing regimen) showed a significant association with the number of women's health specialists (p&#x2009;=&#x2009;0.002).<br><br>CONCLUSION: This study provides the first comprehensive analysis of real-world LEP prescription patterns in Japan, revealing significant regional disparities.}, }
@article {pmid41047557, year = {2025}, author = {Rausch, P and Ratjen, I and Tittmann, L and Enderle, J and Wacker, EM and Jaeger, K and Rühlemann, MC and Franzpötter, K and Ellul, P and Kruse, R and Halfvarson, J and Roggenbuck, D and Ellinghaus, D and Jacobs, G and Krawczak, M and Schreiber, S and Bang, C and Lieb, W and Franke, A}, title = {First insights into microbial changes within an Inflammatory Bowel Disease Family Cohort study.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2559119}, pmid = {41047557}, issn = {1949-0984}, mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/epidemiology ; Male ; Female ; Adult ; *Bacteria/classification/isolation &amp; purification/genetics ; *Dysbiosis/microbiology ; Prospective Studies ; *Gastrointestinal Microbiome ; Middle Aged ; Cohort Studies ; Feces/microbiology ; Germany/epidemiology ; Young Adult ; }, abstract = {The prospective Kiel Inflammatory Bowel Disease (IBD) Family Cohort Study (KINDRED cohort) was initiated in 2013 to systematically and extensively collect data and biosamples from index IBD patients and their relatives, a population at high risk for IBD development. Regular follow-ups were conducted to collect updated health and lifestyle information, to obtain new biosamples, and to capture the incidence of IBD during development. By combining microbial data collected at successive time points with extensive anthropometric, medical, nutritional, and social information, this study aimed to characterize the factors influencing the microbiota in health and disease via detailed ecological analyses. Using a microbial dysbiosis metric based on the German KINDRED cohort, we identified strong and generalizable gradients within and across different external IBD cohorts for validation. These community gradients correspond strongly with IBD pathologies, physiological manifestations of inflammation (e.g. Bristol stool score, ASCA IgA, ASCA IgG), and genetic risk for IBD. Anthropometric and medical factors influencing fecal transit time strongly modify bacterial communities. Various Enterobacteriaceae (e.g. Klebsiella sp.) and opportunistic Clostridia pathogens (e.g. C. XIVa clostridioforme), characterize in combination with ectopically colonizing oral taxa (e.g. Veillonella sp. Cand. Saccharibacteria sp. Fusobacterium nucleatum) the distinct and chaotic IBD-specific communities. Weak community and physiological changes are further traceable in a small number of individuals, who developed IBD in the study's runtime. Our findings demonstrate broad-scale ecological patterns which indicate drastic state transitions of communities in IBD patients. These patterns appear to be universal across cohorts and influence physiological signs of inflammation, display increased resilience, but show only limited heritability/intrafamily transmission.}, }
@article {pmid41042793, year = {2025}, author = {Du, H and Zahn, MV and Loo, SL and Alleman, TW and Truelove, S and Patenaude, B and Gardner, LM and Papageorge, N and Hill, AL}, title = {Improving policy design and epidemic response using integrated models of economic choice and disease dynamics with behavioral feedback.}, journal = {PLoS computational biology}, volume = {21}, number = {10}, pages = {e1013549}, pmid = {41042793}, issn = {1553-7358}, mesh = {Humans ; *COVID-19/epidemiology/economics/transmission/prevention &amp; control ; Pandemics/economics ; SARS-CoV-2 ; Choice Behavior ; Decision Making ; *Policy Making ; Computational Biology ; *Health Policy ; }, abstract = {Human behavior plays a crucial role in infectious disease transmission, yet traditional models often overlook or oversimplify this factor, limiting predictions of disease spread and the associated socioeconomic impacts. Here we introduce a feedback-informed epidemiological model that integrates human behavior with disease dynamics in a credible, tractable, and extendable manner. From economics, we incorporate a dynamic decision-making model where individuals assess the trade-off between disease risks and economic consequences, and then link this to a risk-stratified compartmental model of disease spread taken from epidemiology. In the unified framework, heterogeneous individuals make choices based on current and future payoffs, influencing their risk of infection and shaping population-level disease dynamics. As an example, we model disease-decision feedback during the early months of the COVID-19 pandemic, when the decision to participate in paid, in-person work was a major determinant of disease risk. Comparing the impacts of stylized policy options representing mandatory, incentivized/compensated, and voluntary work abstention, we find that accounting for disease-behavior feedback has a significant impact on the relative health and economic impacts of policies. Including two crucial dimensions of heterogeneity-health and economic vulnerability-the results highlight how inequities between risk groups can be exacerbated or alleviated by disease control measures. Importantly, we show that a policy of more stringent workplace testing can potentially slow virus spread and, surprisingly, increase labor supply since individuals otherwise inclined to remain at home to avoid infection perceive a safer workplace. In short, our framework permits the exploration of avenues whereby health and wealth need not always be at odds. This flexible and extendable modeling framework offers a powerful tool for understanding the interplay between human behavior and disease spread.}, }
@article {pmid41042792, year = {2025}, author = {Chapman, D and Occhibove, F and Bullock, JM and Beck, PSA and Navas-Cortes, JA and White, SM}, title = {Modelling plant disease spread and containment: Simulation and approximate Bayesian Computation for Xylella fastidiosa in Puglia, Italy.}, journal = {PLoS computational biology}, volume = {21}, number = {10}, pages = {e1013539}, pmid = {41042792}, issn = {1553-7358}, mesh = {*Xylella/pathogenicity/physiology ; *Plant Diseases/microbiology/statistics &amp; numerical data/prevention &amp; control ; Italy ; Bayes Theorem ; Computer Simulation ; Disease Outbreaks ; *Models, Biological ; Olea/microbiology ; Computational Biology ; }, abstract = {Mathematical and computational models play a crucial role in understanding the epidemiology of economically important plant disease outbreaks, and in evaluating the effectiveness of surveillance and disease management measures. A case in point is Xylella fastidiosa, one of the world's most deadly plant pathogens. Since its European discovery in olives in Puglia, Italy in 2013, there remain key knowledge gaps that undermine landscape-scale containment efforts of the outbreak, most notably concerning the year of introduction, the rate of spread, dispersal mechanisms and control efficacy. To address this, we developed a spatially explicit simulation model for the outbreak spreading among olive groves coupled to a simulation of the real surveillance and containment measures. We used Approximate Bayesian Computation to fit the model to surveillance and remote-sensing infection data, comparing the fits for three alternative dispersal mechanisms (isotropic, wind and road). The model accurately explained the rate and spatiotemporal pattern of the outbreak and found weak support for the wind dispersal model over the isotropic model. It suggests that the bacterium may have been introduced as early as 2003 (95% CI [2000, 2009]), earlier than previous estimates and congruent with anecdotal evidence. The isotropic model estimates the pathogen is spreading at 5.7 km y-1 (95% CI [5.4-5.9]) under containment measures, down from 7.2 km y-1 (95% CI [6.9-7.5]) without containment measures. Our estimate of an approximately 10-year lag between introduction and detection highlights the need for stronger biosecurity and surveillance for earlier detection of emerging plant pathogens. The outputs from simulations without any disease management also suggest that while containment measures have caused some slowing of X. fastidiosa spread, stronger measures will be required to contain the outbreak fully.}, }
@article {pmid41041147, year = {2024}, author = {Botham, M and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Small Argent and Sable moth, Epirrhoe tristata (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {541}, pmid = {41041147}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Small Argent and Sable moth Epirrhoe tristata (Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence spans 313.80 megabases. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.92 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,469 protein-coding genes.}, }
@article {pmid41040654, year = {2025}, author = {Boyes, D and Broad, GR and Lees, DC and Boyes, C and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Brindled White-spot moth, Parectropis similaria (Hufnagel, 1767).}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {179}, pmid = {41040654}, issn = {2398-502X}, abstract = {We present a genome assembly from a female Parectropis similaria (Brindled White-spot; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 574.79 megabases. Most of the assembly (99.92%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 16.94 kilobases.}, }
@article {pmid41040651, year = {2025}, author = {Boyes, D and Lees, DC and Boyes, C and ,  and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Triangle-marked Roller, Ancylis achatana (Denis &amp; Schiffermüller), 1775.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {128}, pmid = {41040651}, issn = {2398-502X}, abstract = {We present a genome assembly from a male specimen of Ancylis achatana (Triangle-marked Roller; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence has a total length of 547.27 megabases. Most of the assembly (99.25%) is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 16.0 kilobases.}, }
@article {pmid41040647, year = {2025}, author = {Boyes, D and Boyes, C and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Sycamore-seed Pygmy moth, Ectoedemia decentella (Herrich-Schäffer, 1855) van Nieukerken, 1986.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {182}, pmid = {41040647}, issn = {2398-502X}, abstract = {We present a genome assembly from a female specimen of Ectoedemia decentella (Sycamore-seed Pygmy; Arthropoda; Insecta; Lepidoptera; Nepticulidae). The genome sequence has a total length of 418.14 megabases. Most of the assembly (99.59%) is scaffolded into 31 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled, with a length of 15.25 kilobases.}, }
@article {pmid41038931, year = {2025}, author = {Nganso, BT and Agboka, KM and Atagong, SD and Topé, SF and Massing, T and Landmann, T and Sevgan, S and Mwiza, W and Odera, F and Piiru, ED and Otieno-Ayayo, ZN and Soroker, V and Guimapi, RA}, title = {A Geospatial atlas of honey bee forage plants and their distribution patterns in Africa and beyond.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {34384}, pmid = {41038931}, issn = {2045-2322}, support = {70054//JRS Biodiversity Foundation/ ; }, mesh = {Animals ; Africa ; *Bees/physiology ; Biodiversity ; Conservation of Natural Resources ; Databases, Factual ; Ecosystem ; Pollination ; *Plants ; }, abstract = {Honey bee forage plants are essential for bee nutrition and wellbeing, and they also sustain multifunctional landscapes that support human livelihoods and biodiversity. Despite the critical need to conserve them, information on their identity and distribution across Africa remains limited. Through a systematic literature review, we compiled the first continental database of 1,248 honey bee forage plant species from 91 families and retrieved 1,572,790 occurrence records of these species from open-access biodiversity databases like iNaturalist and the Global Biodiversity Information Facility (GBIF). The database includes native and exotic species, with georeferenced records from Africa and beyond. An interactive web-based dashboard accompanies the database, allowing users to visualize species distributions. The dashboard reveals floral report gaps in Western, Central and Northern Africa, helping inform future conservation priorities. In Southern and Eastern Africa where considerable data exists, this resource promotes pollinator-friendly land management practices, supporting honey bees and other pollinators vital for ecosystem resilience. Overall, this resource provides a foundation for future integration with high-resolution imagery, climate models and field-collected data on plant-pollinator interactions to contextualize species distributions under varying land-use and climatic conditions. It offers a valuable tool to support pollinator conservation and climate-resilient strategies for agriculture and beekeeping across Africa.}, }
@article {pmid41034648, year = {2025}, author = {Weingarten, A and Häusler, M and Serangeli, J and Verheijen, I and Reiter, E and Radzevičiūtė, R and Stoessel, A and Krause, J and Spyrou, MA and Conard, NJ and Nieselt, K and Posth, C}, title = {Mitochondrial genomes of Middle Pleistocene horses from the open-air site complex of Schöningen.}, journal = {Nature ecology &amp; evolution}, volume = {9}, number = {12}, pages = {2248-2258}, pmid = {41034648}, issn = {2397-334X}, mesh = {Animals ; Horses/genetics ; *Genome, Mitochondrial ; Phylogeny ; Fossils ; DNA, Ancient/analysis ; Germany ; DNA, Mitochondrial/genetics ; Biological Evolution ; }, abstract = {Deep-time palaeogenomics offers rare insights into macroevolutionary events for both extant and extinct species. Aside from a Middle Pleistocene genome from North American permafrost (780-560 ka) and a number of Late Pleistocene specimens, most ancient horse DNA studies have focused on tracing the origins of domestication and subsequent periods. Here we present mitochondrial genomes from two Equus mosbachensis specimens from Schöningen, Germany, a Middle Pleistocene archaeological site complex with direct and repeated evidence of hominin-horse interactions on the shore of a palaeolake. Using petrous bone sampling, targeted enrichment and damage-aware and polarization-free mitochondrial DNA reconstruction methods, we extend the range of genome recovery in open-air sites to ~300,000 years ago. Phylogenetic analyses position these mitochondrial DNAs in two distinct, deeply divergent lineages, basal to both previously sequenced ancient Eurasian specimens and all modern-day horses. The Schöningen horse mitochondrial DNA data reveal a previously unrecognized diversification event within the clade, ultimately giving rise to modern-day horses, that is molecularly dated to ~570 ka and provides genetic support for the morphological species assignment. By extending the recoverable limits of ancient DNA from Middle Pleistocene open-air sites, our molecular findings bridge a temporal and geographic gap, providing insights on early evolutionary events within the genus Equus.}, }
@article {pmid41032589, year = {2025}, author = {Yang, M and Adegbite, O and Chang, P and Cheng, J and Wang, Y and Held, M and Zhu, X and Li, Y and Dykes, GF and Chen, Y and Savage, N and Zhang, YZ and Gao, J and Hinton, JCD and Lian, LY and Liu, LN}, title = {Molecular basis of the biogenesis of a protein organelle for ethanolamine utilization.}, journal = {Science advances}, volume = {11}, number = {40}, pages = {eadx9774}, pmid = {41032589}, issn = {2375-2548}, mesh = {*Ethanolamine/metabolism ; *Bacterial Proteins/metabolism/genetics/chemistry ; *Organelles/metabolism ; *Salmonella/metabolism ; }, abstract = {Many pathogenic bacteria use proteinaceous ethanolamine utilization microcompartments (Eut BMCs) to catabolize ethanolamine. This ability gives pathogens a competitive edge over commensal microbiota, which can drive virulence in the inflamed gut. Despite such a critical function, the molecular mechanisms underlying the synthesis of Eut BMCs remain elusive. We report a systematic study for dissecting the molecular basis underlying Eut BMC assembly in Salmonella. We determined the functions of individual constituent proteins in the structure and function of Eut BMCs and demonstrated that EutQ is essential for cargo encapsulation and Eut BMC formation through specific association with the shell and cargo enzymes. We found that Eut proteins can self-assemble to form cargo and shell aggregates independently in vivo and that the biogenesis of Eut BMCs follows a "shell-initiated" pathway. Cargo enzymes exhibit dynamic liquid-like organization within the Eut BMC. Our findings provide mechanistic insights into the structure and assembly of the Eut BMC that serves as a paradigm for membraneless organelles.}, }
@article {pmid41032510, year = {2025}, author = {Zhang, C and Teng, J and Liu, P and Liu, C}, title = {Ecological suitability evaluation of traditional village locations in Jiangxi Province based on multi-model integration using artificial intelligence.}, journal = {PloS one}, volume = {20}, number = {10}, pages = {e0332375}, pmid = {41032510}, issn = {1932-6203}, mesh = {*Artificial Intelligence ; China ; *Ecosystem ; Humans ; *Conservation of Natural Resources/methods ; Geographic Information Systems ; Neural Networks, Computer ; *Ecology ; Support Vector Machine ; }, abstract = {Traditional villages have evolved over time to adapt to their environmental characteristics, demonstrating high ecological suitability. Ideal village locations not only provide comfortable living spaces but also ensure safety and sustainability, reflecting the ancestors' profound understanding of the natural environment and ecological wisdom. This study employs an artificial intelligence-based multi-model integration approach to evaluate the ecological suitability of 413 traditional village sites in Jiangxi Province. Key influencing factors are identified, and the ecological wisdom of ancestral site selection is analyzed, resulting in an ecological suitability evaluation map for traditional village locations in Jiangxi Province. The study draws upon environmental characteristic data of Jiangxi Province, including topography, climate, habitat quality, land use, air quality, vegetation cover, and river network density. GIS technology is utilized for spatial analysis and result visualization, with raster data being extracted and standardized. Machine learning methods, such as Random Forest, Support Vector Machine, and Gradient Boosting Decision Trees, along with deep learning methods like Convolutional Neural Networks and Multilayer Perceptrons, are applied. Multi-model integration techniques combine diverse predictive outputs, thereby enhancing the overall accuracy and robustness of ecological suitability evaluations. Experimental results indicate that elevation, slope, habitat quality, actual distance to water bodies, and average temperature are the main influencing factors for village site selection. The multi-model integration method performs excellently in evaluating ecological suitability, effectively identifying key ecological factors. The model's accuracy and reliability are verified through confusion matrix, feature importance analysis, and ROC curve. By analyzing the impact weights of various ecological factors, this study constructs a Composite Suitability Index (CSI) and generates an ecological suitability evaluation map that clearly displays suitability levels. This provides a scientific basis for the protection and rational development of traditional villages and serves as a reference for ecological site selection studies in other regions.}, }
@article {pmid41030989, year = {2025}, author = {Carroll, RA and Ricemeyer, ES and Hillier, LW and DaCosta, JM and Osipova, E and Smith, S and Jamie, GA and Martinez, JG and Molina-Morales, M and Marques-Bonet, T and Manthey, JD and Haddad, D and Fuxjager, MJ and Lynch, KS and Wood, JMD and Jarvis, E and Masterson, P and Thibaud-Nissen, F and Hauber, M and Spottiswoode, CN and Sackton, TB and Balakrishnan, CN and Sorenson, MD and Warren, WC}, title = {Genomic resources for comparative analyses of obligate avian brood parasitism.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41030989}, issn = {2692-8205}, abstract = {Examples of convergent evolution, wherein distantly related organisms evolve similar traits, including behaviors, underscore the adaptive power of natural selection. In birds, obligate brood parasitism, and the associated loss of parental care behaviors, has evolved independently in seven different lineages, though little is known about the genetic basis of the complex suite of traits associated with this rare life history strategy. We generated genome assemblies for ten brood parasitic species plus eight species representatives of their parental/nesting outgroups. This includes nine long-read chromosome-level assemblies, with scaffold N50 sizes ranging from 38.1 to 72.6 MB, and gene representation completeness measures >97%. Leveraging this new catalog of avian genomes, we constructed clade-level alignments that reveal variation in chromosomal synteny, provide first-time or improved annotations of protein-coding and non-coding genes, and define cross-species ortholog reference sets. We also refine estimates for the timing of the seven independent origins of brood parasitism, ranging from recent events such as 1.6 to 4.5 million years ago in Molothrus cowbirds to much earlier origins over 30 million years ago in two of the three cuckoo lineages. These genomic resources lay the foundation for investigating the genetic and genomic underpinnings of brood parasitism, including the loss of parental care, shifts in mating systems, perhaps resulting in heightened sperm competition, elevated annual fecundity, improved spatial cognition related to nest-finding, and the diverse adaptations shaped by intense coevolution with host species.}, }
@article {pmid41030122, year = {2025}, author = {Robinson, JM and Brame, J and Cando-Dumancela, C and Deshmukh, S and Fickling, NW and Hawken, S and Hayward, C and Kuhn, E and Lee, K and Liddicoat, C and Ramesh, S and Robinson, K and Sun, X and Breed, MF}, title = {Mapping and Cataloguing Microbial and Biochemical Determinants of Health: Towards a 'Database of Salutogenic Potential'.}, journal = {Microbial biotechnology}, volume = {18}, number = {10}, pages = {e70243}, pmid = {41030122}, issn = {1751-7915}, support = {//National Environmental Science Program/ ; 32361143523//National Natural Science Foundation of China/ ; UOWX2101//New Zealand Ministry of Business Innovation and Employment/ ; 322GJHZ2022028FN//International Partnership Program of Chinese Academy of Sciences/ ; 2023YFF1304600//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Microbiota ; *Environmental Microbiology ; *Databases, Factual ; *Bacteria/metabolism/classification/genetics ; }, abstract = {Microbial and biochemical research has historically focused on pathogenic agents due to their clear association with disease. This is a perspective that has saved countless lives but encourages a skewed, threat-centered view of microbes and biogenic compounds. Emerging evidence shows that exposure to diverse environmental microbiomes and natural biochemical products is also salutogenic-promoting health and resilience. Here we introduce the 'Database of Salutogenic Potential', a prototype relational repository cataloguing environmental microbes and biochemical compounds linked to health benefits. Drawing from more than 200 articles, we identified 124 potentially salutogenic microbial taxa, 14 biochemical compounds and 63 associated benefits. By creating a structured and open platform, we aim to shift the balance between pathogen-centric and salutogenic perspectives, potentially enabling future applications in public health, urban planning and ecosystem restoration. While the current iteration of the database primarily centers on human health outcomes, it is designed to expand into ecosystem health domains, embedding salutogenic thinking into One Health frameworks. We present this as a first step, not a ready-to-use tool, and invite collaborative refinement from the scientific community.}, }
@article {pmid41029229, year = {2025}, author = {Nagy, KN and Károlyi, CE and Bakacsy, L}, title = {Multiscale assessment of conservation management for Amorpha fruticosa invasion in a marsh meadow.}, journal = {BMC ecology and evolution}, volume = {25}, number = {1}, pages = {97}, pmid = {41029229}, issn = {2730-7182}, support = {7616//University of Szeged Open Access Found/ ; 7616//University of Szeged Open Access Found/ ; 7616//University of Szeged Open Access Found/ ; }, mesh = {*Introduced Species ; *Wetlands ; *Conservation of Natural Resources/methods ; Biodiversity ; Animals ; Cattle ; *Fabaceae/physiology ; }, abstract = {This study examined the ecological impact of the invasive shrub Amorpha fruticosa in marsh meadows and assessed the effectiveness of combined conservation management practices, i.e., mowing and cattle grazing, in on restoring native vegetation. Conducted in the Mártély Landscape Protection Area (Hungary), the research used a multiscale approach to compare treated non-invaded and treated invaded wetland vegetation. Information theory-based diversity metrics were employed to evaluate the impact of A. fruticosa on structural complexity and species composition. Results revealed that although A. fruticosa can significantly altered plant community structure, the implemented management strategies effectively reduced its impact. The treated invaded vegetation exhibited diversity levels compareable to native marshland communities, suggesting that mowing and grazing contributed to decreasing A. fruticose dominance. However, in the absence of untreated control stands, this pattern must be interpreted cautiously, as the observed similarity could be conclusively attributed to the applied management alone. A slight, but non-significant shift in structural diversity was also observed, implying a residual effect of invasion. This study underscores the value of active, combined conservation strategies in maintaining biodiversity and ecosystem resilience in wetland habitats. The results contribute to broader discussions on invasive species control, emphasizing the role of traditional land-use practices in mitigating the ecological effects of biological invasions.}, }
@article {pmid41028231, year = {2026}, author = {Ging-Jehli, NR and Pine, DS}, title = {From symptom-based heterogeneity to mechanism-based profiling in youth ADHD: the promise of computational psychiatry.}, journal = {Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology}, volume = {51}, number = {1}, pages = {234-243}, pmid = {41028231}, issn = {1740-634X}, support = {P500PS_214223//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; ZIA-MH002781//U.S. Department of Health &amp; Human Services | NIH | National Institute of Mental Health (NIMH)/ ; }, mesh = {Humans ; *Attention Deficit Disorder with Hyperactivity/diagnosis/therapy ; Models, Theoretical ; *Psychiatry/methods ; *Diagnosis, Computer-Assisted ; }, abstract = {Mental health conditions such as attention-deficit/hyperactivity disorder (ADHD) and mood disorders show marked symptom heterogeneity, complicating diagnosis and treatment. Computational psychiatry offers a way forward by using mathematical models, such as sequential sampling models, applied to trial-by-trial behavior in well-defined neurocognitive tasks, to infer latent mechanisms underlying behavior. In ADHD, this approach has revealed consistent alterations in information integration (reduced drift rates) in attention-demanding tasks and also indicates that combinations of different model parameters (increased drift rate and longer nondecision time) distinguish the different neurocomputational mechanisms that underlie symptom dimensions. Early work in ADHD also suggests that drift rate predicts illness trajectories and provides insights into treatment response. Yet current applications remain preliminary, limited by task constraints, assumptions in model specification, and questions of reliability and generalizability of the derived parameters. Integrating mechanistic modeling with naturalistic tasks, physiological measures, and longitudinal designs may help to disentangle context-specific from generalizable processes. Ultimately, shifting from symptom descriptions to mechanistic models of belief and behavioral adaptation in dynamic environments may pave the way for next-generation assessments in ADHD, and help to support interventions that are ecologically valid, developmentally informed, and adaptive to patients' changing needs across time and context.}, }
@article {pmid41028195, year = {2025}, author = {Yang, M and Wang, M and Cao, L and Zhang, H}, title = {Integrating trade-offs and supply-demand into ecosystem service zoning management to provide more targeted management strategies from the water-food-ecosystem nexus perspective.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {33957}, pmid = {41028195}, issn = {2045-2322}, support = {42401384//National Natural Science Foundation of China/ ; 41971241//National Natural Science Foundation of China/ ; 24YJCZH376//Humanities and Social Sciences Youth Foundation, Ministry of Education/ ; 24YJCZH376//Humanities and Social Sciences Youth Foundation, Ministry of Education/ ; 25IRTSTHN008//Higher Education Institutions Scientific and Technological Innovation Team Support Program in Henan Province/ ; 25A170008//Key Scientific Research Projects of Colleges and Universities in Henan Province/ ; 24B170003//Key Scientific Research Projects of Colleges and Universities in Henan Province/ ; }, abstract = {The water-food-ecosystem nexus (WFE nexus) forms the foundation for achieving sustainable development. Managing ecosystem services (ESs) from this perspective is crucial for maintaining and enhancing ecosystem sustainability. However, synchronously mitigating trade-offs and supply-demand conflicts among ESs poses a significant challenge for sustainable ecosystem management. This study proposes a spatial management zoning framework integrating information on ESs trade-offs and supply-demand relationships from the perspective of the WFE nexus. This framework aims to precisely distinguish regional differences in ESs trade-off characteristics and supply-demand risk levels. We applied this framework to China's Loess Plateau (LP) in China, where the simultaneous safeguarding of water, food, and ecological security has become a major challenge for local sustainable development. Based on analyzing ESs trade-offs and supply-demand matching relationships, our framework divided the LP into ten management zones. Each of these zones faces similar ecological issues internally, while different zones confront distinct ecological problems. Consequently, we propose targeted management strategies for each zone based on their unique ecological issues. Our framework deepens the research on the WFE nexus and provides a new perspective for simultaneously resolving ESs trade-offs and supply-demand conflicts.}, }
@article {pmid41026600, year = {2025}, author = {Liu, L and Han, P and Wang, J and Xiuqin, S and Xu, G and Wang, L and Liu, R and Shen, X and Chen, F}, title = {Approaches to the water environment and aquatic ecology governance in basin systems.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {92}, number = {6}, pages = {894-902}, pmid = {41026600}, issn = {0273-1223}, support = {ZR2024MD117//Natural Science Foundation of Shandong Province/ ; No.0031504//The Shandong Top Talent Special Foundation/ ; X20192Z//The Doctoral research fund project of Shandong Jianzhu University/ ; 42107496//The National Science Fund for Distinguished Young Scholars-Construction and application of remote sensing ecological index model of Tamarix shrubbery forest/ ; }, mesh = {*Ecology ; *Conservation of Natural Resources ; Ecosystem ; Sustainable Development ; }, abstract = {With the development of human civilization and the rapid progress of urbanization, the water environment and aquatic ecology need more systematic treatment to support the construction of ecological civilization and sustainable development. Based on a large number of research results and from the four dimensions including governance concept, governance technology, management and control platform and engineering strategy suggestions, this study systematically analysed the cutting-edge concepts such as reverse-driven governance, explored the application of key technologies such as remote sensing in the water environment and water ecological governance, put forward strategic suggestions on building an intelligent analysis and decision-making platform and avoiding great leap forward-style vanity projects in the water environment and aquatic ecology governance. Finally, six cutting-edge governance concepts, four key technologies, two types of governance and control platforms and two engineering strategies were sorted out and formed a governance system covering concept guidance, technical support, platform integration and application, and engineering strategy guarantee. The research enriches the theory of the water environment and aquatic ecology governance, and has important reference value for policy-making and engineering practice of watershed water environment and aquatic ecology governance.}, }
@article {pmid41021637, year = {2025}, author = {Maity, B and Banerjee, S and Senapati, A and Pitchford, J and Chattopadhyay, J}, title = {Coupling plankton and cholera dynamics: Insights into outbreak prediction and practical disease management.}, journal = {PLoS computational biology}, volume = {21}, number = {9}, pages = {e1013523}, pmid = {41021637}, issn = {1553-7358}, mesh = {*Cholera/epidemiology/transmission/microbiology/prevention &amp; control ; *Disease Outbreaks/statistics &amp; numerical data/prevention &amp; control ; Humans ; Vibrio cholerae/pathogenicity ; Animals ; *Plankton/microbiology ; Zooplankton/microbiology ; Models, Biological ; Phytoplankton ; Computational Biology ; }, abstract = {Despite extensive control efforts over the centuries, cholera remains a globally significant health issue. Seasonal emergence of cholera cases has been reported, particularly in the Bengal delta region, which is often synchronized with plankton blooms. This phenomenon has been widely attributed to the commensal interaction between Vibrio cholerae and zooplankton in aquatic environments. The role of plankton dynamics in cholera epidemiology has been acknowledged but remains poorly understood, and consequently, its importance in effective policymaking is largely overlooked. To this end, we propose and analyze a novel compartment-based transmission model that integrates phytoplankton-zooplankton interactions into a human-bacteria cholera framework. Our study shows that, beyond the reproduction number, the relative contribution of bacterial versus zooplankton-mediated transmission plays a crucial role in shaping epidemic progression and severity. In presence of zooplankton-mediated transmission, an outbreak with a delayed and lower peak may still result in a larger overall outbreak size. Additionally, contrary to common intuition, even for a large and early outbreak, the epidemic overshoot may intensify due to the maintenance of lower-level infections during the post-peak phase. Furthermore, our analysis reveals that the timing of filtration-like interventions can be strategically guided by ecological indicators, such as phytoplankton blooms. Our study underscores the importance of incorporating ecological aspects in epidemiological research to better predict and manage disease outbreaks.}, }
@article {pmid41021230, year = {2025}, author = {Muzekari, B and Cooper, N and Resnick, A and Paul, AM and Torres-Grillo, OE and Andrews, ME and Mattan, B and Scholz, C and Johnson, D and Carreras-Tartak, J and Cakar, ME and Hao, S and Zhou, E and Beard, E and Mesquiti, S and Sayed, F and Fichman, MA and Lydon-Staley, DM and Barnett, IJ and Strasser, AA and Kirchner, TR and Henriksen, L and Falk, EB}, title = {Naturalistic Tobacco Retail Exposure and Smoking Outcomes in Adults Who Smoke Cigarettes Daily.}, journal = {JAMA network open}, volume = {8}, number = {9}, pages = {e2530132}, pmid = {41021230}, issn = {2574-3805}, mesh = {Humans ; Female ; Male ; Adult ; Middle Aged ; *Tobacco Products/economics/statistics &amp; numerical data ; Craving ; *Commerce/statistics &amp; numerical data ; Aged ; *Cigarette Smoking/epidemiology/psychology ; Cohort Studies ; Young Adult ; Ecological Momentary Assessment ; New Jersey/epidemiology ; *Tobacco Industry ; }, abstract = {IMPORTANCE: The tobacco industry spends more than $8 billion annually in the US on marketing at the point of sale. Exposure to tobacco retail has been associated with smoking outcomes, but substantially less is known about how objectively logged everyday tobacco retail exposure is associated with smoking outcomes.<br><br>OBJECTIVE: To assess preregistered hypotheses that individuals would report (1) greater craving and (2) more cigarettes smoked on days when their exposure to tobacco retail is higher than usual.<br><br>This multimodal, within-person cohort study combined objectively logged geolocation tracking, public tobacco retail location records, and ecological momentary assessment data. Eligible participants recruited from the GeoSmoking Study were aged 21 to 65 years, smoked at least 5 cigarettes per day over the previous 6 months, owned a smartphone, and were a resident of Pennsylvania, New Jersey, or Delaware. Data were collected from May 25, 2022, to June 10, 2024.<br><br>EXPOSURE: Exposure to tobacco retail stores was assessed using mobility data matched with locations of tobacco retailers across Pennsylvania, New Jersey, and Delaware.<br><br>MAIN OUTCOMES AND MEASURES: Daily mean craving and daily number of cigarettes smoked were computed using ecological momentary assessment.<br><br>RESULTS: A total of 273 participants were included in the final analyses (mean [SD] age, 42.5 [10.7] years; 151 women [55.3%]). Multilevel models revealed support for both preregistered hypotheses. On days when individuals had more tobacco retail exposure than their own average, they reported significantly higher levels of craving (b&#x2009;=&#x2009;0.04; 95% CI, 0.01-0.07; t3457&#x2009;=&#x2009;2.72; P&#x2009;=&#x2009;.01) and smoking significantly more cigarettes (b&#x2009;=&#x2009;0.01; 95% CI, 0.0002-0.01; t3469&#x2009;=&#x2009;2.05; P&#x2009;=&#x2009;.04).<br><br>CONCLUSIONS AND RELEVANCE: In this cohort study of individuals who smoke cigarettes daily, exposure to tobacco retail in their everyday lives was associated with increases in craving and smoking. These findings highlight the importance of retail exposure and smoking outcomes, information that is critical for developing effective tobacco control interventions and lays the foundation for broader health research on environmental factors that shape health behaviors.}, }
@article {pmid41020379, year = {2025}, author = {Vázquez, E and Duong, I and Rabin, BA and Stadnick, NA and Watson, PL and Cain, KL and Pozar, M and Cheney, A}, title = {Ripple Effects Mapping: Evaluating Multilevel Perspectives and Impacts of a Statewide Community-Academic Partnership Network on Covid-19 Health Disparities.}, journal = {Health expectations : an international journal of public participation in health care and health policy}, volume = {28}, number = {5}, pages = {e70446}, pmid = {41020379}, issn = {1369-7625}, support = {//This paper was supported by the following funding NIH/NHLBI CEAL grant #21-312-0217571-66106L./ ; }, mesh = {Humans ; *COVID-19/epidemiology/ethnology ; *Health Status Disparities ; California/epidemiology ; Community-Based Participatory Research ; *Community-Institutional Relations ; Universities/organization &amp; administration ; *Community Networks/organization &amp; administration ; SARS-CoV-2 ; Female ; }, abstract = {INTRODUCTION: Community-academic partnerships played an important role in addressing Covid-19-related health disparities in historically marginalised groups such as racial ethnic minorities and low-income and rural communities in the pandemic. Part of the federal response involved establishing regional community academic networks that engaged highly impacted communities in health disparities research. The statewide Share, Trust, Organize, Partner COVID-19 California Alliance (STOP COVID-19 CA) network was part of the federal response.<br><br>METHODS: In spring 2024, ripple effects mapping (REM), a participatory action research method, was used to conduct an evaluation of the impact of the STOP COVID-19 network on the capacity of community-academic partnerships to carry out Covid-19-related health disparities research. This method uses group interviews to capture direct and indirect outcomes, that is, ripples, of community-based programmes. Short-, medium- and long-term changes and conditions related to community-academic partnerships in the statewide network were mapped onto the spheres of influence of the social ecological model.<br><br>RESULTS: A total of 24 participants took part in one of three REM sessions. Community and academic partners were represented in all sessions, and most had been involved in community-engaged research for 3 to 10+&#x2009;years. Most identified as female, Hispanic/Latino, and between the ages of 40 and 49. Qualitative analysis of sessions indicated that most changes occurred at the individual and interpersonal levels and involved medium-term changes (e.g., increased capacity to partner in research and shared understanding). Neighbourhood- or community-level changes included identification of culturally and linguistically responsive intervention and dissemination efforts (e.g., promotora model). Policy and built environment conditions reveal the inequities in higher education and the need for structural-level changes to university infrastructure and grant administration.<br><br>CONCLUSION: Most outcomes were observed at the individual and interpersonal (group) levels and involved primarily medium-term changes. However, the network itself served as a platform to discuss the need for structural-level changes within university infrastructure to facilitate community-engaged scholarship. Such networks have the potential to facilitate capacity building for community-academic partnerships to collaborate in health disparities research that can generate evidence to move forward public health policy change.<br><br>Community partners, including grassroots leaders and staff of community-based organisations, were involved in the development of the research questions, the design of the study, and data collection, analysis and interpretation of the findings. Community partners also contributed to manuscript development.}, }
@article {pmid41013991, year = {2025}, author = {Formanack, A and Ogle, K and Peltier, D}, title = {Flashy, decoupled, or declining? Single theories fail to explain the diversity of drought mortality signals in tree rings.}, journal = {The New phytologist}, volume = {248}, number = {6}, pages = {2795-2808}, doi = {10.1111/nph.70605}, pmid = {41013991}, issn = {1469-8137}, mesh = {*Droughts ; *Trees/growth &amp; development/physiology ; Bayes Theorem ; Species Specificity ; Models, Biological ; Climate ; }, abstract = {Growth patterns recorded in tree rings may predict drought 'winners' and 'losers'. Past studies of drought-killed trees have produced conflicting evidence. Some show killed trees were highly responsive to climate, while others suggest killed trees were climate-insensitive or became less sensitive over time. We leveraged ring width data from 2934 drought-killed and -surviving trees of seven species to compute growth sensitivity to seasonal climate variables via a Bayesian mixed effects model. Aided by clustering analyses, we evaluated how species conformed to three alternative hypotheses (theories): relative to surviving trees, killed trees (H1) have 'flashy' climate responses, (H2) are 'decoupled' from climate, or (H3) have 'declining' sensitivity over time. Differences in growth patterns were not consistent across species or status (surviving/killed). Drought-killed subalpine fir and Engelmann spruce exhibited 'flashy' growth - higher sensitivity of growth to climate over time - compared with survivors. Drought-killed aspen, Scots pine, and Norway spruce showed stable, climate-insensitive growth compared with survivors, suggesting 'decoupling' from climate. Most species showed nonstationary sensitivities, but rather than declining, some sensitivities increased, even in surviving trees. Our flashy-decoupled-declining framework links predictions for future drought-induced mortality to potential mechanisms, enhancing ecological and physiological understanding of growth-climate patterns preceding drought mortality events.}, }
@article {pmid41013625, year = {2025}, author = {Li, M and Yang, H}, title = {Exploring spatial-temporal heterogeneity in new-type urbanization's impact on health expenditure: a GTWR analysis.}, journal = {International journal of health geographics}, volume = {24}, number = {1}, pages = {26}, pmid = {41013625}, issn = {1476-072X}, mesh = {Humans ; *Urbanization/trends ; *Health Expenditures/trends/statistics &amp; numerical data ; China/epidemiology ; *Spatio-Temporal Analysis ; *Geographic Information Systems/trends ; }, abstract = {BACKGROUND: To address challenges arising from rapid urban development, China has formulated and implemented the New-Type Urbanization strategy. However, empirical research on the specific impacts between New-Type Urbanization and health expenditures remains limited.<br><br>METHODS: Using panel data from 31 Chinese provinces (2012-2019), this study constructed a comprehensive evaluation index system for New-Type Urbanization across four dimensions: demographic, economic, social, and ecological. Geographically and Temporally Weighted Regression was employed to examine the spatial effects, influencing factors, and spatial heterogeneity of New-Type Urbanization's impact on health expenditures.<br><br>RESULTS: The results show that China's health expenditures primarily exhibit High-High and Low-Low clustering patterns with spatial fluctuations. Meanwhile, the impact of New-Type Urbanization on health expenditures demonstrates spatiotemporal heterogeneity and non-stationarity. As urbanization levels increase, the negative effects of health expenditure clustering expand, while the influence of economic urbanization weaken.<br><br>CONCLUSIONS: Our findings fill the research gap regarding the impacts between New-Type Urbanization and health expenditures, while also providing direction for New-Type Urbanization development to support the implementation of health policies aimed at controlling health expenditure growth.}, }
@article {pmid41011672, year = {2025}, author = {Song, C and Yan, M and Lin, S and Li, J and Zou, H and Hu, Z and Yan, X}, title = {Dual-Ionization SPME-GC-HRMS Metabolomic Profiling of Broccoli Volatiles for the Construction of a Broccoli Metabolic Database.}, journal = {Molecules (Basel, Switzerland)}, volume = {30}, number = {18}, pages = {}, pmid = {41011672}, issn = {1420-3049}, support = {2022YFE0108300//National Key R&amp;D Program of China/ ; N20220013//the Basic Agricultural Research Project of Wenzhou/ ; }, mesh = {*Volatile Organic Compounds/analysis/metabolism/chemistry ; *Brassica/metabolism/chemistry ; Gas Chromatography-Mass Spectrometry/methods ; *Metabolomics/methods ; Solid Phase Microextraction/methods ; *Metabolome ; Principal Component Analysis ; Databases, Factual ; }, abstract = {Volatile organic compounds (VOCs) play critical roles in broccoli's sensory attributes, defense mechanisms, and ecological interactions, yet comprehensive profiling of its volatilome remains limited. This study aimed to construct a robust and inclusive volatile metabolite database for broccoli using advanced analytical techniques. A pooled sample comprising florets from 191 cultivars was prepared to capture broad chemical diversity and analyzed using solid-phase microextraction-gas chromatography-high-resolution mass spectrometry (SPME-GC-HRMS) under dual ionization modes: electron ionization (EI) and chemical ionization (CI). A total of 206 VOCs spanning nine chemical classes were detected, with 37 compounds further confirmed through synchronized CI analysis. To validate the database, broccoli florets from seven distinct cultivars were analyzed using the same workflow. Of the 206 compounds, 187 (90.78%) were detected in at least one cultivar, while 38 were consistently found across all samples, indicating a conserved core volatilome. Principal component analysis revealed distinct VOC profiles among cultivars, and freeze-dried samples were found suitable for reproducible large-scale analysis. This study demonstrates that a pooled-sample strategy coupled with dual-ionization GC-HRMS provides comprehensive and reliable VOC coverage. The resulting database offers a valuable resource for metabolomics studies in Brassica, with applications in cultivar differentiation, flavor research, and environmental response profiling.}, }
@article {pmid41009797, year = {2025}, author = {Cheng, L and Shi, N and Du, X and Huang, T and Zhang, Y and Zhao, C and Zhao, K and Lin, Z and Ma, D and Li, Q and Wang, F and Yao, H and Shen, H}, title = {Bioinformatics Analysis and Expression Profiling Under Abiotic Stress of the DREB Gene Family in Glycyrrhiza uralensis.}, journal = {International journal of molecular sciences}, volume = {26}, number = {18}, pages = {}, pmid = {41009797}, issn = {1422-0067}, support = {KY2025JBGS03//the Science and Technology Plan Project of the Third Division/ ; 32260083//the National Natural Science Foundation of China/ ; 2023AB052 and 2023CB008-17//a Science and Technology Project of Bingtuan/ ; RCZK202595//Scientific Research Startup Project for High-Level Talents, Shihezi University/ ; }, mesh = {*Gene Expression Regulation, Plant ; *Glycyrrhiza uralensis/genetics/metabolism ; *Stress, Physiological/genetics ; *Plant Proteins/genetics/metabolism ; *Computational Biology/methods ; Phylogeny ; *Transcription Factors/genetics/metabolism ; Gene Expression Profiling ; Droughts ; *Multigene Family ; Promoter Regions, Genetic ; Transcriptome ; }, abstract = {Glycyrrhiza uralensis is an important medicinal plant exhibiting strong tolerance to abiotic stresses, including drought and salinity. DREB (Dehydration-Responsive Element-Binding) transcription factors, key members of the AP2/ERF family, play crucial roles in plant growth, development, and stress responses. Based on transcriptome data, we identified 18 DREB transcription factors in G. uralensis, designated GuDREB1 to GuDREB18. Bioinformatics analysis revealed genomic sequences ranging from 534 to 2864 bp and coding sequence (CDS) lengths between 525 and 1509 bp. All GuDREB proteins contain a single AP2 domain, including the conserved YRG and RAYD elements, and were predicted to localize to the nucleus. Phylogenetic analysis clustered the G. uralensis DREBs with 61 Arabidopsis thaliana DREBs into five subgroups, indicating evolutionary conservation. Promoter analysis detected seventeen stress-responsive cis-acting elements, encompassing hormone-responsive and abiotic stress-responsive motifs, suggesting diverse biological functions. Tissue-specific expression profiling revealed GuDREB transcription in both aerial and underground parts. Drought stress induced varying degrees of GuDREB expression, confirming their involvement in stress responses. Notably, GuDREB10 expression increased significantly in underground parts, while GuDREB15 showed pronounced upregulation in aerial parts under drought; the GuDREB15 promoter contained the highest number of light-responsive elements (23), potentially explaining its aerial tissue specificity. Drought stress significantly increased abscisic acid (ABA) content. Underground parts exhibited higher initial sensitivity to drought, whereas aerial parts displayed a more sustained response; ABA levels overall showed an initial increase followed by a decline. This study expands the G. uralensis DREB gene database, provides a foundation for selecting stress-resistance genes, and offers insights into DREB functional roles in abiotic stress responses in this key medicinal species.}, }
@article {pmid41007943, year = {2025}, author = {Zhu, Y and Zhao, Y and He, Y and Wu, B and Su, X}, title = {YOLO-WildASM: An Object Detection Algorithm for Protected Wildlife.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {18}, pages = {}, pmid = {41007943}, issn = {2076-2615}, support = {QNTD202308//Outstanding Youth Team Project of Central Universities/ ; 2023YFD2201700//National Key R&amp;D Program of China/ ; }, abstract = {Wild animals are an essential component of natural ecosystems, and the accurate identification of wildlife targets plays a critical role in ecological conservation and species monitoring. However, the effectiveness of conventional object detection algorithms is often limited by the challenges posed by complex outdoor environments, small target sizes, and group occlusions. To address these issues, this study constructs a dataset comprising over 8000 images of 10 protected wildlife species and investigates effective detection methods for wildlife in natural habitats. We propose a novel deep learning-based detection framework, YOLO-WildASM, which incorporates three key improvements to the YOLOv8 architecture: a P2 detection layer for small objects, a multi-head self-attention (MHSA) mechanism, and a bidirectional feature pyramid network (BiFPN). Experimental results demonstrate that YOLO-WildASM significantly outperforms YOLOv8 and other state-of-the-art models on the custom wildlife dataset, achieving a mAP50 of 94.1%, which is 2.8% higher than the baseline model and superior to the latest YOLOv12 model (92.2%). Furthermore, ablation and generalization experiments validate the model's enhanced performance and adaptability in multi-scale wildlife detection tasks. The proposed deep learning-based detection framework provides an efficient and robust solution for wildlife monitoring and ecological conservation in complex natural ecosystems.}, }
@article {pmid41006295, year = {2025}, author = {van Galen, LG and Smith, GR and Margenot, AJ and Waldrop, MP and Crowther, TW and Peay, KG and Jackson, RB and Yu, K and Abrahão, A and Ahmed, TA and Alatalo, JM and Anslan, S and Anthony, MA and Araujo, ASF and Ascher-Jenull, J and Bach, EM and Bahram, M and Baker, CCM and Baldrian, P and Bardgett, RD and Barrios-Garcia, MN and Bastida, F and Beggi, F and Benning, LG and Bragazza, L and Broadbent, AAD and Cano-Díaz, C and Cates, AM and Cerri, CEP and Cesarz, S and Chen, B and Classen, AT and Dahl, MB and Delgado-Baquerizo, M and Eisenhauer, N and Evgrafova, SY and Fanin, N and Fornasier, F and Francisco, R and Franco, ALC and Frey, SD and Fritze, H and García, C and García-Palacios, P and Gómez-Brandón, M and Gonzalez-Polo, M and Gozalo, B and Griffiths, R and Guerra, C and Hallama, M and Hiiesalu, I and Hossain, MZ and Hu, Y and Insam, H and Jassey, VEJ and Jiang, L and Kandeler, E and Kohout, P and Kõljalg, U and Krashevska, V and Li, X and Lu, JZ and Lu, X and Luo, S and Lutz, S and Mackie-Haas, KA and Maestre, FT and Malmivaara-Lämsä, M and Mangelsdorf, K and Manjarrez, M and Marhan, S and Martin, A and Mason, KE and Mayor, J and McCulley, RL and Moora, M and Morais, PV and Muñoz-Rojas, M and Murugan, R and Nottingham, AT and Ochoa, V and Ochoa-Hueso, R and Oja, J and Olsson, PA and Öpik, M and Ostle, N and Peltoniemi, K and Pennanen, T and Pescador, DS and Png, GK and Poll, C and Põlme, S and Potapov, AM and Priemé, A and Pritchard, W and Puissant, J and Rocha, SMB and Rosinger, C and Ruess, L and Sayer, EJ and Scheu, S and Sinsabaugh, RL and Slaughter, LC and Soudzilovskaia, NA and Sousa, JP and Stanish, L and Sugiyama, SI and Tedersoo, L and Trivedi, P and Vahter, T and Voriskova, J and Wagner, D and Wang, C and Wardle, DA and Whitaker, J and Yang, Y and Zhong, Z and Zhu, K and Ziolkowski, LA and Zobel, M and van den Hoogen, J}, title = {A global database of soil microbial phospholipid fatty acids and enzyme activities.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1568}, pmid = {41006295}, issn = {2052-4463}, support = {DEB-1845544//National Science Foundation (NSF)/ ; DEB-1926335//National Science Foundation (NSF)/ ; DGE 1450271//National Science Foundation (NSF)/ ; QUEX-CAS-QP-RD-18/19//Qatar Petroleum (QP)/ ; QUEX-CAS-QP-RD-18/19//Qatar Petroleum (QP)/ ; 305069/2018-7//Ministry of Science, Technology and Innovation | Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (National Council for Scientific and Technological Development)/ ; I989-B16//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; I989-B16//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; I989-B16//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; CZ.02.01.01/00/22_008/0004635//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy (Ministry of Education, Youth and Sports)/ ; NE/N009452/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/N009452/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/I027037/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/I027037/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/N009452/1//RCUK | Natural Environment Research Council (NERC)/ ; PICT 2014-2838//Ministry of Science, Technology and Productive Innovation, Argentina | Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica (National Agency for Science and Technology, Argentina)/ ; 315260_149807//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; BIPD_01_2021_FCT-PTDC/BIA-CBI/2340/2020, UIDB/05937/2020, UIDP/05937/2020//NOVA | Faculdade de Ci&#xea;ncias e Tecnologia, Universidade Nova de Lisboa (FCT/UNL)/ ; UID/EMS/00285/2020//NOVA | Faculdade de Ci&#xea;ncias e Tecnologia, Universidade Nova de Lisboa (FCT/UNL)/ ; UID/EMS/00285/2020//NOVA | Faculdade de Ci&#xea;ncias e Tecnologia, Universidade Nova de Lisboa (FCT/UNL)/ ; DFG- FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG- FZT 118, 202548816, Ei 862/29-1 and Ei 862/31-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG- FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 192626868-SFB 990//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 316045089//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 192626868-SFB 990//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 315415//Academy of Finland (Suomen Akatemia)/ ; PTDC/BIA-CBI/2340/2020//Ministry of Education and Science | Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia (Portuguese Science and Technology Foundation)/ ; ANR; MIXOPEAT; ANR-17-CE01-0007//Agence Nationale de la Recherche (French National Research Agency)/ ; 31872994//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41922056//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32101286//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32061143027//National Natural Science Foundation of China (National Science Foundation of China)/ ; CIDEGENT/2018/041//Generalitat Valenciana (Regional Government of Valencia)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; NE/T012226//National Eye Research Centre (NERC)/ ; PRG1065, PRG1789, PSG784//Ministry of Education and Research | Estonian Research Competency Council (Research Competency Council)/ ; 2021M693360//China Postdoctoral Science Foundation/ ; }, mesh = {*Soil Microbiology ; *Phospholipids ; *Fatty Acids ; *Databases, Factual ; *Enzymes ; Soil/chemistry ; Ecosystem ; }, abstract = {Soil microbes drive ecosystem function and play a critical role in how ecosystems respond to global change. Research surrounding soil microbial communities has rapidly increased in recent decades, and substantial data relating to phospholipid fatty acids (PLFAs) and potential enzyme activity have been collected and analysed. However, studies have mostly been restricted to local and regional scales, and their accuracy and usefulness are limited by the extent of accessible data. Here we aim to improve data availability by collating a global database of soil PLFA and potential enzyme activity measurements from 12,258 georeferenced samples located across all continents, 5.1% of which have not previously been published. The database contains data relating to 113 PLFAs and 26 enzyme activities, and includes metadata such as sampling date, sample depth, and soil pH, total carbon, and total nitrogen. This database will help researchers in conducting both global- and local-scale studies to better understand soil microbial biomass and function.}, }
@article {pmid41004955, year = {2025}, author = {Qin, J and Wang, Q and Li, W}, title = {Incorporating regional green spaces into greenspace exposure assessment: A nationwide study of 244 Chinese cities.}, journal = {Journal of environmental management}, volume = {394}, number = {}, pages = {127369}, doi = {10.1016/j.jenvman.2025.127369}, pmid = {41004955}, issn = {1095-8630}, mesh = {Cities ; China ; Urbanization ; Humans ; Ecosystem ; Transportation ; *Conservation of Natural Resources ; }, abstract = {Green spaces are essential components of urban ecosystems, offering ecological services that support environmental sustainability and enhance human well-being. However, rapid urbanization has caused substantial declines in green space, particularly in rapidly growing cities. In this context, regional green spaces (RGSs), which are defined as green areas located beyond the boundaries of built-up areas, have gained attention for their ecological value and strategic role in enhancing urban resilience. Despite their importance, RGSs remain underrepresented in current greenspace exposure assessment frameworks. To fill this gap, we propose a novel transportation-weighted global greenspace exposure model that integrates RGSs, urban green spaces, and transportation proximity. Using greenspace exposure (GE) as an indicator, the model assesses the spatial distribution and exposure contribution of RGSs. We applied this model to 244 Chinese cities and obtained the following findings: (1) Incorporating RGSs significantly improves GE levels in many cities, particularly in southern and western regions, while also amplifying spatial disparities; (2) The compensatory effect of RGSs was validated, as substantial GE increases were observed under larger RGSs buffer zones; (3) Nighttime light intensity, elevation, and land surface temperature correlate strongly with GE, indicating the influence of both anthropogenic and natural factors. The proposed framework enhances the accuracy of GE assessments by integrating RGSs and transportation networks. Its scalable structure and moderate data requirements enable its application across diverse regions, supporting international efforts toward sustainable urban development.}, }
@article {pmid41003170, year = {2025}, author = {Francesconi, L and Conti, M and Martellos, S and Di Nuzzo, L and Gheza, G and Nimis, PL and Pistocchi, C and Nascimbene, J}, title = {Dolichens: An Information System on the Lichens of the Dolomites.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {11}, number = {9}, pages = {}, pmid = {41003170}, issn = {2309-608X}, support = {DOT199RYN9-2//Ministero dell'universit&#xe0; e della ricerca/ ; }, abstract = {Lichens, despite their key role as environmental indicators and their ecological importance, remain underrepresented in conservation policies, largely due to fragmented exploration of several areas, as well as limited availability of data in digital platforms. The UNESCO World Heritage area of the Dolomites (N Italy) is well-investigated as far as lichen diversity is concerned, with a long history of lichenological exploration since the 19th century. However, the relevant amount of data produced by these efforts was scattered and often not accessible in digital format, thus hindering data accessibility and usability. In this paper, we present Dolichens, a novel web platform designed to aggregate data about lichen diversity in the Dolomites. The platform aims at making available a comprehensive resource to support research, monitoring, and conservation of lichen diversity in the Dolomites, while ensuring data interoperability with the most relevant global repositories.}, }
@article {pmid41001881, year = {2026}, author = {Rutz, A and Probst, D and Aguilar, C and Akiyama, DY and Alberti, F and Augustijn, HE and Avalon, NE and Beemelmanns, C and Barbieri, HB and Biermann, F and Bridge, AJ and Girón, EC and Cox, R and Crüsemann, M and D'Agostino, PM and Feuermann, M and Gerke, J and García, KG and Holme, JE and Hwang, JY and Iacovelli, R and Jeronimo Barbosa, JC and Kaur, N and Klapper, M and Köhler, AM and Korenskaia, A and Kubach, N and Lee, BT and Loureiro, C and Mantri, S and Narula, S and Meijer, D and Navarro-Muñoz, JC and Nguyen, GS and Paliyal, S and Panghal, M and Rao, L and Sieber, S and Sokolova, N and Sowa, ST and Szenei, J and Terlouw, BR and Weddeling, HG and Yu, J and Ziemert, N and Weber, T and Blin, K and van der Hooft, JJJ and Medema, MH and Zdouc, MM}, title = {MITE: the Minimum Information about a Tailoring Enzyme database for capturing specialized metabolite biosynthesis.}, journal = {Nucleic acids research}, volume = {54}, number = {D1}, pages = {D635-D642}, pmid = {41001881}, issn = {1362-4962}, support = {101 072 485//Marie Sk&#x142;odowska-Curie/ ; //German Research Foundation/ ; 102 029 187//SINTEF/ ; 2023/06874-4//S&#xe3;o Paulo Research Foundation/ ; //Department of Biotechnology/ ; 101 000 392//Horizon 2020/ ; //National Agri-Food and Biomanufacturing Institute (NABI)/ ; //University Grants Commission/ ; //the Werner Siemens Foundation/ ; //DFG/ ; KICH1.LWV04.21.013//Netherlands Organisation for Scientific Research/ ; F32AT011475/GF/NIH HHS/United States ; //NWO/ ; //State Secretariat for Education, Research and Innovation/ ; 948770-DECIPHER/ERC_/European Research Council/International ; //Horizon Europe programme/ ; //Danish National Research Foundation/ ; MR/V022334/1//UKRI/ ; NNF20CC0035580//Novo Nordisk Foundation/ ; 102 022 750//SINTEF/ ; NNF23OC0086472//Novo Nordisk Foundation/ ; //Hans-Fischer-Gesellschaft/ ; //German Center for Infection Research/ ; 495740318//German Research Foundation/ ; 802736, MORPHEUS//Horizon 2020/ ; 239748522//Deutsche Forschungsgemeinschaft/ ; 2021/08947-3//S&#xe3;o Paulo Research Foundation/ ; 101 072 485//Horizon Europe Marie Sk&#x142;odowska-Curie/ ; 21/07038-0//S&#xe3;o Paulo Research Foundation/ ; 102 029 407//SINTEF/ ; 102024676-14//SINTEF/ ; F32 AT011475/AT/NCCIH NIH HHS/United States ; 862 923//Horizon 2020/ ; 101 081 957//Horizon 2020/ ; }, mesh = {*Enzymes/metabolism/chemistry/genetics ; Substrate Specificity ; *Software ; Humans ; Machine Learning ; Computational Biology/methods ; Internet ; *Databases, Protein ; }, abstract = {Secondary or specialized metabolites show extraordinary structural diversity and potent biological activities relevant for clinical and industrial applications. The biosynthesis of these metabolites usually starts with the assembly of a core 'scaffold', which is subsequently modified by tailoring enzymes to define the molecule's final structure and, in turn, its biological activity profile. Knowledge about reaction and substrate specificity of tailoring enzymes is essential for understanding and computationally predicting metabolite biosynthesis, but this information is usually scattered in the literature. Here, we present MITE, the Minimum Information about a Tailoring Enzyme database. MITE employs a comprehensive set of parameters to annotate tailoring enzymes, defining substrate and reaction specificity by the expressive reaction SMARTS (Simplified Molecular Input Line Entry System Arbitrary Target Specification) chemical pattern language. Both human and machine readable, MITE can be used as a knowledge base, for in silico biosynthesis, or to train machine-learning applications, and tightly integrates with existing resources. Designed as a community-driven and open resource, MITE employs a rolling release model of data curation and expert review. MITE is freely accessible at https://mite.bioinformatics.nl/.}, }
@article {pmid41001448, year = {2025}, author = {Evans, LM and Arehart, CH and Gibson, RA and Bowman, GI and Gignoux, CR}, title = {A simple approach for multiple observations improves power to detect genetic effects and genomic prediction accuracy.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {41001448}, support = {R01 AG046938/AG/NIA NIH HHS/United States ; T32 MH016880/MH/NIMH NIH HHS/United States ; U01 AG009740/AG/NIA NIH HHS/United States ; }, abstract = {Many datasets, including widely used biobanks, have more than one observation of numerous phenotypes for at least a portion of their sample. The majority of GWAS utilize only a single observation per individual, even when more than one observation may be available, and apply a standard model in which the additive allelic effect being estimated is assumed to be constant across the age or time range in the sample. Here, we test a set of simple approaches to utilize multiple observations per individual, under this same assumption. We find that utilizing the mean or median of the available observations rather than a single observation improves power to detect associated loci and enriched gene sets and yields higher out-of-sample polygenic score prediction accuracy. Despite growing biobanks, many deeply phenotyped samples are relatively small but have multiple observations. While explicitly modeling age- or time-dependent genetic effects can estimate time- or age-specific genetic effects, most GWAS apply a standard, additive-only model; a simple approach of using the mean or median can improve power by reducing "noise" in the phenotype, utilize standard, optimized software, and be particularly impactful for smaller samples, including samples of diverse genetic ancestry currently existing in widely used biobanks.}, }
@article {pmid40998880, year = {2025}, author = {Le Scornec, E and Chimienti, M and Corbeau, A and Pajot, A and Weimerskirch, H and Collet, J}, title = {Predicting fisheries from albatross movements requires accounting for individual variability in interaction.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {32807}, pmid = {40998880}, issn = {2045-2322}, mesh = {Animals ; *Fisheries ; *Birds/physiology ; Geographic Information Systems ; *Animal Migration ; }, abstract = {Fisheries have major ecological impacts including bycatch of foraging seabirds, but it is often difficult to obtain comprehensive information on the presence of fishing vessels. Automatic Identification System (AIS) data can be used to monitor fisheries and their interactions with GPS-tracked seabirds, but not all vessels have their AIS operational. Bird-tied radar detectors can overcome this limit and complement monitoring, but the technology is recent and costly. We used both methods combined as a training dataset for classification algorithms, to extend the identification of interactions to GPS tracks without radar detectors nor AIS. We studied over 3 years wandering albatrosses from the French Southern Territories, interacting with toothfish and tuna longliners. We used 196 GPS tracks combined with radar detectors, to calculate different movement variables over various scales (time spent in an area, sinuosity, speed) and used a Random Forest to distinguish behaviour in presence or absence of fishing vessels. Our model reached high classification accuracy (ca. 85%) for individual birds included in the training dataset. However, we lost predictive power (around 72% of accuracy, with a drop of specificity from 76 to 59%) when predicting on individuals not included in the training dataset. Our results emphasize the importance of documenting and accounting for individual variations to use animals as sentinels. We discuss the pros and cons of different research avenues (data sampling, classification model, bird species, etc.) to eventually get to predict fisheries from bird movements only.}, }
@article {pmid40997916, year = {2025}, author = {Zhong, H and Chi, S and Magaña, AA and Fordwour, OB and Foster, LJ}, title = {Integrative Omics and AI-Driven Systems Biology: Multilayer Networks Decoding Apis mellifera Health and Resilience.}, journal = {Journal of proteome research}, volume = {24}, number = {11}, pages = {5305-5318}, pmid = {40997916}, issn = {1535-3907}, mesh = {Bees/physiology/metabolism/genetics ; Animals ; *Systems Biology/methods ; *Artificial Intelligence ; *Proteomics/methods ; *Metabolomics/methods ; Lipidomics/methods ; Machine Learning ; Multiomics ; }, abstract = {Honey bees (Apis mellifera) are vital pollinators essential for maintaining ecosystem stability and global food production, but they face escalating threats from pathogens, agrochemicals, and climate change. Although proteomics has advanced our understanding of bee physiology, single-omics approaches are insufficient to capture the complexity of colony health. This review highlights the rise of integrative multiomics frameworks─combining proteomics, metabolomics, and lipidomics─with artificial intelligence (AI)-based strategies to decode molecular resilience in bees. We summarize recent advances in omics technologies, including spatial and single-cell platforms, mass spectrometry innovations, and customized computational pipelines. Furthermore, we highlight how AI-enhanced multiomics integration facilitates biomarker discovery, elucidates regulatory networks, especially in nonmodel organisms like honey bees. Emerging computational methods such as deep learning, graph neural networks, and multilayer network models offer predictive, scalable, and interpretable insights. Despite challenges like limited sample input and cross-omics heterogeneity, the convergence of omics and machine learning represents a transformative paradigm for decoding complex biological systems. These integrative approaches offer not only a deeper molecular understanding of bee biology but also generalizable frameworks for systems biology in other ecologically relevant species.}, }
@article {pmid40997859, year = {2025}, author = {Hu, J and Bao, G and Wu, J and Chen, S and Xu, Y and Wang, H and Tian, L and Fu, Z and Li, N and Yuan, Y}, title = {Freeze-Thaw Cycles Accelerate Plastic Pollution Invasion in Agriculture: Trojan Horse Effect of Microplastic-Plasticizer Contamination Revealed in Rye via Computational Chemistry and Multiomics.}, journal = {Journal of agricultural and food chemistry}, volume = {73}, number = {40}, pages = {25285-25300}, doi = {10.1021/acs.jafc.5c08155}, pmid = {40997859}, issn = {1520-5118}, mesh = {*Soil Pollutants/chemistry/metabolism/toxicity ; *Microplastics/metabolism/chemistry/toxicity/analysis ; *Secale/metabolism/drug effects/chemistry/genetics/growth &amp; development ; *Plasticizers/metabolism/chemistry/toxicity ; Freezing ; Phthalic Acids/metabolism/chemistry/toxicity ; Bacteria/genetics/metabolism/isolation &amp; purification/classification/drug effects ; Agriculture ; Plant Roots/metabolism/drug effects/microbiology ; Multiomics ; }, abstract = {Climate change-related freeze-thaw (FT) cycles intensify combined contamination from diethyl phthalate (DEP) and microplastics (MPs) in agricultural systems. This study examines their synergistic phytotoxicity in hydroponic rye using multidisciplinary approaches, including physiology, transcriptomics, and computational modeling. FT dramatically increased cocontamination risks. Notably, DEP promoted MP uptake into plants by elevating MP surface charge─an effect intensified by FT─resulting in disrupted root function and nutrient absorption. Molecular analyses showed that DEP binds strongly to key proteins (e.g., HSP70; ΔG = -7.6 kcal/mol), inhibiting photosynthesis (net rate reduced by 20.1-64.5%) and altering antioxidant activity. MPs adsorbed DEP, reducing its mobility, while simultaneously reshaping the root microbiome to favor DEP-degrading bacteria (e.g., Rhizobium). Transcriptomic changes were observed in stress-responsive and phytohormone pathways. These results demonstrate that FT cycles exacerbate combined pollutant toxicity through surface charge modification, molecular disruption, and microbial community adaptation, offering important insights for assessing ecological risks under climate-induced stressors.}, }
@article {pmid40997692, year = {2025}, author = {Zang, H and Feng, Y and Yang, F and Gao, S and Su, M and Li, H}, title = {Multi-media distribution, partitioning behavior, and environmental risk of per- and polyfluoroalkyl substances (PFASs) in the southern coastal zone of Shandong Peninsula, China.}, journal = {Marine environmental research}, volume = {212}, number = {}, pages = {107562}, doi = {10.1016/j.marenvres.2025.107562}, pmid = {40997692}, issn = {1879-0291}, abstract = {Per- and polyfluoroalkyl substances (PFASs) pose significant ecological threats due to their persistence and toxicity. This study investigates the occurrence, partitioning behavior, and environmental risks of 33 legacy and emerging PFASs in the southern coastal zone of Shandong Peninsula, China. Paired water and sediment samples were collected from 55 sites across groundwater, river, estuarine, tourist beaches and marine ranches. PFASs were ubiquitously detected, with total concentrations (∑PFASs) ranging from 23.41 to 80.62 ng/L in water and 0.38-6.49 ng/g dry weight (dw) in sediment. Except perfluorooctanoic acid (PFOA), perfluorobutanoic acid (PFBA) (6.42 ± 2.26 ng/L) and perfluorobutanesulfonic acid (PFBS) (3.03 ± 1.44 ng/L) dominated aqueous phases, reflecting phased-out replacements of long-chain homologs. Sediments accumulated long-chain compounds (e.g., Perfluorohexanoic acid (PFHxA): 0.92 ± 1.08 ng/g dw; perfluorooctane sulfonic acid (PFOS): 0.45 ± 0.28 ng/g dw), driven by hydrophobic partitioning. Strong positive correlations among long-chain PFASs (e.g., Perfluorododecanoic acid (PFDoDA)- perfluorotetradecanoic acid (PFTeDA), r = 0.882) indicated co-accumulation in organic-rich sediments. Spatial analysis revealed land-to-sea concentration gradients, with maxima in estuaries (52.72 ng/L) and industrial-adjacent sediments (6.48 ng/g dw). Groundwater infiltration (up to 51.53 ng/L) highlighted subsurface transport risks. Sediment-water partition coefficients (log Kd) increased with carbon chain length and salinity, consistent with salting-out effects and reduced electrostatic repulsion. Organic carbon-normalized log Koc values (Kow method) aligned with model predictions for most PFASs. Risk assessment identified high ecological risk for sediment-bound PFOS (RQ > 1) near river discharges, while PFOA posed greater aqueous-phase risks. Emerging PFASs (e.g., 6:2 chlorinated polyfluoroalkyl ether sulfonic acid (6:2 Cl-PFESA)) showed negligible risks. Coastal sediments act as significant PFASs reservoirs, with resuspension potential enabling secondary pollution.}, }
@article {pmid40996892, year = {2025}, author = {Njoroge, SM and Kulohoma, BW and Falzon, LC and Kamanu, TK and Momanyi, K and Muinde, P and Murungi, MK and Ogendo, A and Ogola, J and Wambua, L and Kangethe, E and Rushton, J and Woolhouse, M and Thomson, NR and Kariuki, S and von Mentzer, A and Fèvre, EM}, title = {Genomic profiling of enterotoxigenic Escherichia coli toxins and adhesins in livestock isolates from Kenya.}, journal = {Microbial genomics}, volume = {11}, number = {9}, pages = {}, doi = {10.1099/mgen.0.001515}, pmid = {40996892}, issn = {2057-5858}, mesh = {*Enterotoxigenic Escherichia coli/genetics/isolation &amp; purification/pathogenicity ; Kenya/epidemiology ; Animals ; *Livestock/microbiology ; *Escherichia coli Infections/microbiology/veterinary ; *Enterotoxins/genetics ; *Escherichia coli Proteins/genetics ; *Adhesins, Bacterial/genetics ; *Bacterial Toxins/genetics ; Virulence Factors/genetics ; Whole Genome Sequencing ; Humans ; Feces/microbiology ; Cattle ; *Adhesins, Escherichia coli/genetics ; }, abstract = {Enterotoxigenic Escherichia coli (ETEC) is a significant cause of diarrhoea in livestock and humans. The epidemiology of ETEC in animals remains understudied, prompting an investigation into the virulence factors and associated adhesins of ETEC in livestock from Western Kenya. Also, there is limited evidence supporting the role of livestock as possible zoonotic reservoirs for ETEC. ETEC strains harbour colonization factors/adhesins and enterotoxins, with animal ETECs exhibiting various adhesins (F4, F5, F6, F17, F18 and F41). Enterotoxins include heat-labile (LT) and heat-stable (ST) toxins and are further divided into LT-I and LT-II and STa and STb, respectively. Additional toxin combinations occur, with ETEC and Shiga toxin-producing E. coli (STEC) hybrids garnering public health significance. Here, we analysed faecal and mesenteric lymph node samples from diverse livestock across three Western Kenyan counties (Busia, Bungoma and Kakamega), using whole-genome sequencing. In silico screening determined the presence of AB5 and A2B5-like toxin genes, including cytolethal distending toxin (cdtABC) along with associated adhesins. To broaden the screening panel, adhesin genes identified were further characterized to identify both known and novel alleles, particularly focusing on human-ETEC colonization factors. Two estA alleles (estA-4-06, estA-6-02) and six eltAB-II toxin alleles (eltAB-II-a2-01, eltAB-II-a3-01, eltAB-II-c1-02, eltAB-II-c6-03, eltAB-II-c6-04 and eltAB-II-c7-02) were identified in livestock. Hybrid ETECs identified were ETEC/STEC present in 6.7% (4/60) of ETEC strains and ETEC with cdtABC type I. An A2B5-like tripartite toxin, potentially resembling the typhoid toxin, was detected in 8.7% (4/46) of the eltAB-II-positive strains. It may have unique effects on enterocytes distinct from known toxins. These findings expand our understanding of ETEC pathogenicity and genetic diversity in animal reservoirs, while also highlighting potential zoonotic risks. They broaden the toxin repertoire, offer adhesin-based vaccine candidates for livestock and provide valuable insights for future vaccine development and public health strategies in the Lake Victoria Crescent ecosystem and beyond.}, }
@article {pmid40996715, year = {2025}, author = {Fruggiero, I and Maisto, A and Passaro, S and Gentile, D and Nunziata, A and D'Agostino, N}, title = {A new database of chestnut DNA fingerprints for genetic diversity assessment, precise varietal identification, and traceability.}, journal = {Database : the journal of biological databases and curation}, volume = {2025}, number = {}, pages = {}, pmid = {40996715}, issn = {1758-0463}, support = {//Italy-Rural Development Programme/ ; //Italian Ministry of Agriculture/ ; }, mesh = {*Fagaceae/genetics ; *Genetic Variation ; Polymorphism, Single Nucleotide ; *DNA Fingerprinting ; *Databases, Genetic ; *DNA, Plant/genetics ; }, abstract = {The European chestnut (Castanea sativa Mill., Fagaceae) is ecologically and economically important, particularly in countries like Italy, Greece, Spain, and Turkey, where it supports rural economies and ecosystems. Accurate varietal recognition is crucial for managing chestnut groves but is hindered by the limitations of traditional methods, which require costly expertise and struggle to identify young, dormant, or scion trees. Recent advances in molecular tools, particularly single nucleotide polymorphism (SNP) markers identified through Kompetitive Allele-Specific PCR (KASP) technology, have transformed cultivar identification. To harness this potential, we developed KASTRACKdb, a genetic fingerprinting database for European chestnut that now integrates genotypic and phenotypic data for 150 chestnut accessions. Designed to translate KASP analysis results into practical and actionable insights, KASTRACKdb serves as a powerful tool for cultivar identification and management. The database offers three primary query modes and is designed for continuous upgrades, serving a crucial role in cataloguing the genetic diversity of chestnut trees, characterized by broad geographic distributions and significant genetic variation. This diversity is critical for conservation and breeding programs, enabling precise varietal identification and traceability to protect intellectual property, verify authenticity, and support the commercialization of high-value cultivars. Database URL: KASTRACKdb is available online at https://kastrack.crea.gov.it/kastrackdb/?lang=en.}, }
@article {pmid40996703, year = {2025}, author = {Sierra, MA and Ryon, K and Arikatla, MR and Elshafey, R and Bhaskar, H and Proszynski, J and Bhattacharya, C and Shaaban, H and Danko, DC and Ambrose, P and Spaulding, SA and Zambrano, MM and Consortium, TMD and Mason, CE}, title = {The Microbe Directory: a centralized database for biological interpretation of microbiome data.}, journal = {Database : the journal of biological databases and curation}, volume = {2025}, number = {}, pages = {}, pmid = {40996703}, issn = {1758-0463}, support = {U01DA053941/NH/NIH HHS/United States ; U54AG089334/NH/NIH HHS/United States ; R01AI151059/NH/NIH HHS/United States ; 80NSSC24K0728/NASA/NASA/United States ; 80NSSC24K1052/NASA/NASA/United States ; //WorldQuant Foundation/ ; }, mesh = {*Microbiota/genetics ; Humans ; *Databases, Genetic ; Data Curation ; Metadata ; Animals ; Metagenomics ; }, abstract = {The Microbe Directory (TMD) is a centralized database of metadata for microbes from all domains that helps with the biological interpretation of metagenomic data. The database comprises phenotypical and ecological traits of microorganisms, which have been verified by independent manual annotations. This effort has been possible by the help of a community of volunteer students worldwide who were trained in manual curation of microbiology data. To summarize this information, we have built an interactive browser that makes the database accessible to everyone, including non-bioinformaticians. We used the TMD data to analyse microbiome samples from different projects such as MetaSUB, TARA Oceans, Human Microbiome Project, and Sponge Microbiome Project, showcasing the utility of TMD. Furthermore, we compare our microbial annotations with annotations collected by artificial intelligence (AI) and demonstrate that despite the high speed of AI in reviewing and collecting microbial data, annotation requires domain knowledge and therefore manual curation. Collectively, TMD provides a unique source of information that can help to interpret microbiome data and uncover biological associations. Database URL: www.themicrobedirectory.com/.}, }
@article {pmid40995615, year = {2025}, author = {Kuhara, S and Matsugaki, R and Itoh, H and Oginosawa, Y and Fushimi, K and Matsuda, S and Saeki, S}, title = {Factors Influencing the Availability of Cardiopulmonary Exercise Testing for Patients Undergoing Cardiac Resynchronization Therapy in Japan.}, journal = {Journal of arrhythmia}, volume = {41}, number = {5}, pages = {e70198}, pmid = {40995615}, issn = {1880-4276}, abstract = {BACKGROUND: This study aimed to investigate the implementation rate of cardiopulmonary exercise testing (CPET) in patients undergoing cardiac resynchronization therapy (CRT) or cardiac resynchronization therapy-defibrillator (CRT-D), as well as the associated factors, using real-world data.<br><br>METHODS AND RESULTS: Data from the Diagnostic Procedure Combination System in Japan (2014-2018) was analyzed. The participants were cardiac patients who underwent CRT or CRT-D device implantation (n&#x2009;=&#x2009;3859). The primary outcome was whether CPET was performed after device implantation. Unpaired t-tests and chi-squared tests were used to compare the characteristics of the CPET (+) and CPET (-) groups. Multivariate analysis was used to identify factors associated with CPET performance. CPET was performed in 134 patients (3%). The CPET (-) group was older and had lower Barthel Index (BI) scores at discharge. CPET (+) patients had a higher rate of cardiac rehabilitation. Multivariate analysis revealed that age&#x2009;<&#x2009;70&#x2009;years and BI score&#x2009;&#x2265;&#x2009;85 at discharge were associated with CPET implementation. In-hospital cardiac rehabilitation is also an important determinant.<br><br>CONCLUSIONS: The CPET implementation after CRT or CRT-D was low. Emphasizing the importance of CPET may improve these rates. Future studies should explore strategies to increase its use in this patient population.}, }
@article {pmid40993501, year = {2025}, author = {Garnier, &#xc9; and Delalandre, L and Segrestin, J and Barkaoui, K and Kazakou, E and Navas, ML and Vile, D and Violle, C and Bernard-Verdier, M and Birouste, M and Blanchard, A and Bumb, I and Cruz, P and Debain, S and Fayolle, A and Fortunel, C and Grigulis, K and Laurent, G and Lavorel, S and Lloret, F and Pérez-Ramos, IM and Prieto, I and Roumet, C}, title = {FAIRTraits: An enriched, FAIR-compliant database of plant traits from Mediterranean populations of 240 species.}, journal = {Ecology}, volume = {106}, number = {9}, pages = {e70219}, pmid = {40993501}, issn = {1939-9170}, support = {AAPFNSO2019OpenMetaPaper-14026//Minist&#xe8;re de l'Enseignement sup&#xe9;rieur et de la Recherche (FNSO Project)/ ; }, mesh = {*Plants/classification ; Mediterranean Region ; *Databases, Factual ; *Plant Physiological Phenomena ; }, abstract = {Trait-based ecology relies on high-quality, well-documented data to explore how plant traits relate to environmental conditions, community assembly, and ecosystem functioning. However, the reuse and synthesis of trait data across studies remain limited by several constraints: a lack of detailed metadata, heterogeneous protocols, absence of individual-level measurements, and underrepresentation of certain trait types-particularly below-ground traits. Many existing datasets also lack the environmental details necessary to investigate trait-environment relationships at local scales. Here, we present FAIRTraits, a comprehensive dataset that addresses these limitations by compiling 189,452 records of quantitative trait measurements collected between 1997 and 2023 from 1955 populations of 240 vascular plant species in the Northern Mediterranean Basin, a region known both for its exceptional biodiversity and as a climate change hotspot. All data were collected by a single research group using consistent and well-documented field and laboratory protocols, ensuring internal consistency across traits, species, sites, and years. FAIRTraits includes 180 traits measured at the individual or replicate level, with no aggregation. It features an unprecedented diversity of traits spanning all major plant organs-leaves, stems, roots, and reproductive parts. These include widely used traits such as specific leaf area and plant height, but also traits that are rarely reported, especially below-ground traits related to root morphology, as well as mechanical properties, phenology, and microbial associations. In addition to raw measurements, species are annotated with categorical descriptors (e.g., life form, photosynthetic pathway, and successional status), and species-level values taken from a Mediterranean flora, for key traits such as reproductive phenology and maximum height. To support analyses that account for environmental variability, each observation is linked to detailed descriptors of the plot where the individual was sampled, including climate data, soil physicochemical properties, and disturbance regime. Full metadata on sampling protocols and measurement methods are provided for every trait and environmental variable. FAIRTraits was built in compliance with the FAIR principles of data management (Findable, Accessible, Interoperable, and Reusable). Metadata are described using the Ecological Metadata Language (EML); trait definitions are standardized using community-endorsed semantic resources. The data are archived across two interoperable repositories: GBIF (via Darwin Core and trait-specific extensions) for taxon-trait associations and InDoRES for environmental and contextual data. These efforts ensure long-term preservation, data traceability, and seamless integration with plant trait databases such as BROT or TRY, and cross-organism initiatives such as the Open Traits Network or the Encyclopedia of Life. FAIRTraits offers a robust, richly documented, and reusable resource for investigating plant functional strategies, trait-environment relationships, and scaling from individuals to communities and ecosystems. It also provides a concrete example of how trait datasets can meet the highest standards of data quality and interoperability-serving as a model for future community-led initiatives in functional ecology. The FAIRTraits database is released under the CC-BY Attribution 4.0 International license.}, }
@article {pmid40991430, year = {2025}, author = {Pascal, LV and Chadès, I and Adams, MP and Helmstedt, KJ}, title = {Developing new technologies to protect ecosystems: Planning with adaptive management.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {39}, pages = {e2422002122}, pmid = {40991430}, issn = {1091-6490}, support = {DE200101791//Department of Education and Training | Australian Research Council (ARC)/ ; DE200100683//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005//Department of Education and Training | Australian Research Council (ARC)/ ; }, mesh = {*Conservation of Natural Resources/methods ; *Ecosystem ; Climate Change ; Biodiversity ; Australia ; Coral Reefs ; }, abstract = {Technology development is an essential investment for policymakers to address contemporary global crises, including climate change, biodiversity loss, the energy transition, and emergent infectious diseases. However, investing limited resources in the development of new technologies is risky. The research and development process is unpredictable, with unknown timelines and outcomes. In addition, even after successful development, the effects of deploying a new technology remain uncertain. When confronted with these uncertainties, policymakers must determine how long they should allocate resources to developing new technologies. Informed decisions require anticipating possible successes and failures of both technology development and deployment, which is a challenging optimization task when managing dynamic systems, such as threatened ecological systems. Using an adaptive management approach from AI, we find a time limit new technologies should be developed for, which balances costs, benefits, and uncertainties during development and deployment. We extract clear and transparent general rules for investing in new technologies, building on an analytical approximation. Using Australia's Great Barrier Reef as a case study, we demonstrate that the development time limit ranges between 0 to 45 y before surrendering. We also show how characteristics of an ecological system influence the optimal investment strategy. Our approach can inform the development of new technologies in multiple domains including biodiversity conservation, public health, energy production, and the technology industry more broadly.}, }
@article {pmid40990718, year = {2025}, author = {Sabino, AU and Guerreiro, DM and Kim, AR and Ramos, AF and Reinitz, J}, title = {Characterizing the regulatory logic of transcriptional control at the DNA sequence level by ensembles of thermodynamic models.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {10}, pages = {}, pmid = {40990718}, issn = {1367-4811}, support = {R01 OD010936/OD/NIH HHS/United States ; R01 OD010936/NH/NIH HHS/United States ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior-Brasil (CAPES)/ ; //Programa Unificado de Bolsas-USP/ ; }, mesh = {Thermodynamics ; Animals ; Transcription Factors/metabolism ; *Transcription, Genetic ; Drosophila/genetics ; *Gene Expression Regulation ; Enhancer Elements, Genetic ; Drosophila Proteins/genetics/metabolism ; Binding Sites ; *Models, Genetic ; *DNA/chemistry/genetics ; *Sequence Analysis, DNA/methods ; Computational Biology/methods ; Base Sequence ; }, abstract = {MOTIVATION: Understanding how the genome encodes the regulatory logic of transcription is a main challenge of the post-genomic era, and can be overcome with the aid of customized computational tools.<br><br>RESULTS: We report an automated framework for analyzing an ensemble of fits to data of a thermodynamics-based sequence-level model for transcriptional regulation. The fits are clustered accordingly with their intrinsic regulatory logic. A multiscale analysis enables visualization of quantitative features resulting from the deconvolution of the regulatory profile provided by multiple transcription factors interacting with the locus of a gene. Quantitative experimental data on reporters driven by the whole locus of the even-skipped gene in the blastoderm of Drosophila embryos was used for validating our approach. A few clusters of highly active DNA binding sites within the enhancers collectively modulate even-skipped gene transcription. Analysis of variable enhancers' length shows the importance of bound protein-protein interactions for transcriptional regulation. The interplay between activation and quenching enables function conservation of enhancers despite length variations.<br><br>The transcription factor level data used for performing the reported study is accessible in the input files in Zenodo and GitHub as well the full code. Additional data from formerly FlyEx database will be available under request.}, }
@article {pmid40986865, year = {2025}, author = {Sun, Y and Jaiswal, A and Slade, C and Phillips, KT and Benzo, RM and Washington, P}, title = {Associations Between Social Determinants of Health and Adherence in Mobile-Based Ecological Momentary Assessment: Scoping Review.}, journal = {Journal of medical Internet research}, volume = {27}, number = {}, pages = {e69831}, pmid = {40986865}, issn = {1438-8871}, mesh = {Humans ; Male ; *Ecological Momentary Assessment ; Mobile Applications ; *Patient Compliance ; *Social Determinants of Health ; Telemedicine ; }, abstract = {BACKGROUND: Ecological momentary assessment (EMA) involves repeated prompts to capture real-time self-reported health outcomes and behaviors via mobile devices. With the rise of mobile health (mHealth) technologies, EMA has been applied across diverse populations and health domains. However, the extent to which EMA engagement and data quality vary across social determinants of health (SDoH) remains underexplored. Emerging evidence suggests that EMA adherence and data completeness may be sometimes associated with participant characteristics such as socioeconomic status, race/ethnicity, and education level. These associations may sometimes influence who engages with EMA protocols and the types of contextual data captured. Despite growing interest in these patterns, no review to date has synthesized evidence on how SDoH relate to EMA compliance and engagement.<br><br>OBJECTIVE: We conducted a scoping review to study two research questions: (R1) how EMA compliance rates in health studies can differ across SDoH and (R2) what types of SDoH have been identified through EMA health studies.<br><br>METHODS: Following PRISMA-ScR guidelines, we searched PubMed, Web of Science, and EBSCOhost using two sets of queries targeting EMA and its relationship to SDoH. Eligible studies were peer reviewed, were published in English between 2013 and 2024, and used mobile-based EMA methods. Studies were included if they (1) reported on differences in EMA compliance by SDoH or (2) reported at least one SDoH observed or uncovered during an EMA study. We used the social ecological model (SEM) as a guiding framework to categorize and interpret SDoH across individual, interpersonal, community, and societal levels. A qualitative thematic synthesis was conducted to iteratively and collaboratively extract, categorize, and review determinants.<br><br>RESULTS: We analyzed 48 eligible studies, of which 35 addressed R1 by examining compliance patterns across various SDoH. Using the SEM, we identified 13 determinants categorized across 4 levels: individual (eg, daily routine, biological sex, age, socioeconomic status, language, education, and race or ethnicity), interpersonal (eg, social support), community and organizational (eg, social context, social acceptance, stigmatization, and youth culture), and policy or societal (eg, systemic and structural barriers). These studies described differences in EMA response rates, compliance, and dropout associated with these determinants, often among vulnerable populations. The remaining 13 studies addressed R2, demonstrating examples of the types of SDoH that EMA research can uncover, including family culture, social support, social contexts, stigmatization, gender norms, heroic narratives, LGBTQ+ culture, racial discrimination, and systematic and structural barriers.<br><br>CONCLUSIONS: This scoping review illustrates how EMA compliance rates can differ across SDoH and highlights the potential of EMA to uncover social and cultural factors linked to health behaviors and outcomes. Our findings underscore the importance of integrating SDoH considerations into EMA study designs to capture context-specific sociocultural dynamics.}, }
@article {pmid40986480, year = {2025}, author = {Constant, A and Paquin, V and Ackerman, RA and Depp, CA and Moore, RC and Harvey, PD and Pinkham, AE}, title = {Exploring the clinical utility of rhythmic digital markers for schizophrenia.}, journal = {PLOS digital health}, volume = {4}, number = {9}, pages = {e0001010}, pmid = {40986480}, issn = {2767-3170}, abstract = {This study investigates the clinical utility of rhythmic digital markers (RDMs) in schizophrenia. RDMs are digital markers capturing behavioral rhythms over different timescales - within 24 hours span (ultradian), at a span of 24 hours (circadian), or over cycles of more than 24 hours (infradian). While previous research has explored digital markers for schizophrenia, the focus has primarily been on sensor data variability rather than rhythmic patterns. This study introduces two RDMs: an entropy RDM, which quantifies uncertainty in activity distribution over the infradian cycles, and a dynamic RDM, which is derived from models of transitions in entropy and psychotic symptom intensity using Markov chain analysis. Data were ecological momentary assessments (EMAs) of 39 activities collected from 390 individuals diagnosed with schizophrenia (N = 153) or bipolar disorder (N = 192) and controls (N = 45). We assessed associations between RDMs and symptom severity and whether participants could be differentiated based on these RDMs. We found that participants with schizophrenia significantly differed on dynamic RDMs, suggesting a potential diagnostic utility. However, dynamic RDMs were not associated with symptom severity, and entropy RDM had no significant clinical correlate. Our findings contribute to the growing evidence on digital markers in psychiatry and highlight the potential of rhythmic digital markers (RDMs) in characterizing digital phenotypes for schizophrenia.}, }
@article {pmid40979437, year = {2025}, author = {Atagong, SD and Tonnang, H and Senagi, K and Wamalwa, M and Agboka, KM and Odindi, J}, title = {A review on knowledge and information extraction from PDF documents and storage approaches.}, journal = {Frontiers in artificial intelligence}, volume = {8}, number = {}, pages = {1466092}, pmid = {40979437}, issn = {2624-8212}, abstract = {INTRODUCTION: Automating the extraction of information from Portable Document Format (PDF) documents represents a major advancement in information extraction, with applications in various domains such as healthcare, law, or biochemistry. However, existing solutions face challenges related to accuracy, domain adaptability, and implementation complexity.<br><br>METHODS: A systematic review of the literature was conducted using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) methodology to examine approaches and trends in PDF information extraction and storage approaches.<br><br>RESULTS: The review revealed three dominant methodological categories: rule-based systems, statistical learning models, and neural network-based approaches. Key limitations include the rigidity of rule-based methods, the lack of annotated domain-specific datasets for learning-based approaches, and issues such as hallucinations in large language models.<br><br>DISCUSSION: To overcome these limitations, a conceptual framework is proposed comprising nine core components: project manager, document manager, document pre-processor, ontology manager, information extractor, annotation engine, question-answering tool, knowledge visualizer, and data exporter. This framework aims to improve the accuracy, adaptability, and usability of PDF information extraction systems.}, }
@article {pmid40976215, year = {2025}, author = {Kakuma, M and Wada, T and Murakami, M and Tatsuno, T and Ishii, N and Kobayashi, NI and Kurosawa, T and Sayama, Y and Nihei, N and Ohte, N}, title = {Environmental and biological drivers of [137]Cs accumulation in freshwater fish across forested and downstream sites in Fukushima.}, journal = {Journal of environmental radioactivity}, volume = {290}, number = {}, pages = {107810}, doi = {10.1016/j.jenvrad.2025.107810}, pmid = {40976215}, issn = {1879-1700}, mesh = {Animals ; *Cesium Radioisotopes/analysis/metabolism ; *Fukushima Nuclear Accident ; *Water Pollutants, Radioactive/metabolism/analysis ; *Radiation Monitoring ; *Fishes/metabolism ; Japan ; Forests ; Rivers ; Fresh Water ; }, abstract = {To elucidate ecological factors governing [137]Cs accumulation in freshwater fish, we examined 10 species collected from forested headwater streams and downstream reaches of rivers flowing through the Fukushima evacuation zone between 2020 and 2022. By integrating land cover data with isotopic and body size metrics, our study clarifies mechanisms shaping radiocesium distribution across fish communities in post-accident environments. Individuals exceeding the Japanese regulatory limit of 100 Bq/kg-wet were found at all sites, and fish/water concentration ratios of [137]Cs varied widely, from 9.7 × 10 L/kg-wet in a sea-run masu salmon to 1.2 × 10[6] L/kg-wet in a Japanese dace. White-spotted charr and masu salmon, both typical stream-dwelling salmonids, exhibited significantly higher concentration ratios than the other species. Fish from areas with greater forest cover exhibited consistently elevated [137]Cs concentrations, indicating that forests serve as persistent sources of radiocesium to aquatic food webs more than a decade after the accident. Stable isotope analysis showed a significant positive association between terrestrial carbon contribution and [137]Cs concentration, demonstrating that individuals assimilating more terrestrial-derived resources tended to accumulate higher contamination. A positive relationship was also observed between relative body size and [137]Cs concentration, suggesting that growth-related traits influence accumulation. These results suggest that forest connectivity, dietary reliance on allochthonous resources, and individual growth characteristics collectively influence the accumulation of [137]Cs in freshwater fish. The approach and findings provide quantitative evidence for species- and site-specific processes underlying long-term radiocesium dynamics in forested river networks, informing risk assessment and fisheries management in radiologically impacted landscapes.}, }
@article {pmid40972996, year = {2025}, author = {Paladan, S and Kumbar, B and Govindasamy, D and Patil, S and Chethan Kumar, HB and Yogisharadhya, R and Yadav, P and Vivian, TJW and Gaekwad, SS and Kumar, N and Gulati, BR and Shivachandra, SB and Chanda, MM}, title = {Unravelling ecological factors influencing phylodynamics of Kyasanur Forest Disease in India.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {135}, number = {}, pages = {105831}, doi = {10.1016/j.meegid.2025.105831}, pmid = {40972996}, issn = {1567-7257}, mesh = {India/epidemiology ; *Kyasanur Forest Disease/epidemiology/virology/transmission ; Phylogeny ; *Encephalitis Viruses, Tick-Borne/genetics/classification ; Humans ; Genome, Viral ; Animals ; }, abstract = {Kyasanur Forest Disease Virus (KFDV) is a tick-borne flavivirus endemic to the Western Ghats region of India, with increasing reports of geographic expansion. This study employs phylogenetic analysis and spatial diffusion modeling to understand the evolutionary dynamics and transmission patterns of KFDV. Whole genome and E-gene sequences were analysed to identify major phylogenetic clusters, transmission velocity, and environmental factors influencing viral spread. The analysis revealed two primary phylogenetic clusters: Cluster A, originating in Karnataka, and linked to initial outbreaks (1957-1972) and subsequent re-emergence post-2010 in Karnataka, Kerala, and Goa; and Cluster B, which expanded from Maharashtra in the late 1970s into Tamil Nadu, Karnataka, and Kerala. Phylogenetic findings indicated a slow mutation rate, indicative of long-term viral persistence in sylvatic reservoirs rather than sustained human-human transmission. Spatial diffusion analysis estimated a median transmission velocity of 59.67 km/year. Environmental factors such as deforestation, land cover change, and livestock density acted as facilitators of viral spread, while urbanization, open water bodies, and precipitation served as resistance factors. The findings underscore the need for enhanced surveillance, ecological monitoring, and public health interventions to mitigate the increasing risk of KFD outbreaks. This study provides a comprehensive framework for understanding KFDV transmission and evolution, integrating phylogenetic and ecological data to improve risk assessment and guide control strategies in both endemic and emerging regions.}, }
@article {pmid40971902, year = {2025}, author = {Gontjes, KJ and Singh, A and Sansom, SE and Boyko, JD and Smith, SA and Lautenbach, E and Snitkin, E}, title = {Phylogenetic Context of Antibiotic Resistance Provides Insights into the Dynamics of Resistance Emergence and Spread.}, journal = {The Journal of infectious diseases}, volume = {232}, number = {6}, pages = {e992-e1002}, pmid = {40971902}, issn = {1537-6613}, support = {F31-AI186288//National Institute of Allergy and Infectious Diseases/ ; U19AI181767//National Institute of Allergy and Infectious Diseases/ ; T32-HG000040/HG/NHGRI NIH HHS/United States ; T32 HG000040/HG/NHGRI NIH HHS/United States ; 2217116//National Science Foundation/ ; U19 AI181767/AI/NIAID NIH HHS/United States ; 5R01AI148259//National Institute of Allergy and Infectious Diseases/ ; F31 AI186288/AI/NIAID NIH HHS/United States ; R01 AI148259/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Phylogeny ; *Anti-Bacterial Agents/pharmacology ; *Klebsiella pneumoniae/drug effects/genetics/classification/isolation &amp; purification ; *Klebsiella Infections/microbiology/epidemiology/transmission/drug therapy ; Whole Genome Sequencing ; Microbial Sensitivity Tests ; Carbapenems/pharmacology ; Male ; *Drug Resistance, Bacterial/genetics ; Female ; Drug Resistance, Multiple, Bacterial/genetics ; Aged ; Middle Aged ; }, abstract = {BACKGROUND: To ameliorate the antibiotic resistance crisis, the drivers of resistance emergence and resistance spread must be better understood.<br><br>METHODS: Whole-genome sequencing and susceptibility testing were performed on clinical carbapenem-resistant Klebsiella pneumoniae isolates collected from August 2014 to July 2015 across 12 long-term acute care hospitals. Ancestral state reconstruction partitioned patients with resistant strains into those that likely acquired resistance via de novo evolution or cross-transmission. Logistic regression was used to evaluate the associations between patient characteristics/exposures and these 2 pathways: resistance due to predicted within-host emergence of resistance and resistance due to predicted cross-transmission. This framework is available in the user-friendly R package, phyloAMR (https://github.com/kylegontjes/phyloAMR).<br><br>RESULTS: Phylogenetic analysis of 386 epidemic lineage carbapenem-resistant K. pneumoniae sequence type 258 isolates revealed differences in the relative contribution of de novo evolution and cross-transmission to the burden of resistance to 5 antibiotics. Clade-specific variations in rates of resistance emergence and their frequency and magnitude of spread were detected for each antibiotic. Phylogenetically informed regression modeling identified distinct clinical risk factors associated with each pathway. Exposure to the cognate antibiotic was an independent risk factor for resistance emergence (trimethoprim-sulfamethoxazole, colistin, and novel beta-lactam/beta-lactamase inhibitors) and resistance spread (trimethoprim-sulfamethoxazole, amikacin, and colistin). In addition to antibiotic exposures, comorbidities (eg, stage IV + decubitus ulcers) and indwelling medical devices (eg, gastrostomy tubes) were detected as unique risk factors for resistance spread.<br><br>CONCLUSIONS: Phylogenetic contextualization generated insights and hypotheses into how bacterial genetic background, patient characteristics, and clinical practices influence the emergence and spread of antibiotic resistance.}, }
@article {pmid40971701, year = {2025}, author = {Schumann, PG and Bundy, J and Haggard, DE and Everett, L and Harrill, JA and Harris, F and Ryoo, D and Collins, J and Rivetti, C and Campos, B and Hodges, G and LaLone, CA}, title = {Zebrafish cell lines and high-throughput transcriptomics: advancing in vitro and bioinformatics methods for supporting environmental risk assessment.}, journal = {Toxicological sciences : an official journal of the Society of Toxicology}, volume = {208}, number = {2}, pages = {343-356}, pmid = {40971701}, issn = {1096-0929}, support = {//Cooperative Research and Development Agreement/ ; # 1289-20//Unilever Global IP Limited/ ; }, mesh = {*Zebrafish/genetics ; Animals ; Risk Assessment ; *Computational Biology/methods ; Cell Line ; *Transcriptome/drug effects ; *High-Throughput Screening Assays ; *Gene Expression Profiling ; *Toxicity Tests/methods ; *Water Pollutants, Chemical/toxicity ; }, abstract = {Historic animal-based toxicity testing methods cannot keep pace with the need for prioritizing new and existing chemicals for comprehensive risk assessment. New approach methodologies such as high-throughput in vitro transcriptomics screening have emerged to address this challenge. However, most in vitro methods were developed using mammalian cell lines, including human, and may not adequately represent environmental species, potentially limiting the utility of this methodology for supporting environmental risk assessment. The objective of this study was to evaluate whether zebrafish cell lines can generate biologically meaningful chemical effects data in a high-throughput transcriptomics pipeline that is protective of toxicologically relevant aquatic apical endpoints. Forty-two test chemicals were screened in 2 commercially available zebrafish cell lines (ZFL liver and ZEM2S embryonic fibroblast) using the TempO-Seq zS1500+ platform. Transcriptomic points-of-departure (tPODs) were derived using 2 methods: Gene-level analysis (tPODgenes) with BMDExpress software and biological pathway-altering concentrations (BPACs/tPODsignatures) from signature-based dose-response analysis. When converted to predicted external water concentrations using quantitative in vitro-in vivo extrapolation models, tPODs were generally protective of aquatic in vivo endpoints from the ECOTOX Knowledgebase. Differential gene expression and biological pathway analysis revealed potential cell-type-specific effects for several chemicals, highlighting the value of using multiple cell types for capturing tissue-specific responses. Lastly, the biological pathway information was used to extrapolate the chemical effects data across species through an integration of protein-protein interaction network analysis and the Sequence Alignment to Predict Across Species Susceptibility tool, which has significant implications for improving the ecological relevance of these methods.}, }
@article {pmid40971328, year = {2025}, author = {Bock, O and Huang, JY and Wigge, M and Bieche, C and Kehm, C and Richter, N and Fink, GR and Onur, OA}, title = {Route-following deficits in amnestic mild cognitive impairment: Is the dual encoding of route-following strategies impaired?.}, journal = {Journal of Alzheimer's disease : JAD}, volume = {108}, number = {2}, pages = {606-615}, doi = {10.1177/13872877251378658}, pmid = {40971328}, issn = {1875-8908}, mesh = {Humans ; *Cognitive Dysfunction/psychology/complications/physiopathology ; Aged ; Male ; Female ; Neuropsychological Tests ; *Amnesia/psychology ; Maze Learning/physiology ; Cues ; Aged, 80 and over ; Middle Aged ; }, abstract = {BackgroundOne of the earliest signs of amnestic mild cognitive impairment (MCI) and neurodegenerative dementia (ND) is spatial disorientation, e.g., getting lost on previously familiar routes. Healthy individuals often follow routes by combining two strategies, serial recall of directions and cue-direction associations, but the integration of these two strategies may be degraded in amnestic MCI and ND.ObjectiveTo evaluate whether impaired integration of the two strategies (dual encoding) contributes to the route-following deficits in amnestic MCI.MethodsTwenty-five patients with amnestic MCI and 25 age-matched healthy controls (HC) followed routes through virtual mazes that allowed the use of the serial order strategy only (maze S), the associative cue strategy only (maze A), or both strategies (maze SA).ResultsFor longer routes, accuracy in maze SA exceeded that in mazes S and A, confirming the existence of a dual encoding benefit. The magnitude of this benefit was comparable in both groups. In contrast, performance on an additional dual-task test was poorer in MCI than in HC.ConclusionsWe attribute the dissociation between preserved dual encoding and impaired dual-tasking in amnestic MCI not to fundamental differences in the underlying mechanisms, but rather to the different ecological validity of the two experimental paradigms. Our findings suggest that spatial orientation training in amnestic MCI need not target dual encoding.}, }
@article {pmid40970218, year = {2024}, author = {Finn, RD and Balech, B and Burgin, J and Chua, P and Corre, E and Cox, CJ and Donati, C and Dos Santos, VM and Fosso, B and Hancock, J and Heil, KF and Ishaque, N and Kale, V and Kunath, BJ and Médigue, C and Nogueira, T and Pafilis, E and Pesole, G and Richardson, L and Santamaria, M and Strepis, N and Van Den Bossche, T and Vizcaíno, JA and Zafeiropoulos, H and Willassen, NP and Pelletier, E and Batut, B}, title = {Establishing the ELIXIR Microbiome Community.}, journal = {F1000Research}, volume = {13}, number = {}, pages = {}, pmid = {40970218}, issn = {2046-1402}, mesh = {Computational Biology ; *Metagenomics/methods ; *Microbiota ; }, abstract = {Microbiome research has grown substantially over the past decade in terms of the range of biomes sampled, identified taxa, and the volume of data derived from the samples. In particular, experimental approaches such as metagenomics, metabarcoding, metatranscriptomics and metaproteomics have provided profound insights into the vast, hitherto unknown, microbial biodiversity. The ELIXIR Marine Metagenomics Community, initiated amongst researchers focusing on marine microbiomes, has concentrated on promoting standards around microbiome-derived sequence analysis, as well as understanding the gaps in methods and reference databases, and identifying solutions to the computational overheads of performing such analyses. Nevertheless, the methods used and the challenges faced are not confined to marine microbiome studies, but are broadly applicable to other biomes. Thus, expanding this Marine Metagenomics Community to a more inclusive ELIXIR Microbiome Community will enable it to encompass a broader range of biomes and link expertise across 'omics technologies. Furthermore, engaging with a large number of researchers will improve the efficiency and sustainability of bioinformatics infrastructure and resources for microbiome research (standards, data, tools, workflows, training), which will enable a deeper understanding of the function and taxonomic composition of the different microbial communities.}, }
@article {pmid40968609, year = {2025}, author = {Kim, EM and Koh, DH and Sung, S and Hong, Y and Moon, S and Lee, JE and Ko, KP and Park, SK and Min, J and Choi, S and Park, JH and Lee, SG and Kim, HC and Park, DU and Kim, I}, title = {Fraction of Cancer Attributable to Occupational Carcinogens in Korea between 2015 and 2030.}, journal = {Cancer research and treatment}, volume = {}, number = {}, pages = {}, doi = {10.4143/crt.2025.193}, pmid = {40968609}, issn = {2005-9256}, abstract = {PURPOSE: To estimate the contribution of occupational carcinogens to cancer incidence and mortality in the Korean population between 2015 and 2030.<br><br>MATERIALS AND METHODS: We selected occupational carcinogens classified as International Agency for Research on Cancer (IARC) Group 1 and estimated the prevalence of exposure using data from the Korean CARcinogen EXposure (K-CAREX) and previous studies. Relative risks were calculated using published literature through a meta-analysis. Levin's formula was used to estimate population attributable fraction (PAF) while considering a 15-year latency period between exposure, cancer incidence, and death. Additionally, trends in cancer PAF were calculated up to 2030, assuming constant relative risks and a 15-year latency period.<br><br>RESULTS: In 2015, the PAFs for occupational carcinogen-related cancer incidence and mortality were 1.00% (men: 1.75%, women: 0.15%) and 1.97% (men: 2.97%, women: 0.33%), respectively, with asbestos being the largest contributor (incidence: 0.48%; mortality: 0.98%). In 2030, the PAFs for occupational carcinogen-related cancer incidence and mortality were 0.34% (men: 0.62%, women: 0.07%) and 0.80% (men: 1.22%; women: 0.15%), respectively, with diesel engine exhaust being projected to become the largest contributor by 2030 (incidence: 0.16%, mortality: 0.41%).<br><br>CONCLUSION: The PAFs of occupational carcinogens in Korea between 2015 and 2030 were estimated to be very low in the general population, and the values are expected to decrease over time owing to various regulations to prevent exposure to occupational carcinogens. Therefore, while regulating well-known occupational carcinogens, efforts should be made to monitor newly identified ones to ensure prompt implementation of preventive measures.}, }
@article {pmid40966233, year = {2025}, author = {Lee, J and Suh, Y}, title = {Physical activity and its associated factors among adults with chronic kidney disease in a community setting: A secondary data analysis.}, journal = {PloS one}, volume = {20}, number = {9}, pages = {e0332604}, pmid = {40966233}, issn = {1932-6203}, mesh = {Humans ; Male ; Female ; *Renal Insufficiency, Chronic/physiopathology/epidemiology ; *Exercise/physiology ; Middle Aged ; Adult ; Aged ; Republic of Korea/epidemiology ; Nutrition Surveys ; Glomerular Filtration Rate ; Quality of Life ; Secondary Data Analysis ; }, abstract = {BACKGROUND: Physical activity in patients with chronic kidney disease is important as it helps lowers blood pressure, reduces inflammatory markers, improves cognitive function, and improves health-related quality of life. However, there is a lack of studies accurately assess physical activity levels in this population.<br><br>OBJECTIVE: This study aimed to examine the characteristics of chronic kidney disease patients across eGFR stages, assess the proportion of Korean adults with chronic kidney disease meeting recommended physical activity levels, and identify the factors associated with meeting the weekly physical activity recommendation.<br><br>METHODS: We conducted a secondary analysis of data from the 2016-2020 Korean National Health and Nutrition Examination Survey. Descriptive statistics and logistic regression were used to examine physical activity patterns and associated factors.<br><br>RESULTS: Among CKD patients, 79.5% engaged in insufficient physical activity. Factors significantly associated with sufficient activity included sex, smoking status, activity limitation, and eGFR.<br><br>CONCLUSIONS: Tailoring physical activity interventions is crucial, considering the patient's clinical condition, physical performance, and demographic factors.}, }
@article {pmid40965697, year = {2025}, author = {Serpico, J and Choi, KH and Zambrano-Luna, BA and Wang, TX and Wang, H}, title = {Decoding the spatial spread of cyanobacterial blooms in an epilimnion.}, journal = {Journal of mathematical biology}, volume = {91}, number = {4}, pages = {44}, pmid = {40965697}, issn = {1432-1416}, support = {Individual Discovery Grant RGPIN-2020-03911//Natural Sciences and Engineering Research Council of Canada/ ; Discovery Accelerator Supplement Award RGPAS-2020-00090//Natural Sciences and Engineering Research Council of Canada/ ; Tier 1 Canada Research Chair Award//Canada Research Chairs/ ; }, mesh = {*Cyanobacteria/growth &amp; development ; *Lakes/microbiology ; *Models, Biological ; Ecosystem ; Biomass ; Mathematical Concepts ; Geographic Information Systems ; *Eutrophication ; Computer Simulation ; Environmental Monitoring/statistics &amp; numerical data ; *Harmful Algal Bloom ; }, abstract = {Cyanobacterial blooms (CBs) pose significant global challenges due to their harmful toxins and socio-economic impacts, with nutrient availability playing a key role in their growth, as described by ecological stoichiometry (ES). However, real-world ecosystems exhibit spatial heterogeneity, limiting the applicability of simpler, spatially uniform models. To address this, we develop a spatially explicit partial differential equation model based on ES to study cyanobacteria in the epilimnion of freshwater systems. We establish the well-posedness of the model and perform a stability analysis, showing that it admits two linearly stable steady states, leading to either extinction or a spatially uniform positive equilibrium where cyanobacterial biomass stabilizes at its carrying capacity. Further, we discuss the possibility of long-term spatially nonuniform solution with small diffusion and space-dependent parameters. We use the finite elements method (FEM) to numerically solve our system on a real lake domain derived from Geographic Information System (GIS) data and realistic wind conditions extrapolated from ERA5-Land. Additionally, we use a cyanobacteria estimation (CE) obtained from Sentinel-2 to set initial conditions, and we achieve strong model validation metrics. Our numerical results highlight the importance of lake shape and size in bloom monitoring, while global sensitivity analysis using Sobol Indices identifies light attenuation and intensity as primary drivers of bloom variation, with water movement influencing early bloom stages and nutrient input becoming critical over time. This model supports continuous water-quality monitoring, informing agricultural, recreational, economic, and public health strategies for mitigating CBs.}, }
@article {pmid40965023, year = {2025}, author = {Li, S and Chen, P and Zhang, J and Wang, B}, title = {MBLEformer: Multi-Scale Bidirectional Lesion Enhancement Transformer for Cervical Cancer Image Segmentation.}, journal = {Current medical imaging}, volume = {21}, number = {}, pages = {e15734056357180}, doi = {10.2174/0115734056357180250516022218}, pmid = {40965023}, issn = {1573-4056}, mesh = {Humans ; Female ; *Uterine Cervical Neoplasms/diagnostic imaging ; Neural Networks, Computer ; *Image Interpretation, Computer-Assisted/methods ; Deep Learning ; Colposcopy ; Iodides ; *Image Processing, Computer-Assisted/methods ; }, abstract = {BACKGROUND: Accurate segmentation of lesion areas from Lugol's Iodine Staining images is crucial for screening pre-cancerous cervical lesions. However, in underdeveloped regions lacking skilled clinicians, this method may lead to misdiagnosis and missed diagnoses. In recent years, deep learning methods have been widely applied to assist in medical image segmentation.<br><br>OBJECTIVE: This study aims to improve the accuracy of cervical cancer lesion segmentation by addressing the limitations of Convolutional Neural Networks (CNNs) and attention mechanisms in capturing global features and refining upsampling details.<br><br>METHODS: This paper presents a Multi-Scale Bidirectional Lesion Enhancement Network, named MBLEformer, which employs the Swin Transformer encoder to extract image features at multiple stages and utilizes a multi-scale attention mechanism to capture semantic features from different perspectives. Additionally, a bidirectional lesion enhancement upsampling strategy is introduced to refine the edge details of lesion areas.<br><br>RESULTS: Experimental results demonstrate that the proposed model exhibits superior segmentation performance on a proprietary cervical cancer colposcopic dataset, outperforming other medical image segmentation methods, with a mean Intersection over Union (mIoU) of 82.5%, accuracy, and specificity of 94.9% and 83.6%.<br><br>CONCLUSION: MBLEformer significantly improves the accuracy of lesion segmentation in iodine-stained cervical cancer images, with the potential to enhance the efficiency and accuracy of pre-cancerous lesion diagnosis and help address the issue of imbalanced medical resources.}, }
@article {pmid40963762, year = {2025}, author = {Dey, D and Lateef, HA and Leroux, A and Zipunnikov, V and Merikangas, K}, title = {Associations Between Daily Outdoor Temperature and Subjective Real-time Ratings of Emotional States and Sleep in Mood Disorder Subtypes.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {40963762}, support = {Z01 MH002804/ImNIH/Intramural NIH HHS/United States ; ZIA MH002804/ImNIH/Intramural NIH HHS/United States ; ZIA MH002954/ImNIH/Intramural NIH HHS/United States ; }, abstract = {Growing evidence for the influence of weather on mental health at both the aggregate level indices of mental health statistics of hospitalizations, morbidity, and mortality, and individual level dynamics of mood states. Most research on this topic has focused on light exposure and depressed mood as the sole indicators of seasonal fluctuations of mood disorders. This paper evaluates the association between daily maximum outdoor temperature (DMOT) and contemporaneously reported mood, energy, anxiousness, and sleep quality assessed with Ecological Momentary Assessment (EMA) in a community-based sample of 452 people, aged 11 to 85 years, comprising people with or without a history of mood disorders. After controlling for demographics, daily activity levels, and daytime cloud coverage as an index of light exposure, we found that higher DMOT was associated with better mood, increased energy, and better sleep quality among those with with a history of mood disorders, particularly in the spring among people with a history of Bipolar Disorder (BD) who tended to exhibit more seasonal changes than controls. These findings suggest that the dynamics of mood, energy, and sleep may underlie the aggregate population-level influences of temperature and correlated environmental influences on negative mental health outcomes, particularly among those with BD. Therefore, the conceptualization of risk and intervention for mood disorders should consider both the aggregate influences of temperature and light and associated environmental conditions, as well as individual-level sleep quality and energy as potential mechanisms for seasonal patterns of emotional states.}, }
@article {pmid40962773, year = {2025}, author = {Zhao, ZL and Jiang, X and Su, Y and Yin, LJ and Luo, T and Zhao, WQ and Luo, JH}, title = {[Analysis of Vegetation Changes and Influencing Factors in Guiyang City over the Past 33 Years Based on the kNDVI and OPGD Model].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {46}, number = {9}, pages = {5839-5849}, doi = {10.13227/j.hjkx.202408129}, pmid = {40962773}, issn = {0250-3301}, mesh = {China ; *Ecosystem ; *Environmental Monitoring/methods ; *Remote Sensing Technology ; Cities ; *Models, Theoretical ; *Conservation of Natural Resources ; *Plant Development ; Geographic Information Systems ; Satellite Imagery ; }, abstract = {The vegetation index is a critical indicator for monitoring changes in terrestrial ecosystems， and understanding the spatiotemporal characteristics of vegetation changes and their potential driving factors is essential for improving regional ecological protection and management. This study utilized eight periods of Landsat remote sensing images from 1990 to 2023 to calculate the kernel normalized difference vegetation index （kNDVI） for Guiyang City using the Google Earth engine （GEE） platform. The Theil-Sen + Mann-Kendall trend analysis method was applied to assess the trends and significance levels of kNDVI changes， and the Hurst index was used to evaluate the persistence and future trends of kNDVI. Additionally， the optimal parameters geographic detector （OPGD） was employed to analyze the driving mechanisms behind the spatial differentiation of kNDVI. The study produced the following results： ① From 1990 to 2023， the kNDVI in Guiyang City exhibited a fluctuating upward trend over four distinct phases， with significant spatial differentiation， generally displaying a north-high， south-low distribution pattern. ② Over the 33 years， 74.62% of the area in Guiyang City experienced improvement in vegetation cover， while 25.14% showed signs of degradation. ③ The average Hurst index was 0.610 2， indicating weak persistence and suggesting a trend of continued improvement into the future for vegetation kNDVI in Guiyang City. ④ The land-use type factor （0.231 2） showed the strongest explanatory power for the spatial differentiation of vegetation kNDVI. The interactions between factors exhibited both nonlinear enhancement and bi-factor enhancement， with the combination of land use and other factors synergistically explaining the spatial differentiation of kNDVI more effectively.}, }
@article {pmid40959203, year = {2025}, author = {Beene, D and Lin, Y and Hoover, JH and Shi, X}, title = {Deconstructing rurality to better "place" health data.}, journal = {International journal of geographical information science : IJGIS}, volume = {}, number = {}, pages = {}, pmid = {40959203}, issn = {1365-8816}, support = {P30 ES032755/ES/NIEHS NIH HHS/United States ; P42 ES025589/ES/NIEHS NIH HHS/United States ; P50 MD015706/MD/NIMHD NIH HHS/United States ; UH3 OD023344/OD/NIH HHS/United States ; }, abstract = {Rural-urban classification schemes are frequently used in ecological studies of population health. However, the algorithms used to produce these classifications as well as their underlying assumptions may not match their intended use in health research. Here, we focus on the spatial distribution of features of the physical environment that are related to health - such as healthcare - to examine the extent to which eight classification schemes capture the heterogeneous context of rural places. We further explore how well rural-urban classifications distinguish between different types of rural places by comparing rural Tribal reservations with other rural areas in the American southwest. Because health services and infrastructure are often distributed through state and federal programs to underserved populations in rural areas, this approach speaks to the broader political implications in how rural communities are defined and represented. Results indicate that rural-urban classifications do not adequately reflect heterogeneous contexts within and across rural places. We advocate for more appropriate population health models that explain contextual differences in the relationship between health and place.}, }
@article {pmid40958166, year = {2025}, author = {Ghaly, TM and Rajabal, V and Russell, D and Colombi, E and Tetu, SG}, title = {EcoFoldDB: Protein Structure-Guided Functional Profiling of Ecologically Relevant Microbial Traits at the Metagenome Scale.}, journal = {Environmental microbiology}, volume = {27}, number = {9}, pages = {e70178}, pmid = {40958166}, issn = {1462-2920}, support = {CE200100029//ARC Centre of Excellence in Synthetic Biology/ ; //Macquarie University Research Fellowship/ ; }, mesh = {*Metagenome ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism ; Soil Microbiology ; Phylogeny ; *Microbiota/genetics ; Computational Biology/methods ; *Bacterial Proteins/genetics/chemistry ; *Databases, Protein ; Protein Conformation ; }, abstract = {Microbial communities are fundamental to planetary health and ecosystem processes. High-throughput metagenomic sequencing has provided unprecedented insights into the structure and function of these communities. However, functionally profiling metagenomes remains constrained due to the limited sensitivity of existing sequence homology-based methods to annotate evolutionarily divergent genes. Protein structure, more conserved than sequence and intrinsically tied to molecular function, offers a solution. Capitalising on recent breakthroughs in structural bioinformatics, we present EcoFoldDB, a database of protein structures curated for ecologically relevant microbial traits, and its companion pipeline, EcoFoldDB-annotate, which leverages Foldseek with the ProstT5 protein language model for rapid structural homology searching directly from sequence data. EcoFoldDB-annotate outperforms state-of-the-art sequence-based methods in annotating metagenomic proteins, in terms of sensitivity and precision. To demonstrate its utility and scalability, we performed structure-guided functional profiling of 32 million proteins encoded by 8000 high-quality metagenome-assembled genomes from the global soil microbiome. EcoFoldDB-annotate could resolve the phylogenetic partitioning of important nitrogen cycling pathways, from taxonomically restricted nitrifiers to more widespread denitrifiers, as well as identifying novel, uncultivated bacterial taxa enriched in plant growth-promoting traits. We anticipate that EcoFoldDB will enable researchers to extract ecological insights from environmental genomes and metagenomes and accelerate discoveries in microbial ecology.}, }
@article {pmid40957742, year = {2026}, author = {Seven, OF and Bicer, M and Adli, MA}, title = {Experimental insights into muscle and joint roles in stumble recovery: A scoping review.}, journal = {Gait &amp; posture}, volume = {123}, number = {}, pages = {109963}, doi = {10.1016/j.gaitpost.2025.08.081}, pmid = {40957742}, issn = {1879-2219}, mesh = {Humans ; Biomechanical Phenomena ; *Muscle, Skeletal/physiology ; *Accidental Falls ; *Gait/physiology ; *Walking/physiology ; Electromyography ; *Joints/physiology ; Lower Extremity/physiology ; Recovery of Function ; }, abstract = {INTRODUCTION: A major concern, often resulting in serious injuries and loss of independence, is caused by falls due to stumbling. Previous works, investigating stumble recovery responses isolated to joint or muscle responses, lacks a comprehensive view of coordinated whole-body recovery.<br><br>METHODS: A scoping review, on Web of Science, Scopus and PubMed, was conducted using keywords related to recovery from anteriorly-directed stumbles induced by physical obstruction of the swing limb during healthy human walking. Extracted data were experimental cohort, swing phase during stumble, perturbation apparatus, recovery strategies, biomechanical responses including joint kinematics, kinetics and muscle activity. A narrative synthesis was provided to summarize findings across studies.<br><br>RESULTS: 23 of 337 identified studies met inclusion criteria. Limited focus on older adults or comparing them to young adults were found. Rigid and stationary obstacles were commonly used, while compliant/movable obstacles were rarely examined, limiting ecological validity. Recovery strategies varied by perturbation timing: foot elevation and lowering in early/mid-swing and late swing stumbles, respectively. Rare responses like delayed lowering and reaching were underexplored. Sagittal plane lower-limb kinematics were frequently reported, with often missing trunk motion, joint moments and EMG from proximal muscles.<br><br>CONCLUSION: This review highlights the importance of rapid and coordinated whole-body responses in stumble recovery, particularly involving the support limb and trunk. Findings suggest rehabilitation should target hip extensor strength, trunk control and support limb engagement to improve recovery. Future research should investigate underexplored strategies, trunk and upper-limb involvement and age-related adaptations to enhance intervention design.}, }
@article {pmid40954274, year = {2025}, author = {Moore, TR and Krobath, DM and Chang Chusan, YA and Sanga, U and Webb, P and Pachucki, M and Cuevas, A and Roland, HB and Grant, B and Economos, CD and Nicholson, V and Kumanyika, S}, title = {Systems science methods reveal and address links between discrimination and health disparities in US food systems.}, journal = {Nature food}, volume = {6}, number = {9}, pages = {821-826}, pmid = {40954274}, issn = {2662-1355}, support = {K99 HD109456/HD/NICHD NIH HHS/United States ; K99HD109456//U.S. Department of Health &amp; Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; }, abstract = {Discriminatory practices are well documented and deeply rooted in food systems. Systems science methods such as social network analysis, system dynamics modeling, and agent-based modeling can help elicit how discriminatory processes arise, interact, and accumulate to contribute to diet-related health disparities. Such methodological approaches can reveal leverage points for advancing equity driven solutions.}, }
@article {pmid40952102, year = {2025}, author = {Guillén Matus, DG and Donaghy, CM and Vijayan, N and Lane, ZT and Howell, M and Glavin, GG and Angeles-Boza, AM and Nyholm, SV and Balunas, MJ}, title = {Multi-omics analysis reveals important role for microbial-derived metabolites from Botryllus schlosseri in metal interactions.}, journal = {mSystems}, volume = {10}, number = {10}, pages = {e0079325}, pmid = {40952102}, issn = {2379-5077}, support = {Convergence Awards for Research in Interdisciplinary Centers (CARIC)//University of Connecticut/ ; DGE-1747453//NSF | National Science Foundation Graduate Research Fellowship Program (GRFP)/ ; }, mesh = {*Urochordata/microbiology/metabolism ; Animals ; *Microbiota ; *Metals/metabolism ; *Metabolome ; *Bacteria/metabolism/classification ; Metabolomics/methods ; Multiomics ; }, abstract = {Marine microbial communities govern many of the biological and chemical processes in the ocean, including element cycles, ecosystem health, and disease. Marine organisms are surrounded by microbes, with complex molecular interactions occurring between bacterial symbionts, eukaryotic hosts, and their pathogens or prey. Trace metals in the ocean can be either beneficial or detrimental to marine life depending on their concentrations and bioavailability. Multiple marine tunicate species are known to bioaccumulate trace metals in their mantel, and research suggests that tunicate microbiota plays an important role in this process. Botryllus schlosseri, a marine colonial tunicate, has become a model organism for cellular and developmental studies, yet its ecological interactions are still not well understood. Using an integrated multidisciplinary approach, we established a comprehensive baseline and explored correlations between members of the B. schlosseri microbiome, metabolome, and metallome to elucidate the ecological effects of trace metals in host-microbe-pathogen interactions. We identified significant correlations between metals, including manganese, nickel, cerium, zinc, and cobalt, with various metabolites and bacterial taxa. These findings offer insights into B. schlosseri's biological and chemical interactions with microorganisms and their environment, contributing to bridging the knowledge gap of host-microbiome-environment interactions and establishing a foundation for continuing research on the ecological effects of trace metals in these biological systems.IMPORTANCEGiven the importance of marine invertebrates and their microbial communities in marine ecosystems, we sought to characterize the largely unknown microbial associates, metal sequestration, and metabolite production of the marine colonial tunicate, Botryllus schlosseri, a model organism for cellular and developmental studies. Using an integrated multidisciplinary approach, we identified significant correlations between metals, metabolites, and bacterial taxa. B. schlosseri tissue was highly enriched in metals compared to seawater, and B. schlosseri microbiome beta-diversity was significantly different from seawater. We also introduced the concept of the pan-metabolome to classify metabolites based on their presence or absence across complex samples and found microbial metabolites in both the core and flexible metabolome. These findings offer insights into B. schlosseri's biological and chemical interactions with microorganisms and their environment, bridging the knowledge gap of host-microbiome-environment interactions and establishing a foundation for continuing research on the ecological effects of trace metals in these biological systems.}, }
@article {pmid40952002, year = {2025}, author = {Guan, R and Garrido-Oter, R}, title = {Integrated diversity and network analyses reveal drivers of microbiome dynamics.}, journal = {mSystems}, volume = {10}, number = {10}, pages = {e0056425}, pmid = {40952002}, issn = {2379-5077}, support = {2048/1//German Excellence Strategy/ ; }, mesh = {*Microbiota/genetics ; *Biodiversity ; *Plants/microbiology ; Ecosystem ; Microbial Interactions ; Bacteria/genetics/classification ; Computational Biology/methods ; }, abstract = {UNLABELLED: Microbial communities are key components of ecosystems, where interactions among microbes drive biodiversity and productivity. An increased number of microbiome data sets are available, owing to advances in sequencing; however, standard analyses often focus on community composition, neglecting the complex interactions between co-occurring microbes. To address this, we developed a computational framework integrating compositional and co-occurrence network analyses. We applied this approach to extensive microbial amplicon data sets, focusing on plant microbiota, which typically exhibits high diversity and remains challenging to characterize due to the large number of low-abundance taxa. We show that identifying a subset of representative microbial taxa captures the overall community structure and increases the statistical power. From these taxa, we inferred a large-scale co-occurrence network and clustered microbes with co-varying abundances into units for diversity measurement. This approach not only reduces unexplained variance in diversity assessments but also captures the key microbe-microbe relationships that govern assembly patterns. Furthermore, we introduced a bootstrap- and permutation-based statistical approach to compare microbial networks from diverse conditions. Our method robustly distinguishes meaningful differences and pinpoints specific microbes and features driving those differences. These results highlight the importance of incorporating microbe-microbe interactions in microbiota studies, leading to more accurate and ecologically meaningful insights. Our framework, available as an R package ("mina"), enables researchers to identify condition-specific interactions via network comparison and gain a deeper understanding of community ecology. With broad applicability beyond plant systems, this package provides a valuable tool for leveraging microbiome data across disciplines, from agriculture to ecosystem resilience and human health.<br><br>IMPORTANCE: Understanding microbiome dynamics requires capturing not only changes in microbial composition but also interactions between community members. Traditional approaches frequently overlook microbe-microbe interactions, limiting their ecological interpretation. Here, we introduce a novel computational framework that integrates compositional data with network-based analyses, significantly improving the detection of biologically meaningful patterns in community variation. By applying this framework to a large data set from the plant microbiota, we identify representative groups of interacting microbes driving differences across microhabitats and environmental conditions. Our analysis framework, implemented in an R package "mina," provides robust tools allowing researchers to assess statistical differences between microbial networks and detect condition-specific interactions. Broadly applicable to microbiome data sets, our framework is aimed at enabling advances in our understanding of microbial interactions within complex communities.}, }
@article {pmid40951316, year = {2025}, author = {Zhang, B and Sheng, Z and Bu, C and Wang, L and Lv, W and Wang, Y and Xu, Y and Yan, G and Gong, M and Liu, L and Hu, W}, title = {Whipworm infection remodels the gut microbiome ecosystem and compromises intestinal homeostasis in elderly patients revealed by multi-omics analyses.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1663666}, pmid = {40951316}, issn = {2235-2988}, mesh = {*Gastrointestinal Microbiome ; Animals ; Humans ; *Homeostasis ; RNA, Ribosomal, 16S/genetics ; Aged ; Metabolomics/methods ; Metagenomics ; *Trichuriasis/parasitology/microbiology ; *Trichuris ; Female ; Male ; Bacteria/classification/genetics/isolation &amp; purification ; Metabolic Networks and Pathways ; Aged, 80 and over ; Metabolome ; *Intestines/microbiology ; Multiomics ; }, abstract = {INTRODUCTION: Whipworm (Trichuris trichiura) coexists with symbiotic microbiota in the gastrointestinal ecosystem. There is a paucity of data on the association between whipworm infection and the gut microbiota composition in elderly individuals. This study was designed to investigate changes in gut microbiota and function and its metabolite profile in patients with whipworm infection.<br><br>METHODS: We used 16S rRNA gene sequencing to identify microbial signatures associated with whipworm infection. Subsequently, shotgun metagenomic sequencing revealed functional changes that highlighted disruptions in microbial gene expression and metabolic pathways influencing host health. Ultraperformance liquid chromatography-mass spectrometry metabolomics was used to characterize whipworm infectioninduced metabolic perturbations and elucidate metabolite dynamics linked to microbial activity. Collectively, this multi-omics approach deciphered structural, functional, and metabolic remodeling of the gut ecosystem that distinguished whipworm-infected patients from healthy controls.<br><br>RESULTS: Analyses of the gut microbiome in patients with whipworm infection revealed significantly increased observed species richness and ACE indices, along with an enrichment of Prevotella 9-driven enterotypes. Additionally, metagenomic and metabolomic analyses indicated enrichment in metabolic pathways related to amino acid, energy and carbohydrate metabolism. Metabolic network analysis further suggested that the upregulated Prevotella copri and Siphoviridae sp. were positively correlated with elevated levels of myristic acid and DL-dipalmitoylphosphatidylcholine.<br><br>CONCLUSION: These findings suggest that whipworm infection significantly remodels the gut microbiome ecosystem and compromises intestinal homeostasis.}, }
@article {pmid40950394, year = {2025}, author = {Sambo, B and Sperotto, A and Aznarez, C and Terzi, S and Pittore, M and Critto, A and Torresan, S}, title = {Managing the water-energy-food nexus in the adige river basin: impacts of climate and land use change on ecosystem services bundles.}, journal = {Climatic change}, volume = {178}, number = {9}, pages = {168}, pmid = {40950394}, issn = {0165-0009}, abstract = {UNLABELLED: The Water-Energy-Food (WEF) nexus framework highlights the interdependencies among water, energy, and food systems. Integrating Ecosystem Services (ESs) enhances this approach by incorporating ecological benefits for more holistic assessments. This study applies a spatially explicit ESs-based WEF nexus analysis in the Adige River Basin (Northern Italy), focusing on five ESs: water provisioning, crop yield, sediment retention, carbon storage, and landscape diversity, under two future scenarios (SSP1-RCP 2.6 and SSP5-RCP 8.5) from 2018 to 2050. Using Self-Organizing Maps, sub-basins were clustered into ESs bundles enabling the identification of tailored management strategies. Results reveal spatial heterogeneity and shifts in ESs bundles, with synergies often found in upstream, forested areas. Under high-emission scenarios, regulating services decline and provisioning services face trade-offs, especially with intensified agriculture. Key strategies suggested include maintaining environmental flows, reducing synthetic fertilizers, promoting reforestation, crop diversification, and expanding protected areas. These are structured into physical, economic, and climatic pathways aligned with EU restoration goals. Findings demonstrate the value of an ESs-bundles approach for optimizing synergies and managing trade-offs across the WEF nexus.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10584-025-04013-3.}, }
@article {pmid40947031, year = {2026}, author = {Onyeka, OC and Cheng, JS and Sanei, S and Clark, SL and Pinciotti, CM and Guzick, AG and Storch, EA and Stewart, S and Sandoval, JF and Taylor, L and Riddle, D and Garza, C and Liberzon, I and Rousseau, J and Shahidullah, JD and Newport, DJ and Wagner, KD and Nemeroff, C}, title = {Exploring resource profiles among trauma exposed youth: An identity-focused, cultural, and person-centered approach.}, journal = {Journal of affective disorders}, volume = {393}, number = {Pt A}, pages = {120298}, doi = {10.1016/j.jad.2025.120298}, pmid = {40947031}, issn = {1573-2517}, mesh = {Humans ; Female ; Male ; Adolescent ; *Resilience, Psychological ; *Stress Disorders, Post-Traumatic/psychology/ethnology ; Anxiety/psychology ; Depression/psychology ; Social Support ; Longitudinal Studies ; Texas ; *Social Identification ; Child ; }, abstract = {OBJECTIVE: Resilience is a multi-faceted construct comprised of both internal and external resources that support adaptive functioning following trauma exposure. The role of resilience in ameliorating internalizing symptoms may depend on its typology as opposed to its presence alone, suggesting the existence of distinct subpopulations with heterogeneous resource profiles. The current study employs Latent Profile Analysis (LPA) to identify and characterize profiles of resilience-related resources among youth exposed to trauma from an identity-focused, cultural lens.<br><br>METHOD: Patterns of resources were examined in 1,538 youth (Mage = 13.4, 51.9% female) from a large longitudinal registry of trauma exposed youth in Texas using LPA. Profiles were related to demographic variables and internalizing symptoms (post-traumatic stress symptoms [PTSS], depression, and anxiety) using multinomial regression.<br><br>RESULTS: Results demonstrated an optimal four-class solution (Low Social Support and Average ERI, 31.2&#xa0;%; Average Level of Protective Factors, 27.4&#xa0;%; Ethnic Identity Diffusion, 18.1&#xa0;%; Social Support Dominant, 23.2&#xa0;%). Depressive symptoms significantly differentiated between classes in the four-class model as well as youth race, age, and ethnicity. Anxiety symptoms and PTSS did not differentiate the classes as clearly.<br><br>CONCLUSION: Person-centered analyses such as LPA underscore the value of examining resilience as a multi-faceted and heterogenous pattern of resources shaped by socio-ecological and cultural contexts among trauma-exposed youth. Implications for clinical intervention are discussed.}, }
@article {pmid40946389, year = {2025}, author = {Siuda, P and Aaltonen, M and Haasio, A and Bancroft, A and Nurmi, J and Shi, H and Harviainen, JT}, title = {Digital drug trading ecologies in context: Technological, geographic, and linguistic variation across darknet platforms.}, journal = {The International journal on drug policy}, volume = {145}, number = {}, pages = {104984}, doi = {10.1016/j.drugpo.2025.104984}, pmid = {40946389}, issn = {1873-4758}, mesh = {*Drug Trafficking ; Humans ; Datasets as Topic ; *Internet/economics ; Language ; *Illicit Drugs/economics ; Commerce ; Internationality ; }, abstract = {BACKGROUND: Previous research on darknet drug markets has primarily concentrated on large, English-language cryptomarkets, often overlooking regionally oriented platforms that operate in national languages. This study adopts a comparative, exploratory approach to examine how drug trade practices vary across linguistic, geographic, and technological contexts. We introduce the concept of "drug trading ecologies" to describe how platform features, communication norms, and localized settings together shape distinct trading environments.<br><br>METHODS: Using a mixed-methods approach, we analyzed web-crawled data from three Tor-based platforms: Tsatti (Finnish-language chat), Cebulka (Polish-language forum), and Nemesis (English-language cryptomarket). Data were collected through customized web scraping and analyzed using statistical tools and qualitative content coding to examine platform-specific patterns. Our comparative approach highlights structural and localization-specific variations without attempting exhaustive conceptual definitions.<br><br>RESULTS: Each platform displayed a distinct configuration shaped by its technical affordances and localization-specific user practices. Tsatti supported fast, hyperlocal, and highly anonymized exchanges with minimal user identity or community features. Cebulka enabled semi-public vendor-buyer interactions, trust-building through discourse, and diverse product bundling. Nemesis functioned as a transnational, professionalized cryptomarket with standardized listings, formalized trust mechanisms, and branding strategies.<br><br>CONCLUSIONS: Rather than attributing differences solely to local, transnational, or design factors in isolation, we argue that darknet drug trading ecologies emerge from the intersection of platform architecture, localization (geographic scope), and language. Our findings underscore the importance of considering these factors when conducting digital ethnography in illicit economies and providing concrete entry points for tailoring harm reduction interventions responsive to the diverse realities of online drug trading.}, }
@article {pmid40941648, year = {2025}, author = {Pantelić, M and Cvetković, D and Jovankić, J and Soldatović, I and Pantelić, M and Dujović, M and Vučinić, T and Cvetković, A}, title = {Predictive Value of Serum HMGB1, NF-κB, and IL-17 Gene Expression in Acute Pancreatitis Outcomes.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {15}, number = {17}, pages = {}, pmid = {40941648}, issn = {2075-4418}, abstract = {Background/Objectives: This study investigated the gene expression levels of High Mobility Group Box 1 (HMGB1), nuclear factor kappa B (NF-κB) and interleukin-17 (IL-17) in the serum of patients with acute pancreatitis (AP) and analyzed the correlation of these three with the severity of AP, local and systemic complications, transfer to intensive care unit (ICU) and death. Methods: AP was diagnosed and stratified according to the revised Atlanta classification. The diagnosis of AP requires two of the following three features: abdominal pain (acute onset of persistent severe, epigastric pain often radiating to the back); serum lipase/or amylase activity at least three times higher than normal; characteristic findings of AP on computed tomography or abdominal ultrasonography. Results: This study confirmed that NF-kB is a significant marker of AP severity, as well as for ICU transfer, and correlates with acute respiratory distress syndrome (ARDS), while IL-17 is shown as a significant marker of systemic complications (pleural effusions, ARDS, and renal failure). HMGB1 correlates with pancreatic necrosis, systemic inflammatory response syndrome, and ICU transfer. Conclusions: Over the past years, the role of HMGB1, NF-kB, and IL-17 in the pathogenesis of AP has been under intense scrutiny, and they have been proposed as prognostic biomarkers for AP severity, poor prognosis, and death outcome. The advantage of this research is that changes in gene expression can be detected before the increase in serum concentrations of these biomarkers, and it allows early prediction of a severe form of AP, as well as the development of complications.}, }
@article {pmid40938934, year = {2025}, author = {Attar, MI and Naseer, S and Pandey, Y and Khan, JN and Bangroo, SA and Hasan, MA and Khan, ZA and Khan, AH and Tantray, AM}, title = {Morphometric analysis for prioritizing critical areas of Urpash watershed in Sindh catchment of the lesser Himalayas using RS and GIS approach.}, journal = {PloS one}, volume = {20}, number = {9}, pages = {e0330503}, pmid = {40938934}, issn = {1932-6203}, mesh = {*Geographic Information Systems ; *Rivers ; *Remote Sensing Technology ; Hydrology ; Conservation of Natural Resources ; Environmental Monitoring/methods ; Soil Erosion ; Himalayas ; }, abstract = {Effective soil and water conservation is critical in fragile watersheds prone to erosion. However, assessing erosion susceptibility in ungauged watersheds remains challenging due to the lack of observed hydrological data This study addresses this gap by employing a comprehensive morphometric analysis integrated with remote sensing (RS) and Geographic Information Systems (GIS) to prioritize erosion-prone sub-watersheds within the ecologically sensitive and data-scarce Urpash watershed. Shuttle Radar Topography Mission (SRTM) Digital Elevation Model (DEM) data and ArcGIS 10.7 were used to analyze a 21.37 km[2] area. Key morphometric parameters-including linear, areal, and relief aspects-were assessed to understand watershed hydrology and erosion susceptibility. A total of 32 streams were identified, categorized into 1st to 3rd orders. Watershed shape indices, such as elongation ratio (Re = 0.65), form factor (Rf = 0.33) and circularity ratio (Rc = 0.295), indicate an elongated shape, indicative of reduced surface runoff and erosion potential, along with higher sub-soil permeability. However, drainage parameters like drainage density (Dd = 1.67 km/km2), stream frequency (Fs = 1.49 km-2) and drainage intensity (Di = 0.89 km-1) pointed to the watershed's susceptibility to flooding, gully erosion, and landslides due to slow surface runoff dispersion. Relief parameters such as basin relief (H = 1742.87 m), relief ratio (Rh = 0.22) and ruggedness number (Rn = 2.9) reflect the watershed's high relief and steep terrain, indicating a greater susceptibility to erosion. Using a compound parameter approach, the sub-watershed prioritisation ranked WS3 as the highest priority, followed by WS4, WS5, WS6, WS2, and WS1. By using RS and GIS-based morphometric analysis in an ungauged Urpash watershed, this study provides a geospatial framework for targeted soil and water conservation strategies, contributing to more precise watershed management in data-scarce and erosion-vulnerable regions.}, }
@article {pmid40936754, year = {2025}, author = {Ward, EJ and English, PA and Rooper, CN and Ferriss, BE and Whitmire, CE and Wetzel, CR and Barnett, LAK and Anderson, SC and Thorson, JT and Johnson, KF and Indivero, J and Markowitz, EH}, title = {surveyjoin: a standardized database of scientific trawl surveys in the Northeast Pacific Ocean.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19964}, pmid = {40936754}, issn = {2167-8359}, mesh = {Pacific Ocean ; *Fisheries/statistics &amp; numerical data ; *Databases, Factual/standards ; Animals ; Gadiformes ; Biomass ; Surveys and Questionnaires ; Conservation of Natural Resources ; }, abstract = {Fisheries management faces challenges due to political, spatial, and ecological complexities, which are further exacerbated by variation or shifts in species distributions. Effective management depends on the ability to integrate fisheries data across political and geographic boundaries. However, such efforts may be hindered by inconsistent data formats, limited data sharing, methodological differences in sampling, and regional governance differences. To address these issues, we introduce the surveyjoin R package, which combines and provides public access to bottom trawl survey data collected in the Northeast Pacific Ocean by NOAA Fisheries and Fisheries and Oceans Canada. This initial database integrates over 3.3 million observations from 14 bottom trawl surveys spanning Alaska, British Columbia, Washington, Oregon, and California from the 1980s to present. This database standardizes variables such as catch-per-unit-effort (CPUE), haul data, and in-situ measurements of bottom temperature. We demonstrate the utility of this database through three case studies. Our first case study develops a coastwide biomass index for Pacific hake (Merluccius productus) using geostatistical index standardization, comparing results to independent acoustic survey estimates. The second case study examines spatial patterns in groundfish community structure, highlighting breakpoints between assemblages in their mixture of life histories and trophic compositions. Our third example applies spatially varying coefficient models to assess sablefish (Anoplopoma fimbria) biomass trends, identifying regional variability in increases in occurrence and biomass. Together, these case studies demonstrate how the surveyjoin R package and database may improve species and ecosystem assessments by providing insights into population trends across geopolitical boundaries. This database and package represent an important step toward offering a scalable framework that can be extended to include additional data types, surveys, and species. By fostering collaboration, transparency, and data-driven decision making, surveyjoin supports international efforts to sustainably manage shared marine resources under dynamic environmental conditions.}, }
@article {pmid40934430, year = {2025}, author = {Tejada-Llacsa, PJ and Alarcón, GS and Ugarte-Gil, MF}, title = {Prevalence of systemic lupus erythematosus in Peru and its association with environmental and healthcare factors: An ecological study.}, journal = {Lupus}, volume = {34}, number = {13}, pages = {1406-1412}, doi = {10.1177/09612033251379313}, pmid = {40934430}, issn = {1477-0962}, mesh = {Humans ; Peru/epidemiology ; Female ; Male ; Adult ; *Lupus Erythematosus, Systemic/epidemiology ; Prevalence ; Middle Aged ; Young Adult ; Adolescent ; Altitude ; Child ; Temperature ; Registries ; Physicians/supply &amp; distribution ; Aged ; Sex Factors ; Risk Factors ; }, abstract = {ObjectiveTo estimate the prevalence of Systemic Lupus Erythematosus (SLE) in Peru in 2017 and its association with altitude, environmental temperature, and physician density.MethodsThis ecological study was performed using population data from the 2017 Peruvian census. The number of SLE cases for each department was obtained from the National Health Registries using the ICD-10 code M32. Altitude, environmental temperature and physician density were obtained for each department from the National Institute of Statistics and Informatic (Instituto Nacional de Estadística e Informática) registries. The prevalence for each department was calculated adjusting for age and sex. Then a negative binomial regression was performed to estimate the prevalence ratio (PR) and evaluate factors associated with the prevalence of SLE.ResultsThe national prevalence of SLE was 40.2 per 100,000 people. Two age groups had the highest prevalence: 12-17 years and 30-59 years. Females exhibited a higher prevalence than males, particularly in the 30-59 age group (113.9 vs 16.1 per 100,000, respectively). An inverse relationship was observed between the age- and sex-adjusted prevalence in each department and altitude (PR 0.97; 95% CI: 0.94-0.99). On the other hand, there was a direct relationship with physician density (PR: 1.04; 95% CI: 1.01-1.07). No association was found between the adjusted prevalence and environmental temperature or latitude.ConclusionThe prevalence of SLE in Peru aligns with global estimates. The inverse relationship with altitude and the direct association with physician density suggest that environmental and healthcare access factors may influence disease distribution. Further research is needed to explore the underlying mechanisms driving these associations.}, }
@article {pmid40932046, year = {2025}, author = {Matsumoto, Y and Okada, G and Ohta, M}, title = {Can Augmented Reality be Used as a Portion Size Estimation Aid Tool? A Pilot Randomized Controlled Trial.}, journal = {Journal of human nutrition and dietetics : the official journal of the British Dietetic Association}, volume = {38}, number = {5}, pages = {e70125}, doi = {10.1111/jhn.70125}, pmid = {40932046}, issn = {1365-277X}, support = {//This study was supported by PUH Research Grant Program./ ; }, mesh = {Humans ; Pilot Projects ; *Portion Size/psychology ; Female ; Male ; Young Adult ; Adult ; *Augmented Reality ; *Dietetics/education/methods ; Students ; Feasibility Studies ; }, abstract = {BACKGROUND: Evidence on the effectiveness of augmented reality (AR)-based tools for portion size estimation as an educational aid remains limited. In this pilot study, we developed a 3D food model using AR and assessed the feasibility of using this application to teach portion size estimation skills.<br><br>METHODS: This intervention study involved 43 students (including 38 females) from two dietetic education institutions. Participants were randomly assigned into four groups: (1) text only, (2) text and pictures, (3) food model and (4) AR. Learning effectiveness was evaluated using a pretest of 10 different foods, followed by a 10-min instructional session with the assigned tool, and then a post-test. Participants rated each learning tool for enjoyment, usefulness and recommendation to others on an 11-point Likert scale. Outcomes included the change in the number of correct answers within &#xb1;&#x2009;10% or &#xb1;&#x2009;20% of the true food weight.<br><br>RESULTS: Mean acceptability ratings for the text only, text and picture, food model and AR groups were enjoyment (4.1, 5.6, 7.0 and 7.9), usefulness (5.5, 7.4, 8.4 and 8.3) and recommendation to others (3.6, 6.3, 6.3 and 7.1), respectively. The mean changes in correct answers for text only, text and picture, food model and AR groups were 0.7, -1.1, 1.5 and 0.1, respectively, within a 10% error margin, and 1.2, -1.9, 2.0 and 0.8, respectively, within a 20% error margin.<br><br>CONCLUSIONS: This pilot study suggests that AR-based tools have potential as educational aids for portion size estimation among future dietitians, with acceptability ratings comparable to conventional methods, such as text only, text and pictures, and food models.<br><br>TRIAL REGISTRATION: The study was registered with the University Hospital Medical Information Network; UMIN000054307.}, }
@article {pmid40931350, year = {2025}, author = {Ye, G and Hong, H and Li, T and Li, J and Wu, JQ and Jiang, S and Meng, ZT and Yuan, HT and Xue, W and Li, AL and Zhou, T and Li, TT and Li, T}, title = {MAGdb: a comprehensive high quality MAGs repository for exploring microbial metagenome-assemble genomes.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {276}, pmid = {40931350}, issn = {1474-760X}, support = {No. 32100421//China National Natural Science Foundation/ ; No. 82341098//China National Natural Science Foundation/ ; No. 82130052//China National Natural Science Foundation/ ; No. NSS2021CI05002//Nanhu Laboratory/ ; No. 2024ZYYDSA400333//The Central Government Guides Local Science and Technology Development Fund Projects/ ; }, mesh = {*Metagenome ; *Metagenomics/methods ; *Databases, Genetic ; *Microbiota ; }, abstract = {Metagenomic analyses of microbial communities have unveiled a substantial level of interspecies and intraspecies genetic diversity by reconstructing metagenome-assembled genomes (MAGs). The MAG database (MAGdb) boasts an impressive collection of 74 representative research papers, spanning clinical, environmental, and animal categories and comprising 13,702 paired-end run accessions of metagenomic sequencing and 99,672 high quality MAGs with manually curated metadata. MAGdb provides a user-friendly interface that users can browse, search, and download MAGs and their corresponding metadata information. It represents a valuable resource for researchers in discovering potential novel microbial lineages and understanding their ecological roles. MAGdb is publicly available at https://magdb.nanhulab.ac.cn/ .}, }
@article {pmid40930298, year = {2026}, author = {Slack, SD and Esquinca, E and Arehart, CH and Boorgula, MP and Szczesny, B and Romero, A and Campbell, M and Chavan, S and Rafaels, N and Watson, H and Landis, RC and Hansel, NN and Rotimi, CN and Olopade, CO and Figueiredo, CA and Ober, C and Liu, AH and Kenny, EE and Kammers, K and Ruczinski, I and Taub, MA and Daya, M and Gignoux, CR and Kechris, K and Barnes, KC and Mathias, RA and Johnson, RK}, title = {Prediction and characterization of genetically regulated expression of asthma tissues from African-ancestry populations.}, journal = {The Journal of allergy and clinical immunology}, volume = {157}, number = {1}, pages = {253-261}, doi = {10.1016/j.jaci.2025.07.035}, pmid = {40930298}, issn = {1097-6825}, mesh = {Female ; Humans ; Male ; *Asthma/genetics/immunology ; *Black People/genetics ; *CD4-Positive T-Lymphocytes/immunology ; Gene Expression Profiling ; *Gene Expression Regulation ; Genetic Predisposition to Disease ; *Nasal Mucosa/metabolism/immunology ; Transcriptome ; }, abstract = {BACKGROUND: Genetic control of gene expression in asthma-related tissues is not well characterized, particularly for African-ancestry populations, limiting advancement in our understanding of the increased prevalence and severity of asthma in these populations.<br><br>OBJECTIVE: We sought to create novel transcriptome prediction models for asthma tissues (nasal epithelium and CD4[+] T cells) and apply them in a transcriptome-wide association study (TWAS) to discover candidate asthma genes.<br><br>METHODS: We developed and validated gene expression prediction databases for unstimulated CD4[+] T cells and nasal epithelium using an elastic net framework. Combining these with existing prediction databases (N = 51), we performed a TWAS of 9284 individuals of African ancestry to identify tissue-specific and cross-tissue candidate genes for asthma.<br><br>RESULTS: Novel databases for CD4[+] T cells and nasal epithelial gene expression prediction contain 8,351 and 10,296 genes, respectively, including 4 asthma loci (SCGB1A1, MUC5AC, ZNF366, and LTC4S) not predictable with existing public databases. Prediction performance was comparable to existing databases and was most accurate for populations sharing ancestry with the training set (eg, African ancestry). From the TWAS, we identified 17 candidate causal asthma genes (adjusted P < .1), including genes with tissue-specific (IL33 in nasal epithelium) and cross-tissue (CCNC and FBXW7) effects.<br><br>CONCLUSIONS: Expression of IL33, CCNC, and FBXW7 may affect asthma risk in African- ancestry populations by mediating inflammatory responses. The addition of CD4[+] T cell and nasal epithelium prediction databases to the public sphere will improve ancestry representation and power to detect novel gene-trait associations from TWAS.}, }
@article {pmid40928529, year = {2025}, author = {Lawler, T and Kwekkeboom, K and Warren Andersen, S and Sethi, AK and Tevaarwerk, AJ and Litzelman, K and Pophali, PA and Gangnon, RE and Hampton, JM and LoConte, NK and Trentham-Dietz, A}, title = {Self-efficacy for cancer self-management in the context of COVID-19: a cross-sectional survey study.}, journal = {Supportive care in cancer : official journal of the Multinational Association of Supportive Care in Cancer}, volume = {33}, number = {10}, pages = {843}, pmid = {40928529}, issn = {1433-7339}, support = {P30 CA014520/CA/NCI NIH HHS/United States ; UL1 TR002373/TR/NCATS NIH HHS/United States ; P30CA014520/CA/NCI NIH HHS/United States ; UL1TR002373//National Institutes of Health, United States/ ; }, mesh = {Humans ; *Self Efficacy ; *COVID-19/epidemiology/psychology ; Middle Aged ; Male ; Female ; Cross-Sectional Studies ; Adult ; Aged ; *Neoplasms/therapy/psychology ; *Self-Management/psychology ; Adolescent ; *Cancer Survivors/psychology ; Aged, 80 and over ; Young Adult ; Surveys and Questionnaires ; }, abstract = {PURPOSE: For cancer survivors, self-efficacy is needed to manage the disease and the effects of treatment. The COVID-19 pandemic disrupted cancer-related healthcare, which may have impacted self-management self-efficacy. We investigated self-efficacy reported by cancer survivors during COVID-19, including associations with healthcare disruptions, distress, and general health.<br><br>METHODS: Between 2020 and 2021, 1902 individuals aged 18-80&#xa0;years with a recent cancer diagnosis completed a survey regarding the effects of COVID-19 on healthcare, self-efficacy for managing cancer and social interactions, cancer-related distress, and perceived general health. Linear and logistic models estimated odds ratios and 95% confidence intervals (CIs) between self-efficacy scores, healthcare disruptions, significant distress, and general health.<br><br>RESULTS: Mean self-efficacy for managing cancer was 7.58 out of 10. Greater self-efficacy was associated with lower odds for distress (OR 0.18 [95% CI 0.13-0.26], quartile 4 vs. 1) and for worse general health (0.05 [0.03-0.09]). Participants with disruptions to cancer-related healthcare had lower self-efficacy for managing cancer compared to those without (6.62 vs. 7.09, respectively, P&#x2009;<&#x2009;0.001) and higher odds for distress (1.70 [1.36-2.14]), but not worse general health (1.13 [0.39-1.44]). Lower self-efficacy mediated 27% of the association between healthcare disruptions and increased distress (15-47%). Associations with self-efficacy for managing social interactions trended in the same direction.<br><br>CONCLUSIONS: During COVID-19, disruptions to cancer-related healthcare were associated with lower self-efficacy, increased distress, and worse general health. Psychosocial interventions designed to overcome barriers and target self-efficacy may be important for enhancing outcomes among cancer survivors experiencing disruptions in healthcare access.}, }
@article {pmid40927873, year = {2025}, author = {Blackman Carr, LT and Ard, J and Shanks, CB and Forman, EM and Goldstein, SP and Haire-Joshu, D and Jastreboff, AM and Johnson, S and Kandula, NR and Katzmarzyk, PT and Keyserling, TC and Kumanyika, SK and Lee, BY and Lewis, KH and Martin, MY and Mozaffarian, D and Newton, RL and Odoms-Young, A and Panza, E and Pronk, NP and Rosas, LG and Samuel-Hodge, C and Schmidt, LA and Sherwood, NE and Spring, B and Cooksey Stowers, K and Baskin, ML}, title = {Toward Health Equity: A Workshop Report on the State of the Science of Obesity Interventions for Adults.}, journal = {Obesity (Silver Spring, Md.)}, volume = {33}, number = {12}, pages = {2235-2245}, doi = {10.1002/oby.70035}, pmid = {40927873}, issn = {1930-739X}, support = {/HL/NHLBI NIH HHS/United States ; //Office of Disease Prevention/ ; /NH/NIH HHS/United States ; /HL/NHLBI NIH HHS/United States ; /NH/NIH HHS/United States ; }, mesh = {Humans ; *Obesity/prevention &amp; control/epidemiology/therapy ; *Health Equity ; Adult ; United States ; Health Promotion ; }, abstract = {OBJECTIVE: From October 18 to 20, 2022, the National Institutes of Health held a workshop to examine the state of the science concerning obesity interventions in adults to promote health equity. The workshop had three objectives: (1) convene experts from key institutions and the community to identify gaps in knowledge and opportunities to address obesity, (2) generate recommendations for obesity prevention and treatment to achieve health equity, and (3) identify challenges and needs to address obesity prevalence and disparities and develop a diverse workforce.<br><br>METHODS: A three-day virtual convening.<br><br>RESULTS: Several key themes emerged from the workshop discussions that describe directions to build on the currently limited amount of research on obesity, disparities, and equity. Key themes centered on the determinants of health, leveraging technology, clinical, community, commercial, and policy approaches. Community-engaged work, particularly in populations that have received little focus (e.g., sexual gender minorities, Asian communities), was also discussed.<br><br>CONCLUSIONS: Future research may be impactful when multilevel approaches are undertaken that leverage equity-minded tools and can be scaled up to meet community-informed population needs in a variety of settings. Funding priorities and workforce development will be critical to realizing health equity.}, }
@article {pmid40926576, year = {2025}, author = {Achury, R and Staab, M and Seibold, S and Müller, J and Heidrich, L and Püls, M and Hacker, H and Fonseca, CR and Fischer, M and Blüthgen, N and Weisser, W}, title = {Habitat and land-use intensity shape moth community structure across temperate forest and grassland.}, journal = {The Journal of animal ecology}, volume = {94}, number = {11}, pages = {2308-2321}, pmid = {40926576}, issn = {1365-2656}, support = {//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Animals ; *Grassland ; *Moths/physiology ; *Forests ; Germany ; *Biodiversity ; Ecosystem ; }, abstract = {Land-use change and intensification are major drivers of biodiversity loss, yet their effects on diversity have usually been studied within a single habitat type or land-use category, limiting our understanding of cross-habitat patterns. Moths, a species-rich taxon worldwide, represent a significant portion of the biodiversity in both temperate forests and grasslands, functioning as pollinators and herbivores. While increasing land-use intensity (LUI) in both habitats is expected to negatively impact moth assemblages, the strength of this effect remains uncertain. Moreover, land-use intensification interacts with broader environmental factors, such as weather conditions and the spread of artificial light at night (ALAN), but their combined effects on moth community diversity and turnover across habitats remain poorly understood. We sampled moth communities across 150 grassland and 150 forest plots along land-use gradients in Germany. We quantified plot- and landscape-scale LUI and tested the role of plant diversity, temperature and precipitation during the night of sampling and the preceding season, and ALAN in shaping moth diversity (standardized by coverage) along Hill numbers. Forests supported significantly higher moth abundance, biomass and diversity than grasslands, with habitat type being the main driver of moth community composition. LUI at the plot scale had contrasting effects on moth abundance, increasing it in forests but reducing it in grasslands. Impacts of LUI were more pronounced at the landscape level, reducing moth diversity particularly in areas dominated by grasslands. Plant diversity and temperature were key determinants for moth communities, increasing alpha diversity across diversity metrics, that is Hill numbers. ALAN had no significant influence on moth abundance or biomass but significantly decreased Simpson diversity. Beta diversity increased with geographic distance, habitat change and LUI but decreased with weather differences among plots. Our results highlight the interplay between LUI, habitat type and abiotic factors in shaping moth communities across large spatial scales. Effective conservation strategies should consider maintaining habitat heterogeneity and promoting plant diversity, particularly in temperate habitats exposed to high land-use intensification.}, }
@article {pmid40924543, year = {2025}, author = {Baele, G and Carvalho, LM and Brusselmans, M and Dudas, G and Ji, X and McCrone, JT and Lemey, P and Suchard, MA and Rambaut, A}, title = {HIPSTR: highest independent posterior subtree reconstruction in TreeAnnotator X.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {10}, pages = {}, pmid = {40924543}, issn = {1367-4811}, support = {//Research Foundation-Flanders/ ; }, mesh = {*Software ; *Phylogeny ; *SARS-CoV-2/genetics/classification ; Bayes Theorem ; *Ebolavirus/genetics/classification ; Algorithms ; Humans ; *Computational Biology/methods ; COVID-19/virology ; }, abstract = {SUMMARY: In Bayesian phylogenetic and phylodynamic studies, it is common to summarize the posterior distribution of trees with a time-calibrated summary phylogeny. While the maximum clade credibility (MCC) tree is often used for this purpose, we here show that a novel summary tree method-the highest independent posterior subtree reconstruction, or (HIPSTR)-contains consistently higher supported clades over MCC. We also provide faster computational routines for estimating both summary trees in an updated version of TreeAnnotator X, an open-source software program that summarizes the information from a sample of trees and returns many helpful statistics such as individual clade credibilities contained in the summary tree.<br><br>RESULTS: HIPSTR and MCC reconstructions on two Ebola virus and two SARS-CoV-2 datasets show that HIPSTR yields summary trees that consistently contain clades with higher support compared to MCC trees. The MCC trees regularly fail to include several clades with very high posterior probability (&#x2265;0.95) as well as a large number of clades with moderate to high posterior probability (&#x2265;50%), whereas HIPSTR-in particular its majority-rule extension MrHIPSTR-achieves near-perfect performance in this respect. HIPSTR and MrHIPSTR also exhibit favourable computational performance over MCC in TreeAnnotator X. Comparison to the recent CCD0-MAP algorithm yielded mixed results and requires a more in-depth investigation in follow-up studies.<br><br>TreeAnnotator X is available as part of the BEAST X (v10.5.0) software package, available at https://github.com/beast-dev/beast-mcmc/releases, and on Zenodo (DOI: https://doi.org/10.5281/zenodo.4895234).}, }
@article {pmid40923094, year = {2025}, author = {Sze, JS and Sauls, LA}, title = {Prospects and perils in the geospatial turn of conservation.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {39}, number = {6}, pages = {e70145}, pmid = {40923094}, issn = {1523-1739}, support = {ES/Y002660/1//Economic and Social Research Council/ ; ERC-2021-ADG/ERC_/European Research Council/International ; CONDJUST/ERC_/European Research Council/International ; 101054259/ERC_/European Research Council/International ; }, mesh = {*Conservation of Natural Resources/methods ; *Biodiversity ; *Big Data ; }, abstract = {Conservation has embraced advances in big data and related digital technologies as key to preventing biodiversity loss, especially in the identification of areas of conservation priority based on spatial data, which we call the big geospatial data turn. This turn has led to the proliferation of useful methods and tools, including global geospatial maps. But these methods may also undermine moves toward rights-based and inclusive conservation approaches that consider plural values and perspectives. We built on the burgeoning literature to call for greater attention to be paid to the datasets, methodological choices, and the assumptions global mapping for biodiversity conservation is based on. In increasingly prioritizing the use of big geospatial data, conservation professionals risk forgetting that maps show only partial information and limit the diversity of ways of seeing and representing the world. Big geospatial data collected through remotely sensed technologies must still be situated in time and place and provided with appropriate political-economic and sociocultural contexts. Further, global mapping efforts remain primarily the purview of Global North researchers, even given the push to make data open access. Instead of uncritically calling for more data, we urge conservationists to contextualize and situate big geospatial data carefully so as to build a field that achieves socially just and ecologically effective conservation outcomes.}, }
@article {pmid40921753, year = {2025}, author = {Wang, F and Xue, M and Zhou, L and Doughty, CE and Ciais, P and Reich, PB and Shang, J and Chen, JM and Liu, J and Green, JK and Hao, D and Tao, S and Su, Y and Liu, L and Xia, J and Wang, H and Yu, K and Zhu, Z and Zhu, P and Li, X and Liu, H and Zeng, Y and Yan, K and Liu, L and Lafortezza, R and Su, Y and Meng, Y and Pan, Y and Yang, X and Fu, YH and He, N and Yuan, W and Chen, X}, title = {Contrasting age-dependent leaf acclimation strategies drive vegetation greening across deciduous broadleaf forests in mid- to high latitudes.}, journal = {Nature plants}, volume = {11}, number = {9}, pages = {1748-1758}, pmid = {40921753}, issn = {2055-0278}, mesh = {*Plant Leaves/physiology/growth &amp; development ; *Forests ; *Acclimatization ; *Trees/physiology ; Seasons ; Climate Change ; Photosynthesis ; North America ; Europe ; }, abstract = {Increasing leaf area and extending vegetation growing seasons are two primary drivers of global greening, which has emerged as one of the most significant responses to climate change. However, it remains unclear how these two leaf acclimation strategies would vary across forests at a large spatial scale. Here, using multiple satellite-based datasets and field measurements, we analysed the temporal changes (Δ) in maximal leaf area index (LAImax) and length of the growing season (LOS) from 2002 to 2021 across deciduous broadleaf forests (DBFs) in the middle to high latitudes. Contrary to the widely held assumption of coordination, our results revealed a negative correlation between ΔLAImax and ΔLOS. Notably, the trade-offs between ΔLAImax and ΔLOS were strongly explained by stand age. Younger DBFs, with lower baseline LAImax, predominantly located in eastern Asia, displayed an increase in LAImax with small changes in LOS. This acquisitive strategy facilitated younger DBFs to grow more photosynthetically efficient leaves with low leaf mass per area, enhancing their light use efficiency. Conversely, older DBFs with a higher baseline LAImax, primarily located in North America and Europe, extended their LOS by increasing leaf mass per area. This conservative strategy facilitated older DBFs to produce thicker, but less photosynthetically efficient leaves, resulting in decreased light use efficiency. Our findings offer new insights into the contrasting changes in leaf area and growing season length and highlight their divergent impacts on ecosystem functioning.}, }
@article {pmid40920919, year = {2025}, author = {Li, Y and Meng, L and Richardson, AD and Lee, X and Menzel, A and Mao, J and Diehl, JL and Wang, A}, title = {Cooling outweighs warming across phenological transitions in the Northern Hemisphere.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {37}, pages = {e2501844122}, pmid = {40920919}, issn = {1091-6490}, mesh = {Seasons ; Forests ; Temperature ; *Climate Change ; *Global Warming ; Plant Leaves/physiology ; Trees ; }, abstract = {Vegetation phenology, i.e., seasonal biological events such as leaf-out and leaf-fall, regulates local climate through biophysical processes like evapotranspiration (ET) and albedo. However, the net surface temperature impact of these processes-whether ET cooling or albedo-induced warming predominates-and how the dominance changes across phenological transitions and regions remains poorly understood. Here, we investigated the effects of vegetation foliage on daytime land surface temperature (LST) following six phenological transitions, spanning from the start of season to end of season, in deciduous and mixed forests across the mid- to high-latitude Northern Hemisphere during 2013-2021 using multiple satellite products and ground observations. We quantified vegetation effect as the difference between observed LST and LST estimates from the Annual Temperature Cycle (ATC) model, representing a no-foliage scenario. We found that vegetation-induced cooling consistently outweighs warming following all phenological transitions except for the end of the season. Cooling intensity increased with vegetation greenness, ranging from 1.0 ± 0.5 °C (mean ± 0.15 SD) in 59% of forests after the start of the season (SOS) to 6.1 ± 0.8 °C in 89% of forests following the onset of maturity, before declining toward the end of the season. Over half of the regions experiencing cooling showed intensification of surface cooling with climate warming, suggesting an amplified vegetation-mediated cooling under future climate change. The findings provide a more precise understanding of the role of vegetation in modulating climate at the intraseasonal scale, highlighting the importance of integrating phenological impacts into climate adaptation strategies and Earth system modeling.}, }
@article {pmid40920894, year = {2025}, author = {Kawam, B and Ostner, J and McElreath, R and Schülke, O and Redhead, D}, title = {A causal framework for the drivers of animal social network structure.}, journal = {PLoS computational biology}, volume = {21}, number = {9}, pages = {e1013370}, pmid = {40920894}, issn = {1553-7358}, mesh = {Animals ; Bayes Theorem ; *Behavior, Animal/physiology ; Computational Biology ; *Social Behavior ; Computer Simulation ; Models, Biological ; }, abstract = {A major goal of behavioural ecology is to explain how phenotypic and ecological factors shape the networks of social relationships that animals form with one another. This inferential task is notoriously challenging. The social networks of interest are generally not observed, but must be approximated from behavioural samples. Moreover, these data are highly dependent: the observed network edges correlate with one another, due to biological and sampling processes. Failing to account for the resulting uncertainty and biases can lead to dysfunctional statistical procedures, and thus to incorrect results. Here, we argue that these problems should be understood-and addressed-as problems of causal inference. For this purpose, we introduce a Bayesian causal modelling framework that explicitly defines the links between the target interaction network, its causes, and the data. We illustrate the mechanics of our framework with simulation studies and an empirical example. First, we encode causal effects of individual-, dyad-, and group-level features on social interactions using Directed Acyclic Graphs and Structural Causal Models. These quantities are the objects of inquiry, our estimands. Second, we develop estimators for these effects-namely, Bayesian multilevel extensions of the Social Relations Model. Third, we recover the structural parameters of interest, map statistical estimates to the underlying causal structures, and compute causal estimates from the joint posterior distribution. Throughout the manuscript, we develop models layer by layer, thereby illustrating an iterative workflow for causal inference in social networks. We conclude by summarising this workflow as a set of seven steps, and provide practical recommendations.}, }
@article {pmid40920814, year = {2025}, author = {Bergman, DR and Jackson, T and Jain, HV and Norton, KA}, title = {An efficient and flexible framework for inferring global sensitivity of agent-based model parameters.}, journal = {PLoS computational biology}, volume = {21}, number = {9}, pages = {e1013427}, pmid = {40920814}, issn = {1553-7358}, support = {U01 CA243075/CA/NCI NIH HHS/United States ; }, mesh = {*Models, Biological ; Humans ; Computational Biology/methods ; Computer Simulation ; Cell Proliferation/physiology ; Algorithms ; Neoplasms/pathology ; Reproducibility of Results ; }, abstract = {Agent-based models (ABMs) have become essential tools for simulating complex biological, ecological, and social systems where emergent behaviors arise from the interactions among individual agents. Quantifying uncertainty through global sensitivity analysis is crucial for assessing the robustness and reliability of ABM predictions. However, most global sensitivity methods demand substantial computational resources, making them impractical for highly complex models. Here, we introduce SMoRe GloS (Surrogate Modeling for Recapitulating Global Sensitivity), a novel, computationally efficient method for performing global sensitivity analysis of ABMs. By leveraging explicitly formulated surrogate models, SMoRe GloS allows for comprehensive parameter space exploration and uncertainty quantification without sacrificing accuracy. We demonstrate our method's flexibility by applying it to two biological ABMs: a simple 2D in vitro cell proliferation model and a complex 3D vascular tumor growth model. Our results show that SMoRe GloS is compatible with simpler methods like the Morris one-at-a-time method, and more computationally intensive variance-based methods like eFAST. SMoRe GloS accurately recovered global sensitivity indices in each case while achieving substantial speedups, completing analyses in minutes. In contrast, direct implementation of eFAST amounted to several days of CPU time for the complex ABM. Remarkably, our method also estimates sensitivities for ABM parameters representing processes not explicitly included in the surrogate model, further enhancing its utility. By making global sensitivity analysis feasible for computationally expensive models, SMoRe GloS opens up new opportunities for uncertainty quantification in complex systems, allowing for more in depth exploration of model behavior, thereby increasing confidence in model predictions.}, }
@article {pmid40920559, year = {2025}, author = {Abdugheni, R and Li, WJ}, title = {EzBioCloud 16S rRNA Gene Sequence Formatter: a Python-based sequence formatting tool for systematic microbiology.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {75}, number = {9}, pages = {}, doi = {10.1099/ijsem.0.006890}, pmid = {40920559}, issn = {1466-5034}, mesh = {*RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Bacteria/classification/genetics ; *Software ; Sequence Analysis, DNA/methods ; *Computational Biology/methods ; }, abstract = {EzBioCloud is one of the practical reference databases and analytical platforms for systematic microbiology research. The EzBioCloud database provides convenient services in this regard, especially for performing sequence analysis using the 16S rRNA genes. However, '.fasta' files of 16S rRNA sequences obtained after the alignment in EzBioCloud need manual formatting for further analysis and phylogenetic tree construction, which is labourious and time-consuming. To address this issue, we have developed a Python-based tool, EzBioCloud 16S rRNA Gene Sequence Formatter (version 1.0), designed to assist in sequence formatting. Here, we report the development and application of the tool and present this tool publicly to support the researchers in the relevant field.}, }
@article {pmid40920446, year = {2025}, author = {Jackson, K and Gabrielli, J and Colby, S and Wray, T and Janssen, T and Rogers, M and Delapaix, C}, title = {Real-Time Exposure to Alcohol Content in Digital Media in Adolescents: Protocol for a Multiburst Ecological Momentary Assessment Study.}, journal = {JMIR research protocols}, volume = {14}, number = {}, pages = {e50649}, pmid = {40920446}, issn = {1929-0748}, support = {R01 AA027968/AA/NIAAA NIH HHS/United States ; }, mesh = {Humans ; Adolescent ; *Ecological Momentary Assessment ; Male ; Female ; *Social Media/statistics &amp; numerical data ; Prospective Studies ; *Alcohol Drinking/psychology ; *Adolescent Behavior/psychology ; Surveys and Questionnaires ; *Underage Drinking/psychology ; Digital Media ; }, abstract = {BACKGROUND: Digital media frequently contains positive portrayals of alcohol content, which has been shown to be associated with alcohol-related cognitions and behaviors. Because youth are heavy media consumers and have access to unsupervised, repeat viewing of media content on their personal mobile devices, it is critical to understand the frequency of encountering alcohol content in adolescents' daily lives and how adolescents engage with the content.<br><br>OBJECTIVE: This paper outlines the study protocol for examining adolescents' exposure to alcohol-related content in digital media within their natural environments.<br><br>METHODS: Adolescents (N=302; 31.8% boys, 16.2% nonbinary, 51.3% girls; 25.8% Asian, 3.6% American Indian, 21.5% Black, 4.6% other, 52% White, 25.8% Hispanic or Latinx; mean age 16.21, SD 0.77 y) enrolled in high school were recruited through social media to participate in a prospective study involving bursts of ecological momentary assessment (EMA) reports coupled with longer surveys. We conducted group orientation sessions via videoconference and online surveys, followed by a 21-day EMA period that included scheduled reports across 4 daily time blocks, as well as self-initiated reports on media exposure. Reports of alcohol content exposure included details about the platform, level of engagement, source characteristics, beliefs and perceived norms about the content, the viewing context, and whether the content was sponsored or branded. The participants submitted exposures to alcohol content as an image (screenshot or photo) or text description to be objectively coded. The participants completed a weekly online survey assessing alcohol use and related cognitions. EMA reports will be merged with coded image and text entries and with data from baseline, weekly, and follow-up surveys. Self-reported alcohol exposure will be explored descriptively, and differences in exposure tested across subgroups. Event-level data will be compared with random prompt data to examine differences at times of exposure versus nonexposure. Prospective associations between media alcohol content exposure and alcohol use will be explored over 1-week and 4-month time frames. Mediation of the association between media alcohol exposure and drinking will be tested to explore putative mechanisms.<br><br>RESULTS: EMA data collection took place from February 2022 to August 2023. Data management and preliminary analysis are ongoing. Preliminary data were disseminated through conference presentations in 2024-2025 and manuscripts are ongoing with full results anticipated to be published in 2025-2026.<br><br>CONCLUSIONS: By characterizing adolescents' real-world exposure to alcohol content in the media, the study provides critical information to develop and implement interventions to target youth behavior that are well suited to delivery via mobile devices. Next steps are to conduct focus groups to understand participants' lived experience of exposure to media alcohol content and reactions to proposed intervention targets. This study and subsequent qualitative work will launch a program of research to counter the effects of alcohol-related media exposure as experienced by adolescents in an effort to minimize underage alcohol involvement.<br><br>DERR1-10.2196/50649.}, }
@article {pmid40920239, year = {2026}, author = {Kröger, K and Wiemes, K and Santosa, F and Böhner, H and Lax, H and Stolpe, S and Kowall, B and Stang, A}, title = {Prescription of lipid-lowering drugs and their association with hospitalization for ST-elevation myocardial infarction (STEMI) in Germany in 2010-2022.}, journal = {Clinical research in cardiology : official journal of the German Cardiac Society}, volume = {115}, number = {2}, pages = {313-321}, pmid = {40920239}, issn = {1861-0692}, mesh = {Humans ; Germany/epidemiology ; *ST Elevation Myocardial Infarction/epidemiology/therapy ; *Hospitalization/trends/statistics &amp; numerical data ; Male ; *Hypolipidemic Agents/therapeutic use ; Female ; Aged ; Middle Aged ; *Drug Prescriptions/statistics &amp; numerical data ; }, abstract = {OBJECTIVES: We investigated changes in lipid-lowering drug prescriptions in Germany as a whole and in the 16 federal states over the last 13 years and their association with hospitalization rates for acute myocardial infarction.<br><br>DESIGN: Ecological study.<br><br>SETTING: Nationwide German hospitalization, Diagnosis-Related Groups Statistic.<br><br>PATIENTS/PARTICIPANTS: German population in the years 2010 through 2022.<br><br>INTERVENTION: All prescriptions of lipid-lowering drugs in the years 2010 to 2022 by federal state in Germany.<br><br>MAIN OUTCOME MEASURES: Hospitalization rates for the treatment of transmural infarction per calendar year and federal state (STEMI&#x2009;=&#x2009;ST-elevation myocardial infarction).<br><br>RESULTS: The age-standardized prescription rates of lipid-lowering drugs per 1000 person-years increased from 77.4 in 2010 to 145.2 in 2022 (reference population: Germany 2011). Within the same period, the STEMI hospitalization rate per 100,000 person-years decreased from 143.7 to 100.1. Based on the prescription and hospitalization rates of the 16 federal states, it is shown that the STEMI hospitalization rate decreased the more the prescription rate of lipid-lowering drugs in a federal state increased over time (beta&#x2009;=&#x2009;0.38, 95% confidence interval&#x2009;-&#x2009;0.64;&#x2009;-&#x2009;0.12; adjusted explained variance 0.362).<br><br>CONCLUSION: Increasing prescription rates of lipid-lowering drugs have correlated with decreasing rates of hospitalized cases for STEMI in Germany in the last decade.}, }
@article {pmid40919732, year = {2026}, author = {Milligan, PD and Rossiter, J and Zare, A and Palmer, TM and Lemboi, J and Mizell, GM and Mosiany, J and Riginos, C and Goheen, JR and Pringle, EG}, title = {Mutualism, herbivory, and invasive ants as seasonally dependent drivers of root surface area in a foundational savanna ant-plant.}, journal = {The New phytologist}, volume = {249}, number = {2}, pages = {777-791}, doi = {10.1111/nph.70553}, pmid = {40919732}, issn = {1469-8137}, support = {1556905//Division of Environmental Biology/ ; 1935498//Division of Environmental Biology/ ; 2010075//National Science Foundation Division of Biological Infrastructure/ ; }, mesh = {Animals ; *Acacia/growth &amp; development ; *Ants ; Convolutional Neural Networks ; Grassland ; *Herbivory ; *Introduced Species ; Mammals ; Models, Biological ; *Plant Roots/growth &amp; development ; Rain ; Seasons ; *Symbiosis ; *Myrmecophytes/growth &amp; development ; }, abstract = {Many plants are defended from herbivory by costly insect mutualists. Understanding positive associations between plants and mutualists requires a whole-plant perspective including roots. We hypothesized that root surface area increases with mutualist activity (to a saturation threshold) and recent rainfall but that this relationship shifts when herbivores are excluded. We also hypothesized that invasive ants limit root surface area and that mutualism breakdown driven by invaders blunts root responses to rainfall and herbivore exclusion. Using minirhizotrons (est. 2021), we surveyed root surface area of ant-acacias during a dry (2022) and then a wet (2023) season. Study plots either excluded or permitted vertebrate browsers, within a natural experiment comparing mutualist-defended ant-acacias to those invaded by a mutualism-disrupting ant. Root area increased with mutualist activity to a threshold, but this positive association was less apparent during rainy periods. Megabrowser exclusion increased overall root area but reduced the threshold for a positive association with mutualist activity and reduced the steepness of the root area-rainfall correlation. Ant-invaded acacias had smaller root areas that correlated less steeply with rainfall. Positive associations between insect defense and root area were thus contingent on rainfall, herbivory, and biotic invasion, drivers that are shifting under global change.}, }
@article {pmid40915583, year = {2026}, author = {Zhang, Y and Wang, B and Hassan, M and Zhang, X}, title = {Biochar-calcium alginate composite immobilizing Pseudomonas sp. H6 for phosphate and ammonium recovery: Multi-omics insights and practical application evaluation.}, journal = {Bioresource technology}, volume = {439}, number = {}, pages = {133274}, doi = {10.1016/j.biortech.2025.133274}, pmid = {40915583}, issn = {1873-2976}, mesh = {*Alginates/chemistry ; *Charcoal/chemistry ; *Ammonium Compounds/isolation &amp; purification ; *Phosphates/isolation &amp; purification ; *Pseudomonas/metabolism ; Wastewater/chemistry ; Glucuronic Acid/chemistry ; Hexuronic Acids/chemistry ; Cells, Immobilized/metabolism ; Adsorption ; Water Purification/methods ; Biodegradation, Environmental ; Water Pollutants, Chemical/isolation &amp; purification ; Multiomics ; }, abstract = {Water eutrophication has emerged as a pervasive ecological challenge worldwide. To realize the resource utilization of waste and nutrients, a novel rape straw-derived biochar-calcium alginate composite (M-CA-RBC) immobilized Pseudomonas sp. H6 was synthesized to simultaneously remove phosphate (PO4[3-]) and ammonium (NH4[+]) from distillery wastewater. The removal performance of PO4[3-] and NH4[+] by M-CA-RBC were investigated. The removal mechanisms were explored by using different adsorption models combined with microbial degradation kinetics, analysis of dissolved organic matter components, electrochemical analysis, metagenomics, and metabolomics. The resource application potential of M-CA-RBC was evaluated. The results showed that M-CA-RBC had good removal performance for PO4[3-] (17.81 mg/g) and NH4[+] (25.78 mg/g). Surface precipitation, electrostatic attraction, Poly-P accumulation, microbial-induced calcium precipitation, and microbial assimilation were the main removal mechanisms of PO4[3-] by M-CA-RBC. The removal mechanisms of NH4[+] were micropore filling, ion exchange, electrostatic attraction, and heterotrophic nitrification-aerobic denitrification (HN-AD). M-CA-RBC had a good application potential in the practical distillery wastewater, with removal rates of PO4[3-] and NH4[+] reaching 88% and 65%, respectively. After adsorption saturation, M-CA-RBC exhibited good stability, which could be used as a slow-release fertilizer to promote the growth of mung beans. This study provides practical significance for the efficient removal and recovery of nitrogen and phosphorus in wastewater.}, }
@article {pmid40914230, year = {2025}, author = {Xu, Y and Chevreul, K and Dindorf, C and Bismuth, &#xc9; and Carel, JC and Michel, M}, title = {Association of socioeconomic status and hospital efficiency in Type-1 diabetic patients with ketoacidosis or diabetic coma: a secondary data analysis comparing nation-wide paediatric and adult admissions in France.}, journal = {Diabetes research and clinical practice}, volume = {229}, number = {}, pages = {112450}, doi = {10.1016/j.diabres.2025.112450}, pmid = {40914230}, issn = {1872-8227}, mesh = {Humans ; France/epidemiology ; *Diabetes Mellitus, Type 1/complications/economics/epidemiology/therapy ; Adult ; Male ; Female ; *Diabetic Ketoacidosis/economics/epidemiology/therapy ; Child ; Adolescent ; Length of Stay/statistics &amp; numerical data/economics ; *Social Class ; Young Adult ; Middle Aged ; Child, Preschool ; *Diabetic Coma/economics/epidemiology/therapy ; *Hospitalization/statistics &amp; numerical data/economics ; Secondary Data Analysis ; }, abstract = {AIMS: To study the association between socioeconomic status (SES) and hospital efficiency in Type 1 diabetes mellitus patients admitted for ketoacidosis or diabetic coma in mainland France, overall and in adults versus children.<br><br>METHODS: An observational study was carried out using exhaustive national hospital discharge databases. It included all admissions discharged from 2013 to 2019. SES was assessed using an ecological measure divided into national quintiles, and efficiency by variations in patients' length of stay (LOS) compared to mean national LOS and a comparison of production costs and revenues. Multilevel multivariable analyses were carried out to study the association.<br><br>RESULTS: 67,100 admissions were included. Multivariable analyses found a significant association between efficiency outcomes, SES and age. Compared to other age groups, children under 5 had higher LOS than the national mean and incurred higher costs than what hospitals were paid regardless of SES. In adults, there was a significant interaction between SES and age group, leading to significantly increased LOS and costs in adults from intermediate and/or lower SES groups.<br><br>CONCLUSIONS: Current payment methods using diagnosis-related groups may not adequately reflect the burden of Type 1 diabetes mellitus patients admitted for ketoacidosis or diabetic coma on hospitals.}, }
@article {pmid40911670, year = {2025}, author = {Wan, N and Duan, Q and Cai, Z and Zhu, Z and Wang, J and Tian, Y and Shen, W and Li, B and Kuang, Z and Liang, X and Liu, S and An, X and Yang, X and Liu, X and Mao, L and Chen, J and Wang, Y and Feng, Z and Liu, W and Bu, Y and Nevo, E and Papa, R and Meyer, A and Liu, J and Li, K}, title = {Aplf/Dna2 variants drive chromosomal fission and accelerate speciation in zokors.}, journal = {Science advances}, volume = {11}, number = {36}, pages = {eadt2282}, pmid = {40911670}, issn = {2375-2548}, mesh = {Multiomics ; Chromosomes ; Animals ; *Rodentia/classification/genetics ; *DNA-(Apurinic or Apyrimidinic Site) Lyase/genetics ; *DNA Helicases/genetics ; *Endodeoxyribonucleases/genetics ; Genome ; Molecular Sequence Annotation ; Synteny ; Genomic Structural Variation ; Genetic Speciation ; Genetics, Population ; Telomere ; Phylogeny ; Base Sequence ; Genetic Variation ; }, abstract = {Chromosomal fissions and fusions are common, yet the molecular mechanisms and implications in speciation remain poorly understood. Here, we confirm a fission event in one zokor species through multiple-omics and functional analyses. We traced this event to a mutation in a splicing enhancer of the DNA repair gene Aplf in the fission-bearing species, which caused exon skipping and produced a truncated protein that disrupted DNA repair. An intronic deletion in Dna2, known to facilitate neo-telomere formation when knocked out, reduced gene activity. These variants collectively drove chromosomal fission in this zokor species. The newly formed chromosome became fixed due to carrying essential genes and strong selective pressure. While geographic isolation likely initiated the divergence of this species and the sister one, the fission event and associated decline at the chromosome level in gene flow probably exacerbated the speciation process. Our work elucidates the genetic basis of chromosomal fission and underscores its role in speciation dynamics.}, }
@article {pmid40910796, year = {2025}, author = {Gaun, N and Pietroni, C and Martin-Bideguren, G and Lauritsen, J and Aizpurua, O and Fernandes, JM and Ferreira, E and Aubret, F and Sarraude, T and Perry, C and Wauters, L and Romeo, C and Spada, M and Tranquillo, C and Sutton, AO and Griesser, M and Warrington, MH and Pérez I de Lanuza, G and Abalos, J and Aguilar, P and de la Cruz, F and Juste, J and Alonso-Alonso, P and Groombridge, J and Louch, R and Ruhomaun, K and Henshaw, S and Cabido, C and Barrio, IG and Šunje, E and Hosner, P and Prates, I and While, GM and García-Roa, R and Uller, T and Feiner, N and Bonaccorso, E and Klein-Ipsen, P and Rotovnik, RM and Alberdi, A and Eisenhofer, R}, title = {The Earth Hologenome Initiative: Data Release 1.}, journal = {GigaScience}, volume = {14}, number = {}, pages = {}, pmid = {40910796}, issn = {2047-217X}, support = {DNRF143//Danmarks Grundforskningsfond/ ; CF20-0460//Carlsbergfondet/ ; 101066225//HORIZON EUROPE Framework Programme/ ; PD/BD/150645/2020//Ag&#xea;ncia Regional para o Desenvolvimento da Investiga&#xe7;&#xe3;o, Tecnologia e Inova&#xe7;&#xe3;o/ ; 25925//Villum Fonden/ ; }, mesh = {Animals ; *Metagenomics/methods ; *Metagenome ; *Microbiota/genetics ; Earth, Planet ; *Vertebrates/genetics/microbiology ; Databases, Genetic ; }, abstract = {BACKGROUND: The Earth Hologenome Initiative (EHI) is a global endeavor dedicated to revisit fundamental ecological and evolutionary questions from the systemic host-microbiota perspective, through the standardized generation and analysis of joint animal genomic and associated microbial metagenomic data.<br><br>RESULTS: The first data release of the EHI contains 968 shotgun DNA sequencing read files containing 5.2 TB of raw genomic and metagenomic data derived from 21 vertebrate species sampled across 12 countries, as well as 17,666 metagenome-assembled genomes reconstructed from these data.<br><br>CONCLUSIONS: The dataset can be used to address fundamental questions about host-microbiota interactions and will be available to the research community under the EHI data usage conditions.}, }
@article {pmid40909344, year = {2025}, author = {Polak, I and Stryiński, R and Paukszto, &#x141; and Jastrzębski, JP and Bogacka, I and Łopieńska-Biernat, E}, title = {Diversity, expression, and structural modeling of sugar transporters in Anisakis simplex s. s. L3 and L4 larvae: an in vitro and in silico study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1621051}, pmid = {40909344}, issn = {2235-2988}, mesh = {Animals ; Larva/genetics/metabolism ; *Anisakis/genetics/metabolism/growth &amp; development ; *Glucose Transport Proteins, Facilitative/genetics/metabolism/chemistry ; Computer Simulation ; Computational Biology ; Glucose/metabolism ; Phylogeny ; *Monosaccharide Transport Proteins/genetics/metabolism/chemistry ; Biological Transport ; *Helminth Proteins/genetics/metabolism/chemistry ; Gene Expression Profiling ; Models, Molecular ; }, abstract = {INTRODUCTION: Glucose transporter (GLUT) research in parasitic nematodes focuses on identifying and characterizing developmentally regulated isoforms, elucidating their regulatory and structural properties, and evaluating their potential as drug targets. While glucose transport mechanisms have been well characterized in the free-living nematode Caenorhabditis elegans, data on parasitic species remain limited. Anisakis simplex s. s., a parasitic nematode, relies on host-derived glucose to maintain energy metabolism. It is hypothesized that A. simplex s. s. utilizes specific glucose transporters to facilitate sugar uptake under varying nutritional conditions.<br><br>MATERIALS AND METHODS: In silico analysis identified five putative facilitated glucose transporter genes (fgt-1, fgt-2, fgt-3, fgt-5, fgt-9) and one Sugars Will Eventually be Exported Transporter (sweet-1) gene. The FGTs were classified as members of the solute carrier family 2 (SLC2), while sweet-1 belonged to the SWEET transporter family. Full-length cDNA sequences were obtained, and encoded proteins structurally characterized using bioinformatic modeling. Expression of transporter genes was assessed in A. simplex s. s. larvae at stages L3 and L4 cultured in vitro under different glucose concentrations and time points.<br><br>RESULTS: Structural and phylogenetic analyses revealed that fgt-1 and fgt-3 share high similarity with class I GLUTs found in nematodes and vertebrates. Gene expression profiling demonstrated differential regulation between larval stages. Most notably, FGT genes were stably expressed in L4 larvae, whereas in L3 larvae, gene activation was more variable and dependent on glucose concentration, showing a dynamic transcriptional response to nutrient levels. Sweet-1 was expressed in both stages, but its regulation differed over time and with glucose availability. Glucose supplementation altered trehalose and glycogen levels, and trehalase activity varied across stages and treatments, indicating stage-specific metabolic adaptation.<br><br>DISCUSSION: The observed transcriptional and biochemical differences between L3 and L4 larvae suggest a shift in glucose uptake mechanisms, from transcuticular absorption in L3 to intestinal glucose uptake in L4 following intestine activation. FGT1 and FGT3 are proposed as key facilitators of glucose uptake, with roles varying across developmental stages. These findings indicate that glucose transporters are regulated in response to changing environmental conditions and may represent targets for rational anthelmintic drug design.}, }
@article {pmid40908443, year = {2025}, author = {Kaplan, DM and Alvarez, SJA and Palitsky, R and Choi, H and Clifford, GD and Crozier, M and Dunlop, BW and Grant, GH and Greenleaf, MN and Johnson, LM and Maples-Keller, J and Levin-Aspenson, HF and Mascaro, JS and McDowall, A and Pozzo, NS and Raison, CL and Zarrabi, AJ and Rothbaum, BO and Lam, WA}, title = {Correction: Fabla: A voice-based ecological assessment method for securely collecting spoken responses to researcher questions.}, journal = {Behavior research methods}, volume = {57}, number = {10}, pages = {274}, doi = {10.3758/s13428-025-02818-9}, pmid = {40908443}, issn = {1554-3528}, }
@article {pmid40906521, year = {2025}, author = {Selten, G and Gómez-Repollés, A and Lamouche, F and Radutoiu, S and de Jonge, R}, title = {SyFi: generating and using sequence fingerprints to distinguish SynCom isolates.}, journal = {Microbial genomics}, volume = {11}, number = {9}, pages = {}, pmid = {40906521}, issn = {2057-5858}, mesh = {*Microbiota/genetics ; *Plant Roots/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; *Computational Biology/methods ; High-Throughput Nucleotide Sequencing ; *DNA Fingerprinting/methods ; Sequence Analysis, DNA/methods ; }, abstract = {The plant root microbiome is a complex community shaped by interactions among bacteria, the plant host and the environment. Synthetic community (SynCom) experiments help disentangle these interactions by inoculating host plants with a representative set of culturable microbial isolates from the natural root microbiome. Studying these simplified communities provides valuable insights into microbiome assembly and function. However, as SynComs become increasingly complex to better represent natural communities, bioinformatics challenges arise. Specifically, accurately identifying and quantifying SynCom members based on, for example, 16S rRNA amplicon sequencing becomes more difficult due to the high similarity of the target amplicon, limiting downstream interpretations. Here, we present SynCom Fingerprinting (SyFi), a bioinformatics workflow designed to improve the resolution and accuracy of SynCom member identification. SyFi consists of three modules: the first module constructs a genomic fingerprint for each SynCom member based on its genome sequence and, when available, raw genomic reads, accounting for both copy number and sequence variation in the target gene. The second module extracts the target region from this genomic fingerprint to create a secondary fingerprint linked to the relevant amplicon sequence. The third module uses these fingerprints as a reference to perform pseudoalignment-based quantification of SynCom member abundance from amplicon sequencing reads. We demonstrate that SyFi outperforms standard amplicon analysis by leveraging natural intragenomic variation, enabling more precise differentiation of closely related SynCom members. As a result, SyFi enhances the reliability of microbiome experiments using complex SynComs, which more accurately reflect natural communities. This improved resolution is essential for advancing our understanding of the root microbiome and its impact on plant health and productivity in agricultural and ecological settings. SyFi is available at https://github.com/adriangeerre/SyFi.}, }
@article {pmid40904625, year = {2025}, author = {Hébert-Dufresne, L and Ahn, YY and Allard, A and Colizza, V and Crothers, JW and Dodds, PS and Galesic, M and Ghanbarnejad, F and Gravel, D and Hammond, RA and Lerman, K and Lovato, J and Openshaw, JJ and Redner, S and Scarpino, SV and St-Onge, G and Tangherlini, TR and Young, JG}, title = {One pathogen does not an epidemic make: a review of interacting contagions, diseases, beliefs, and stories.}, journal = {Npj complexity}, volume = {2}, number = {1}, pages = {26}, pmid = {40904625}, issn = {2731-8753}, support = {P20 GM125498/GM/NIGMS NIH HHS/United States ; }, abstract = {From pathogens and computer viruses to genes and memes, contagion models have found widespread utility across the natural and social sciences. Despite their success and breadth of adoption, the approach and structure of these models remain surprisingly siloed by field. Given the siloed nature of their development and widespread use, one persistent assumption is that a given contagion can be studied in isolation, independently from what else might be spreading in the population. In reality, countless contagions of biological and social nature interact within hosts (interacting with existing beliefs, or the immune system) and across hosts (interacting in the environment, or affecting transmission mechanisms). Additionally, from a modeling perspective, we know that relaxing these assumptions has profound effects on the physics and translational implications of the models. Here, we review mechanisms for interactions in social and biological contagions, as well as the models and frameworks developed to include these interactions in the study of the contagions. We highlight existing problems related to the inference of interactions and to the scalability of mathematical models and identify promising avenues of future inquiries. In doing so, we highlight the need for interdisciplinary efforts under a unified science of contagions and for removing a common dichotomy between social and biological contagions.}, }
@article {pmid40904542, year = {2025}, author = {Zhang, L and Xiong, A and Li, C and Liu, X and Zhang, X and Gong, S and Yan, M and Qin, X and Liu, Y and Hu, Z and Fang, JK and Duan, H and Liu, H and Chan, LL and Jin, LN}, title = {Ecological pattern of microalgal communities and associated risks in coastal ecosystems.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf109}, pmid = {40904542}, issn = {2730-6151}, abstract = {Eukaryotic harmful and toxic microalgae, along with their derived toxins, pose significant threats to seafood safety, human health, and marine ecosystems. Here, we developed a novel full-length 18S rRNA database for harmful and toxic microalgae and combined metabarcoding with toxin analyses to investigate the ecological patterns of phytoplankton communities and the underlying mechanism of associated toxic microalgae risks. We identified 79 harmful and toxic species in Hong Kong's coastal waters, with dinoflagellates and diatoms representing the majority of toxic and harmful taxa, respectively. Distinct seasonal succession patterns were observed in phytoplankton communities, driven by different ecological assembly processes. Deterministic processes dominated during the dry season, correlating with elevated toxic microalgae abundance and temperature stress. Seasonal shifts in temperature played a pivotal role in shaping toxic algal communities. The dominance of dinoflagellates, particularly Alexandrium spp., Dinophysis spp., Prorocentrum spp., and Karenia spp., during the dry season was consistent with elevated toxin concentrations. These toxin profiles highlight the heightened risk in a warming climate, where the prevalence and impacts of toxigenic algae are expected to intensify.}, }
@article {pmid40904416, year = {2025}, author = {Hutchinson, F and Crowley, LM and Broad, GR and ,  and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Brown Moss-moth, Bryotropha terrella (Denis &amp; Schiffermüller), 1775.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {310}, pmid = {40904416}, issn = {2398-502X}, abstract = {We present a genome assembly from a female specimen of Bryotropha terrella (Brown Moss-moth; Arthropoda; Insecta; Lepidoptera; Gelechiidae). The genome sequence has a total length of 756.35 megabases. Most of the assembly (99.62%) is scaffolded into 31 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled, with a length of 15.29 kilobases.}, }
@article {pmid40904111, year = {2025}, author = {Kupczok, A and Gavriilidou, A and Paulitz, E and Guerrero-García, L and Baumdicker, F}, title = {Gene co-occurrence and its association with phage infectivity in bacterial pangenomes.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {380}, number = {1934}, pages = {20240070}, pmid = {40904111}, issn = {1471-2970}, support = {//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Bacteriophages/physiology ; *Bacteria/genetics/virology ; *Genome, Bacterial ; Host Specificity ; *Genes, Bacterial ; Phylogeny ; }, abstract = {Phages infect bacteria and have recently re-emerged as a promising strategy to combat bacterial infections. However, there is a lack of methods to predict whether and why a particular phage can or cannot infect a bacterial strain based on their genome sequences. Understanding the complex interactions between phages and their bacterial hosts is thus of considerable interest. We recently developed Goldfinder, a phylogenetic method to discover gene co-occurrences across bacterial pangenomes. Here, we expand Goldfinder to infer which gene presences or absences influence bacterial sensitivity to phages. By integrating a bacterial pangenome with an experimentally determined host range matrix, we infer associations between phage infectivity and the presence of accessory genes in bacterial pangenomes. The presented approach can be applied to predict bacterial genes that potentially enable phage infection, bacterial genes that prevent phage infection, and potential interactions between particular bacterial and phage accessory genes. Finally, the predicted interactions are clustered and visualized with the software Cytoscape. Here, we present a method to identify candidate genes within the pool of mobile accessory genes that may contribute to phage-host interactions. This approach will help to set up follow-up experiments and to understand the complex interactions between phages and bacteria.This article is part of the discussion meeting issue 'The ecology and evolution of bacterial immune systems'.}, }
@article {pmid40900722, year = {2025}, author = {Jones, OE and Beckett, H and Abraham, AJ and Makunga, NP and Midgley, GF}, title = {Endozoochory by Black Rhinoceroses Enhances Germination of a Key Arid Savanna Tree Species.}, journal = {Ecology and evolution}, volume = {15}, number = {9}, pages = {e71951}, pmid = {40900722}, issn = {2045-7758}, abstract = {Megaherbivores are typically regarded as agents of top-down control, limiting woody encroachment through destructive foraging. Yet they also possess traits and engage in behaviours that facilitate plant success. For example, megaherbivores can act as effective endozoochorous seed dispersers. However, studies on facilitative roles are heavily biased towards the African savanna elephant (Loxodonta africana), with little attention paid to other species or to effects beyond germination, across early ontogenic stages. The African black rhinoceros (Diceros bicornis), an obligate browser that exhibits frugivory and defecates in fixed dung middens, may offer ecologically distinct dispersal services. We conducted controlled experiments to test whether black rhino interactions with Vachellia erioloba, a leguminous tree of ecological importance in arid savannas, enhance germination, early seedling development or seedling resilience to herbivory. Germination was compared among dung-derived seeds, untreated controls and chemically scarified seeds. Seedling growth was assessed in dung versus sand and under simulated black rhino herbivory. Dung-derived seeds germinated most steadily and produced the highest cumulative germination (+40%) over the longest period (+13 days). Growth trials revealed that dung substrates did not enhance initial growth. Rather, seedlings being older conferred greater resilience to biomass loss than exposure to different substrate conditions. Our results provide the first experimental evidence of an apparent mutualism between black rhino and V. erioloba. This relationship is not driven by enhanced seedling development through legacy effects of gut passage, nor by dung conditions, as expected. Instead, it stems from gut passage effects on germination. In addition to increasing total germination, gut passage accelerates germination and extends the germination period, producing a seedling cohort with both older individuals and greater age variation-a population structure that may enhance persistence beyond the germination bottleneck. This research supports a more nuanced view of megaherbivores as both disturbance agents and mutualists in arid ecosystems.}, }
@article {pmid40899150, year = {2025}, author = {Ürel, H and Benassou, S and Marti, H and Reska, T and Sauerborn, E and Pinheiro Alves De Souza, Y and Perlas, A and Rayo, E and Biggel, M and Kesselheim, S and Borel, N and Martin, EJ and Venegas, CB and Schloter, M and Schröder, K and Mittelstrass, J and Prospero, S and Ferguson, JM and Urban, L}, title = {Nanopore- and AI-empowered microbial viability inference.}, journal = {GigaScience}, volume = {14}, number = {}, pages = {}, pmid = {40899150}, issn = {2047-217X}, support = {//Helmholtz Principal Investigator Grant/ ; HIDSS-006//Munich School for Data Science/ ; BB/M010996/1//BBSRC/ ; //STFC Food Network+ Scoping Grant/ ; //Helmholtz Association Initiative and Networking Fund/ ; 1336/2004//Vontobel-Stiftung/ ; //University of Zurich/ ; }, mesh = {*Microbial Viability ; *Nanopores ; *Artificial Intelligence ; *Nanopore Sequencing/methods ; Metagenomics/methods ; Escherichia coli/genetics ; Computational Biology/methods ; }, abstract = {BACKGROUND: The ability to differentiate between viable and dead microorganisms in metagenomic data is crucial for various microbial inferences, ranging from assessing ecosystem functions of environmental microbiomes to inferring the virulence of potential pathogens from metagenomic analysis. Established viability-resolved genomic approaches are labor-intensive as well as biased and lacking in sensitivity.<br><br>RESULTS: We here introduce a new fully computational framework that leverages nanopore sequencing technology to assess microbial viability directly from freely available nanopore signal data. Our approach utilizes deep neural networks to learn features from such raw nanopore signal data that can distinguish DNA from viable and dead microorganisms in a controlled experimental setting of UV-induced Escherichia cell death. The application of explainable artificial intelligence (AI) tools then allows us to pinpoint the signal patterns in the nanopore raw data that allow the model to make viability predictions at high accuracy. Using the model predictions as well as explainable AI, we show that our framework can be leveraged in a real-world application to estimate the viability of obligate intracellular Chlamydia, where traditional culture-based methods suffer from inherently high false-negative rates. This application shows that our viability model captures predictive patterns in the nanopore signal that can be utilized to predict viability across taxonomic boundaries. We finally show the limits of our model's generalizability through antibiotic exposure of a simple mock microbial community, where a new model specific to the killing method had to be trained to obtain accurate viability predictions.<br><br>CONCLUSIONS: While the potential of our computational framework's generalizability and applicability to metagenomic studies needs to be assessed in more detail, we here demonstrate for the first time the analysis of freely available nanopore signal data to infer the viability of microorganisms, with many potential applications in environmental, veterinary, and clinical settings.}, }
@article {pmid40897761, year = {2025}, author = {Rodal, M and Luyssaert, S and Balzarolo, M and Campioli, M}, title = {A global database of net primary production of terrestrial ecosystems.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1534}, pmid = {40897761}, issn = {2052-4463}, mesh = {*Ecosystem ; *Databases, Factual ; *Biomass ; Soil ; Forests ; Grassland ; }, abstract = {Net primary production (NPP) is a fundamental measure of biomass production in ecosystems. In terrestrial biomes, NPP lacks standard measuring protocols and is difficult to measure. Thus, despite decades of research efforts, NPP data are limited and heterogenous. Moreover, there continues to be a lack of global NPP databases containing harmonized estimates for all major ecosystem types and which account for both above- and belowground production. We present a global database containing records for both above- and belowground production for forests, grasslands, arid shrublands, northern peatlands and tundra at 456 sites. The records are reported as annual production (g m[-2]yr[-1]). The NPP data are complemented with detailed site and methodological information, including a method specific estimate for the measurement uncertainty, as well as ancillary data on climatic conditions, soil fertility and management status. This database provides a basis for comparative studies on local, regional and global scales, and may serve as an important benchmarking dataset for the development of DGVMs.}, }
@article {pmid40897756, year = {2025}, author = {Zhang, F and Liang, Y and Hu, Z}, title = {Research on the inversion model of soil moisture content based on a novel ReMPDI index in mining areas.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {32330}, pmid = {40897756}, issn = {2045-2322}, support = {N25XQD015//Basic Research Operations in Higher Education/ ; }, abstract = {The excavation of subterranean coal has led to a plethora of ecological and environmental issues, which seriously restrict the sustainable development of society. As one of the important physical indicators of soil, soil moisture content needs to be scientific, real-time, and comprehensively monitored. Due to the low efficiency of manual measurement, methods based on remote sensing data inversion have received widespread attention and in-depth research in recent years. In this study, a new ReMPDI index (Red edge Modified Perpendicular Drought Index) is constructed, and six retrieval models of soil moisture content based on machine learning algorithms are compared and analyzed, and the accuracy is verified by measured sampling data. The following conclusions were obtained: (1) Using the red edge band as the horizontal axis, and the near infrared band NIR as the vertical axis is the optimal spatial band combination of spectral characteristics for constructing soil lines; (2) The determination coefficient (R2) of ReMPDI index based on REdge-NIR spectral feature space and adding vegetation cover factor is the highest, which is-0. 798, and there is a significant correlation, which is better than MPDI and PDI index; (3) The model inversion accuracy of the RF is significantly higher than SVM, BPNN, PLSR, CNN, and RBFNN, with an error of only 9.52% compared to the measured results. The results of this study can provide a theoretical basis and technical support for the fine monitoring of surface soil moisture content on a large scale in mining areas.}, }
@article {pmid40894110, year = {2025}, author = {Whiteford, S and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the virgin bagworm, Luffia ferchaultella (Stephens, 1850).}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {108}, pmid = {40894110}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Luffia ferchaultella (the Virgin Bagworm; Arthropoda; Insecta; Lepidoptera; Psychidae). The genome sequence spans 645.30 megabases. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.37 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,416 protein-coding genes.}, }
@article {pmid40894108, year = {2025}, author = {de Goeij, JM and Mueller, B and Achlatis, M and Campana, S and Hudspith, M and Kornder, NA and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and ,  and ,  and ,  and ,  and , }, title = {The scaffold-level genome sequence of an encrusting sponge, Halisarca caerulea Vacelet &amp; Donadey, 1987, and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {344}, pmid = {40894108}, issn = {2398-502X}, abstract = {We present a scaffold-level genome assembly from a Halisarca caerulea specimen (encrusting sponge; Porifera; Demospongiae; Chondrillida; Halisarcidae). The genome sequence is 195.70 megabases in span. The mitochondrial genome has also been assembled and is 19.15 kilobases in length. Gene annotation of this assembly on Ensembl identified 26,722 protein-coding genes. The metagenome of the specimen was also assembled and four binned bacterial genomes related to the relevant sponge symbiont clades Alphaproteobacteria bacterium GM7ARS4 and Gammaproteobacteria bacterium AqS2 ((Tethybacterales) were identified.}, }
@article {pmid40892914, year = {2025}, author = {Rowntree, LC and Allen, LF and Hagen, RR and McQuilten, HA and Quadeer, AA and Chaurasia, P and Kaewpreedee, P and Lee, KWK and Cohen, CA and Petersen, J and Littler, DR and Habel, JR and Zhang, W and Cheng, SMS and Chan, KKP and Kwok, JSY and Leung, KSM and Wu, JT and Lee, CK and Davies, J and Pannaraj, PS and Kaity Allen, E and Thomas, PG and Tosif, S and Crawford, NW and Lappas, M and Thevarajan, I and Lewin, SR and Kent, SJ and Juno, JA and Bond, KA and Williamson, DA and Holmes, NE and Smibert, OC and Gordon, CL and Trubiano, JA and Kotsimbos, TC and Cheng, AC and Efstathiou, C and Turtle, L and Thwaites, RS and Brightling, CE and ,  and Rossjohn, J and McKay, MR and Tian, J and Liu, WJ and Gao, GF and Xu, J and Sonehara, K and Ishii, KJ and Namkoong, H and Okada, Y and Peiris, M and Hui, DSC and Poon, LLM and Doherty, PC and Nguyen, THO and Valkenburg, SA and Kedzierska, K}, title = {HLA-B*15:01-positive severe COVID-19 patients lack CD8[+] T cell pools with highly expanded public clonotypes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {36}, pages = {e2503145122}, pmid = {40892914}, issn = {1091-6490}, support = {U01 AI144616/AI/NIAID NIH HHS/United States ; 1173871//Federal Government | DHAC | National Health and Medical Research Council (NHMRC)/ ; }, mesh = {Humans ; *COVID-19/immunology/genetics ; *CD8-Positive T-Lymphocytes/immunology ; *SARS-CoV-2/immunology ; Male ; Female ; Middle Aged ; Adult ; Aged ; Spike Glycoprotein, Coronavirus/immunology ; }, abstract = {Understanding host factors driving asymptomatic versus severe disease outcomes is of key importance if we are to control emerging and re-emerging viral infections. HLA-B*15:01 has been associated with asymptomatic SARS-CoV-2 infection in nonhospitalized individuals of European ancestry, with protective immunity attributed to preexisting cross-reactive CD8[+] T-cells directed against HLA-B*15:01-restricted Spike-derived S919-927 peptide (B15/S919[+]CD8[+] T-cells). However, fundamental questions remained on the abundance and clonotypic nature of CD8[+] T-cell responses in HLA-B*15:01-positive patients who succumbed to life-threatening COVID-19. Here, we analyzed B15/S919[+]CD8[+] T-cell responses in COVID-19 patients from independent HLA-typed COVID-19 patient cohorts across three continents, Australia, Asia and Europe. We assessed B15/S919[+]CD8[+] T-cells in COVID-19 patients across disease outcomes ranging from asymptomatic to hospitalized critical illness. We found that severe/critical COVID-19 patients mounted B15/S919[+]CD8[+] T-cell responses lacking a highly expanded key public B15/S919[+]CD8[+] T-cell receptor (TCR; TRAV9-2/TRBV7-2) which recurred across multiple individuals in COVID-19 patients with a mild disease. Instead, B15/S919[+]CD8[+] T-cell responses in life-threatening disease had a prevalence of an alternate TCR clonotypic motif (TRAV38-2/DV8/TRBV20-1), potentially contributing, at least in part, to why B15/S919[+]CD8[+] T-cells in severe COVID-19 patients were less protective. Interestingly, the frequency, memory phenotype, and activation profiles of circulating B15/S919[+]CD8[+] T-cells did not differ across disease severity. Moreover, B15/S919[+]CD8[+] T-cells were better maintained into convalescence compared to other SARS-CoV-2-specificities. Our study thus provides evidence on the differential nature of the TCR clonal repertoire in 22.37% of HLA-B*15:01-positive COVID-19 patients who developed severe or critical disease in our cohorts, comparing to HLA-B*15:01-expressing individuals with mild COVID-19.}, }
@article {pmid40892908, year = {2025}, author = {Araujo, G and Lurgi, M}, title = {Mutualism provides a basis for biodiversity in eco-evolutionary community assembly.}, journal = {PLoS computational biology}, volume = {21}, number = {9}, pages = {e1013402}, pmid = {40892908}, issn = {1553-7358}, mesh = {*Biodiversity ; *Symbiosis/physiology ; *Biological Evolution ; *Models, Biological ; *Ecosystem ; Computational Biology ; Animals ; Computer Simulation ; }, abstract = {Unveiling the ecological and evolutionary mechanisms underpinning the assembly of stable and complex ecosystems is a main focus of community ecology. Ecological theory predicts the necessity of structural constraints on the network of species interactions to allow for growth and persistence of multi-species communities. However, the mechanisms behind their emergence are not well understood. An understanding of how the coexistence of diverse species interaction types could influence the development of complexity and how a persistent composition of interactions could arise in nature is needed. Using an eco-evolutionary model, we investigate the assembly of complex species interaction networks with multiple interaction types and its consequences for ecosystem stability. Our results show that highly mutualistic communities promote complex and stable network configurations, thus resulting in a positive complexity-stability relationship. We show that evolution by speciation enhances the emergence of such conditions compared to a purely ecological assembly scenario of repeated invasions by migrating species. Furthermore, communities evolved in isolation promote a disproportionately higher complexity and a larger diversity of outcomes. Our results produce valuable theoretical insight into the mechanisms behind the emergence of ecological complexity and into the roles of mutualism and speciation in community formation.}, }
@article {pmid40892020, year = {2025}, author = {Ng, S and Brown, JP and Straub, L and Bateman, B and Gray, KJ and Huybrechts, KF and Hernández-Díaz, S}, title = {Leveraging Health Insurance Claims Data to Complement the Centers for Disease Control and Prevention Surveillance System for Birth Defects.}, journal = {Birth defects research}, volume = {117}, number = {9}, pages = {e2523}, doi = {10.1002/bdr2.2523}, pmid = {40892020}, issn = {2472-1727}, support = {R01 HD097778/HD/NICHD NIH HHS/United States ; }, mesh = {Humans ; United States/epidemiology ; *Congenital Abnormalities/epidemiology ; Female ; Prevalence ; Centers for Disease Control and Prevention, U.S. ; Infant, Newborn ; *Insurance, Health/statistics &amp; numerical data ; Pregnancy ; Databases, Factual ; Male ; Insurance Claim Review ; Population Surveillance/methods ; Infant ; Adult ; }, abstract = {BACKGROUND: Birth defect surveillance can help identify temporo-spatial clusters and teratogenic signals to inform subsequent investigations or interventions. In the United States, state surveillance systems exist but collect limited information, prompting a complementary use of health insurance claims data to describe national birth defect prevalence trends and investigate signals.<br><br>METHODS: The Merative MarketScan Commercial Claims and Encounters (MarketScan) database was used to identify liveborn infants from 2016 to 2022, with linkage to maternal health care records during pregnancy. Birth defects were identified using ICD-10-CM codes recorded in the first 3&#x2009;months of life, and prevalence estimates with 95% confidence intervals were generated for birth defect categories and select birth defects.<br><br>RESULTS: The study population included 943,855 liveborn infants. From 2016 to 2022, the prevalence increased for cardiac, central nervous system, ear, genital, urinary, musculoskeletal, and limb birth defect categories. Stable prevalence over the study period was observed for chromosomal, oral cleft, respiratory, gastrointestinal, vascular, and eye defects. For specific defects, we observed an increased prevalence of both ankyloglossia and lip-tie over the study period and a transient higher prevalence of omphalocele over 2017 and 2018. Within genital birth defects, we observed increasing prevalence trends for congenital malformations of the penis, while hypospadias and cryptorchidism remained relatively stable.<br><br>CONCLUSION: Health care utilization databases can complement existing surveillance systems by generating, confirming, or refuting signals based on ecological trends or clusters. The availability of patient information in claims databases can allow for further investigation of signals to inform birth defect etiology.}, }
@article {pmid40889349, year = {2025}, author = {Moraitou, M and Richards, JL and Bolyos, C and Saliari, K and Gilissen, E and Timmons, Z and Kitchener, AC and Pauwels, OSG and Sabin, R and Kokkini, P and Portela Miguez, R and Guschanski, K}, title = {Host Traits Impact the Outcome of Metagenomic Library Preparation From Dental Calculus Samples Across Diverse Mammals.}, journal = {Molecular ecology resources}, volume = {25}, number = {8}, pages = {e70039}, pmid = {40889349}, issn = {1755-0998}, support = {2019-00275//Svenska Forskningsr&#xe5;det Formas/ ; }, mesh = {*Metagenomics/methods ; *Dental Calculus/microbiology ; *Mammals/microbiology/classification ; Animals ; *Microbiota ; *Gene Library ; Metagenome ; Computational Biology ; }, abstract = {Dental calculus metagenomics has emerged as a valuable tool for studying the oral microbiomes of humans and a few select mammals. With increasing interest in wild animal microbiomes, it is important to understand how widely this material can be used across the mammalian tree of life, refine the related protocols and understand the expected outcomes and potential challenges of dental calculus sample processing. In this study, we significantly expand the breadth of studied host species, analysing laboratory and bioinformatics metadata of dental calculus samples from 32 ecologically and phylogenetically diverse mammals. Although we confirm the presence of an oral microbiome signature in the metagenomes of all studied mammals, the fraction recognised as oral varies between host species, possibly because of both biological differences and methodological biases. The overall success rate of dental calculus processing, from extractions to sequencing, was ~74%. Although input sample weight was positively associated with the number of produced library molecules, we identify a negative impact of enzymatic inhibition on the library preparation protocol. The inhibition was most prevalent in herbivores and frugivores and is likely diet-derived. In contrast, hosts with an animalivore diet posed fewer challenges during laboratory processing and yielded more DNA relative to sample weight. Our results translate into recommendations for future studies of dental calculus metagenomics from a variety of host species, identifying required sample amounts, and emphasising the utility of dental calculus in exploring the oral microbiome in relation to broader ecological and evolutionary questions.}, }
@article {pmid40888850, year = {2026}, author = {Chasapi, MN and Chasapi, IN and Aplakidou, E and Baltoumas, FA and Karatzas, E and Iliopoulos, I and Stravopodis, DJ and Emiris, IZ and Buluç, A and Georgakopoulos-Soares, I and Kyrpides, NC and Pavlopoulos, GA}, title = {metagRoot: a comprehensive database of protein families associated with plant root microbiomes.}, journal = {Nucleic acids research}, volume = {54}, number = {D1}, pages = {D1733-D1742}, pmid = {40888850}, issn = {1362-4962}, support = {23592//Hellenic Foundation for Research and Innovation/ ; //European Union's Horizon 2020/ ; 945405//Marie Sk&#x142;odowska-Curie/ ; //Penn State College of Medicine/ ; //Huck Innovative and Transformational Seed/ ; //Huck Institutes of the Life Sciences/ ; 16718-PRPFOR//Hellenic Foundation for Research and Innovation/ ; TAEDR-0539180//Hellenic Foundation for Research and Innovation/ ; DE-AC02-05CH11231//U.S. Department of Energy Office of Science/ ; //Nikos Kyrpides JGI-LBNL/ ; }, mesh = {*Plant Roots/microbiology ; *Microbiota/genetics ; *Databases, Protein ; Metagenomics ; Molecular Sequence Annotation ; Metagenome ; }, abstract = {The plant root microbiome is vital in plant health, nutrient uptake, and environmental resilience. To explore and harness this diversity, we present metagRoot, a specialized and enriched database focused on the protein families of the plant root microbiome. MetagRoot integrates metagenomic, metatranscriptomic, and reference genome-derived protein data to characterize 71 091 enriched protein families, each containing at least 100 sequences. These families are annotated with multiple sequence alignments, CRISPR elements, hidden Markov models, taxonomic and functional classifications, ecosystem and geolocation metadata, and predicted 3D structures using AlphaFold2. MetagRoot is a powerful tool for decoding the molecular landscape of root-associated microbial communities and advancing microbiome-informed agricultural practices by enriching protein family information with ecological and structural context. The database is available at https://pavlopoulos-lab.org/metagroot/ or https://www.metagroot.org.}, }
@article {pmid40887834, year = {2025}, author = {Han, Y and Yu, J and Liu, X and Zhang, F and Huang, X and Lu, Y and Zhang, W and Zimmerman, R and Rudich, Y and Li, Q and Chen, J and Chen, Y and Jin, LN}, title = {Generation of More Potent Components at Higher Temperatures Offsets Toxicity Reduction despite Reduced Mass Emissions during Biomass Burning.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {36}, pages = {19244-19256}, doi = {10.1021/acs.est.5c05710}, pmid = {40887834}, issn = {1520-5851}, mesh = {*Biomass ; Humans ; Temperature ; Aerosols ; Air Pollutants/toxicity ; Reactive Oxygen Species ; }, abstract = {Biomass burning organic aerosols (BBOAs) represent a major global health hazard. Their toxicity varies significantly due to the diversity of combustion conditions, which shape mixtures of components with differing toxic potency. We quantified component-specific contributions to intracellular reactive oxygen species generation in human bronchial epithelial cells exposed to BBOAs produced under controlled combustion conditions. Elevated combustion temperatures substantially reduced organic carbon (OC) mass emissions (by 20-fold) but resulted in a more modest reduction in OC toxicity emissions (by 5-fold). The toxicity emission reduction was primarily attributed to water-extractable OC (WOC), while methanol-extractable OC (MOC) limited this effect. The reduced emission of WOC toxicity was driven by the decreased mass emission of polar compounds such as methoxylates, as the toxicity per unit mass of WOC showed negligible changes across temperatures. In contrast, the toxicity per unit mass of MOC increased 10-fold from low to high temperatures, partially due to the formation of more potent aromatic derivatives, despite their smaller mass contribution. These findings underscore the importance of identifying key toxicity drivers to guide targeted source apportionment and refine strategies for reducing toxic emissions.}, }
@article {pmid40886889, year = {2025}, author = {Furxhi, I and Perucca, M and Baldi, G and Dami, V and Cioni, A and Koivisto, AJ and Bengalli, R and Mantecca, P and Motta, G and Carriere, M and Kose, O and Nicosia, A and Ravegnani, F and Burrueco-Subirà, D and Candalija, A and Cabellos, J and Vázquez-Campos, S and Lahive, E and Eagles, E and de Ipiña, JL and Oliveira, J and Conin, P and Zanoni, I and Brigliadori, A and Faccani, L and Syed, T and Haq, EU and O'Mahony, C and Serantoni, M and Blosi, M and Exner, T and Costa, A}, title = {The fruits of data shepherding: A collection of open FAIR datasets for titanium dioxide coated photocatalytic surfaces.}, journal = {NanoImpact}, volume = {39}, number = {}, pages = {100583}, doi = {10.1016/j.impact.2025.100583}, pmid = {40886889}, issn = {2452-0748}, mesh = {*Titanium/chemistry ; Catalysis ; *Databases, Factual ; Surface Properties ; *Nanostructures/chemistry ; Information Dissemination ; }, abstract = {This paper presents a large-scale collaborative effort within a multi-partner consortium, to systematically structure, curate, and openly share data in alignment with the FAIR principles. The data result from a case study of titanium dioxide (TiO2) nanomaterials (NMs) for photocatalytic depolluting surfaces, produced via various spray coating techniques under the Safe and Sustainable by Design (SSbD) approach. The data are publicly available through a dedicated Zenodo community (https://zenodo.org/communities/asina/records), comprising of individual records that separately host the data and the corresponding metadata. Each dataset is systematically named to reflect its context beginning with "ASINA dataset," followed by i) the relevant life cycle stage (LCS) from synthesis to end-of-life, ii) the SSbD dimension (i.e., functionality, safety, and environmental aspects), and iii) the assessed features (e.g., physicochemical properties, hazard evaluation, functionality assessment) facilitating searchability. The data files include "descriptors" excel tab, which is a harmonized version derived from primary data for visualization, data integration and future modeling applications. Metadata are provided in separate records and include detailed information such as contributor name and affiliations, experimental protocols, instrumentation, dictionary definitions, ontologies, and licensing terms. The data and metadata files are mutually paired in Zenodo using related identifiers, where each data file includes the DOI of its corresponding metadata file, and vice versa. In total, 43 interlinked records are provided capturing the case study, offering structured and machine-actionable resources that support modeling, data integration and harmonization efforts within the nanosafety and nanoinformatics communities. This effort was coordinated through dedicated data shepherding, which enabled trust-building, metadata alignment, and consistent FAIR implementation across partners.}, }
@article {pmid40885803, year = {2025}, author = {Simonienko, K and Jermakowicz, E and Szefer, P and Wróbel, K and Suprunowicz, U and Cwalina, U and Kostro-Ambroziak, A}, title = {The impact of urban flower meadows on the well-being of city dwellers provides hints for planning biophilic green spaces.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {31981}, pmid = {40885803}, issn = {2045-2322}, support = {SKN/SP/495977/2021//Ministry of Science and Higher Education/ ; SKN/SP/495977/2021//Ministry of Science and Higher Education/ ; SKN/SP/495977/2021//Ministry of Science and Higher Education/ ; SKN/SP/495977/2021//Ministry of Science and Higher Education/ ; }, mesh = {Humans ; Female ; Male ; *Flowers/growth &amp; development ; Adult ; Middle Aged ; Cities ; *Urban Population ; Emotions ; Young Adult ; Aged ; }, abstract = {Living surrounded by greenery has a relaxing effect and reduces physiological and psychological symptoms of stress. In view of the exponential growth of the urban population and disconnection with nature, supporting the physical and mental health of city dwellers is a huge challenge nowadays. In this context, urban flower meadows (UFMs), a relatively new management strategy cultivated in many cities, can be a very important component of urban greenery, which support human well-being. We investigated the emotional reception of UFMs, taking into account the features of different types of UFMs and the socio-demographic characteristics of respondents. Our research shows that urban flower meadows evoke positive emotions regardless of the age, gender and place of origin of respondents. While some structural variables of UFMs, particularly the proportion of green in relation to other colours, the representation of various flower colours, the proportion of yellow flowers, and the presence of alien plant species-influence people's perception. Fewer colours and the absence of alien plant species tend to shift perception towards less positive emotions. The dominance of yellow flowers evokes positive emotions. These results are helpful for the further planning of UFMs to better reinforce the well-being of all city dwellers.}, }
@article {pmid40854001, year = {2025}, author = {Khajehnejad, M and García, J and Meyer, B}, title = {Age polyethism can emerge from social learning: A game-theoretic investigation.}, journal = {PLoS computational biology}, volume = {21}, number = {8}, pages = {e1013415}, pmid = {40854001}, issn = {1553-7358}, mesh = {Animals ; *Social Learning/physiology ; *Game Theory ; Behavior, Animal/physiology ; Social Behavior ; Computational Biology ; Models, Biological ; }, abstract = {Age-polyethism-the age-based allocation of tasks in social insect colonies-is a key feature of division of labour. While its hormonal underpinnings have been studied extensively, the behavioural and environmental mechanisms driving age-polyethism remain poorly understood, especially under ecological stress. We present a novel modelling framework that integrates social learning with task-related environmental feedback to explain the emergence and breakdown of age-polyethism. We develop two models: a Social Learning (SL) model, in which individuals adapt task preferences by copying similar peers, and a Stimulus-Response Threshold Social Learning (SRT-SL) model, which extends this framework by incorporating task-related dynamic stimuli and response thresholds that regulate collective task demand. Our models demonstrate that age-polyethism can emerge from simple social imitation processes, without the need for fixed hormonal schedules. We show that under increasing environmental pressure (e.g., resource scarcity), age-polyethism collapses as younger individuals are forced into tasks typically handled by older workers. Importantly, we find that age-polyethism does not necessarily optimize immediate colony efficiency; instead, it appears to reflect a trade-off between environmental constraints and behavioural coordination. These findings provide a mechanistic and ecologically grounded explanation for empirical observations linking environmental stress to dysfunctional division of labour and colony collapse.}, }
@article {pmid40872272, year = {2025}, author = {Bugingo, C and Infantino, A and Okello, P and Perez-Hernandez, O and Petrović, K and Turatsinze, AN and Moparthi, S}, title = {From Morphology to Multi-Omics: A New Age of Fusarium Research.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {8}, pages = {}, pmid = {40872272}, issn = {2076-0817}, mesh = {*Fusarium/genetics/classification/pathogenicity ; Genomics/methods ; *Plant Diseases/microbiology ; Mycotoxins ; Humans ; Crops, Agricultural/microbiology ; Host-Pathogen Interactions ; *Fusariosis/microbiology ; Multiomics ; }, abstract = {The Fusarium genus includes some of the most economically and ecologically impactful fungal pathogens affecting global agriculture and human health. Over the past 15 years, rapid advances in molecular biology, genomics, and diagnostic technologies have reshaped our understanding of Fusarium taxonomy, host-pathogen dynamics, mycotoxin biosynthesis, and disease management. This review synthesizes key developments in these areas, focusing on agriculturally important Fusarium species complexes such as the Fusarium oxysporum species complex (FOSC), Fusarium graminearum species complex (FGSC), and a discussion on emerging lineages such as Neocosmospora. We explore recent shifts in species delimitation, functional genomics, and the molecular architecture of pathogenicity. In addition, we examine the global burden of Fusarium-induced mycotoxins by examining their prevalence in three of the world's most widely consumed staple crops: maize, wheat, and rice. Last, we also evaluate contemporary management strategies, including molecular diagnostics, host resistance, and integrated disease control, positioning this review as a roadmap for future research and practical solutions in Fusarium-related disease and mycotoxin management. By weaving together morphological insights and cutting-edge multi-omics tools, this review captures the transition into a new era of Fusarium research where integrated, high-resolution approaches are transforming diagnosis, classification, and management.}, }
@article {pmid40874445, year = {2026}, author = {Liang, M and Pan, W and Feng, Z and Cui, Y and Su, H and Guo, C and He, J}, title = {IVCDB: a comprehensive database of iridoviruses for epidemiology, genetic evolution, and disease management.}, journal = {Nucleic acids research}, volume = {54}, number = {D1}, pages = {D790-D800}, pmid = {40874445}, issn = {1362-4962}, support = {2022YFE0203900//National Key Research and Development Program of China/ ; CARS-46//Earmarked Fund for China Agriculture Research System/ ; 32473201//National Natural Science Foundation of China/ ; 2022B1111030001//Special Project for Research and Development in Key areas of Guangdong Province/ ; 2024B1212040007//Science and Technology Planning Project of Guangdong Province/ ; 2023A1515110395//Basic and Applied Basic Research Foundation of Guangdong Province/ ; }, mesh = {Animals ; *Iridovirus/genetics/classification/pathogenicity ; Phylogeny ; Genome, Viral ; *Databases, Genetic ; *Evolution, Molecular ; *DNA Virus Infections/epidemiology/virology/veterinary ; Viral Proteins/genetics ; }, abstract = {Iridoviruses, a globally distributed group of double-stranded DNA viruses, exhibit remarkable environmental adaptability and host-switching capabilities, infecting over 200 species of ectothermic vertebrates and invertebrates, including reptiles, amphibians, fish, crustaceans, and insects. These characteristics have led to substantial economic losses in global aquaculture and population declines in amphibian and invertebrate species. Despite accumulating genomic data, research progress remains constrained by three critical limitations: fragmented multidimensional data resources, ambiguous taxonomic levels, and insufficient spatiotemporal visualization tools. To address these challenges, we present the Iridovirus Comprehensive Database (IVCDB; https://www.iridovirus.com/), a comprehensive database consolidating multidimensional iridovirus-related data. IVCDB provides curated comprehensive information on 310 geographically distinct virus isolates complemented by an interactive geospatial visualization system and a nonredundant protein database containing 4378 viral proteins, including 162 core genes/proteins, derived from a standardized genome annotation pipeline. This database also contains phylogenetic relationships across various viral taxonomic levels within the family Iridoviridaeanda viral genome collinearity analysis tool, facilitating taxonomic analysis and supporting novel species identification. Furthermore, IVCDB integrates an application-oriented knowledge base including host range data, experimentally validated vaccines, and field-deployable visual detection methods. IVCDB offers substantial support for disease control and host conservation while addressing systemic bottlenecks in viral cross-species transmission research.}, }
@article {pmid40862956, year = {2025}, author = {Yoon, HJ and Seo, JH and Shin, SH and Abdelhamid, MAA and Pack, SP}, title = {Bioinformation and Monitoring Technology for Environmental DNA Analysis: A Review.}, journal = {Biosensors}, volume = {15}, number = {8}, pages = {}, pmid = {40862956}, issn = {2079-6374}, support = {RS-2021NR060107//the National Research Foundation of Korea funded by the Ministry of Science and ICT/ ; RS-2022-NR074662//the National Research Foundation of Korea funded by the Ministry of Education/ ; }, mesh = {*Environmental Monitoring/methods ; *DNA, Environmental/analysis ; *Computational Biology ; Ecosystem ; }, abstract = {Environmental DNA (eDNA) analysis has emerged as a transformative tool in environmental monitoring, enabling non-invasive detection of species and microbial communities across diverse ecosystems. This study systematically reviews the role of bioinformation technology in eDNA analysis, focusing on methodologies and applications across air, soil, groundwater, sediment, and aquatic environments. Advances in molecular biology, high-throughput sequencing, bioinformatics tools, and field-deployable detection systems have significantly improved eDNA detection sensitivity, allowing for early identification of invasive species, monitoring ecosystem health, and tracking pollutant degradation processes. Airborne eDNA monitoring has demonstrated potential for assessing microbial shifts due to air pollution and tracking pathogen transmission. In terrestrial environments, eDNA facilitates soil and groundwater pollution assessments and enhances understanding of biodegradation processes. In aquatic ecosystems, eDNA serves as a powerful tool for biodiversity assessment, invasive species monitoring, and wastewater-based epidemiology. Despite its growing applicability, challenges remain, including DNA degradation, contamination risks, and standardization of sampling protocols. Future research should focus on integrating eDNA data with remote sensing, machine learning, and ecological modeling to enhance predictive environmental monitoring frameworks. As technological advancements continue, eDNA-based approaches are poised to revolutionize environmental assessment, conservation strategies, and public health surveillance.}, }
@article {pmid40858627, year = {2025}, author = {Ge, S and Li, J and Ma, H and Sánchez-Bermúdez, M and Wu, S and Lv, Q and Guo, F and Dong, J and Ma, G and Li, QQ and Satheesh, V and Lei, M}, title = {A cis-natural antisense RNA regulates alternative polyadenylation of SlSPX5 under Pi starvation in tomato.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {7981}, pmid = {40858627}, issn = {2041-1723}, support = {U24A20385//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32270344//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2025JCXK01//Hangzhou Normal University (HNU)/ ; 2347540//National Science Foundation (NSF)/ ; }, mesh = {*Polyadenylation/genetics ; *Solanum lycopersicum/genetics/metabolism ; Gene Expression Regulation, Plant ; *RNA, Antisense/genetics/metabolism ; *Plant Proteins/genetics/metabolism ; *Phosphates/deficiency/metabolism ; RNA, Messenger/metabolism/genetics ; Transcription Factors/metabolism/genetics ; RNA Polymerase II/metabolism ; }, abstract = {Alternative polyadenylation (APA) generates transcript diversity by producing mRNA isoforms with distinct 3' ends. Despite the critical roles that APA plays in various biological processes, the mechanisms regulating APA in response to stresses have remained poorly understood in plants. Here, we perform comprehensive analysis of APA in tomato, and focus on a phosphate (Pi)- regulated APA gene SlSPX5, encoding a putative Pi sensor protein. SlSPX5 interacts with and sequesters the transcription factor SlPHL1 in the cytosol, thereby inhibiting the expression of Pi starvation inducible genes. We discover that a cis-natural antisense RNA (cis-NAT) is activated from SlSPX5 to promote its proximal polyadenylation under Pi-depleted conditions. The transcription of this cis-NAT induces RNA Polymerase II pausing, generating Ser2 phosphorylation signals that recruit polyadenylation machinery to the 5' end of SlSPX5. Our findings demonstrate that a cis-NAT regulates APA of its cognate gene in response to Pi starvation.}, }
@article {pmid40855644, year = {2025}, author = {Panneerselvam, K and Tiwari, KK and Licata, L and Panni, S and Ricard-Blum, S and Balu, S and Huget, S and Medina Reyes, JJ and Ragueneau, E and Perfetto, L and Meldal, B and Orchard, S and Hermjakob, H}, title = {Mining Alzheimer's Interactomes, Macromolecular Complexes and Pathways for Drug Discovery.}, journal = {Proteomics}, volume = {25}, number = {21-22}, pages = {102-150}, pmid = {40855644}, issn = {1615-9861}, support = {203149/WT_/Wellcome Trust/United Kingdom ; 218294/WT_/Wellcome Trust/United Kingdom ; U24 HG012198/AOU_/AOU NIH HHS/United States ; U24 HG012198/HG/NHGRI NIH HHS/United States ; 3367/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; //BBSRC - National Science Foundation/Directorate for Biological Sciences/ ; 212925/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; //European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) core funding/ ; }, mesh = {*Alzheimer Disease/metabolism/genetics/drug therapy ; Humans ; *Drug Discovery/methods ; Amyloid beta-Protein Precursor/metabolism/genetics ; Protein Interaction Maps ; MicroRNAs/metabolism/genetics ; Data Mining ; Mutation ; }, abstract = {Alzheimer's disease (AD) is a progressive neurodegenerative disorder that leads to dementia. Many cases are diagnosed annually and there is no currently available cure. Understanding the underlying disease biology of AD through the study of molecular networks, particularly by mapping clinical variants to tissue-specific interactomes and regulatory macromolecular assemblies, offers a promising avenue to elucidate altered disease pathways. In this study, we applied differential interactome analysis using a manually curated AD dataset to identify how disease-associated mutations alter both transient and stable protein interactions. By focussing on variant-specific associations detected in brain-relevant tissues, we mapped disruptions in stable macromolecular assemblies and performed Reactome enrichment analysis to uncover perturbed pathways unique to each variant. Additionally, we explored therapeutic insights through the analysis of amyloid precursor protein (APP) physical interactors, identifying potential intervention points that influence amyloidogenic processing. Complementing protein-level data, we integrated microRNA (miRNA)-mediated regulatory interactions, revealing an additional layer of posttranscriptional control over key AD genes. Together, this multilayered strategy provides a framework for precision therapeutics in AD.}, }
@article {pmid40851520, year = {2025}, author = {Naseri, C and Hill, AM and Xu, D and Francis-Coad, J and Vaz, S and Garswood, L and Meakes, R and Umbella, J and O'Brien, G and Starling, T and Weselman, T}, title = {What influences older people to join a community hub to engage in healthy ageing programs? An exploratory study.}, journal = {Australasian journal on ageing}, volume = {44}, number = {3}, pages = {e70079}, pmid = {40851520}, issn = {1741-6612}, support = {//Royal Perth Hospital Medical Research Foundation/ ; //Australian Association of Gerontology Research Trust/ ; }, mesh = {Humans ; *Healthy Aging/psychology ; Aged ; Female ; Male ; Western Australia ; Aged, 80 and over ; Age Factors ; Middle Aged ; *Health Services for the Aged/organization &amp; administration ; Social Support ; Social Networking ; Interviews as Topic ; *Community Health Services ; *Health Promotion ; Qualitative Research ; *Community Networks/organization &amp; administration ; }, abstract = {OBJECTIVES: Most people seek to stay connected to their community as they age; this has been a major focus in the development of innovative community programs in Australia. This study aimed to explore what influences older people to join a community hub to engage in healthy ageing programs.<br><br>METHODS: Semi-structured interviews (n&#x2009;=&#x2009;29) were conducted during an Open Day in early 2023 at an urban community hub in Western Australia, followed by telephone interviews (n&#x2009;=&#x2009;9) of a purposive sample of older individuals, community hub facilitators and coordinators of national community hubs. Analysis used a socio-ecological framework.<br><br>RESULTS: Deductive content analysis identified social prescribing as an overarching influencer for older people to join and engage in healthy ageing programs and main themes of (i) supporting community hub facilitators to harness community assets, (ii) link-supports provided to older members by paid community hub concierges triggered positive outcomes at individual and community levels, (iii) online and in-person social and physical healthy ageing activities tailored to member interests and (iv) nurturing social networks and reciprocity between members sustained engagement in healthy ageing activities.<br><br>CONCLUSIONS: The dynamic process of social prescribing was a central influencer for older adults to engage in healthy ageing programs, and the social network perpetuated through community hubs was an immeasurable social investment that boosted the resilience of intergenerational populations in Australian communities. Policy support is required for communities to meet the challenge of being responsive to the needs of members who seek to remain independent as they age in place.}, }
@article {pmid40846910, year = {2025}, author = {Lu, M and Wang, S and Zhou, Y and Wang, X and Su, H and Gong, Y and De, J}, title = {Multi-omics profiling reveals single-seed mutants of Ephedra saxatilis as dominant variants in high-altitude Xizang.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {1118}, pmid = {40846910}, issn = {1471-2229}, support = {32060087//National Natural Science Foundation of China/ ; 32060087//National Natural Science Foundation of China/ ; 32060087//National Natural Science Foundation of China/ ; XZ202402ZD0005//Science and Technology Projects of Xizang Autonomous Region, China/ ; XZ202402ZD0005//Science and Technology Projects of Xizang Autonomous Region, China/ ; XZ202501ZY0101//Xizang Autonomous Region Science and Technology Department project, China/ ; XZ202501ZY0101//Xizang Autonomous Region Science and Technology Department project, China/ ; }, mesh = {*Altitude ; *Ephedra/genetics/metabolism/physiology ; Germination/genetics ; *Seeds/genetics/metabolism/ultrastructure/physiology ; Tibet ; Mutation ; Metabolomics ; Transcriptome ; Multiomics ; }, abstract = {Ephedra species, important Tibetan medicinal plants, are widely distributed across the Qinghai-Tibet Plateau at altitudes of 2700-5000 m. Their adaptation to high-altitude environments, such as low temperatures, strong UV radiation and low oxygen, is still poorly understood. This study investigated the morphological, metabolic, and genetic mechanisms underlying the reproductive advantage of a unique single-seed variant observed in high-germination-rate Ephedra species. Seeds from six Ephedra species were collected for germination assays and electron microscopic analysis. Results showed that E. saxatilis, E. intermedia, and E. monosperma exhibited significantly higher germination rates (Germination rates > 65%) and predominantly produced single-seed variants, while others mainly produced double seeds. Analysis of burr and fold numbers of phenotypic traits showed a significant positive correlation with germination rates. Time-course metabolomics analysis identified 762 KEGG annotated metabolites, and revealed E. saxatilis as the dominant species due to its faster metabolic rate, particularly simulated high-altitude conditions. Absolute hormone quantification highlighted the single-seed variant of E. saxatilis as the dominant type, with ABA content peaking in the shed seed coat. ABA exhibited antagonistic interactions with 2MeScZR, SA, IAA, GA7, IPR, and t-CA, suggesting a complex hormonal regulation network. Co-expression network analysis integrating transcriptome and hormone data predicted 23 key genes regulating seed germination adaptation. This study provides novel insights into the ecological and evolutionary significance of single-seed variation in high-altitude adaptation. The findings have potential applications in high-altitude plant breeding, conservation, and sustainable utilization of Ephedra species. Future research should focus on the genetic basis of single-seed variation and its role in other high-altitude plant species.}, }
@article {pmid40841825, year = {2025}, author = {De Rovere, F and Mastropierro, M and Jungclaus, JH and Khodri, M and Rubino, A and Zanchettin, D}, title = {Future Atlantification of the European Arctic limited under sustained global warming.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {30802}, pmid = {40841825}, issn = {2045-2322}, support = {2022CCRN7R, "ATTRACTION - ATlantificaTion dRiven by polAr-subpolar ConnecTIONs", CUP: H53D23001550006//Next-GenerationEU - PNRR - M.4 C.2, INVESTIMENTO 1.1 - PRIN22/ ; }, abstract = {Atlantification is an ongoing oceanic phenomenon characterised by the expansion of the typical Atlantic domain towards the Arctic, driving rapid oceanic and ecological changes in the European Arctic. Using reanalyses and a multi-model ensemble of unperturbed and transient preindustrial, historical and future-scenario simulations, this study shows that modern Atlantification possibly initiated in the late nineteenth century, preceded by several "Arctification" episodes in the preindustrial millennium. In the historical period, Atlantification and pan-Arctic warming superposed constructively to drive upper-ocean warming and salinification in the Barents Sea. Modern Atlantification is projected to continue in the next few decades, fully revealing its exceptional character in the context of the past millennium. However, Atlantification halts during the second half of the twenty-first century, decoupling from pan-Arctic warming. The northward expansion of the Atlantic domain is hindered by the onset of a damping mechanism where the Atlantic-Arctic density gradient increases progressively, which sustains a countercurrent by baroclinic adjustment pushing the Arctic polar front southward. As the evolution of this density gradient is intertwined with the retreat of the sea-ice edge, a late-summer ice-free Barents Sea may mark the end of modern Atlantification.}, }
@article {pmid40848298, year = {2025}, author = {Jia, Y and Chen, L and Jin, LN and Zhang, P and Chen, L and Fan, C and Liu, H and Ji, Y and Li, D and Chen, J}, title = {Environmentally Relevant Levels of Ozone Enhance Klebsiella pneumoniae Pulmonary Colonization and Cross-Organ Translocation.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {35}, pages = {18424-18439}, doi = {10.1021/acs.est.5c02782}, pmid = {40848298}, issn = {1520-5851}, mesh = {*Klebsiella pneumoniae ; *Ozone/toxicity ; Animals ; Lung/microbiology ; Mice ; Klebsiella Infections ; }, abstract = {Ozone (O3) is a major global air pollutant. Recent epidemiological studies have suggested links between O3 exposure and outbreaks of infectious diseases. However, whether environmentally relevant levels of O3 exacerbate the colonization and infection of airborne pathogens remains unclear. This study demonstrated that exposure to environmentally relevant levels of O3 (0.15 and 0.60 ppm) significantly enhanced pulmonary colonization of low-dose Klebsiella pneumoniae (1 × 10[3] CFU/mouse) in mice, which failed to colonize without O3 exposure. Unexpectedly, in vivo and in vitro coculture experiments with BEAS-2B bronchial epithelial cells demonstrated that O3 exposure also enhanced the ability of K. pneumoniae to penetrate the lung-blood barrier, thereby inducing bacteremia that spread to the liver and caused severe liver injury. O3 exposure reduced the proportions of T cells, B cells, and macrophages in the lungs and altered the expression of key pulmonary genes (Tlr4, Il-18, Traf6, and Tgf-β1) involved in resisting K. pneumoniae colonization. In addition, lipid peroxidation product MDA in plasma acted as a mediator in the signal transmission along the lung-liver axis. This study underscores the critical role of air pollutants in pathogen colonization and infection, emphasizing the urgent need to address air quality to mitigate respiratory health risks.}, }
@article {pmid40840460, year = {2025}, author = {Carlozzi, NE and Troost, J and Lombard, WL and Miner, JA and Graves, CM and Choi, SW and Wu, Z and Sen, S and Sander, AM}, title = {Completion and Compliance Rates for an Intensive mHealth Study Design to Promote Self-Awareness and Self-Care Among Care Partners of Individuals With Traumatic Brain Injury: Secondary Analysis of a Randomized Controlled Trial.}, journal = {JMIR mHealth and uHealth}, volume = {13}, number = {}, pages = {e73772}, pmid = {40840460}, issn = {2291-5222}, mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Awareness ; *Brain Injuries, Traumatic/psychology/therapy ; *Caregivers/psychology/statistics &amp; numerical data ; Mobile Applications/statistics &amp; numerical data/standards ; *Patient Compliance/statistics &amp; numerical data/psychology ; *Self Care/methods/psychology/standards/statistics &amp; numerical data ; Surveys and Questionnaires ; Telemedicine/standards/statistics &amp; numerical data ; *Treatment Adherence and Compliance/statistics &amp; numerical data/psychology ; Secondary Data Analysis ; }, abstract = {BACKGROUND: Compliance rates for mobile health (mHealth) studies that involve intensive study designs are highly variable. Both person- and study-specific factors likely contribute to this variability. We were interested in understanding the impact that care partner characteristics and demographics have on study engagement, given that engagement is critical to the success of mHealth interventions.<br><br>OBJECTIVE: The primary objective of this report was to analyze the overall and component-specific completion and compliance rates for an intensive 6-month mHealth intervention (CareQOL app) designed to promote self-awareness and self-care among care partners of individuals with traumatic brain injury.<br><br>METHODS: This randomized controlled trial was designed to test the CareQOL app, an mHealth app designed to promote care partner self-awareness (through self-monitoring) and self-care (through personalized self-care push notifications). The study design consisted of a baseline assessment, a 6-month home-monitoring period that included 3 daily ecological momentary assessment (EMA) questions, monthly patient-reported outcome (PRO) surveys, continuous activity and sleep monitoring using a Fitbit, and 2 follow-up PRO surveys at 3 and 6 months posthome monitoring. Three participants withdrew prior to the initiation of the home-monitoring period, resulting in a final analytical sample size of 254. All participants had access to a self-monitoring dashboard (CareQOL app) that included graphical displays of the daily survey scores, as well as daily steps and sleep data from the Fitbit.<br><br>RESULTS: Overall compliance for the different aspects of the study was high. On average, the full-sample daily EMA PRO completion rate was 84% (SD 19%), Fitbit-based step count compliance was 90% (SD 21%), and Fitbit-based sleep duration compliance was 75% (SD 32%); there was no difference between the study arms for daily EMA PROs and Fitbit compliance rates. Completion rates for monthly and follow-up PRO surveys were even higher, with average end-of-month completion rates ranging from 97% to 100%, and follow-up completion rates of 95% for both time points. Again, these rates did not differ by study arm. The data were represented by 3 engagement groups: high-compliance-all data; high-compliance-PROs and steps only; and moderate PRO compliance-low Fitbit compliance. Group membership was predicted by both race (P<.001) and relationship to the care recipient (P=.001), but not by the other person-specific variables.<br><br>CONCLUSIONS: The compliance rates for this intensive study design are consistent, but at the high end, with what has been reported previously in the literature for studies with shorter time durations. Except for race and relationship to the care recipient, person-specific factors did not appear to be significantly associated with the engagement group. As such, we anticipate that the high compliance rates observed in this study are likely due to several study-specific design elements that were used to encourage study engagement.}, }
@article {pmid40843346, year = {2025}, author = {Xia, K and Hu, Y and Cai, S and Lin, M and Lu, M and Lu, H and Ye, Y and Lin, F and Gao, L and Xia, Q and Tian, R and Lin, W and Xie, L and Tan, D and Lu, Y and Lin, X and Yang, X and Zhong, L and Xu, L and Zhang, Z and Wang, L and Ren, J and Xu, H}, title = {GastritisMIL: An interpretable deep learning model for the comprehensive histological assessment of chronic gastritis.}, journal = {Patterns (New York, N.Y.)}, volume = {6}, number = {8}, pages = {101286}, pmid = {40843346}, issn = {2666-3899}, abstract = {The comprehensive histological assessment of chronic gastritis is imperative for guiding endoscopic follow-up strategies and surveillance of early-stage gastric cancer, yet rapid and objective assessment remains challenging in clinical workflows. We propose a powerful deep learning model (GastritisMIL) to effectively identify pathological alterations on H&amp;E-stained biopsy slides, thereby expediting pathologists' evaluation and improving decision-making regarding follow-up intervals. We have trained and tested GastritisMIL by using retrospective data from 2,744 patients and evaluated discriminative performance across three medical centers (467 patients). GastritisMIL attained areas under the receiver operating curve greater than 0.971 in four tasks (inflammation, activity, atrophy, and intestinal metaplasia) and superior performance comparable to that of two senior pathologists. Specifically, interpretable attention heatmaps generated by GastritisMIL effectively assist junior pathologists in locating suspicious lesion regions across the entire field and minimizing missed diagnosis risk. Moreover, the high generalizability of this developed model across multiple external cohorts demonstrates its potential translational value.}, }
@article {pmid40841201, year = {2025}, author = {Sena, AVDS and Telles, L and Melo, PHM and Salomão, SL and Uzeda, TS and Pereira Lima, BL and Kratky, L and Mooney, DP and Bustorff-Silva, J}, title = {The management of cryptorchidism in Brazil: An ecological overview.}, journal = {Journal of pediatric urology}, volume = {21}, number = {6}, pages = {1813-1819}, doi = {10.1016/j.jpurol.2025.07.025}, pmid = {40841201}, issn = {1873-4898}, mesh = {Humans ; *Cryptorchidism/surgery/epidemiology ; Male ; Brazil/epidemiology ; *COVID-19/epidemiology ; Child ; Child, Preschool ; *Orchiopexy/statistics &amp; numerical data ; Infant ; Adolescent ; Infant, Newborn ; }, abstract = {INTRODUCTION: Cryptorchidism refers to the extra-scrotal location of the testicle and is the most common male genital anomaly. Although the recommended age ranges for both hormonal and surgical treatments are well-established, within the Brazilian Unified Health System (SUS), children with cryptorchidism undergo surgery at varying ages across the country. As a time-sensitive procedure, delayed orchidopexy has consequences such as an increased risk of infertility or even testicular cancer. Correlating data on cryptorchidism treatment in SUS with geographic and socioeconomic indicators may help to understand how a population's profile influences the public healthcare system. This study explores the potential relationship between the age at which orchiopexy is performed and the quality of public healthcare services in Brazil while also assessing the impact of the COVID-19 pandemic on this surgery's backlog.<br><br>METHODS: To achieve this, we collected data from the Department of Informatics of the Brazilian Public Health System (DATASUS) and indicators provided by the Brazilian Institute of Geography (IBGE) and the Institute for Applied Economic Research (IPEA). We cataloged and compiled the data for comprehensive analysis.<br><br>RESULTS: Between 2008 and 2022, 94,237 orchiopexies were performed in SUS in patients aged 0-15. Nationwide, this represents only 47.6 % of the expected procedures, ranging from 22.75 % in the North to 68.18 % in the South. The proportion of surgeries performed before age 2 was very low, ranging from 12 % in the North and Northeast to 24 % in the South. Most orchiopexies in Brazil were performed after the age of five. The COVID-19 pandemic significantly worsened this situation, causing a 44.45 % decline in surgeries in 2020 compared to 2019, disproportionately affecting all age groups and exacerbating the backlog of surgeries.<br><br>CONCLUSION: Our study indicates that many children with cryptorchidism remain undiagnosed or receive delayed treatment. The COVID-19 pandemic further worsened this scenario, temporarily reducing the number of operations. These findings underscore the urgent need for comprehensive public policies to improve healthcare access and prevent complications associated with untreated cryptorchism.}, }
@article {pmid40840863, year = {2025}, author = {Zong, Z and Sun, X and Chen, J and Yu, Y and Ni, Z and Wang, Y}, title = {Identification of the full-length GbERD7 gene family in Gossypium barbadense and functional analysis of the role of the GbERD7g gene in drought and salt tolerance.}, journal = {Plant science : an international journal of experimental plant biology}, volume = {360}, number = {}, pages = {112715}, doi = {10.1016/j.plantsci.2025.112715}, pmid = {40840863}, issn = {1873-2259}, mesh = {*Gossypium/genetics/physiology ; Plant Proteins/genetics ; *Salt Tolerance/genetics/physiology ; Droughts ; Dehydration/genetics/metabolism ; *Stress, Physiological/genetics/physiology ; Computational Biology ; Genes, Plant ; *Acclimatization/genetics/physiology ; Sodium Chloride ; Polyethylene Glycols ; Hot Temperature ; Malondialdehyde/metabolism ; }, abstract = {ERD (early response to dehydration) genes are promptly upregulated under dehydration stress and are pivotal in plant development. Nonetheless, the precise impact of the ERD7 gene on the response of cotton to abiotic stress remains unclear. The physical and chemical characteristics, gene architecture, gene collinearity, and transcriptomic profiles were examined. Using bioinformatics techniques, we investigated the evolutionary relationships among the genes within the GbERD7 gene family of sea island cotton. The GbERD7 genes are unevenly distributed across the seven chromosomes of sea island cotton, with multiple gene duplications. The GbERD7 gene family was subjected to phylogenetic analysis, leading to the classification of its members into the SENA and SENB subfamilies. The expression of the GbERD7 genes was investigated in relation to heat, low-temperature, salt (NaCl), and polyethylene glycol (PEG) treatments. Some genes presented greater expression in specific organs and different periods of fiber development. The functional role of GbERD7g was subsequently investigated using molecular biological techniques. GbERD7g exhibited pronounced expression in sea island cotton leaves and was upregulated following exposure to PEG, NaCl, and ABA. Subcellular localization studies revealed that the GbERD7g protein is located within the nucleus as well as the plasma membrane of the cell. When the GbERD7g gene was silenced under drought and salt stress, the sea island cotton plants were significantly less resistant to drought and salinity and exhibited lower survival than the control plants. The proline levels, catalase activity, and superoxide dismutase activity were reduced, and the malondialdehyde and hydrogen peroxide levels were elevated. In addition, compared with those in the control plants, the expression of all three stress-responsive genes, namely, GbRD22, GbRD26, and GbCDPK1, was significantly lower in the mutant plants.}, }
@article {pmid40840423, year = {2025}, author = {Bozeman, BB and Matson, PG and DeRolph, CR and DeNeale, ST}, title = {The HydroBio Dataset: a new data resource for evaluating existing and potential hydropower capacity and freshwater biodiversity in the conterminous United States.}, journal = {Journal of environmental management}, volume = {393}, number = {}, pages = {127042}, doi = {10.1016/j.jenvman.2025.127042}, pmid = {40840423}, issn = {1095-8630}, mesh = {*Biodiversity ; Conservation of Natural Resources ; Ecosystem ; *Fresh Water ; *Power Plants ; Rivers ; United States ; *Datasets as Topic ; }, abstract = {Hydropower is a critical source of affordable and reliable electricity and energy system stability services in the United States. Opportunities to expand US hydropower production include retrofitting existing non-powered dams to produce power, retrofitting existing hydropower dams to improve efficiency or increase capacity, or constructing new hydropower infrastructure on currently unregulated river reaches. We created the HydroBio Dataset, which summarizes existing and potential hydropower capacity and freshwater biodiversity at the sub-basin scale in the conterminous US to contextualize existing and potential grid contributions with the freshwater ecosystems in which dams are situated. We demonstrate a use-case of this dataset by rescaling and comparing potential non-powered dam nominal capacity to rarity-threat-weighted freshwater species richness for sub-basins where both types of data exist. On average, normalized freshwater biodiversity exceeded normalized potential non-powered dam nominal capacity in these sub-basins. Potential non-powered dam nominal capacity was concentrated in sub-basins in the Upper Mississippi and Ohio hydrologic regions while freshwater biodiversity was concentrated in the South Atlantic-Gulf, Ohio, and Tennessee hydrologic regions. Additionally, non-powered dams and existing hydropower dams are located in sub-basins with similar indices of freshwater biodiversity. The HydroBio Dataset adds an additional ecological dimension of context to our understanding of current and potential future US hydropower capabilities and is a valuable decision support tool for stakeholders tasked with balancing gains in services to the US power grid with the public and environmental benefits of freshwater ecosystems.}, }
@article {pmid40838167, year = {2025}, author = {Boyes, D and Fletcher, C and Phillips, D and Sivess, L and Boyes, C and ,  and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Tortix moth, Archips podanus (Scopoli, 1763).}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {189}, pmid = {40838167}, issn = {2398-502X}, abstract = {We present a genome assembly from a male specimen of Archips podanus (Tortix moth; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence has a total length of 549.00 megabases. Most of the assembly (99.72%) is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 15.45 kilobases.}, }
@article {pmid40833038, year = {2026}, author = {De Neef, E and Velásquez-Zapata, V and Gordon, ERL and Narva, K and Mc Cahon, P and Mézin, L and Lester, PJ and Romeis, J and Fletcher, S and Mitter, N and Devisetty, UK and Sridharan, K}, title = {A bioinformatic ecological risk assessment framework for externally applied double-stranded RNA-based biopesticides.}, journal = {Integrated environmental assessment and management}, volume = {22}, number = {1}, pages = {116-131}, doi = {10.1093/inteam/vjaf116}, pmid = {40833038}, issn = {1551-3793}, mesh = {*RNA, Double-Stranded/toxicity ; Risk Assessment/methods ; *Computational Biology/methods ; *Biological Control Agents/toxicity ; *Pest Control, Biological/methods ; Animals ; *Pesticides/toxicity ; }, abstract = {Double-stranded RNA (dsRNA)-based biopesticides are a promising new method of pest management. These biopesticides leverage the endogenous RNA interference pathway to selectively regulate expression of key genes involved in growth and development in pests, providing the potential to minimize harmful environmental effects by highly specific targeting. As dsRNA-based biopesticides are presented for regulatory review, evaluating potential off-target effects on nontarget organisms (NTOs) in a manner that may be unique to this novel sequence-specific mode of action is crucial. To address this, we propose here a bioinformatics framework for consideration of sequence-specific off-target effects in NTOs. This framework includes careful consideration of NTOs based on potential exposure and susceptibility and recommends standardizing analyses to search for 21-nucleotide stretches of perfect identity and 80% overall identity between the dsRNA and off-target transcripts. We recommend a three-pronged approach to ensure a comprehensive risk assessment: (a) phylogenetic analysis of gene orthologs that defines the taxonomic scope of sequence similarity, (b) broad searches of large databases to identify potential unexpected similarity in distantly related species, and (c) full transcriptome analyses in NTO species of particular concern for a thorough understanding of all potential hazards. Finally, we recommend considering the results of bioinformatic analyses in the context of risk characterization, which means considering likely exposure to the dsRNA-based pesticide and potential susceptibility or barriers to dsRNA uptake. This approach enables a robust ecological risk assessment for dsRNA-based biopesticides and a regulatory path forward for this promising new pest management tool.}, }
@article {pmid40829560, year = {2025}, author = {McKnight, JC and Solms, B and Jensen, M and Turnbull, J and Balfour, S and Laagland, M and Bronkhorst, M and Lee, HJ and Kang, G and Lee, JY and Bell, A and Hastie, G and Ilardo, M}, title = {Diving behaviour and physiology of the Korean Haenyeo.}, journal = {Current biology : CB}, volume = {35}, number = {16}, pages = {R797-R798}, doi = {10.1016/j.cub.2025.06.066}, pmid = {40829560}, issn = {1879-0445}, mesh = {Adult ; Female ; Humans ; *Diving/physiology ; Republic of Korea ; *Breath Holding ; }, abstract = {There is a long history of breath-hold diving cultures in East Asia, with references in Japanese chronicles as early as the third century BC. Given evidence of genetic adaptations for phenotypes associated with enhanced diving capacity within such populations[1], it is likely they hold the most prodigious human diving abilities - abilities that may be akin to semi-aquatic mammals, and even some marine mammals. Yet, a dearth of fine-scale information exists on the combined natural diving behaviour and physiological responses within these diving populations. One such extraordinary population is the all-female Haenyeo. Here, we assess the fine-scale diving behaviours and physiological responses of these women during natural harvest diving. Our results show that Haenyeo divers demonstrate the highest proportions of time underwater of any humans, also exceeding those of semi-aquatic mammals and being comparable with some marine mammals. Additionally, they do not exhibit an overt cardiovascular depression, or 'dive response', classically associated with consummate diving mammals.}, }
@article {pmid40828878, year = {2025}, author = {Fong, LJM and Johnson, BD and Darolti, I and Sandkam, BA and Mank, JE}, title = {Genome report: Genome of the Amazon guppy (Poecilia bifurca) reveals conservation of sex chromosomes and dosage compensation.}, journal = {G3 (Bethesda, Md.)}, volume = {15}, number = {10}, pages = {}, pmid = {40828878}, issn = {2160-1836}, support = {//NSERC/ ; //UBC/ ; //BRC Informatics/ ; }, mesh = {Animals ; *Poecilia/genetics ; *Dosage Compensation, Genetic ; Male ; Female ; *Sex Chromosomes/genetics ; *Genome ; *Genomics/methods ; X Chromosome/genetics ; }, abstract = {The Amazon guppy, Poecilia bifurca, is a small live-bearing fish. The close relatives Poecilia reticulata, Poecilia picta, and Poecilia parae all share the same sex chromosome system, but with substantial diversity in the degree of Y degeneration and the extent of X chromosome dosage compensation. In order to identify if P. bifurca shares the same sex chromosome system, we built a female (XX) draft genome with 55X coverage of PacBio HiFi data, resulting in a 785 Mb assembly with 94.4% BUSCO completeness. We used this genome and found that P. bifurca shares the same sex chromosomes as related species and shows substantial Y chromosome degeneration. We combined this with RNA-Seq data and found similar expression of X-linked genes between sexes, revealing that P. bifurca also exhibits complete X chromosome dosage compensation. We further identify 11 putative autosome-to-Y gene duplications, 5 of which show gene expression in guppy male germ cells.}, }
@article {pmid40828862, year = {2025}, author = {Kubota, Y and Fukiage, T}, title = {Human-like monocular depth biases in deep neural networks.}, journal = {PLoS computational biology}, volume = {21}, number = {8}, pages = {e1013020}, pmid = {40828862}, issn = {1553-7358}, mesh = {Humans ; *Neural Networks, Computer ; *Depth Perception/physiology ; *Vision, Monocular/physiology ; Computational Biology ; Male ; Female ; Adult ; }, abstract = {Human depth perception from 2D images is systematically distorted, yet the nature of these distortions is not fully understood. By examining error patterns in depth estimation for both humans and deep neural networks (DNNs), which have shown remarkable abilities in monocular depth estimation, we can gain insights into constructing functional models of this human 3D vision and designing artificial models with improved interpretability. Here, we propose a comprehensive human-DNN comparison framework for a monocular depth judgment task. Using a novel human-annotated dataset of natural indoor scenes and a systematic analysis of absolute depth judgments, we investigate error patterns in both humans and DNNs. Employing exponential-affine fitting, we decompose depth estimation errors into depth compression, per-image affine transformations (including scaling, shearing, and translation), and residual errors. Our analysis reveals that human depth judgments exhibit systematic and consistent biases, including depth compression, a vertical bias (perceiving objects in the lower visual field as closer), and consistent per-image affine distortions across participants. Intriguingly, we find that DNNs with higher accuracy partially recapitulate these human biases, demonstrating greater similarity in affine parameters and residual error patterns. This suggests that these seemingly suboptimal human biases may reflect efficient, ecologically adapted strategies for depth inference from inherently ambiguous monocular images. However, while DNNs capture metric-level residual error patterns similar to humans, they fail to reproduce human-level accuracy in ordinal depth perception within the affine-invariant space. These findings underscore the importance of evaluating error patterns beyond raw accuracy, providing new insights into how humans and computational models resolve depth ambiguity. Our dataset and methodology provide a framework for evaluating the alignment between computational models and human perceptual biases, thereby advancing our understanding of visual space representation and guiding the development of models that more faithfully capture human depth perception.}, }
@article {pmid40828283, year = {2025}, author = {Aceto, S and Perrini, S and Varone, M and Lucibelli, F and Volpe, G and Di Lillo, P and Carfora, A and Mazzucchiello, SM and Saccone, G and Salvemini, M}, title = {Identification of Sex-Specific and Sex-Biased Transcripts for Genetic Sexing.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2935}, number = {}, pages = {273-298}, pmid = {40828283}, issn = {1940-6029}, mesh = {Animals ; Male ; Female ; *Computational Biology/methods ; *Sex Determination Analysis/methods ; *Transcriptome ; }, abstract = {Sex-specific transcripts are RNA molecules expressed predominantly or exclusively in one sex, providing insights into molecular and physiological differences between males and females. This knowledge underpins the development of precise and efficient genetic sexing methods applicable in various contexts. In agriculture and livestock management, early sex determination could enhance resource management and productivity. In ecology and conservation, genetic sexing informs population monitoring and species management. In applied entomology, it could improve biological control strategies, such as the sterile insect technique. Here, we describe a bioinformatic framework to identify sex-specific transcripts using RNA-seq sequencing data in eukaryotic species with or without a sequenced reference genome.}, }
@article {pmid40828279, year = {2025}, author = {Vizueta, J and Pisarenco, VA and Rozas, J}, title = {Evolutionary Genomics of Gene Families: A Case Study of Insect Gustatory Receptors.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2935}, number = {}, pages = {179-209}, pmid = {40828279}, issn = {1940-6029}, mesh = {Animals ; *Genomics/methods ; *Evolution, Molecular ; *Multigene Family ; Phylogeny ; *Receptors, Cell Surface/genetics ; *Ants/genetics ; Computational Biology/methods ; *Insect Proteins/genetics ; Molecular Sequence Annotation ; }, abstract = {Gene families, which are groups of genes that share common ancestry and are often functionally related, constitute a substantial proportion of the protein-coding sequences within eukaryotic genomes. In insects, genes involved in chemoperception belong to gene families characterized by numerous copies that arise from episodic bursts of gene duplication. This biological process is crucial for insect survival, as it enables the perception of environmental chemical cues. In this chapter, we analyze the gustatory receptors in the fire ant Solenopsis invicta and present a protocol for bioinformatic analyses. First, we employ BITACORA to identify and annotate gene family members in the genome assembly, providing tools for the annotation and subsequent validation. Then, we use GALEON to explore the genomic arrangement of gene family members in the chromosome-level assembly and visualize the distribution of gene clusters. To gain insights into the evolution and function of these genes, we conduct multiple-sequence alignment and reconstruct the phylogeny, incorporating data from two other insects. Finally, we integrate physical and evolutionary distances of the gustatory receptors to further understand the dynamics of this gene family.}, }
@article {pmid40828274, year = {2025}, author = {Ramos-Onsins, SE and Guirao-Rico, S and Hafez, A and Ferretti, L}, title = {npstat: An Efficient Tool to Explore the Population Genome Variability and Divergence Using Pool Sequencing Data.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2935}, number = {}, pages = {51-66}, pmid = {40828274}, issn = {1940-6029}, mesh = {*Software ; *Genetic Variation ; *Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; *Genetics, Population/methods ; *Computational Biology/methods ; }, abstract = {Pool sequencing has emerged as a valuable approach in ecological studies, particularly when dealing with very small organisms (with limited amount of DNA available), when distinguishing individual organisms is a challenge (e.g., in colonies, microbiome), when there is a trade-off between the sequencing cost and the number of individuals to sequence, when the main goal is to estimate nucleotide variability and variant frequency patterns at the population level (that is, when individual information is not required). Estimates of variability can be efficiently explored by analyzing sequences of pooled individuals sampled from the population. When using this approach, the number of pooled individuals and the mean read depth are key choices in the experimental design.The software npstat calculates different estimates of nucleotide variability and neutrality tests.It also calculates the number of synonymous and nonsynonymous variants and the proportion of beneficial substitutions (alpha) using the MKT approach when GTF annotation file and an outgroup is provided.}, }
@article {pmid40827702, year = {2025}, author = {Chung, J and Moloney, ME and Seixas, AA and Jackson, CL}, title = {The environment around the sleeper is changing: a perspective.}, journal = {Sleep}, volume = {48}, number = {11}, pages = {}, pmid = {40827702}, issn = {1550-9109}, support = {5R01HL152453-05/GF/NIH HHS/United States ; }, mesh = {Humans ; *Sleep/physiology ; Weather ; *Environmental Exposure/adverse effects ; *Environment ; Circadian Rhythm/physiology ; Temperature ; }, abstract = {Sleep is shaped by a complex interplay of biological, behavioral, and environmental factors. While substantial attention has been paid to the first two factors, the role of environmental exposures, particularly weather patterns, ambient temperature variability, and other dynamic atmospheric conditions, remains relatively underexplored in sleep research. This gap is notable given the increasing availability of high-resolution environmental data and growing evidence that ambient conditions can influence circadian regulation, thermal comfort, and sleep continuity. This perspective paper reviews emerging evidence linking environmental factors to sleep patterns, highlighting both direct effects (e.g. thermal disruptions) and indirect pathways (e.g., displacement or stress from extreme weather events). Recent advances in environmental sensing, geospatial data, and real-time monitoring offer new opportunities to capture high-resolution environmental data relevant to sleep. This perspective highlights the need for data infrastructure capable of integrating these dynamic environmental inputs with sleep metrics from, for instance, wearables, surveys, and clinical records. We also examine the methodological and informatics challenges of integrating environmental data with sleep measures and suggest directions for future research. As environmental conditions evolve, understanding their influence on sleep holds promise for advancing both scientific knowledge and public health relevance, particularly in identifying affected populations, designing responsive interventions, and contextualizing sleep within broader ecological systems.}, }
@article {pmid40826054, year = {2025}, author = {Quintanilha, D and Moura, E and Xavier, D}, title = {Hospitalisations in Brazil: an ecological time series analysis of the impact of medical decision support data as an exogenous variable.}, journal = {BMC public health}, volume = {25}, number = {1}, pages = {2827}, pmid = {40826054}, issn = {1471-2458}, mesh = {Brazil/epidemiology ; Humans ; *Hospitalization/statistics &amp; numerical data ; *Decision Support Systems, Clinical/statistics &amp; numerical data ; *Public Health Surveillance/methods ; }, abstract = {PURPOSE: Public health surveillance depends on continuous monitoring to guide interventions and allocate resources effectively. This study aimed to evaluate whether structured medical search data from the Afya Whitebook®, a clinical decision-support platform, can serve as exogenous variables to enhance the explanatory capacity of time series models characterising hospitalisation patterns within Brazil's public health system.<br><br>METHODS: An ecological time series analysis was conducted using hospitalisation data (SIH/SUS) and Afya Whitebook&#xae; search volumes from 2021 to 2024. SARIMAX models assessed temporal associations between search activity and hospital admissions across Brazilian states, compared to univariate SARIMA models to evaluate the added value of search data.<br><br>RESULTS: In 278 of the 478 time series, SARIMAX models provided a better fit than univariate SARIMA models, particularly for conditions such as chronic obstructive pulmonary disease, dengue, urinary tract infections, type 2 diabetes, asthma, depression, and chronic kidney disease. Model fit varied by disease and region, underscoring the influence of contextual factors in the association between search behaviour and hospital admissions.<br><br>CONCLUSION: This study demonstrates that structured medical search data can serve as exogenous variables to improve the explanatory capacity of time series models of hospitalisation patterns. Despite variation between diseases and regions, this approach shows promise in supporting public health surveillance and could be strengthened by incorporating contextual data in future studies.}, }
@article {pmid40825407, year = {2025}, author = {Tarandek, A and Boštjančić, LL and Francesconi, C and Bonassin, L and Schardt, L and Jussila, J and Kokko, H and Schwenk, K and Hudina, S and Lecompte, O and Theissinger, K}, title = {Characterisation of the noble crayfish immune response to oomycete-derived immunostimulants.}, journal = {Fish &amp; shellfish immunology}, volume = {166}, number = {}, pages = {110666}, doi = {10.1016/j.fsi.2025.110666}, pmid = {40825407}, issn = {1095-9947}, mesh = {Animals ; *Astacoidea/immunology/genetics/microbiology ; *Aphanomyces/chemistry/physiology/immunology ; *Adjuvants, Immunologic/pharmacology ; *Glucans/pharmacology ; *Immunity, Innate ; Hemocytes/immunology ; }, abstract = {The invasive oomycete pathogen Aphanomyces astaci significantly threatens native European crayfish populations, prompting investigations towards the effects of protective immunostimulation on the immune response of the vulnerable noble crayfish (Astacus astacus). Here, we evaluate the effect of three oomycete-derived immunostimulant treatments: laminarin (β-1,3-glucan found within the Ap. astaci cell wall), inactivated Ap. astaci spores and Ap. astaci hyphal homogenate. Our findings reveal immediate changes in the noble crayfish total haemocyte count (THC), differential haemocyte count (DHC), and gene expression. A short-term increase in the THC was observed in all treatments, with a gradual return to normal values 8 h post immunostimulation. Granular haemocytes seem to be involved in response to immunostimulation with inactivated Ap. astaci spores, while the number of semi-granular and hyaline haemocytes increased in response to laminarin and Ap. astaci hyphal homogenate. Analysis of the differentially expressed genes showed that the Prophenoloxidase pathway genes and Toll pathway genes are involved in the response to oomycete-derived immunostimulants. Prolonged effects of immunostimulation were reflected in the decreased C/EBP and Kr-h1 gene expression in the hyphal homogenate group as well as decreased Kr-h1 expression in the spore group. Taken together, our results indicate that immunostimulation causes a dynamic change in the noble crayfish immune system response, with similarities in the gene expression patterns between immunostimulated and Ap. astaci infected noble crayfish. As a future research focus, we highlight the importance of molecular characterisation of the genes involved in the anti-oomycete response which could provide valuable insights into pathogen resistance in freshwater crayfish. In the context of the Ap. astaci mediated downfall of the noble crayfish stocks across Europe, further exploration is needed regarding the benefits of the oomycete-derived immunostimulation that can potentially support conservation and aquacultural efforts.}, }
@article {pmid40824055, year = {2025}, author = {Grigson, SR and Bouras, G and Dutilh, BE and Olson, RD and Edwards, RA}, title = {Computational function prediction of bacteria and phage proteins.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {89}, number = {3}, pages = {e0002225}, pmid = {40824055}, issn = {1098-5557}, support = {865694/ERC_/European Research Council/International ; 390713860//Deutsche Forschungsgemeinschaft/ ; RC2DK116713/DK/NIDDK NIH HHS/United States ; DP250103825//Australian Research Council/ ; DP220102915//Australian Research Council/ ; FL250100019//Australian Research Council/ ; }, mesh = {*Bacteriophages/genetics/metabolism ; *Computational Biology/methods ; *Viral Proteins/genetics/metabolism/chemistry ; *Bacteria/genetics/metabolism ; *Bacterial Proteins/genetics/metabolism/chemistry ; Machine Learning ; Molecular Sequence Annotation/methods ; }, abstract = {SUMMARYUnderstanding protein functions is crucial for interpreting microbial life; however, reliable function annotation remains a major challenge in computational biology. Despite significant advances in bioinformatics methods, ~30% of all bacterial and ~65% of all bacteriophage (phage) protein sequences cannot be confidently annotated. In this review, we examine state-of-the-art bioinformatics tools and methodologies for annotating bacterial and phage proteins, particularly those of unknown or poorly characterized function. We describe the process of identifying protein-coding regions and the systems to classify protein functionalities. Additionally, we explore a range of protein annotation methods, from traditional homology-based methods to cutting-edge machine learning models. In doing so, we provide a toolbox for confidently annotating previously unknown bacterial and phage proteins, advancing the discovery of novel functions and our understanding of microbial systems.}, }
@article {pmid40822726, year = {2025}, author = {Piršelová, B and Jakubčinová, J}, title = {Plant cyanogenic glycosides: from structure to properties and potential applications.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1612132}, pmid = {40822726}, issn = {1664-462X}, abstract = {Cyanogenic glycosides (CGs) represent an important group of secondary metabolites predominantly of plant origin, characterized by their ability to release hydrogen cyanide upon enzymatic hydrolysis. These compounds are widely distributed across the plant kingdom, where they play a crucial role in defense against herbivores and pathogens. In recent years, advanced analytical tools have greatly expanded our knowledge of CGs by enabling the identification of less abundant forms. Based on the latest data from published scientific studies, this review presents a comprehensive overview of CGs, with a focus on their structural variability, biosynthetic pathways, ecological functions, and inherent toxicity. Special attention is given to the quantity and distribution of significant CGs in plants, as the available data is often heterogeneous, fragmented, and dispersed across the literature. Furthermore, the review explores emerging evidence regarding the biomedical relevance of selected CGs, including their putative anticancer properties and broader therapeutic potential. The findings presented in this review may be applied in fields such as pharmacology, toxicology, food safety, and plant biotechnology - either to enhance CG content for crop protection or, conversely, to eliminate such content in order to improve food safety.}, }
@article {pmid40821442, year = {2025}, author = {Motlagh, SH and Momtazi, F and Saeedi, H}, title = {Senckenberg dogger bank long-term monitoring: First dataset on amphipods.}, journal = {Data in brief}, volume = {62}, number = {}, pages = {111931}, pmid = {40821442}, issn = {2352-3409}, abstract = {This dataset includes unique occurrence records of amphipod specimens collected during the 2024 annual Senckenberg Long-Term Monitoring Project in Dogger Bank (a shallow sand bank in the central North Sea), Cruise DOG24. This cruise was part of an ongoing effort to monitor biodiversity, which has occurred annually from 1991 to 2024 by the Marine Zoology Department at the Senckenberg Research Institute and Natural History Museum. Amphipods, key components of marine benthic ecosystems, were sampled by beam trawl over the Dogger Bank's stable sandy substrate. A total of 8444 specimens of ten species belonging to 13 families and 14 genera were identified using morphological methods with Leica M60 and DM750 microscopes. This study presents the first species-level identification of benthic amphipods in the Dagger Bank, providing a taxonomically resolved dataset that serves as a reliable identification key for future monitoring efforts in the area. Data were structured and published to the Ocean Biodiversity Information System (OBIS) and the Global Biodiversity Information Facility (GBIF) following the Darwin Core (DwC) standard. This dataset is the first-hand data ever published open-access from the Senckenberg Long Term Monitoring Project since 1991. This dataset also supports a broader research project aimed at (i) revealing the distribution pattern of amphipods in the North Sea, (ii) identifying environmental drivers of species distribution and diversity, and (iii) evaluating the response of the amphipod community to ecosystem changes.}, }
@article {pmid40820776, year = {2025}, author = {Stansberry, TT and Myers, CR and Tran, L and Roberson, PNE and Ahn, S}, title = {Impacts of Access to Hospital and Emergency Care on Rural Mortality in Tennessee, 2010-2019: A GIS-Informed Study.}, journal = {Journal of health care for the poor and underserved}, volume = {36}, number = {3}, pages = {787-814}, doi = {10.1353/hpu.2025.a967333}, pmid = {40820776}, issn = {1548-6869}, mesh = {Humans ; Tennessee/epidemiology ; *Health Services Accessibility/statistics &amp; numerical data ; Retrospective Studies ; *Rural Population/statistics &amp; numerical data ; Cross-Sectional Studies ; Middle Aged ; Geographic Information Systems ; Female ; Male ; COVID-19/epidemiology ; Adult ; Aged ; *Mortality/trends ; *Emergency Medical Services/statistics &amp; numerical data ; }, abstract = {Rural Tennessee's health and economic disparities have worsened since 2010 (while the state led the nation in hospital closures per capita). Guided by the Vulnerable Populations Conceptual Model, we examined the relationship between Tennessee's county-level rural mortality rates and declining access to hospital and emergency care in the decade preceding the COVID-19 pandemic (avoiding pandemic-related delayed data releases and potential statistical modeling issues). We conducted a retrospective, ecological correlational study using geographic information systems and annual cross-sectional secondary data, employing aspatial and spatial negative binomial generalized linear mixed-effects models (GLMMs). Our bivariate models revealed significant correlations between hospital and emergency care access and mortality rates, but the effect decreased when adjusted for rurality, median household income, age, and other covariates. While access to hospital and emergency care influences mortality, our findings indicate that socioeconomic and demographic factors have a greater impact, underscoring the strong health-wealth connection in rural Tennessee.}, }
@article {pmid40820130, year = {2025}, author = {Sehi, GT and Birhanie, SK and Hans, J and Brown, MQ and Parker, DM}, title = {Environmental correlates of Aedes aegypti abundance in the West Valley region of San Bernardino County, California, USA, from 2017 to 2023: an ecological modeling study.}, journal = {Parasites &amp; vectors}, volume = {18}, number = {1}, pages = {349}, pmid = {40820130}, issn = {1756-3305}, support = {U01 CK000649/CK/NCEZID CDC HHS/United States ; U01CK000649/ACL/ACL HHS/United States ; }, mesh = {Animals ; *Aedes/physiology/virology ; California/epidemiology ; *Mosquito Vectors/physiology/virology ; Geographic Information Systems ; Temperature ; *Environment ; Ecosystem ; Dengue/transmission ; Mosquito Control ; Humans ; }, abstract = {BACKGROUND: Aedes mosquitoes, particularly Aedes aegypti and Ae. albopictus, are major vectors of globally significant diseases such as dengue, Zika, and chikungunya. Since 2013, Ae. aegypti populations have rapidly expanded in California, making control efforts difficult due to their widespread, small-scale breeding sites and strong adaptation to urban environments.<br><br>METHODS: Remote sensing technologies, coupled with Geographic Information Systems (GIS), offer innovative solutions for mosquito surveillance and control. However, understanding the environmental drivers of mosquito abundance, particularly in California's diverse ecological settings, remains an important gap. To address this gap, we analyzed Ae. aegypti abundance (2017 to 2023) in relation to environmental variables, such as temperature, precipitation, surface water, elevation, and built environment. We applied hotspot analysis to identify spatial clusters of high mosquito abundance and used a generalized additive model (GAM) with a negative binomial distribution to assess environmental and meteorological influences on mosquito counts.<br><br>RESULTS: Hotspot analyses revealed clusters of Ae. aegypti hotspots near residential areas. Aedes aegypti counts increased with higher surface water availability and temperature.<br><br>CONCLUSIONS: Our study characterizes the spatial and temporal dynamics of Ae. aegypti mosquito abundance in the West Valley region of San Bernardino County from 2017 to 2023, shedding light on the influence of environmental factors and human activities on temporal trends. Our findings emphasize the critical role of temperature and water availability in shaping mosquito population dynamics, highlighting the need for proactive vector control strategies in response to environmental changes.}, }
@article {pmid40819189, year = {2025}, author = {Alhashmi, AA and Elhessewi, GMS and Ghaleb, M and Ahmad, N and Aljehane, NO and Alkhaldi, TM and Almansour, H and Al Zanin, S}, title = {Enhancing medical response efficiency in real-time large crowd environments via smart coverage and deep learning for stable ecological health monitoring.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {30000}, pmid = {40819189}, issn = {2045-2322}, mesh = {*Deep Learning ; Humans ; Geographic Information Systems ; *Crowding ; Algorithms ; }, abstract = {Festivals and city-wide mass events are prevalent in human societies worldwide, drawing large crowds. Such events range from concerts with a dozen attendees to large-scale actions with thousands of viewers. It is the highest priority for each organizer of such an occasion to be capable of upholding a higher standard of safety and minimizing the danger of events, especially medical emergencies. Therefore, establishing sufficient safety measures is significant. There is a requirement for event organizers and emergency response personnel to identify developing, potentially critical crowd situations at an early stage during city-wide mass assemblies. In general, the localization of the global positioning system (GPS) and proximity-based tracking is employed to capture intricate crowd dynamics throughout an event. Recently, technology has been used in numerous diverse ways to achieve these large crowds. For example, computer vision-based models are employed to observe the flexibility and behaviour of crowds. In this manuscript, a model for Medical Response Efficiency in Real-Time Large Crowd Environments via Smart Coverage and Hiking Optimisation (MRELC-SCHO) is presented, aiming to maintain stable ecological health. The primary objective of this paper is to propose an effective method for enhancing medical response efficiency in large crowd environments by utilizing advanced optimization algorithms. Initially, the MRELC-SCHO model utilizes min-max normalization to transform the input data into a structured format. Furthermore, the Chimp Optimisation Algorithm (CHOA) model is employed for the feature selection (FS) process to select the most significant features from the dataset. Additionally, the MRELC-SCHO technique utilizes the bidirectional long short-term memory with an auto-encoder (BiLSTM-AE) method for classification. Finally, the parameter selection for the BiLSTM-AE model is performed by using the Hiking Optimisation Algorithm (HOA) model. The experimentation of the MRELC-SCHO approach is accomplished under the Ecological Health dataset. The comparison analysis of the MRELC-SCHO approach revealed a superior accuracy value of 98.56% compared to existing models.}, }
@article {pmid40818234, year = {2025}, author = {Poudel, B and Xie, J and Guo, C and Watt, OE and Pulster, EL and Patel, RJ and Steevens, JA and Xu, D}, title = {Real-time oil spill concentration assessment through fluorescence imaging and deep learning.}, journal = {Journal of hazardous materials}, volume = {496}, number = {}, pages = {139374}, doi = {10.1016/j.jhazmat.2025.139374}, pmid = {40818234}, issn = {1873-3336}, abstract = {Oil spills may pose severe ecological and socioeconomic threats, necessitating rapid and accurate environmental assessment. Traditional assessment methods used to determine the extent of a spill including gas chromatography-mass spectrometry, satellite imaging, and visual surveys, are often time-consuming, expensive, and limited by weather conditions or sampling constraints. Furthermore, these methods frequently struggle to provide real-time data crucial for prompt decision-making during spill emergencies. This study addresses these limitations by combining fluorescence imaging, deep learning, a mobile application, and a data management system for automated and real-time oil spill assessment. Our approach leverages a convolutional neural network architecture for feature extraction coupled with a custom regression model, trained and evaluated on a self-curated comprehensive dataset of 1530 fluorescence images from two distinct oil types, a napthalenic crude oil and an aromatic-napthalenic crude oil, at concentrations ranging from 0 to 500 mg/L. The proposed approach demonstrates superior performance compared to both traditional machine learning models and more complex deep learning architectures, achieving an R[2] score of 0.9958 and RMSE of 9.28. The application enables rapid, cost-effective field measurements with robust data tracking and analysis capabilities. This research advances oil spill monitoring technology with a scalable solution that balances accuracy, speed, and accessibility for real-time environmental assessment and emergency response.}, }
@article {pmid40817347, year = {2025}, author = {Rajpal, H and Stengel, CV and Mediano, PAM and Rosas, FE and Viegas, E and Marquet, PA and Jensen, HJ}, title = {Information dynamics and the emergence of high-order individuality in ecosystems.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {1231}, pmid = {40817347}, issn = {2399-3642}, support = {EP/W024020/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; EP/X03870X/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; EP/W007142/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; ES/T005319/2//RCUK | Economic and Social Research Council (ESRC)/ ; }, mesh = {*Ecosystem ; *Biological Evolution ; *Selection, Genetic ; Mutation ; Population Dynamics ; *Information Theory ; }, abstract = {At what level does natural selection occur? When considering the reproductive dynamics of interacting and mutating agents, it has long been debated whether selection is better understood by focusing on the individual or if hierarchical selection emerges as a consequence of joint adaptation. Despite longstanding efforts in theoretical ecology, there is still no consensus on this fundamental issue, most likely due to the difficulty in obtaining adequate data spanning a sufficient number of generations and the lack of adequate tools to quantify the effect of hierarchical selection. Here, we capitalise on recent advances in information-theoretic data analysis to advance this state of affairs by investigating the emergence of high-order structures- such as groups of species- in the collective dynamics of the Tangled Nature model of evolutionary ecology. Our results show that evolutionary dynamics can lead to clusters of species that act as a self-perpetuating group that exhibits greater information-theoretic agency than a single species for a broad range of stable mutation rates. However, this higher-order organization breaks down for mutation rates close to the error threshold, where increased information processing is observed at the level of a single species. For mutation rates higher than the error threshold, no stable population of species are observed in time, and all individuality is lost in the ecosystem. Overall, our findings provide quantitative evidence supporting the emergence of higher-order structures in evolutionary ecology from relatively simple processes of adaptation and reproduction.}, }
@article {pmid40816181, year = {2025}, author = {Xu, Z and Xu, D and Ma, J and Wang, J and Yan, S and Fu, R and Cui, Y}, title = {The risk assessment for metal(loid)s in soil-slag mixing systems: Coupling sequential extraction, leaching tests, and in vitro bioaccessibility assays.}, journal = {Journal of hazardous materials}, volume = {496}, number = {}, pages = {139544}, doi = {10.1016/j.jhazmat.2025.139544}, pmid = {40816181}, issn = {1873-3336}, mesh = {Risk Assessment ; *Soil Pollutants/analysis/toxicity ; *Metalloids/analysis/toxicity ; Biological Availability ; Humans ; *Industrial Waste/analysis ; Soil/chemistry ; *Metals, Heavy/analysis ; *Metals/analysis ; Arsenic ; Metallurgy ; }, abstract = {The metals and metalloids (metal[loid]s) in the newly formed soil-slag mixing systems (SSMS), formed by the invasion of smelting slag into contaminated soils, may pose potential risks to environment and residents near the smelter sites. In this study, sequential extraction, leaching tests and in vitro bioaccessibility assays were conducted to assess the ecological and human health risk of metal(loid)s in SSMS. The results indicated that the contaminated soils and smelting slags were composed of more than 80 % silicate and oxide minerals, which served as the host phases for metal(loid)s in SSMS. Cd exhibited high mobility and availability, with its exchangeable fraction ranging from 0.15 % to 69.23 %. Leaching tests revealed high leachability and bioavailability of Cd, Mn and Zn. Moreover, metal(loid)s bioaccessibility varied amongst samples: 2.78-46.63 % of As, 11.87-95.25 % of Cd, 37.35-93.88 % of Mn, 1.97-87.84 % of Pb and 0-57.98 % of Zn. Risk assessment calculation results indicated potentially ecological risks posed by Cd, Mn, Pb, and Zn, and unfavorable carcinogenic risks associated with As and Cd, suggesting that remediation efforts were warranted. Overall, this study highlighted how the invasion of smelting slags can affect the accuracy of risk assessments, providing new guidance for risk control and environmental management at slag dumping sites.}, }
@article {pmid40814786, year = {2026}, author = {Misono, S and Nguyen-Feng, VN and Lei, X and Feddema, E and Tella, A and Stockness, A and Frazier, PA and Kummerfeld, E and Lim, KO}, title = {Ecological Momentary Assessment of Voice &amp; Psychological Factors: Group &amp; Individual Mechanisms.}, journal = {The Laryngoscope}, volume = {136}, number = {1}, pages = {324-331}, pmid = {40814786}, issn = {1531-4995}, support = {K23DC016335/DC/NIDCD NIH HHS/United States ; UL1 TR002494/TR/NCATS NIH HHS/United States ; UL1TR002494/TR/NCATS NIH HHS/United States ; KL2 TR000113/TR/NCATS NIH HHS/United States ; K23 DC016335/DC/NIDCD NIH HHS/United States ; KL2TR000113/TR/NCATS NIH HHS/United States ; //American College of Surgeons, Triological Society: Clinical Scientist Development Award/ ; }, mesh = {Humans ; Male ; Female ; Adult ; *Ecological Momentary Assessment ; Middle Aged ; *Dysphonia/psychology/physiopathology ; *Voice Quality ; Cross-Sectional Studies ; Anxiety/psychology ; Stress, Psychological ; Aged ; }, abstract = {OBJECTIVES: Cross-sectional associations between voice and psychological factors are known, but changes over time offer opportunities to refine our understanding of their interactions and consider customized treatment options. Study objectives were to measure relationships between voice and psychological factors using ecological momentary assessment and applying (1) group-level time series analysis and (2) group and (3) individual causal modeling to identify key psychological factors relevant for voice outcomes.<br><br>METHODS: Adults (N&#x2009;=&#x2009;32) with primary muscle tension dysphonia completed multiple assessments daily for 10&#x2009;days. Measures included items from the Voice Handicap Index-10, voice-adapted perceived present control scale, items from NIH PROMIS and the NIH Toolkit to assess distress, and the Positive and Negative Affect Scale. Group-level time series analysis was conducted using dynamic structural equation modeling; causal analysis utilized the Greedy Fast Causal Inference algorithm.<br><br>RESULTS: In group-level time series analyses, neither perceived control nor distress predicted subsequent timepoint voice handicap scores. In group-level causal modeling, anxiety was causal for voice handicap, but perceived control was not. Individual-level analyses identified various causal factors for voice handicap including perceived control and negative affect, and to a lesser extent, serenity, anxiety, somatic arousal, and stress.<br><br>CONCLUSIONS: Group-level analyses may obscure important heterogeneity that is identifiable using individual-level causal analyses. For example, perceived control was not identified as predictive or causal for voice handicap at the group level; but was a salient causal factor for voice handicap in some individuals. Causal modeling using intensive longitudinal datasets offers a potential avenue for individualized treatment approaches.}, }
@article {pmid40812171, year = {2025}, author = {Lundberg, DS and Bergelson, J and Roux, F and Weigel, D and Karasov, TL}, title = {Lab to field: Challenges and opportunities for plant biology.}, journal = {Cell host &amp; microbe}, volume = {33}, number = {8}, pages = {1212-1216}, doi = {10.1016/j.chom.2025.05.027}, pmid = {40812171}, issn = {1934-6069}, mesh = {*Plants/microbiology ; Plant Diseases/microbiology ; *Plant Physiological Phenomena ; }, abstract = {Plant-microbe research offers many choices of model and strain and whether a field-first or lab-first approach is best. However, differences between laboratory studies, offering control and repeatability, versus field experiments, revealing ecological relevance and environmental effects, should not be seen as failure but motivate further inquiry and allow complementary discovery.}, }
@article {pmid40811794, year = {2025}, author = {Shen, S and Qi, W and Zeng, J and Li, S and Liu, X and Zhu, X and Dong, C and Wang, B and Shi, Y and Yao, J and Wang, B and Lou, X and Gu, S and Li, P and Wang, J and Jiang, G and Cao, S}, title = {Passive Sensing for Mental Health Monitoring Using Machine Learning With Wearables and Smartphones: Scoping Review.}, journal = {Journal of medical Internet research}, volume = {27}, number = {}, pages = {e77066}, pmid = {40811794}, issn = {1438-8871}, mesh = {*Wearable Electronic Devices ; Humans ; *Machine Learning ; *Smartphone ; *Mental Health ; *Mental Disorders/diagnosis ; Monitoring, Physiologic ; }, abstract = {BACKGROUND: Mental health issues have become a significant global public health challenge. Traditional assessments rely on subjective methods with limited ecological validity. Passive sensing via wearable devices and smartphones, combined with machine learning (ML), enables objective, continuous, and noninvasive mental health monitoring.<br><br>OBJECTIVE: This study aimed to provide a comprehensive review of the current state of passive sensing-based and ML technologies for mental health monitoring. We summarized the technical approaches, revealed the association patterns between behavioral features and mental disorders, and explored potential directions for future advancements.<br><br>METHODS: This scoping review adhered to the PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews) guidelines and was prospectively registered on the Open Science Framework. We systematically searched 7 databases (Web of Science, PubMed, IEEE Xplore, Embase, PsycINFO, Scopus, and ACM Digital Library) for studies published between January 2015 and February 2025. We included 42 peer-reviewed studies that used passive sensing from wearables or smartphones with ML to monitor clinically diagnosed mental disorders, such as depression and anxiety. Data were synthesized across technical dimensions (data collection, preprocessing, feature engineering, and ML models) and clinical associations, with behavioral features categorized into 8 domains.<br><br>RESULTS: The 42 included studies were predominantly cohort designs (23/42, 55%), with a median sample size of 60.5 (IQR 54-99). Most studies focused on depression (23/42, 55%) and anxiety (9/42, 21%) using primarily wrist-worn devices (32/42, 76%) collecting heart rate (28/42, 67%), movement index (25/42, 60%), and step count (17/42, 40%) as key biomarkers. Deep learning models (eg, convolutional neural networks and long short-term memory) showed high accuracy, while traditional ML (eg, random forest) remained prevalent due to better interpretability. We identified critical limitations, including small samples (32/42, 76% with N<100), short monitoring periods (19/42, 45% <7 days), scarce external validation (1/42, 2%), and limited reporting on data anonymization (6/42, 14%).<br><br>CONCLUSIONS: While passive sensing and ML demonstrate promising accuracy (eg, convolutional neural network-long short-term memory achieving 92.16% in anxiety detection), the evidence remains constrained by three key limitations: (1) methodological heterogeneity (32/42, 76% single-device studies; 19/42, 45% with <7-day monitoring), (2) high risk of bias from small samples (median 60.5, IQR 54-99 participants) and scarce external validation (1/42, 2%), and (3) ethical gaps (only 6/42, 14% addressing anonymization). These findings underscore the technology's potential to transform mental health care through objective, continuous monitoring-particularly for depression (heart rate and step count biomarkers) and anxiety (sleep and social interaction patterns). However, clinical translation requires standardized protocols, larger longitudinal studies (&#x2265;3 months), and ethical frameworks for data privacy. Future work should prioritize multimodal sensor fusion and explainable artificial intelligence to bridge the gap between technical performance and clinical deployability.}, }
@article {pmid40808315, year = {2025}, author = {Navratilova, HF and Whetton, AD and Geifman, N}, title = {Integrating Food Preference Profiling, Behavior Change Strategies, and Machine Learning for Cardiovascular Disease Prevention in a Personalized Nutrition Digital Health Intervention: Conceptual Pipeline Development and Proof-of-Principle Study.}, journal = {Journal of medical Internet research}, volume = {27}, number = {}, pages = {e75106}, pmid = {40808315}, issn = {1438-8871}, mesh = {Humans ; *Cardiovascular Diseases/prevention &amp; control ; *Machine Learning ; *Food Preferences ; Female ; Male ; *Precision Medicine ; Middle Aged ; United Kingdom ; Digital Health ; }, abstract = {BACKGROUND: Personalized dietary advice needs to consider the individual's health risks as well as specific food preferences, offering healthier options aligned with personal tastes.<br><br>OBJECTIVE: This study aimed to develop a digital health intervention (DHI) that provides personalized nutrition recommendations based on individual food preference profiles (FPP), using data from the UK Biobank.<br><br>METHODS: Data from 61,229 UK Biobank participants were used to develop a conceptual pipeline for a DHIs. The pipeline included three steps: (1) developing a simplified food preference profiling tool, (2) creating a cardiovascular disease (CVD) prediction model using the subsequent profiles, and (3) selecting intervention features. The CVD prediction model was created using 3 different predictor sets (Framingham set, diet set, and FPP set) across 4 machine learning models: logistic regression, linear discriminant analysis, random forest, and support vector machine. Intervention functions were designed using the Behavior Change Wheel, and behavior change techniques were selected for the DHI features.<br><br>RESULTS: The feature selection process identified 14 food items out of 140 that effectively classify FPPs. The food preference profile prediction set, which did not include blood measurements or detailed nutrient intake, demonstrated comparable accuracy (across the 4 models: 0.721-0.725) to the Framingham set (0.724-0.727) and diet set (0.722-0.725). Linear discriminant analysis was chosen as the best-performing model. Four key features of the DHI were identified: food source and portion information, recipes, a dietary recommendation system, and community exchange platforms. The FPP and CVD risk prediction model serve as inputs for the dietary recommendation system. Two levels of personalized nutrition advice were proposed: level 1-based on food portion intake and FPP; and level 2-based on nutrient intake, FPP, and CVD risk probability.<br><br>CONCLUSIONS: This study presents proof of principle for a conceptual pipeline for a DHI that empowers users to make informed dietary choices and reduce CVD risk by catering to person-specific needs and preferences. By making healthy eating more accessible and sustainable, the DHI has the potential to significantly impact public health outcomes.}, }
@article {pmid40808268, year = {2025}, author = {Xu, G and Guo, J and Yu, X and Zhao, N and Li, X and Yuan, T and Xu, Z and Zhao, T and Zhao, S and Li, X and Liu, X}, title = {Multi-Omics Analysis Reveals Adaptive Strategies of Meconopsis horridula to UV-B Radiation in the Qinghai-Tibet Plateau.}, journal = {Plant, cell &amp; environment}, volume = {48}, number = {11}, pages = {8249-8263}, doi = {10.1111/pce.70117}, pmid = {40808268}, issn = {1365-3040}, support = {//This study was supported by the Local Development Funds of the Science and Technology Department of Tibet (Grants XZ202001YD0028C and XZ202102YD0031C), and by the Graduate High-Level Talent Training Program of Tibet University (Grant 2025-GSP-B017)./ ; }, mesh = {*Ultraviolet Rays ; Flavonoids/biosynthesis ; Tibet ; *Adaptation, Physiological ; Transcriptome ; Gene Expression Regulation, Plant ; Altitude ; Arabidopsis/genetics ; Multiomics ; Acyltransferases ; Papaveraceae ; }, abstract = {Meconopsis horridula, an endemic medicinal and alpine horticultural species of the Qinghai-Tibet Plateau, exhibits remarkable adaptation to high-altitude UV-B radiation. Despite its ecological and medicinal significance, the mechanisms underlying its UV-B adaptation remain poorly understood. Here, we used a PacBio full-length transcriptome as a reference, integrating RNA-seq and metabolomic data from altitudinal populations, with field-based transcriptomic and microbiome profiling under shade-controlled UV-B gradients, to elucidate UV-B adaptive regulatory networks. KEGG enrichment and environmental correlation analyses highlighted flavonoid biosynthesis as a central pathway in UV-B adaptation at high altitudes. Controlled UV-B gradient experiments identified 10 conserved flavonoid biosynthesis genes, including chalcone synthase (CHS). Overexpression of CHS in Arabidopsis thaliana increased flavonoid content by approximately 1.2-fold. Co-expression analysis further revealed that CHS-associated regulatory factors mediate coordinated responses, including reduced light signalling, enhanced antioxidant capacity and suppression of defence genes and anthocyanin biosynthesis inhibitors. CHS, in coordination with immune regulation, modulates high-centrality microbes, contributing to differential network regulation and microbiome stability. Enriched key microbes may mitigate the growth-defence trade-off under UV-B stress through antimicrobial, growth-promoting and antioxidant activities. Collectively, our findings reveal a flavonoid-centred adaptation framework that deepens our understanding of UV-B resilience in alpine plants and offers potential resources for crop improvement.}, }
@article {pmid40807726, year = {2025}, author = {Ye, G and Yu, R}, title = {Spatiotemporal Mapping of Grazing Livestock Behaviours Using Machine Learning Algorithms.}, journal = {Sensors (Basel, Switzerland)}, volume = {25}, number = {15}, pages = {}, pmid = {40807726}, issn = {1424-8220}, support = {Project No. 72104065//National Natural Science Foundation of China/ ; Project No. NHXXRCXM202303//Hainan New Star Projects/ ; Project No. KC20230018//Natural Resources Comprehensive Survey Command Centre Science and Technology Innovation Fund/ ; Project No. 2022KJCX04//Sanya Science and Technology Special Fund/ ; }, mesh = {Animals ; *Machine Learning ; *Livestock/physiology ; China ; Grassland ; Spatio-Temporal Analysis ; Algorithms ; Geographic Information Systems ; *Behavior, Animal/physiology ; *Herbivory/physiology ; Ecosystem ; }, abstract = {Grassland ecosystems are fundamentally shaped by the complex behaviours of livestock. While most previous studies have monitored grassland health using vegetation indices, such as NDVI and LAI, fewer have investigated livestock behaviours as direct drivers of grassland degradation. In particular, the spatial clustering and temporal concentration patterns of livestock behaviours are critical yet underexplored factors that significantly influence grassland ecosystems. This study investigated the spatiotemporal patterns of livestock behaviours under different grazing management systems and grazing-intensity gradients (GIGs) in Wenchang, China, using high-resolution GPS tracking data and machine learning classification. the K-Nearest Neighbours (KNN) model combined with SMOTE-ENN resampling achieved the highest accuracy, with F1-scores of 0.960 and 0.956 for continuous and rotational grazing datasets. The results showed that the continuous grazing system failed to mitigate grazing pressure when grazing intensity was reduced, as the spatial clustering of livestock behaviours did not decrease accordingly, and the frequency of temporal peaks in grazing behaviour even showed an increasing trend. Conversely, the rotational grazing system responded more effectively, as reduced GIGs led to more evenly distributed temporal activity patterns and lower spatial clustering. These findings highlight the importance of incorporating livestock behavioural patterns into grassland monitoring and offer data-driven insights for sustainable grazing management.}, }
@article {pmid40805736, year = {2025}, author = {Lu, F and Yi, B and Ma, JX and Wang, SN and Feng, YJ and Qin, K and Tu, Q and Bu, ZJ}, title = {Drought and Shrub Encroachment Accelerate Peatland Carbon Loss Under Climate Warming.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {15}, pages = {}, pmid = {40805736}, issn = {2223-7747}, support = {U23A2003//The National Nature Science Foundation of China/ ; 42407354//The National Nature Science Foundation of China/ ; 42371050//The National Nature Science Foundation of China/ ; 20230203002SF and 20210402032GH//Jilin Provincial Science and Technology Development Project/ ; 2024QN1081//Fundamental Research Funds for the Central Universities/ ; }, abstract = {Peatlands store substantial amounts of carbon (C) in the form of peat, but are increasingly threatened by drought and shrub encroachment under climate warming. However, how peat decomposition and its temperature sensitivity (Q10) vary with depth and plant litter input under these stressors remains poorly understood. We incubated peat from two depths with different degrees of decomposition, either alone or incubated with Sphagnum divinum shoots or Betula ovalifolia leaves, under five temperature levels and two moisture conditions in growth chambers. We found that drought and Betula addition increased CO2 emissions in both peat layers, while Sphagnum affected only shallow peat. Deep peat alone or with Betula exhibited higher Q10 than pure shallow peat. Drought increased the Q10 of both depths' peat, but this effect disappeared with fresh litter addition. The CO2 production rate showed a positive but marginal correlation with microbial biomass carbon, and it displayed a rather similar responsive trend to warming as the microbial metabolism quotient. These results indicate that both deep and dry peat are more sensitive to warming, highlighting the importance of keeping deep peat buried and waterlogged to conserve existing carbon storage. Additionally, they further emphasize the necessity of Sphagnum moss recovery following vascular plant encroachment in restoring carbon sink function in peatlands.}, }
@article {pmid40803399, year = {2025}, author = {Jin, L and Lu, Y and Huang, J and Liu, J and Wei, X and Ma, G and Yu, H}, title = {Metabolism exploration of disinfection byproducts halonitromethanes (HNMs) by cytochrome P450 enzymes and toxicity evaluation.}, journal = {Environmental research}, volume = {285}, number = {Pt 4}, pages = {122575}, doi = {10.1016/j.envres.2025.122575}, pmid = {40803399}, issn = {1096-0953}, mesh = {*Cytochrome P-450 Enzyme System/metabolism ; *Disinfectants/toxicity/metabolism ; Animals ; Humans ; Rats ; *Nitroparaffins/toxicity/metabolism ; Disinfection ; Microsomes, Liver/metabolism ; }, abstract = {The nitrogen-contained disinfection by-products, halonitromethanes (HNMs), are known for their high cytotoxicity and genotoxicity. Although HNMs can be metabolized by cytochrome P450 enzymes (P450s), the specific mechanism has remained unclear. To shed light on this, density functional theory (DFT) calculations were performed to elucidate the potential oxidative P450-catalytic activation of the nine HNMs. Our findings reveal that active species of P450s (Cpd I) predominantly react with halogen-substituted nitromethanes via hydrogen abstraction and bromine atom abstraction, rather than chlorosylation. As a result of these reactions, oxidized HNMs are produced and can undergo further hydrolysis, leading to nitro-formaldehyde, nitro formyl halogen, halogen hydride, hypobromous acid, and nitroformic acid. To experimentally validate the computational predictions, in vitro experiments were conducted on five typical nitromethanes using human liver microsomes and the results reveal that DCNM, BCNM and DBCNM form nitroformyl chlorine (NO2CClO), while BCNM, DBNM and TBNM are transferred into nitroformyl bromide (NO2CBrO). Nitroformic acid is also identified as a metabolite in the TBNM metabolism reaction. Toxicity assessment reveals that metabolic transformation leads to an overall reduction in the ecological toxicity. However, metabolites showed similar toxicity to Fathead minnow and even higher acute toxicity to rat, as well as larger probability of hERG inhibition effects than HNMs, underscoring the need for caution in health risk assessment. By integrating in silico and in vitro approaches, this work has provided a comprehensive understanding of the metabolism of HNMs and offered potential toxicity data basis of these compounds.}, }
@article {pmid40801436, year = {2025}, author = {Karaman, MZ and Yetiman, AE and Zhan, J and Fidan, O}, title = {Biochemical Characterization and Genome Analysis of Pseudomonas loganensis sp. nov., a Novel Endophytic Bacterium.}, journal = {MicrobiologyOpen}, volume = {14}, number = {4}, pages = {e70051}, pmid = {40801436}, issn = {2045-8827}, support = {//This study was financially supported by The Scientific and Technological Research Council of Turkiye (TUBITAK) (Grant No: 221Z280)./ ; }, mesh = {*Pseudomonas/genetics/classification/isolation &amp; purification/drug effects/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Genome, Bacterial ; Anti-Bacterial Agents/pharmacology ; DNA, Bacterial/genetics/chemistry ; *Endophytes/genetics/classification/isolation &amp; purification ; Multigene Family ; Microbial Sensitivity Tests ; Carotenoids/metabolism ; Sequence Analysis, DNA ; Computational Biology ; }, abstract = {Pseudomonas species are highly adaptable, thriving in diverse environments and exhibiting remarkable genetic and metabolic diversity. While some strains are pathogenic, others have significant ecological and industrial applications. Bioinformatics and biochemical analyses, including antibiotic sensitivity testing, revealed that Pseudomonas loganensis sp. nov. can tolerate NaCl concentrations up to 5% and pH ranges between 5 and 9. Antibiogram results corroborated genome data, demonstrating resistance to vancomycin, ampicillin, methicillin, oxacillin, and penicillin G. Phylogenetic analysis based on 16S rRNA, rpoB, rpoD, and gyrB genes, combined with average nucleotide identity (ANI) comparisons, confirmed P. loganensis sp. nov. as a novel species within the Pseudomonas genus. Genome analysis further revealed the presence of turnerbactin and carotenoid gene clusters. Turnerbactin, known to contribute to nitrogen fixation in plants, highlights the strain's potential as a biofertilizer. Additionally, the carotenoid gene cluster suggests potential applications in industrial carotenoid production. The discovery of a trehalose synthase (treS) gene indicates the capability for one-step conversion of maltose into trehalose, underscoring its potential utility in trehalose production.}, }
@article {pmid40798830, year = {2025}, author = {Abraham, AJ and Clauss, M and Bailey, MA and Duvall, ES}, title = {Body Mass Scaling of Sodium Regulation in Mammals.}, journal = {Acta physiologica (Oxford, England)}, volume = {241}, number = {9}, pages = {e70090}, doi = {10.1111/apha.70090}, pmid = {40798830}, issn = {1748-1716}, }
@article {pmid40797121, year = {2025}, author = {Kaplan, DM and Alvarez, SJA and Palitsky, R and Choi, H and Clifford, GD and Crozier, M and Dunlop, BW and Grant, GH and Greenleaf, MN and Johnson, LM and Maples-Keller, J and Levin-Aspenson, HF and Mascaro, JS and McDowall, A and Pozzo, NS and Raison, CL and Zarrabi, AJ and Rothbaum, BO and Lam, WA}, title = {Fabla: A voice-based ecological assessment method for securely collecting spoken responses to researcher questions.}, journal = {Behavior research methods}, volume = {57}, number = {9}, pages = {257}, pmid = {40797121}, issn = {1554-3528}, support = {UL1 TR002378/TR/NCATS NIH HHS/United States ; UL1TR002378/NH/NIH HHS/United States ; }, mesh = {Humans ; Female ; Male ; Adult ; *Voice ; Young Adult ; *Mobile Applications ; *Speech ; Middle Aged ; Adolescent ; }, abstract = {This article reports on the validation of Fabla, a researcher-developed and university-hosted smartphone app that facilitates naturalistic and secure collection of participants' spoken responses to researcher questions. Fabla was developed to meet the need for tools that (a) collect longitudinal qualitative data and (b) capture speech biomarkers from participants' natural environments. This study put Fabla to its first empirical test using a repeated-measures experimental design in which participants (n = 87) completed a 1-week voice daily diary via the Fabla app, and an identical 1-week text-entry daily diary administered via Qualtrics, with diary method order counterbalanced and randomized. A preregistered analysis plan investigated (1) adherence, usability, and acceptability of Fabla, (2) concurrent validity of voice diaries (vs. text-entry diaries) by comparing linguistic features obtained via each diary method, and (3) differences in the strength of the association between linguistic features and their known psychological correlates when assessed by voice versus text-entry diary. Voice diaries yielded more than double the mean daily language volume (word count) compared to text-entry diaries and received high usability and acceptability ratings. Linguistic markers consistently associated with depression in prior research were significantly associated with depression symptoms when assessed via voice but not text-entry diaries, and the difference in correlation magnitude was significant. Word-count-adjusted linguistic patterns were highly correlated between diary methods, with statistically significant mean differences observed for some linguistic dimensions in the presence of these associations. Fabla is a promising tool for collecting high-quality speech data from participants' naturalistic environments, overcoming multiple limitations of text-entry responding.}, }
@article {pmid40796641, year = {2025}, author = {Sanad, H and Moussadek, R and Mouhir, L and Lhaj, MO and Dakak, H and Manhou, K and Zouahri, A}, title = {Monte carlo simulation for evaluating spatial dynamics of toxic metals and potential health hazards in sebou basin surface water.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {29471}, pmid = {40796641}, issn = {2045-2322}, mesh = {Monte Carlo Method ; Humans ; *Metals, Heavy/analysis/toxicity ; *Water Pollutants, Chemical/analysis/toxicity ; Risk Assessment ; *Environmental Monitoring/methods ; Morocco ; Geographic Information Systems ; Principal Component Analysis ; }, abstract = {Surface water is vital for environmental sustainability and agricultural productivity but is highly vulnerable to heavy metals (HMs) pollution from human activities. The focus of this research is to provide an analysis of ecological and human exposure to HMs in the Sebou Basin, an agriculturally significant region within Morocco's Gharb Plain. Using a multi-index integration approach, encompassing HM pollution indices, Human Health Risk Assessment (HHRA), Monte Carlo Simulation (MCS), multivariate statistical analysis (MSA), and Geographic Information Systems (GIS), twenty samples of surface water were taken and subjected to analysis. The results demonstrated notable spatial variability, with the northwestern, southwestern, and western parts of the Sebou Basin showing higher contamination levels. Cu exhibited the highest hazard quotient for ingestion, while Cr exceeded the hazard index (HI) threshold in both age categories. Statistical analysis uncovered strong associations, particularly between As and Cr, while principal component analysis (PCA) detected two key factors explaining 74.44% of the overall variability. Pollution indices classified all samples as highly contaminated (HPI > 30), with 65% categorized as "seriously affected" (MI > 6). The HHRA results indicated a heightened non-carcinogenic risk for children and carcinogenic risks exceeding acceptable thresholds (TCR > 10[-4]), with Ni presenting the highest risk (TCR = 2.32 × 10[-3] for children). MCS results revealed that Cu and Cr pose potential risks, with Cu exceeding the safety threshold for ingestion in both adults and children. These results emphasize the urgent necessity for tailored strategies to reduce contamination and foster sustainable agricultural and environmental management practices.}, }
@article {pmid40796553, year = {2025}, author = {Arehart, CH and Lin, M and Gibson, RA and ,  and Raghavan, S and Gignoux, CR and Stanislawski, MA and Grotzinger, AD and Evans, LM}, title = {Modeling the genomic architecture of adiposity and anthropometrics across the lifespan.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {7494}, pmid = {40796553}, issn = {2041-1723}, support = {R01 AG046938/AG/NIA NIH HHS/United States ; T32 MH016880/MH/NIMH NIH HHS/United States ; RF1 AG073593/AG/NIA NIH HHS/United States ; K01 HL157658/HL/NHLBI NIH HHS/United States ; R01 MH120219/MH/NIMH NIH HHS/United States ; }, mesh = {Humans ; *Adiposity/genetics ; Male ; Female ; Genome-Wide Association Study ; *Obesity/genetics ; Multifactorial Inheritance ; Adult ; Middle Aged ; Anthropometry ; *Longevity/genetics ; Genomics ; Polymorphism, Single Nucleotide ; Aged ; Body Size/genetics ; }, abstract = {Obesity-related conditions are among the leading causes of preventable death and are increasing in prevalence worldwide. Body size and composition are complex traits that are challenging to characterize due to environmental and genetic influences, longitudinal variation, heterogeneity between sexes, and differing health risks based on adipose distribution. Here, we construct a 4-factor genomic structural equation model using 18 measures, unveiling shared and distinct genetic architectures underlying birth size, abdominal size, adipose distribution, and adiposity. Multivariate genome-wide associations reveal the adiposity factor is enriched specifically in neural tissues and pathways, while adipose distribution is enriched more broadly across physiological systems. In addition, polygenic scores for the adiposity factor predict many adverse health outcomes, while those for body size and composition predict a more limited subset. Finally, we characterize the factors' genetic correlations with obesity-related traits and examine the druggable genome by constructing a bipartite drug-gene network to identify potential therapeutic targets.}, }
@article {pmid40794746, year = {2025}, author = {Alkhatib, SA and Arya, S and Islayem, D and Nyadzayo, RM and Mohamed, S and Yousef, AF and Hernandez, HH and Pappa, AM}, title = {Revealing bioremediation potential of novel indigenous bacteria from oil-contaminated sites in the UAE: A combined bioinformatics and experimental validation.}, journal = {PloS one}, volume = {20}, number = {8}, pages = {e0329515}, pmid = {40794746}, issn = {1932-6203}, mesh = {*Biodegradation, Environmental ; *Computational Biology/methods ; United Arab Emirates ; Polycyclic Aromatic Hydrocarbons/metabolism ; *Bacteria/metabolism/genetics/isolation &amp; purification ; Phenols/metabolism ; *Soil Pollutants/metabolism ; }, abstract = {Microbial biodegradation of recalcitrant aromatic hydrocarbon pollutants represents an environmentally sustainable strategy for remediating contaminated sites. However, elucidating the metabolic capabilities and genetic determinants of biodegrading strains is crucial for optimizing bioremediation strategies. In this study, we comprehensively characterize the aromatic catabolic potential of two indigenous bacterial isolates, A. xylosoxidans C2 (A. x. C2) and A. xylosoxidans KW38 (A. x. KW38), obtained from hydrocarbon-impacted environments in the United Arab Emirates (UAE). Experimental validation through aromatic hydrocarbons supplemented growth studies confirmed the capability of the isolated bacteria to mineralize bisphenol A, 4-hydroxybenzoic acid, 1-naphthalenemethanol, and the high molecular weight polycyclic aromatic hydrocarbon (PAH), pyrene, in the presence of glucose. Their degradation efficiencies were comparable to or greater than those of Pseudomonas paraeruginosa, a well-characterized model organism for aromatic compound degradation. Integrated bioinformatic analyses uncovered fundamental aromatic catabolic pathways conserved across Achromobacter species, along with strain-specific genes that potentially confer specialized degradative capacities, highlighting the genomic basis of the observed metabolic versatility. Further, protein modeling based on the curated sequences revealed unique features of individual catabolic enzymes and their interaction networks. Notably, a dehydrogenase enzyme involved in aromatic ring cleavage was identified exclusively in these UAE isolates. These findings establish A. x. C2 and A. x. KW38 as promising bioremediators of diverse aromatic pollutants. Overall, the study exemplifies a powerful and comprehensive methodological framework that bridges bioinformatic analysis and experimental research to further optimize the effectiveness of experimental design. We achieved a substantial reduction in the number of unknown genetic and metabolic determinants of aromatic hydrocarbon degradation in the strains, reducing uncertainty by 99.3%, thereby enhancing the overall process and outcomes for systematic biodiscovery of pollutant-degrading environmental microbes to address ecological challenges.}, }
@article {pmid40789383, year = {2025}, author = {Rout, AK and Rout, SS and Panda, A and Tripathy, PS and Kumar, N and Parida, SN and Dey, S and Dash, SS and Behera, BK and Pandey, PK}, title = {Potential applications and future prospects of metagenomics in aquatic ecosystems.}, journal = {Gene}, volume = {967}, number = {}, pages = {149720}, doi = {10.1016/j.gene.2025.149720}, pmid = {40789383}, issn = {1879-0038}, mesh = {*Metagenomics/methods ; *Ecosystem ; Microbiota/genetics ; *Water Microbiology ; Environmental Monitoring/methods ; Computational Biology/methods ; Humans ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; }, abstract = {Metagenomics plays a vital role in advancing our understanding of microbial communities and their functional contributions in various ecosystems. By directly sequencing DNA from environmental samples such as soil, water, air, and the human body. Metagenomics enables the identification of previously uncultivable or unknown microorganisms, offering key insights into their ecological functions. Beyond taxonomic classification, metagenomic analyses reveal functional genes and metabolic pathways, facilitating the discovery of enzymes, bioactive compounds, and other molecules with applications in agriculture, biotechnology, and medicine. This review discusses the broad applications of metagenomics in environmental monitoring, encompassing sample collection, high-throughput sequencing, data analysis and interpretation. We review different sequencing platforms, library preparation methods, and advanced bioinformatics tools used for quality control, sequence assembly, and both taxonomic and functional annotation. Special focus is given to the role of metagenomics in evaluating microbial responses to environmental stress, contaminant degradation, disease emergence, and climate change. The use of microbial bioindicators for aquatic ecosystem monitoring and toxicological assessments is also examined. A comprehensive evaluation of current bioinformatics pipelines is provided for their effectiveness in processing large-scale metagenomic datasets. As global environmental pressures intensify, integrative meta-omics approaches, including whole-genome metagenomics, will become crucial for understanding the complexity, functions, and dynamics of microbiomes in both natural and affected ecosystems.}, }
@article {pmid40788461, year = {2025}, author = {Torres, MC and Breyer, GM and da Silva, MERJ and de Itapema Cardoso, MR and Siqueira, FM}, title = {Metagenomic approaches for the quantification of antibiotic resistance genes in swine wastewater treatment system: a systematic review.}, journal = {Molecular biology reports}, volume = {52}, number = {1}, pages = {816}, pmid = {40788461}, issn = {1573-4978}, support = {408693/2022-3//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico,Brazil/ ; }, mesh = {Swine ; *Wastewater/microbiology ; Animals ; *Metagenomics/methods ; *Drug Resistance, Microbial/genetics ; Metagenome/genetics ; Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; Water Purification/methods ; Computational Biology/methods ; Anti-Bacterial Agents/pharmacology ; }, abstract = {This systematic review aims to identify the metagenomic methodological approaches employed for the detection of antimicrobial resistance genes (ARGs) in swine wastewater treatment systems. The search terms used were metagenome AND bacteria AND ("antimicrobial resistance gene" OR resistome OR ARG) AND wastewater AND (swine OR pig), and the search was conducted across the following electronic databases: PubMed, Scopus, ScienceDirect, Web of Science, Embase, and Cochrane Library. The search was limited to studies published between 2020 and 2024. Of the 220 studies retrieved, eight met the eligibility criteria for full-text analysis. The number of publications in this research area has increased in recent years, with China contributing the highest number of studies. ARGs are typically identified using bioinformatics pipelines that include steps such as quality trimming, assembly, metagenome-assembled genome (MAG) reconstruction, open reading frame (ORF) prediction, and ARG annotation. However, comparing ARGs quantification across studies remains challenging due to methodological differences and variability in quantification approaches. Therefore, this systematic review highlights the need for methodological standardization to facilitate comparison and enhance our understanding of antimicrobial resistance in swine wastewater treatment systems through metagenomic approaches.}, }
@article {pmid40786600, year = {2025}, author = {Boyes, D and Gardiner, A and ,  and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the V-Pug moth, Chloroclystis v-ata (Haworth, 1809).}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {197}, pmid = {40786600}, issn = {2398-502X}, abstract = {We present a genome assembly from a female specimen of Chloroclystis v-ata (V-Pug; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 275.35 megabases. Most of the assembly (99.95%) is scaffolded into 17 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled, with a length of 15.49 kilobases.}, }
@article {pmid40782603, year = {2025}, author = {Benvenuti, MC and Merkle, EC and McCarthy, DM}, title = {Physical context of alcohol use and craving: An EMA exploratory study.}, journal = {Addictive behaviors}, volume = {170}, number = {}, pages = {108450}, pmid = {40782603}, issn = {1873-6327}, support = {R01 AA019546/AA/NIAAA NIH HHS/United States ; T32 AA013526/AA/NIAAA NIH HHS/United States ; }, mesh = {Humans ; *Craving ; Male ; Female ; *Ecological Momentary Assessment ; *Alcohol Drinking/psychology/epidemiology ; Adult ; Young Adult ; Adolescent ; Geographic Information Systems ; Self Report ; }, abstract = {While environmental and physical contextual factors play an important role in alcohol use and motivation for use, assessment of the physical context of use, even when using ecological momentary assessments (EMA), has been limited. While EMA research has examined drinking locations at the event level using categories of drinking locations, there is considerable within-category variability in the attributes of drinking locations. Using data from a 6-week EMA study (N = 207), this exploratory study sought to determine drinking locations through the combination of EMA self-report and GPS coordinates. Through multilevel modeling, we also tested whether specific locations were associated with variability in drinking (self-reported drinking and breathalyzer readings) and craving for alcohol. Results indicated significant differences in both alcohol consumption and craving between home, friend's houses, and on-premises drinking locations. Our results offer proof of concept for using mobile and geospatial data to passively identify on-premise drinking locations. This approach has the potential to aid in the development of targeted intervention strategies that identify and mitigate risks associated with specific drinking environments.}, }
@article {pmid40781446, year = {2025}, author = {Rauniyar, S and Samanta, D and Thakur, P and Saxena, P and Singh, RN and Bazin, A and Bomgni, A and Fotseu, E and Etienne, GZ and Gadhamshetty, V and Peyton, BM and Fields, M and Subramaniam, M and Sani, RK}, title = {Mapping the pangenome of sulfate reducing bacteria: core genes, plasticity, and novel functions in Desulfovibrio spp.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {41}, number = {8}, pages = {305}, pmid = {40781446}, issn = {1573-0972}, support = {5P20GM103443-20/NH/NIH HHS/United States ; 1736255//National Science Foundation/ ; }, mesh = {*Desulfovibrio/genetics/metabolism/classification ; *Genome, Bacterial ; *Sulfates/metabolism ; Phylogeny ; Multigene Family ; Gene Regulatory Networks ; Genes, Bacterial ; Gene Ontology ; }, abstract = {The pangenome of sulfate reducing bacteria represents a genetic reservoir that deciphers the intricate interplay of conserved and variable elements driving their ecological dominance, evolutionary adaptability, and industrial relevance. This study introduces the most comprehensive pangenome analysis of the genus Desulfovibrio till date, incorporating 63 complete and high-quality genomes using the Partitioned Pangenome Graph of Linked Neighbors (PPanGGOLiN) pipeline. The structure and dynamics of core gene families were investigated through gene ontology, KEGG pathway mapping, and gene network analyses, shedding light on the functional organization of the Desulfovibrio genomes. The analysis categorized 799, 4053, and 43,581 gene families into persistent, shell, and cloud groups, respectively. A core set of 326 gene families, conserved across Desulfovibrio genomes, highlights their essential role in community functionality. Genome plasticity analysis identified 4,576 regions of genome plasticity, with 1,322 hotspots enriched in horizontally acquired genes (89% in the cloud partition). Key gene families in these regions included glpE, fdhD, petC, and cooF, linked to sulfur metabolism. Out of 29 hypothetical genes, one was linked to actin nucleation, another contained a TRASH domain, while the other regulates filopodium assembly. Other predicted functions included lnrL, folE, RNA binding, and pyrG/pyrH involvement in CTP biosynthesis. Additionally, genomic islands revealed evolutionary events, such as cheY acquisition in Oleidesulfovibrio alaskensis G20. This study provides a genus-wide view of Desulfovibrio, emphasizing genome plasticity, hypothetical gene functions, and adaptation mechanisms.}, }
@article {pmid40781089, year = {2025}, author = {McDaniel, JH and Patel, V and Olson, ND and He, HJ and He, Z and Cole, KD and Gooden, AA and Schmitt, A and Sikkink, K and Sedlazeck, FJ and Doddapaneni, H and Jhangiani, SN and Muzny, DM and Gingras, MC and Mehta, H and Behera, S and Paulin, LF and Hastie, AR and Yu, HC and Weigman, V and Rojas, A and Kennedy, K and Remington, J and Salas-González, I and Sudkamp, M and Wiseman, K and Lajoie, BR and Levy, S and Jain, M and Akeson, S and Narzisi, G and Steinsnyder, Z and Reeves, C and Shelton, J and Kingan, SB and Lambert, C and Baybayan, P and Wenger, AM and McLaughlin, IJ and Adamson, A and Kingsley, C and Wescott, M and Kim, Y and Paten, B and Park, J and Violich, I and Miga, KH and Gardner, J and McNulty, B and Rosen, GL and McCoy, R and Brundu, F and Sayyari, E and Scheffler, K and Truong, S and Catreux, S and Hannah, LC and Lipson, D and Benjamin, H and Iremadze, N and Soifer, I and Krieger, G and Eacker, S and Wood, M and Cross, E and Husar, G and Gross, S and Vernich, M and Kolmogorov, M and Ahmad, T and Keskus, AG and Bryant, A and Thibaud-Nissen, F and Trow, J and Proszynski, J and Hirschberg, JW and Ryon, K and Mason, CE and Bhakta, MS and Sanborn, JZ and Munding, EM and Wagner, J and Xiao, C and Liss, AS and Zook, JM}, title = {Correction: Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1385}, doi = {10.1038/s41597-025-05752-9}, pmid = {40781089}, issn = {2052-4463}, }
@article {pmid40779849, year = {2025}, author = {Zhu, J and Ding, X and Xu, Q and Fan, Y and Zhu, P and Li, X and Zhang, X and Zhang, Q and Du, X and Zhou, W and Jiao, J and Lu, B and Lu, C}, title = {Insights into the disinfection byproduct bromochloroacetamide-induced cardiotoxicity of zebrafish embryo-larvae: A multiomics approach and comparison of biomarker responsiveness.}, journal = {Ecotoxicology and environmental safety}, volume = {303}, number = {}, pages = {118805}, doi = {10.1016/j.ecoenv.2025.118805}, pmid = {40779849}, issn = {1090-2414}, mesh = {Animals ; *Zebrafish/embryology ; Biomarkers/metabolism ; *Water Pollutants, Chemical/toxicity ; *Cardiotoxicity/etiology ; *Acetamides/toxicity ; Embryo, Nonmammalian/drug effects ; Larva/drug effects ; *Disinfectants/toxicity ; Heart/drug effects ; Metabolomics ; Disinfection ; Multiomics ; }, abstract = {Bromochloroacetamide (BCAcAm), an inevitable byproduct of the water treatment disinfection process, is widely detected in drinking water. Previous toxicological and in silico results suggested that developmental effects are associated with analogous chemical exposure; however, the key molecular events and underlying mechanisms remain unclear, especially in the early stages of aquatic organisms. In the present study, a zebrafish larval model was used to comprehensively assess the developmental toxicity of BCAcAm via transcriptional, metabolic, biochemical and morphological tests. Integration analyses of RNA sequencing and untargeted metabolomic data revealed crucial biological processes related to drug metabolism, cardiac muscle contraction and oxidative phosphorylation, which started from the initial stage, and ferroptosis progressed to the advanced stage in validated cardiac defects. Biochemical assays further verified ATP depletion, ROS and MDA accumulation, and hyperactivation of detoxification (increased GST activity) and the antioxidative system (increased GSH and GSSG levels). Transcriptionally, BCAcAm led to gpx4 downregulation, iron homeostasis perturbation (upregulated tfr and tf and downregulated fth) and lipid peroxidation (elevated alox12 and lpcat3), suggesting the involvement of ferroptosis. Moreover, the application of Fer-1 (a ferroptosis inhibitor) reversed BCAcAm-induced mitochondrial dysfunction and subsequent cardiotoxicity. In addition, the BMD and IBRv2 indices were derived from molecules across various biological levels. The general ranking of the different biomarkers in terms of better responsiveness and sensitivity performance is as follows: transcriptomics > metabolomics > biochemical assays. In the present study, an approach to detecting chemical-induced adverse outcomes and deciphering the underlying mechanisms through high-throughput data analysis is applied. This study provides valuable insights into the responsiveness and sensitivity of biomarkers, which may be instrumental for evaluating the ecological and health risks associated with newly emerged contaminants.}, }
@article {pmid40778113, year = {2025}, author = {Sprint, G and Schmitter-Edgecombe, M and Weaver, R and Wiese, L and Cook, DJ}, title = {CogProg: Utilizing Large Language Models to Forecast In-the-moment Health Assessment.}, journal = {ACM transactions on computing for healthcare}, volume = {6}, number = {2}, pages = {}, pmid = {40778113}, issn = {2637-8051}, support = {R01 AG066748/AG/NIA NIH HHS/United States ; R25 AG046114/AG/NIA NIH HHS/United States ; R01 AG065218/AG/NIA NIH HHS/United States ; R35 AG071451/AG/NIA NIH HHS/United States ; R01 EB009675/EB/NIBIB NIH HHS/United States ; }, abstract = {Forecasting future health status is beneficial for understanding health patterns and providing anticipatory support for cognitive and physical health difficulties. In recent years, generative large language models (LLMs) have shown promise as forecasters. Though not traditionally considered strong candidates for numeric tasks, LLMs demonstrate emerging abilities to address various forecasting problems. They also provide the ability to incorporate unstructured information and explain their reasoning process. In this paper, we explore whether LLMs can effectively forecast future self-reported health state. To do this, we utilized in-the-moment assessments of mental sharpness, fatigue, and stress from multiple studies, utilizing daily responses (N=106 participants) and responses that are accompanied by text descriptions of activities (N=32 participants). With these data, we constructed prompt/response pairs to predict a participant's next answer. We fine-tuned several LLMs and applied chain-of-thought prompting evaluating forecasting accuracy and prediction explainability. Notably, we found that LLMs achieved the lowest mean absolute error (MAE) overall (0.851), while gradient boosting achieved the lowest overall root mean squared error (RMSE) (1.356). When additional text context was provided, LLM forecasts achieved the lowest MAE for predicting mental sharpness (0.862), fatigue (1.000), and stress (0.414). These multimodal LLMs further outperformed the numeric baselines in terms of RMSE when predicting stress (0.947), although numeric algorithms achieved the best RMSE results for mental sharpness (1.246) and fatigue (1.587). This study offers valuable insights for future applications of LLMs in health-based forecasting. The findings suggest that LLMs, when supplemented with additional text information, can be effective tools for improving health forecasting accuracy.}, }
@article {pmid40777262, year = {2025}, author = {Weiss, AS and Santos-Santiago, JA and Keenan, O and Smith, AB and Knight, M and Zackular, JP and Tamayo, R}, title = {Enterococcus faecalis modulates phase variation in Clostridioides difficile.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40777262}, issn = {2692-8205}, support = {R01 AI143638/AI/NIAID NIH HHS/United States ; R01 AI188648/AI/NIAID NIH HHS/United States ; }, abstract = {To adapt and persist in the gastrointestinal tract, many enteric pathogens, including Clostridioides difficile, employ strategies such as phase variation to generate phenotypically heterogeneous populations. Notably, the role of the gut microbiota and polymicrobial interactions in shaping population heterogeneity of invading pathogens has not been explored. Here, we show that Enterococcus faecalis, an opportunistic pathogen that thrives in the inflamed gut during C. difficile infection, can impact the phase variable CmrRST signal transduction system in C. difficile. The CmrRST system controls multiple phenotypes including colony morphology, cell elongation, and cell chaining in C. difficile. Here we describe how interactions between E. faecalis and C. difficile on solid media lead to a marked shift in C. difficile phenotypes associated with phase variation of CmrRST. Specifically, E. faecalis drives a switch of the C. difficile population to the cmr-ON state leading to chaining and a rough colony morphology. This phenomenon preferentially occurs with E. faecalis among the enterococci, as other enterococcal species do not show a similar effect, suggesting that the composition of the polymicrobial environment in the gut is likely critical to shaping C. difficile population heterogeneity. Our findings shed light on the complex role that microbial ecology and polymicrobial interactions can have in the phenotypic heterogeneity of invading pathogens.}, }
@article {pmid40776104, year = {2025}, author = {Bauberg, H and Tachnai, N and Hanan, G and Nehama, D and Tamburis, O and Darmoni, S and Grosjean, J and Benis, A}, title = {Automated Elicitation of Human and Ecological Health Indicators: An LLM-Based Practical Implementation for One Digital Health.}, journal = {Studies in health technology and informatics}, volume = {329}, number = {}, pages = {1488-1492}, doi = {10.3233/SHTI251086}, pmid = {40776104}, issn = {1879-8365}, mesh = {Humans ; *One Health ; *Health Status Indicators ; *Environmental Health/methods ; Digital Health ; }, abstract = {This paper presents a new method for automating the identification of human and ecological health indicators using the One Digital Health framework, which combines One Health and Digital Health principles. By applying mainly Large Language Models, we conduct a systematic literature review on urban freshwater environments. This automation streamlines the process of finding and analyzing relevant research, allowing us to extract vital health indicators related to urban aquatic ecosystems and human wellness. The findings support the OneAquaHealth project's goals, enhancing environmental monitoring and linking human, animal, and environmental health in a digital context.}, }
@article {pmid40774918, year = {2025}, author = {Hung, CC and Hsieh, HH and Chou, WC and Liu, EC and Chow, CH and Chang, Y and Lee, TM and Santsch, PH and Ranatunga, RRMKP and Bacosa, HP and Shih, YY}, title = {Corrigendum to "Assessing CO2 sources and sinks in and around Taiwan: Implication for achieving regional carbon neutrality by 2050" [Mar. Pollut. Bull. 206 (2024) 116664].}, journal = {Marine pollution bulletin}, volume = {220}, number = {}, pages = {118543}, doi = {10.1016/j.marpolbul.2025.118543}, pmid = {40774918}, issn = {1879-3363}, }
@article {pmid40774560, year = {2025}, author = {Guo, J and Lei, W and Liang, X and Wang, H and Qi, W and Huang, S and Chen, X and He, S}, title = {Three-dimensional distribution and key drivers of neonicotinoid residues in hilly agricultural areas.}, journal = {Environmental research}, volume = {285}, number = {Pt 3}, pages = {122524}, doi = {10.1016/j.envres.2025.122524}, pmid = {40774560}, issn = {1096-0953}, mesh = {*Neonicotinoids/analysis ; *Soil Pollutants/analysis ; *Insecticides/analysis ; *Environmental Monitoring ; Agriculture ; *Pesticide Residues/analysis ; Soil/chemistry ; China ; Nitro Compounds/analysis ; Guanidines/analysis ; Thiazoles ; }, abstract = {Neonicotinoids (NNIs) raise global concern due to their substantial soil residues and potential health risks to animal and human health. High water solubility and low soil adsorption enhanced vertical and horizontal migration of NNIs. However, understanding of NNIs' three-dimensional distribution in soils and influencing factors remains limited, limiting accurate risk assessment and remediation strategies for agriculture ecosystems. This study selected typical mountainous farmland soil to investigate the three-dimensional distribution of NNIs contents and composition. The findings indicated that the average detection rate of imidacloprid (IMI) in the 0-20 cm layer was 33 % higher than that in the 30-40 cm layer, whereas clothianidin (CLO) detection rates remained consistent across 0-40 cm layer. The contents of eight NNIs (∑8NNIs) in the study area ranged from 0.09 to 37.08 ng/g, with the 6.58 ± 8.65 ng/g in the 0-10 cm and 2.60 ± 7.78 ng/g in the 30-40 cm layer. The contents of ∑8NNIs, IMI, and CLO decreased by 60 %, 62 %, and 75 %, respectively, with increasing depth. The proportion of IMI and CLO to ∑8NNIs decreased and increased by 35 % and 12 %, respectively, in the 0-40 cm soil, leading to IMI predominance in the topsoil (60 %) and CLO in the deeper soil (29 %). Correlation analysis revealed that soil particle size, slope, and elevation were significantly associated with both the ∑8NNIs and the proportions of IMI and CLO. These results highlighted the substantial influence of topography and soil structure on the vertical distribution of NNIs. Additionally, the ∑8NNIs content in stem mustard soil was higher than in sweet potato, rice, corn, and forest. Overall, the study found very low health risks to humans (hazard index, HI < 1) and no overall potential ecological risk in the study area, though localized sublethal risks to non-target organisms were identified. Furthermore, the spatial correlation between IMI and CLO health risk regions identified overlapping high-risk areas.}, }
@article {pmid40774411, year = {2025}, author = {Zhang, L and Liu, Y and Chen, K and Yue, Q and Wang, C and Xie, L and Molnár, I and Xu, Y}, title = {Genome mining of tailoring enzymes from biosynthetic gene clusters for synthetic biology: A case study with fungal methyltransferases.}, journal = {Metabolic engineering}, volume = {92}, number = {}, pages = {125-135}, doi = {10.1016/j.ymben.2025.08.001}, pmid = {40774411}, issn = {1096-7184}, mesh = {*Methyltransferases/genetics/metabolism ; *Multigene Family ; *Genome, Fungal ; *Fungal Proteins/genetics/metabolism ; *Synthetic Biology/methods ; *Fungi/genetics/enzymology ; *Data Mining/methods ; Biosynthetic Pathways/genetics ; Biological Products/metabolism ; }, abstract = {Harnessing the potential of tailoring enzymes within fungal natural product (NP) biosynthetic gene clusters (BGCs) can significantly enhance NP diversity and production efficiency via artificially constructed microbial cell factories. To achieve this, an efficient genome mining method is crucial, especially since the functions of many putative enzymes in databases are unknown. As a test case, we aimed to identify methyltransferases (MTs) that modify a polyketide substrate without a known cognate MT. 16,748 putative MTs were annotated in 101,321 fungal BGCs and grouped into orthologous families. Three methods were explored to prioritize suitable enzymes. Among these, the machine learning method proved superior, with 11 out of 15 tested MTs successfully methylating the test substrate. This demonstrates the effectiveness of machine learning to mine tailoring enzymes that modify selected compounds, aiding synthetic biology in optimizing NP biosynthesis and facilitating the production of "unnatural products" for pharmaceutical or other bioindustrial applications.}, }
@article {pmid40774342, year = {2025}, author = {Cao, W and Cao, X and Sutherland, AD}, title = {Planning for the Unexpected and Unintended Effects of mHealth Interventions: Systematic Review.}, journal = {Journal of medical Internet research}, volume = {27}, number = {}, pages = {e68909}, pmid = {40774342}, issn = {1438-8871}, mesh = {*Telemedicine ; Humans ; }, abstract = {BACKGROUND: Mobile health (mHealth) interventions can produce both intended and unintended effects. Examining these unintended effects helps create a more complete and objective understanding of mHealth interventions and can reduce potential harm to participants. Existing studies on the unintended effects, which were published several years ago, tend to have either a general focus on health IT or a specific focus on health care providers, thereby excluding other key stakeholders (eg, patients and community health workers). Additionally, these studies did not systematically outline the causes of the unintended effects or strategies for their prevention.<br><br>OBJECTIVE: To address this gap, this systematic review, guided by the ecological framework, aims to systematically identify the unintended effects of mHealth interventions, create a typology for them, investigate the reasons for their occurrence, describe how they were detected, and propose ways to prevent or lessen them.<br><br>METHODS: Following the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines, a systematic review was performed to examine the unintended effects of health interventions that use mobile technology.<br><br>RESULTS: A total of 15 papers were included in the review. An ecological typology of mHealth intervention unintended effects (mHUE) was developed, which includes 26 distinct effects (eg, silencing and boomerang). The majority of these unintended effects (n=20) occur at the individual level and span physical or behavioral (n=7), psychological (n=8), cognitive (n=4), and financial (n=1) domains. Three effects occur at the interpersonal level and another 3 at the community or institutional level. Most of the identified effects (n=22) were negative. Potential causes for these effects include the improper use of mHealth technology, poorly designed interventions, the application of unsuitable intervention mechanisms, or a misalignment between the intended outcomes and the sociocultural context. Strategies and recommendations (eg, considering the context such as cultural norms) were suggested to help prevent or reduce the unintended effects.<br><br>CONCLUSIONS: The unintended effects detailed in the mHUE typology were heterogenous and context-dependent. These effects can influence individuals across different domains and also affect unintended people within the ecological system. As most of the unintended effects are negative, if they are not monitored, mHealth interventions designed to empower participants could paradoxically disempower them (eg, decreasing self-efficacy for disease management, undermining patient control, and engagement). The mHUE typology, together with the proposed recommendations and strategies, can be used as a guide to enhance the planning, design, implementation, and postimplementation evaluation on mHealth interventions. Future research should concentrate on understanding the specific mechanisms behind these unintended effects.}, }
@article {pmid40772610, year = {2025}, author = {Tsuji, S and Kunimatsu, S and Watanabe, K}, title = {Environmental DNA Comparative Phylogeography: Simultaneous Estimation of Population Structures Within a Species-Rich Group of Freshwater Gobies.}, journal = {Molecular ecology}, volume = {34}, number = {18}, pages = {e70059}, doi = {10.1111/mec.70059}, pmid = {40772610}, issn = {1365-294X}, support = {23K13967//Japan Society for the Promotion of Science/ ; //ESPEC Foundation for Global Environment Research and Technology/ ; }, mesh = {Phylogeography ; Animals ; *DNA, Environmental/genetics ; Fresh Water ; Japan ; *Genetics, Population ; Haplotypes ; *Perciformes/genetics/classification ; Cytochromes b/genetics ; Phylogeny ; Biodiversity ; DNA, Mitochondrial/genetics ; Genetic Variation ; Sequence Analysis, DNA ; High-Throughput Nucleotide Sequencing ; }, abstract = {Comparative phylogeography provides crucial insights into evolutionary processes shaping biodiversity patterns by analysing spatial genetic variations across multiple species. However, conventional capture-based methods are often labour-intensive, particularly for multi-species analyses. Environmental DNA (eDNA) analysis has significant advantages in comparative phylogeography, including simplified field surveys requiring only water collection and the potential to simultaneously analyse multiple species from a single sample. To further expand the eDNA application and demonstrate its utility in comparative phylogeographic studies, this study employed eDNA analysis to simultaneously analyse the phylogeographic patterns in a species-rich freshwater goby group (Rhinogobius) in the Japanese Archipelago. DNA amplification was performed on eDNA samples collected from 573 sites across the archipelago using newly designed group-specific primers targeting the mitochondrial cytochrome b region of Rhinogobius. High-throughput sequencing detected haplotypes of all nine known species (or species groups) occurring in this region, followed by phylogenetic and network analyses. The eDNA analysis successfully revealed the genetic population structures across multiple species. A landlocked species, R. flumineus, exhibited fine-scale population differentiation shaped by geomorphological barriers, while amphidromous species showed broader genetic patterns likely influenced by ocean currents and their ecological traits. The phylogenetic and phylogeographic patterns reconstructed by the eDNA analysis were almost completely concordant with previously identified patterns of limited groups based on conventional methods, demonstrating the reliability of eDNA-based comparative phylogeography. This study highlights the potential of eDNA to complement and partially replace conventional methods, facilitating large-scale comparative phylogeographic research to gain new insights into spatial patterns and evolutionary processes of biodiversity.}, }
@article {pmid40772542, year = {2025}, author = {Reddy, S and Wacker, K and Fahmy, M and Hekkala, E and Bates, JM and Goodman, SM and Hackett, SJ and Raherilalao, MJ and Maddox, JD}, title = {VoronaGasyCodes: A Public Database of Mitochondrial Barcodes for Malagasy Birds.}, journal = {Molecular ecology resources}, volume = {25}, number = {8}, pages = {e70027}, pmid = {40772542}, issn = {1755-0998}, mesh = {Animals ; Madagascar ; *Birds/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; *DNA, Mitochondrial/genetics/chemistry ; Biodiversity ; *Databases, Genetic ; }, abstract = {Molecular tools are increasingly being used to survey the presence of biodiversity and their interactions within ecosystems. Indirect methods, like environmental DNA (eDNA) and invertebrate-derived DNA (iDNA), are dependent on sequence databases with accurate and sufficient taxonomic representation. These methods are increasingly being used in regions and habitats where direct detection or observations can be difficult for a variety of reasons. Madagascar is a biodiversity hotspot with a high proportion of endemic species, many of which are threatened or endangered. Here we describe a new resource, VoronaGasyCodes, a curated database of newly published genetic sequences from Malagasy birds. Our database is currently populated with six mitochondrial genes or DNA barcodes for 142 species including 70% of the birds endemic to the island and will be periodically updated as new data become available. We demonstrate the utility of our database with an iDNA study of leech blood meals where we successfully identified 77% of the hosts to species. These types of resources for characterising biodiversity are critical for insights into species distribution, discovery of new taxa, novel ecological connections and advancing conservation and restoration measures.}, }
@article {pmid40770961, year = {2026}, author = {Lopes-Araujo, HF and Guimarães, RL and Carvalho-Silva, WHV}, title = {Correlations between new HIV infections and hospital admissions for non-Hodgkin lymphoma in Brazil.}, journal = {International journal of cancer}, volume = {158}, number = {1}, pages = {84-93}, doi = {10.1002/ijc.70076}, pmid = {40770961}, issn = {1097-0215}, mesh = {Humans ; Brazil/epidemiology ; Male ; *HIV Infections/epidemiology/complications ; Female ; *Lymphoma, Non-Hodgkin/epidemiology/virology ; Adult ; Middle Aged ; *Hospitalization/statistics &amp; numerical data ; Adolescent ; Incidence ; Young Adult ; Aged ; Child ; }, abstract = {Despite advancements in antiretroviral therapy, human immunodeficiency virus (HIV) infections remain a significant global health challenge. With increasing life expectancy among people living with HIV, the emergence of HIV-related malignancies, notably non-Hodgkin lymphoma (NHL), has become a prominent concern. This study aims to investigate the correlation between new HIV infections and NHL hospitalizations in Brazil from 2010 to 2022. Using an ecological time series design, data from authoritative sources, including the Notifiable Diseases Information System and the Department of Unified Health System Informatics, were analyzed. The study cohort comprised individuals admitted to the Brazilian Unified Health System, categorized by geographical region, sex, and age cohorts. Pearson's and Spearman's correlation coefficients were utilized to examine the correlation between new HIV infections and NHL hospitalizations. Our analysis revealed a strong positive and statistically significant correlation between the incidence of new HIV cases and NHL hospitalizations in Brazil (r = 0.8901; p = .0001) and in most regions (r > 0.80; p < .001). Moreover, our findings indicate that this correlation becomes evident from the age of 15 onward, with a discernible tendency to escalate with advancing age from moderate to very strong (r > 0.62; p < .02). Regarding sex, the observed correlations were strong positive for male (r = 0.8681; p = .0003) and female (r = 0.7912; p = .0020). These results underscore the importance of vigilant monitoring for individuals living with HIV. Furthermore, we emphasize the importance of rigorous screening practices and adherence to antiretroviral therapy, which may hold promising implications for managing neoplastic conditions.}, }
@article {pmid40770074, year = {2025}, author = {Myers, T and Song, SJ and Chen, Y and De Pessemier, B and Khatib, L and McDonald, D and Huang, S and Gallo, R and Callewaert, C and Havulinna, AS and Lahti, L and Roeselers, G and Laiola, M and Shetty, SA and Kelley, ST and Knight, R and Bartko, A}, title = {Chronological age estimation from human microbiomes with transformer-based Robust Principal Component Analysis.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {1159}, pmid = {40770074}, issn = {2399-3642}, mesh = {Humans ; *Aging ; *Biometry/methods ; *Deep Learning ; *Gastrointestinal Microbiome ; *Principal Component Analysis/methods ; *Skin Microbiome ; Software Validation ; }, abstract = {Deep learning for microbiome analysis has shown potential for understanding microbial communities and human phenotypes. Here, we propose an approach, Transformer-based Robust Principal Component Analysis(TRPCA), which leverages the strengths of transformer architectures and interpretability of Robust Principal Component Analysis. To investigate benefits of TRPCA over conventional machine learning models, we benchmarked performance on age prediction from three body sites(skin, oral, gut), with 16S rRNA gene amplicon(16S) and whole-genome sequencing(WGS) data. We demonstrated prediction of age from longitudinal samples and combined classification and regression tasks via multi-task learning(MTL). TRPCA improves age prediction accuracy from human microbiome samples, achieving the largest reduction in Mean Absolute Error for WGS skin (MAE: 8.03, 28% reduction) and 16S skin (MAE: 5.09, 14% reduction) samples, compared to conventional approaches. Additionally, TRPCA's MTL approach achieves an accuracy of 89% for birth country prediction across 5 countries, while improving age prediction from WGS stool samples. Notably, TRPCA uncovers a link between subject and error prediction through residual analysis for paired samples across sequencing method (16S/WGS) and body site(oral/gut). These findings highlight TRPCA's utility in improving age prediction while maintaining feature-level interpretability, and elucidating connections between individuals and microbiomes.}, }
@article {pmid40764303, year = {2025}, author = {Xu, Y and Gkoutos, GV}, title = {A computational framework for inferring species dynamics and interactions with applications in microbiota ecology.}, journal = {NPJ systems biology and applications}, volume = {11}, number = {1}, pages = {87}, pmid = {40764303}, issn = {2056-7189}, support = {101095480//HYPERMARKER/ ; 101095480//HYPERMARKER/ ; 731032//Nanocommons H2020-EU/ ; 965286//MAESTRIA/ ; 101057014//PARC/ ; HDRUK/CFC/01//MRC Heath Data Research UK/ ; }, mesh = {Animals ; *Computational Biology/methods ; Mice ; Humans ; *Microbiota ; Computer Simulation ; Machine Learning ; Gastrointestinal Microbiome ; *Ecology/methods ; Ecosystem ; Clostridioides difficile ; Clostridium Infections/microbiology ; Models, Biological ; Microbial Interactions ; }, abstract = {We present MBPert, a generic computational framework for inferring species interactions and predicting dynamics in time-evolving ecosystems from perturbation and time-series data. In this work, we contextualize the framework in microbial ecosystem modeling by coupling a modified generalized Lotka-Volterra formulation with machine learning optimization. Unlike traditional methods that rely on gradient matching, MBPert leverages numerical solutions of differential equations and iterative parameter estimation to robustly capture microbial dynamics. The framework is assessed within the context of two experimental scenarios: (i) paired before-and-after measurements under targeted perturbations, and (ii) longitudinal time-series data with time-dependent perturbations. Extensive simulation studies, benchmarking on standardized MTIST datasets, and application to Clostridium difficile infection in mice and repeated antibiotic perturbations of human gut micribiota, demonstrate that MBPert accurately recapitulates species interactions and predicts system dynamics. Our results highlight MBPert as a powerful and flexible tool for mechanistic insight into microbiota ecology, with broad potential applicability to other complex dynamical systems.}, }
@article {pmid40763614, year = {2025}, author = {Wang, C and Xia, A and Feng, D and Li, L and Zhang, J and Huang, Y and Zhu, X and Zhu, X and Trably, E and Liao, Q}, title = {Impacts of intermittent electrical stimulation on continuous electro-anaerobic digestion from wastewater: performance and multi-omics insights.}, journal = {Water research}, volume = {287}, number = {Pt A}, pages = {124319}, doi = {10.1016/j.watres.2025.124319}, pmid = {40763614}, issn = {1879-2448}, mesh = {*Multiomics ; *Wastewater/chemistry ; Anaerobiosis ; Sewage/microbiology ; *Waste Disposal, Fluid/methods ; Electric Stimulation ; Bioreactors/microbiology ; Methane/analysis/metabolism ; Proteome/metabolism ; }, abstract = {The recently reported electro-anaerobic digestion with intermittent electrical stimulation (IEAD) offers new opportunities for renewable energy storage. However, the mechanistic insights and resilience of long-term continuous and stable IEAD are still yet to be better understood. This study lasted up to 155 days of continuous operation of IEAD in up-flow anaerobic sludge blanket bioreactors to evaluate the long-term effects of different intermittent power periods on IEAD performance. The optimal electrical stimulation period was obtained for 12 h:12 h intermittence, resulting in a 15.9 % improvement of the specific methane yield while achieving an organic removal efficiency higher than 98 %. Intermittent electrical stimulation favored biofilm growth, electroactive substance secretion, and enhanced electrochemical activity and cellular repair. Genomic analysis demonstrated that IEAD microbial community was dominated by Methanothrix, whereas continuous energization promoted Methanobacteriaceae enrichment. Proteomic analysis suggested that intermittent power supply preserved functional proteins and upregulated dominant enzymes such as acetyl-CoA carboxylase biotin carboxyl carrier protein and enoyl-CoA hydratase, while conferring flexible carbon source allocation and electron transfer capacity to the suspension zone. Life cycle assessment results showed that the IEAD system could achieve an energy conversion rate of 20.6 and low carbon emissions of 7.3 g CO2-eq/MJ.}, }
@article {pmid40763572, year = {2025}, author = {Sagawa, N and Ichikawa, K and Furukawa, K and Morita, H and Takahara, A and Hinata, H}, title = {Time-resolved fragmentation pathways of expanded polystyrene microplastics: Intrinsic pathway modulated by sand morphology and degradation state.}, journal = {The Science of the total environment}, volume = {997}, number = {}, pages = {180172}, doi = {10.1016/j.scitotenv.2025.180172}, pmid = {40763572}, issn = {1879-1026}, abstract = {Microplastic fragmentation, driven by ultraviolet exposure, mechanical forces, and sand properties, remains poorly understood in natural settings despite its ecological significance. This study investigates temporal variation (6-240 h) in the shape, size, and number of EPS fragments (size distribution) and their dependence on sand morphology and parent microplastic degradation state based on pot mill experiments. Two experimental setups were employed: Time-Resolved Fragmentation (TRF) experiments using virgin EPS (∼5000 μm) with beach sand (TRF-VB), and virgin or degraded EPS with river sand (TRF-VR/DR). In the TRF-VB, two dominant size classes were identified: size class 1 (5-100 μm), appearing early (6-12 h), and size class 2 (200-1000 μm), emerging at 48-72 h and plateauing at 120 h due to hardened surface layer exfoliation of the parent EPS. The steep slopes of the size distributions (<-3) are explained by a combination of continuous-cascading and leap-cascading fragmentation mechanisms. In the TRF-VR experiment, only size class 1 persisted, whereas in the TRF-DR experiment, degraded EPS produced both classes by 120 h. The fragmentation pathway was influenced by both sand morphology and the parent degradation state. Volume balance analysis revealed the dominance of fine fragments (<5 μm) in both experiments, indicating their environmental relevance. These findings provide a conceptual framework for modeling EPS fragmentation and highlight the ecological risks associated with the rapid generation of fine microplastics. In the future, the continued integration of experimental, numerical, and theoretical approaches will be essential for advancing our understanding of plastic fragmentation processes.}, }
@article {pmid40763003, year = {2025}, author = {Chen, AT and Wang, LC and Pike, KC and Conway, M and Glass, JE}, title = {Comparing the Use Experiences, Contextual Factors, and Recovery Strategies Associated with Different Substances: An Analysis of Social Media Narratives.}, journal = {Substance use &amp; misuse}, volume = {60}, number = {14}, pages = {2287-2298}, doi = {10.1080/10826084.2025.2540938}, pmid = {40763003}, issn = {1532-2491}, mesh = {Humans ; *Social Media/statistics &amp; numerical data ; *Substance-Related Disorders/psychology ; *Opioid-Related Disorders/psychology ; Social Stigma ; }, abstract = {BACKGROUND: Research on use experience and recovery has often focused on a single substance or polysubstance use. However, there can be substance-specific differences; understanding these can be critical to developing targeted interventions. We examined social media relating to alcohol, cannabis, and/or opioids to: 1) construct use profiles highlighting salient settings, actors, and contextual factors; and 2) characterize differences in recovery strategies depending on readiness to change.<br><br>METHODS: We constructed a dataset of Reddit posts from subreddits pertaining to alcohol, cannabis, and opioids, authored between January 2013 and December 2019. We leveraged computational techniques to sample posts containing stigma, logistic regression to compare substance use experiences, and content analysis to identify stages of change and recovery strategies.<br><br>RESULTS: We examined 748 posts (alcohol, n&#x2009;=&#x2009;316; cannabis, n&#x2009;=&#x2009;335; opioids, n&#x2009;=&#x2009;135). Regression models indicated leisure settings, coworkers, health, and legal consequences were associated with alcohol versus other substances. Posts involving cannabis were more likely to include school, and heightened self-awareness, demonstrated through curiosity, disgust, and realization. Posts involving opioids were more likely to include anticipated stigma, anger, healthcare, medications, financial, and religious content; they were less likely to include home and leisure. With respect to recovery strategies, social support seeking and awareness of substance use consequences were more common in earlier stages of readiness. In the action and maintenance stages, there was greater use of recovery strategies overall.<br><br>CONCLUSIONS: Substance-specific use profiles highlighted salient settings, actors, and contextual factors. Recovery strategies were also differentiated across stages of change, affording opportunities for treatment and intervention.}, }
@article {pmid40762139, year = {2025}, author = {Kwong, SLT and Budd, AM and Hung, JY and Villacorta-Rath, C and Uthicke, S}, title = {Methylome Profiling of a Deuterostome Invertebrate Using Oxford Nanopore Technology (ONT).}, journal = {Molecular ecology resources}, volume = {25}, number = {8}, pages = {e70026}, pmid = {40762139}, issn = {1755-0998}, support = {//Australian Institute of Marine Science/ ; }, mesh = {Animals ; *DNA Methylation ; *Epigenome ; Computational Biology/methods ; }, abstract = {DNA methylation is crucial for genome regulation and provides key insights into the interaction between genetics and environmental factors, offering valuable perspectives for ecological research. However, knowledge of DNA methylation patterns in nonmodel invertebrates remains limited. The present study addresses this knowledge gap by conducting the first methylome profiling of the Pacific crown-of-thorns seastar (CoTS; Acanthaster cf. solaris), a coral-eating species that aggravates the decline of Indo-Pacific coral reefs. Using Oxford Nanopore Technology (ONT) we generated long-read sequences, covering over 90% of CpG dinucleotides in the CoTS genome. Our analysis revealed a mosaic methylation landscape with moderate genome-wide methylation levels of 37.7%. Comparative analysis highlights the intermediate methylation state observed in other deuterostome invertebrates, positioning them between the hypomethylated genomes of protostomes and the hypermethylated genomes of vertebrates. Methylation in CoTS was predominantly localised within gene bodies, especially in intronic regions, enabling modulation of gene expression and potentially supporting fitness in dynamic marine environments. Additionally, elevated methylation in repetitive elements suggests a role in genome defence. This study demonstrates the effectiveness of ONT for comprehensive methylome analysis in ecologically important nonmodel species and deepens our understanding of the epigenetic landscape in deuterostome invertebrates. We also present a detailed laboratory and bioinformatics workflow, including modified phenol-chloroform protocols that address the challenge of extracting high molecular weight DNA from marine invertebrates. Together with the methylome profiles, these resources serve as a foundation for future research, enabling investigations into DNA methylation functions, applications for CoTS outbreak management and comparative studies across diverse lineages.}, }
@article {pmid40757428, year = {2025}, author = {Callaway, RM and Pal, RW and Schaar, A and Hooper, D and Auge, H and Hensen, I and Kožić, K and Lekberg, Y and Nagy, DU and Selke, JA and Thoma, AE and Träger, S and Rosche, C}, title = {Exotic Invasive Plant Species Increase Primary Productivity, but Not in Their Native Ranges.}, journal = {Ecology letters}, volume = {28}, number = {8}, pages = {e70187}, doi = {10.1111/ele.70187}, pmid = {40757428}, issn = {1461-0248}, support = {//German Research Foundation/ ; //federal state of Saxony-Anhalt/ ; //German Academic Exchange Service London/ ; }, mesh = {*Introduced Species ; *Biomass ; *Ecosystem ; *Plants ; }, abstract = {Ecosystem net primary productivity is thought to occur near the maximum that abiotic constraints allow; but exotic invasive plants often correlate with increased productivity. However, field patterns and experimental evidence for this come only from the non-native ranges of exotic species. Thus, we do not know if this pattern is caused by exotic invasions per se or whether successful exotic species are disproportionately productive or colonise more productive microsites. We measured aboveground biomass in the field and in common gardens with five plant species in their native and non-native ranges. For all species combined, exotic invaders increased total plot productivity in their non-native ranges by 91% in the field, and by 107% in the common garden, but had much smaller or no such effects in their native ranges. Thus, exotic invaders appear to be a driver of increased productivity, not simply a passenger, but only in their non-native ranges.}, }
@article {pmid40755083, year = {2025}, author = {Koseki, Y and Takeshima, H and Yoneda, R and Katayanagi, K and Ito, G and Yamanaka, H}, title = {gmmDenoise: A New Method and R Package for High-Confidence Sequence Variant Filtering in Environmental DNA Amplicon Analysis.}, journal = {Molecular ecology resources}, volume = {25}, number = {8}, pages = {e70023}, pmid = {40755083}, issn = {1755-0998}, support = {JP21K12329//Japan Society for the Promotion of Science/ ; JP22K14908//Japan Society for the Promotion of Science/ ; JP25K02038//Japan Society for the Promotion of Science/ ; }, mesh = {*DNA, Environmental/genetics ; *DNA Barcoding, Taxonomic/methods ; *Computational Biology/methods ; *Genetic Variation ; *Metagenomics/methods ; *Software ; Sequence Analysis, DNA/methods ; }, abstract = {Assessing and monitoring genetic diversity is vital for understanding the ecology and evolution of natural populations but is often challenging in animal and plant species due to technically and physically demanding tissue sampling. Although environmental DNA (eDNA) metabarcoding is a promising alternative to the traditional population genetic monitoring based on biological samples, its practical application remains challenging due to spurious sequences present in the amplicon data, even after data processing with the existing sequence filtering and denoising (error correction) methods. Here we developed a novel amplicon filtering approach that can effectively eliminate such spurious amplicon sequence variants (ASVs) in eDNA metabarcoding data. A simple simulation of eDNA metabarcoding processes was performed to understand the patterns of read count (abundance) distributions of true ASVs and their polymerase chain reaction (PCR)-generated artefacts (i.e., false-positive ASVs). Based on the simulation results, the approach was developed to estimate the abundance distributions of true and false-positive ASVs using Gaussian mixture models and to determine a statistically based threshold between them. The developed approach was implemented as an R package, gmmDenoise and evaluated using single-species metabarcoding datasets in which all or some true ASVs (i.e., haplotypes) were known. Example analyses using community (multi-species) metabarcoding datasets were also performed to demonstrate how gmmDenoise can be used to derive reliable intraspecific diversity estimates and population genetic inferences from noisy amplicon sequencing data. The gmmDenoise package is freely available in the GitHub repository (https://github.com/YSKoseki/gmmDenoise).}, }
@article {pmid40753432, year = {2025}, author = {Sigrist, C and Bechdolf, A and Bertsch, K and Bullenkamp, R and Busse, M and Darrelmann, UG and Dempfle, A and Driessen, M and Frodl, T and Kersting, JM and Kesik, J and Matzke, B and Neukel, C and Niessen, E and Nückel, S and Oertel, V and Padberg, F and Philipsen, A and Pink, D and Reif, A and Reinhard, M and Steuwe, C and Wolkenstein, L and Herpertz, SC and Consortium, TM}, title = {A mechanism-based group psychotherapy approach to aggressive behavior (MAAP) in borderline personality disorder: a multicenter randomized controlled clinical trial.}, journal = {Trials}, volume = {26}, number = {1}, pages = {265}, pmid = {40753432}, issn = {1745-6215}, support = {462340798//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Humans ; *Borderline Personality Disorder/therapy/psychology/diagnosis ; *Aggression/psychology ; Treatment Outcome ; *Psychotherapy, Group/methods ; Germany ; Adult ; Multicenter Studies as Topic ; Female ; Male ; Randomized Controlled Trials as Topic ; Young Adult ; Time Factors ; }, abstract = {BACKGROUND: High levels of trait anger and aggressive behavior are common and problematic phenomena in patients with borderline personality disorder (BPD). In BPD, patterns of reactive aggression often lead to functional impairment affecting important areas of life. Despite the high burden on individuals and their social environment, there are no specific, cost-effective treatments to reduce aggression in BPD. In previous studies, we and others have been able to infer specific biobehavioral mechanisms underlying patterns of reactive aggression in BPD that can be used as potential treatment targets. To address this, we developed a mechanism-based anti-aggression psychotherapy (MAAP) for the group setting that specifically targets the biobehavioral mechanisms underlying outward-directed aggression in BPD. A previously conducted proof-of-concept study had suggested beneficial effects for this neglected group of patients.<br><br>METHODS: In this multicenter, confirmatory, randomized-controlled-clinical-trial, MAAP, which consists of multifaceted, evidence-based treatment elements adapted from other sophisticated treatment programs such as Dialectical Behavior Therapy and Mentalization-Based Treatment, is tested for efficacy against a non-specific supportive psychotherapy (NSSP) program focusing on non-specific general factors of psychotherapy at seven different sites in Germany. Both treatment arms, based on one individual and 13 group therapeutic sessions (1.5 h per session, twice a week), are delivered over a period of 7-10 weeks. A total of N&#x2009;=&#x2009;186 patients will be recruited, half of whom will be cluster-randomized to MAAP. Outcomes are assessed at baseline, immediately, and 4, 12, 20, and 24&#xa0;weeks post-treatment using ecological momentary assessment, clinical interviews, questionnaires, and online tasks.<br><br>DISCUSSION: If proven superior, MAAP can be incorporated into standard psychiatric care, filling a critical gap in the current therapeutic landscape by offering a structured, cost-effective, and evidence-based treatment that directly targets the biobehavioral mechanisms underlying reactive aggression in BPD. By potentially improving clinical outcomes and reducing the burden of reactive aggression in BPD, MAAP could be beneficial for both individuals and their social environments. The study's large, multicenter design enhances the generalizability of the results, making them more relevant for broader clinical applications.<br><br>TRIAL REGISTRATION: This study was registered in the German Clinical Trials Register DRKS (DRKS00031608) on 31.10.2023 (https://drks.de/search/de/trial/DRKS00031608).}, }
@article {pmid40744438, year = {2025}, author = {Posthuma, L and Price, T and Viljanen, M}, title = {Improving the Ecotoxicological Hazard Assessment of Chemicals by Pairwise Learning.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {31}, pages = {16250-16260}, pmid = {40744438}, issn = {1520-5851}, mesh = {*Ecotoxicology ; *Machine Learning ; Animals ; Risk Assessment ; Environmental Pollutants ; }, abstract = {This study demonstrates how machine learning techniques can bridge data gaps in the ecotoxicological hazard assessment of chemical pollutants and illustrates how the results can be used in practice. The innovation herein consists of the prediction of the sensitivity of all species that were tested for at least one chemical for all chemicals based on all available data. As proof of concept, pairwise learning was applied to 3295 × 1267 (chemical,species) pairs of Observed LC50 data, where only 0.5% of the pairs have experimental data. This yielded more than four million Predicted LC50s for separate exposure durations. These were used to create (1) a novel Hazard Heatmap of Predicted LC50s, (2) Species Sensitivity Distributions (SSD) for all chemicals based on 1267 species each, as well as (3) for taxonomic groups separately, and (4) newly defined Chemical Hazard Distributions (CHD) for all species based on 3295 chemicals each. Validation results and graphical examples illustrate the utility of the results and highlight species and compound selection biases in the input data. The results are broadly applicable, ranging from Safe and Sustainable by Design (SSbD) assessments and setting protective standards to Life Cycle Assessment of products and assessing and mitigating impacts of chemical pollution on biodiversity.}, }
@article {pmid40743301, year = {2025}, author = {Lu, Z and Chen, Z and Zhou, M and Lei, D and Chen, Y}, title = {Spatiotemporal patterns of water and vegetation in Poyang Lake from 2013 to 2021 using remote sensing data.}, journal = {PloS one}, volume = {20}, number = {7}, pages = {e0327579}, pmid = {40743301}, issn = {1932-6203}, mesh = {*Lakes ; *Remote Sensing Technology ; China ; *Environmental Monitoring/methods ; Spatio-Temporal Analysis ; Ecosystem ; Geographic Information Systems ; Support Vector Machine ; *Plants ; Water ; }, abstract = {Continuous monitoring and research on Poyang Lake is essential to understand its ecological dynamics and promote sustainable development. Spatial and temporal dynamic monitoring and analyses of vegetation changes in the water body of Poyang Lake are still limited. This study fills this gap by using remote sensing and GIS techniques for dynamic monitoring and analysing the changes of water bodies and vegetation in Poyang Lake from 2013 to 2021. We used a combination of Maximum Likelihood Classification (MLC) and Support Vector Machine (SVM) to preprocess and classify 42 Landsat 8 OLI images. The results showed that the stability of the water body and vegetation varied greatly, with the water body showing the obvious change pattern of water rises, vegetation recedes and water recedes, vegetation grows, and the high-frequency inundation area was concentrated in the northeastern part of the lake (accounting for 60% of the total inundation area). Vegetation frequency distribution showed a pattern of sparse in the north and dense in the south, with the middle frequency area being the most, accounting for 19.88%, and the low frequency area being the least, accounting for 16.09%. The results show that the spatial and temporal distribution characteristics of water body and vegetation in Poyang Lake show low stability, which is a highly dynamic ecosystem. This study relatively makes up for the missing analysis of the stability change of water body and vegetation in the cycle of Poyang Lake, and provides a solid scientific basis for the protection and sustainable management work.}, }
@article {pmid40736894, year = {2025}, author = {Child, HT and Barber, DG and Maneein, S and Clayton, J and Love, J and Tennant, RK}, title = {Laboratory and In-Field Metagenomics for Environmental Monitoring.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2955}, number = {}, pages = {71-88}, doi = {10.1007/978-1-0716-4702-8_5}, pmid = {40736894}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; *Environmental Monitoring/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Gene Library ; }, abstract = {Direct sequencing of DNA from environmental samples (eDNA) is increasingly utilized to provide a census of natural and industrial habitats. The methodology required to perform metagenomics can be divided into three distinct stages: DNA Purification, Library Preparation and Sequencing, and Bioinformatic Analysis. Here we demonstrate an end-to-end protocol that can be utilized either in the field or laboratory for metagenomic analysis of environmental samples utilizing the Oxford Nanopore Technologies MinION sequencing platform.}, }
@article {pmid40733364, year = {2025}, author = {Onyeagoziri, CA and Minoarivelo, HO and Hui, C}, title = {Mutualism and Dispersal Heterogeneity Shape Stability, Biodiversity, and Structure of Theoretical Plant-Pollinator Meta-Networks.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {14}, pages = {}, pmid = {40733364}, issn = {2223-7747}, support = {89967//National Research Foundation/ ; //PhD bursary of the Southern African Systems Analysis Centre (SASAC), with partial funding from the German Academic Exchange Service (DAAD - Deutscher Akademischer Austauschdienst)/ ; }, abstract = {Mutualistic interactions are crucial to the structure and functioning of ecological communities, playing a vital role in maintaining biodiversity amidst environmental perturbations. In studies of meta-networks, which are groups of local networks connected by dispersal, most research has focused on the effect of dispersal on interaction networks of competition and predation, without much attention given to mutualistic interactions. Consequently, the role of different dispersal rates (between local networks and across species) in stability and network structures is not well understood. We present a competition-mutualism model for meta-networks where mutualistic interactions follow a type II functional response, to investigate stability and species abundance dynamics under varying dispersal scenarios. We specifically assess the impact of mutualism and dispersal heterogeneity, both between local networks and across species, on the structure and stability of meta-networks. We find that mutualistic meta-networks exhibit greater stability, higher total abundance, lower species unevenness, and greater nestedness compared to meta-networks with only competition interactions. Although dispersal heterogeneity across species exerts some influence, dispersal heterogeneity between local networks mainly drives the patterns observed: it reduces total abundance, increases unevenness, and diminishes compositional similarity across the meta-network. These results highlight the pivotal role of both mutualism and spatial dispersal structure in shaping ecological networks. Our work advances understanding of how mutualistic interactions and dispersal dynamics interact to influence biodiversity and stability in complex ecosystems.}, }
@article {pmid40732512, year = {2025}, author = {Adlou, B and Wilburn, C and Weimar, W}, title = {Motion Capture Technologies for Athletic Performance Enhancement and Injury Risk Assessment: A Review for Multi-Sport Organizations.}, journal = {Sensors (Basel, Switzerland)}, volume = {25}, number = {14}, pages = {}, pmid = {40732512}, issn = {1424-8220}, mesh = {Humans ; *Athletic Performance/physiology ; Risk Assessment ; *Athletic Injuries/prevention &amp; control ; *Sports ; Geographic Information Systems ; Movement/physiology ; Motion Capture ; }, abstract = {Background: Motion capture (MoCap) technologies have transformed athlete monitoring, yet athletic departments face complex decisions when selecting systems for multiple sports. Methods: We conducted a narrative review of peer-reviewed studies (2015-2025) examining optical marker-based, inertial measurement unit (IMU) systems, including Global Navigation Satellite System (GNSS)-integrated systems, and markerless computer vision systems. Studies were evaluated for validated accuracy metrics across indoor court, aquatic, and outdoor field environments. Results: Optical systems maintain sub-millimeter accuracy in controlled environments but face field limitations. IMU systems demonstrate an angular accuracy of 2-8° depending on movement complexity. Markerless systems show variable accuracy (sagittal: 3-15°, transverse: 3-57°). Environmental factors substantially impact system performance, with aquatic settings introducing an additional orientation error of 2° versus terrestrial applications. Outdoor environments challenge GNSS-based tracking (±0.3-3 m positional accuracy). Critical gaps include limited gender-specific validation and insufficient long-term reliability data. Conclusions: This review proposes a tiered implementation framework combining foundation-level team monitoring with specialized assessment tools. This evidence-based approach guides the selection of technology aligned with organizational priorities, sport-specific requirements, and resource constraints.}, }
@article {pmid40732191, year = {2025}, author = {Eaton, WD and Hamilton, DA and Lemenze, A and Soteropoulos, P}, title = {Initial Analysis of Plant Soil for Evidence of Pathogens Associated with a Disease of Seedling Ocotea monteverdensis.}, journal = {Microorganisms}, volume = {13}, number = {7}, pages = {}, pmid = {40732191}, issn = {2076-2607}, support = {no number//Fundacion Conservacionista Costarricense Fundacion/ ; 2022-10//Fondation Franklinia/ ; no number//Pace University Dyson College Deans Office/ ; no number//Pace University Dyson College Faculty Research Grant Committee/ ; no number//Pace University Provost Office for Research and Support/ ; }, abstract = {Seedlings of the ecologically important, critically endangered tree Ocotea monteverdensisis experience high mortality in the Monteverde, Costa Rica, cloud forests at the onset of the wet season, yet there are no studies suggesting the disease etiology. Here, healthy and diseased plant root and bulk soils were analyzed for various carbon and nitrogen (N) metrics and respiration levels, and DNA sequence-based bacterial and fungal community compositions. All nitrogen metric levels were greater in diseased vs. healthy plant root soils, which could enhance pathogen growth and pathogenic mechanisms. Greater DNA percentages from several potential pathogens were found in diseased vs. healthy plant root soils, suggesting this disease may be associated with a root pathogen. The DNA of the fungus Mycosphaerella was at greater levels in diseased vs. healthy plant root soils than other potential pathogens. Mycosphaerella causes similar diseases in other plants, including coffee, after onset of the wet season. The O. monteverdensis disease also occurs in seedlings planted within or near former coffee plantations at wet season onset. Distance-based linear model analyses indicated that NO3[-] levels best predicted the pattern of fungal pathogens in the soils, and Mycosphaerella and Tremella best predicted the patterns of the different N metrics in the soils, supporting their possible roles in this disease.}, }
@article {pmid40731321, year = {2025}, author = {Rech de Laval, V and Dainat, B and Engel, P and Robinson-Rechavi, M}, title = {The BeeBiome data portal provides easy access to bee microbiome information.}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {198}, pmid = {40731321}, issn = {1471-2105}, mesh = {Bees/microbiology ; Animals ; *Microbiota/genetics ; Metagenomics/methods ; *Databases, Genetic ; Metagenome ; }, abstract = {Bees can be colonized by a large diversity of microbes, including beneficial gut symbionts and detrimental pathogens, with implications for bee health. Over the last few years, researchers around the world have collected a huge amount of genomic and transcriptomic data about the composition, genomic content, and gene expression of bee-associated microbial communities. While each of these datasets by itself has provided important insights, the integration of such datasets provides an unprecedented opportunity to obtain a global picture of the microbes associated with bees and their link to bee health. The challenge of such an approach is that datasets are difficult to find within large generalist repositories and are often not readily accessible, which hinders integrative analyses. Here we present a publicly-available online resource, the BeeBiome data portal (https://www.beebiome.org), which provides an overview of and easy access to currently available metagenomic datasets involving bee-associated microbes. Currently the data portal contains 33,678 Sequence Read Archive (SRA) experiments for 278 Apoidea hosts. We present the content and functionalities of this portal. By providing access to all bee microbiomes in a single place, with easy filtering on relevant criteria, BeeBiome will allow faster progress of applied and fundamental research on bee biology and health. It should be a useful tool for researchers, academics, funding agencies, and governments, with beneficial impacts for stakeholders.}, }
@article {pmid40730013, year = {2025}, author = {Chen, CF and Zhou, Z and Li, C and Liu, W}, title = {Ecological compensation and breakthrough innovation: Evidence from heavily polluting firms.}, journal = {Journal of environmental management}, volume = {392}, number = {}, pages = {126682}, doi = {10.1016/j.jenvman.2025.126682}, pmid = {40730013}, issn = {1095-8630}, mesh = {China ; *Environmental Pollution ; *Environmental Policy ; Industry ; *Conservation of Natural Resources ; }, abstract = {The continuous deepening of the concept of green development and the increasing pressure of environmental governance leads great theoretical significance and practical value to explore the impact of the ecological compensation (eco-compensation) policy on the innovation behavior of enterprises. Taking the implementation of China's ecological compensation policy as an exogenous shock, this paper adopts a multi-period difference-in-differences (DID) model to systematically assess the impact of eco-compensation on corporate breakthrough innovation based on the data of A-share listed companies in the heavy pollution industry from 2014 to 2023. The findings indicate that eco-compensation significantly promotes breakthrough innovation activities of heavy polluting firms. Mechanism analysis further reveals that the policy indirectly drives the enhancement of firms' breakthrough innovation capability mainly by improving the level of data asset disclosure, reducing innovation risk and enhancing R&amp;D activity. The heterogeneity analysis reveals that the eco-compensation policy promotes breakthrough innovation more significantly in firms located in regions where big data management institutions remain unreformed, data factor utilization is low, or industry-university-research collaboration is absent. This study theoretically expands the understanding of the impact mechanism of environmental regulation on enterprises' green innovation and enriches the research framework of incentives for breakthrough innovation; in practice, it provides policy references for optimizing the design of eco-compensation policies and guiding heavily polluting enterprises to achieve green transformation and high-quality development.}, }
@article {pmid40729790, year = {2025}, author = {Michel, A and Prade, M and De Bandt, D}, title = {Pregabalin and gabapentin use in France from 2012 to 2023, impact of prescription restrictions, a time series analysis.}, journal = {The International journal on drug policy}, volume = {145}, number = {}, pages = {104929}, doi = {10.1016/j.drugpo.2025.104929}, pmid = {40729790}, issn = {1873-4758}, mesh = {*Pregabalin/administration &amp; dosage/economics ; *Gabapentin/administration &amp; dosage/economics ; France ; Humans ; *Practice Patterns, Physicians'/statistics &amp; numerical data/trends ; Prescription Drug Misuse ; Databases, Factual ; Drug Prescriptions/statistics &amp; numerical data ; }, abstract = {INTRODUCTION: Gabapentinoids use is accompanied by increased misuse, particularly for pregabalin. In May 2021, France introduced secure prescription requirements for pregabalin. This paper aims to analyse variations in gabapentinoid dispensing, with a focus on changes in prescription rules.<br><br>MATERIEL AND METHOD: We performed an ecological study using the French national health insurance database from January 2012 to December 2023. We analysed pregabalin and gabapentin doses sold by city pharmacies expressed in monthly defined daily dose per thousand inhabitant a day (DDD/TID) between January 2012 and December 2023. Dose sales trends before and after May 2021 were compared using segmented analysis of Autoregressive Integrated Moving Average models. Descriptive analysis was performed to analyse associated expenses expressed in euros.<br><br>RESULTS: Between 2012 and 2020, pregabalin doses sold rose from 3.228 DDD/TID to 4.908 DDD/TID. After the reform, they declined to 3.923 DDD/TID in 2023. Gabapentin doses sold increased from 1.042 DDD/TID to 1.257 DDD/TID between 2012 and 2020, then rose further post-reform, reaching 1.705 DDD/TID. Costs related to the pregabalin doses sold decreased from &#x20ac;132.47 to &#x20ac;51.36 million from 2012 to 2023. Costs related to gabapentin decrease from &#x20ac;32.31 to &#x20ac;26.84 million between 2012 and 2021, then increase to &#x20ac;37.70 million in 2023.<br><br>DISCUSSION: These data suggest that the May 2021 reform has reduced pregabalin consumption and induced an increase of gabapentin use. Cost implications remain of difficult interpretation due to multiple confounding factors. Further research could clarify these trends and be used to optimize prescription practices.}, }
@article {pmid40728939, year = {2025}, author = {Franco, ME and Araújo, CVM and Cerveny, D and Koubová, A and Danneels, B and Goksøyr, A and Bertram, MG}, title = {The extended chemical defensome: emphasizing mechanisms of defense as key research avenues to tackle priority questions in environmental toxicology.}, journal = {Environmental toxicology and chemistry}, volume = {44}, number = {11}, pages = {3118-3130}, doi = {10.1093/etojnl/vgaf190}, pmid = {40728939}, issn = {1552-8618}, support = {MCIN/AEI/10.13039/501100011033/FEDER//Ministry of Science, Innovation and Universities of Spain/ ; PID2022-137402OB-I00//BeingHavior/ ; 2020-02293//Swedish Research Council Formas/ ; 2020-01052//Swedish Research Council Formas/ ; SMK-1954 and SMK21-0069//Kempe Foundations/ ; 23-07274S//Czech Science Foundation/ ; #334739//Research Council of Norway/ ; }, mesh = {*Ecotoxicology ; Animals ; *Environmental Pollutants/toxicity ; Humans ; }, abstract = {Chemical pollution threatens organismal integrity, affecting growth, reproduction, behavior, and overall fitness, ultimately leading to shifts in biodiversity and the provisioning of ecosystem services. In response to chemical exposure, organisms use specific regions of their genome coding for different defense mechanisms-this collection of genes is termed the "chemical defensome." Specifically, genes associated with efflux transporters, transcription factors, antioxidant systems, and biotransformation pathways, among others, are expressed to reduce toxicity. These sub-individual processes are, for the most part, widely conserved across taxa and play a critical role in enabling organisms to cope with polluted environments. Additionally, we argue that behavioral responses-particularly spatial avoidance-should be recognized as an individual-level defense mechanism and incorporated into an extended chemical defensome framework. Expanding and reinforcing the concept of the chemical defensome beyond traditional studies at the genome level, as well as developing strategies to synthesize existing data, offers a valuable opportunity to link gene composition to physiological and behavioral responses, thereby addressing key research needs in environmental toxicology. These include estimating the impact of chemical mixtures across different exposure scenarios, identifying the main drivers of intra- and interspecific sensitivity to pollution, and assessing large-scale ecological processes, such as biodiversity losses, in polluted habitats in a more integrated manner. In ecotoxicology and environmental risk assessment, understanding not only how chemical pollutants exert toxicity but also how organisms counteract these effects is essential. Indeed, investigating chemical-induced shifts in defense mechanisms can improve predictions of adverse outcomes at higher levels of biological organization and can inform more effective chemical management and regulatory strategies.}, }
@article {pmid40726282, year = {2025}, author = {de Mol, F and Fritzsche, R and Gerowitt, B}, title = {Weed biodiversity and herbicide intensity as linked via a decision support system.}, journal = {Pest management science}, volume = {81}, number = {10}, pages = {6667-6677}, pmid = {40726282}, issn = {1526-4998}, support = {//South Baltic Cross-border cooperation EU programme/ ; //German Federal Agency/ ; FKZ 351984070//Federal Ministry/ ; }, mesh = {*Herbicides ; *Biodiversity ; *Plant Weeds/drug effects ; *Weed Control/methods ; Germany ; *Decision Support Techniques ; Triticum/growth &amp; development ; }, abstract = {BACKGROUND: Extensive herbicide use is one reason for the declining biodiversity of arable weeds. This study aimed to investigate (i) whether herbicide decisions recommended by a decision support system increase the weed species diversity compared to standard recommendations, and (ii) whether high weed species diversity reduces herbicide intensity, which in turn contributes to higher diversity. Data on weeds and herbicide applications in winter wheat fields in north-eastern Germany were collected in 15 field trials over 2 years. Five treatments differed in the way of decision-making for herbicide application, including two treatments according to recommendations of decision support systems.<br><br>RESULTS: Along the Hill's series biodiversity metrics, the untreated control had the highest species richness (13.5&#x2009;m[-2]) per field but showed increasingly stronger dominance structures than the treated plots (equivalent species richness: 1.7-2.0&#x2009;m[-2]). The treatment frequency index as a metric for herbicide intensity was significantly lowest in the decision support system with low reliability (1.07). Path models, including weed diversity and density in autumn, weed diversity in summer, and herbicide intensity as a mediating variable showed a significant decreasing effect of Shannon diversity on herbicide intensity in all treatments. Only the decision support systems reacted to low weed densities with a significant reduction of the herbicide intensity.<br><br>CONCLUSION: Higher weed species diversity contributes to lower herbicide intensity, which is ecologically and economically valuable. Decision support systems for herbicide application should have other target functions than cost reduction for contributing to biodiversity. &#xa9; 2025 The Author(s). Pest Management Science published by John Wiley &amp; Sons Ltd on behalf of Society of Chemical Industry.}, }
@article {pmid40724857, year = {2025}, author = {Piotrowski, M and Pawlaczyk, A and Szynkowska-Jóźwik, MI and Maras, P and Kozicki, M}, title = {Radiation-Sensitive Nano-, Micro-, and Macro-Gels and Polymer Capsules for Use in Radiotherapy Dosimetry.}, journal = {International journal of molecular sciences}, volume = {26}, number = {14}, pages = {}, pmid = {40724857}, issn = {1422-0067}, mesh = {*Polymers/chemistry ; *Radiometry/methods ; Alginates/chemistry ; Capsules/chemistry ; *Hydrogels/chemistry ; Humans ; Iron/chemistry ; *Radiotherapy/methods ; Gels/chemistry ; Radiation, Ionizing ; }, abstract = {This work introduces an original approach to the manufacturing of ionizing radiation-sensitive systems for radiotherapy applications-dosimetry. They are based on the Fricke dosimetric solution and the formation of macro-gels and capsules, and nano- and micro-gels. The reaction of ionic polymers, such as sodium alginate, with Fe and Ca metal ions is employed. Critical polymer concentration (c*) is taken as the criterion. Reaction of ionic polymers with metal ions leads to products related to c*. Well below c*, nano- and micro-gels may form. Above c*, macro-gels and capsules can be prepared. Nano- and micro-gels containing Fe in the composition can be used for infusion of a physical gel matrix to prepare 2D or 3D dosimeters. In turn, macro-gels can be formed with Fe ions crosslinking polymer chains to obtain radiation-sensitive hydrogels, so-called from wall-to-wall, serving as 3D dosimeters. The encapsulation process can lead to capsules with Fe ions serving as 1D dosimeters. This work presents the concept of manufacturing various gel structures, their main features and manufacturing challenges. It proposes new directions of research towards novel dosimeters.}, }
@article {pmid40724441, year = {2025}, author = {Hunyadi, ID and Cismaș, C}, title = {Mining Complex Ecological Patterns in Protected Areas: An FP-Growth Approach to Conservation Rule Discovery.}, journal = {Entropy (Basel, Switzerland)}, volume = {27}, number = {7}, pages = {}, pmid = {40724441}, issn = {1099-4300}, support = {LBUS-IRG-10-2024//Lucian Blaga University of Sibiu/ ; }, abstract = {This study introduces a data-driven framework for enhancing the sustainable management of fish species in Romania's Natura 2000 protected areas through ecosystem modeling and association rule mining (ARM). Drawing on seven years of ecological monitoring data for 13 fish species of ecological and socio-economic importance, we apply the FP-Growth algorithm to extract high-confidence co-occurrence patterns among 19 codified conservation measures. By encoding expert habitat assessments into binary transactions, the analysis revealed 44 robust association rules, highlighting interdependent management actions that collectively improve species resilience and habitat conditions. These results provide actionable insights for integrated, evidence-based conservation planning. The approach demonstrates the interpretability, scalability, and practical relevance of ARM in biodiversity management, offering a replicable method for supporting adaptive ecological decision making across complex protected area networks.}, }
@article {pmid40715537, year = {2025}, author = {Zhang, F and Guo, A and Hu, Z and Liang, Y}, title = {A novel image fusion method based on UAV and Sentinel-2 for environmental monitoring.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {27256}, pmid = {40715537}, issn = {2045-2322}, support = {2018SMHKJ-A-J-03//the Research and Demonstration of Key Technology for Water Resources Protection and Utilization and Ecological Reconstruction in Coal Mining area of Northern Shaanxi/ ; 2018SMHKJ-A-J-03//the Research and Demonstration of Key Technology for Water Resources Protection and Utilization and Ecological Reconstruction in Coal Mining area of Northern Shaanxi/ ; 2018SMHKJ-A-J-03//the Research and Demonstration of Key Technology for Water Resources Protection and Utilization and Ecological Reconstruction in Coal Mining area of Northern Shaanxi/ ; 2018SMHKJ-A-J-03//the Research and Demonstration of Key Technology for Water Resources Protection and Utilization and Ecological Reconstruction in Coal Mining area of Northern Shaanxi/ ; N25XQD015//Funding for Basic Research Operations in Higher Education/ ; N25XQD015//Funding for Basic Research Operations in Higher Education/ ; N25XQD015//Funding for Basic Research Operations in Higher Education/ ; N25XQD015//Funding for Basic Research Operations in Higher Education/ ; }, abstract = {In recent years, with the rapid development of remote sensing technology, environmental monitoring in mining areas using remote sensing imagery has gained increasing attention. Due to the small scale of mining areas, the resolution of satellite remote sensing imagery is insufficient for detailed monitoring needs. UAV remote sensing imagery provides high resolution, but its monitoring range is limited and lacks access to historical data. Furthermore, effectively fusing multi-source data with disparate spatial-temporal characteristics to accurately capture the complex dynamic changes in mining areas remains a key methodological challenge.To address this, this study, utilizing UAV remote sensing imagery and Sentinel-2 satellite imagery acquired on September 5, 2023, from the Erlintu mining area, proposes a novel fusion method aimed at achieving small-scale, long-term environmental monitoring in mining areas.First, the spatial resolution of both UAV and Sentinel-2 imagery is resampled to 0.1 m. Second, a two-layer preprocessing approach is applied to enhance data quality. Third, a stacked inversion model based on an ensemble learning framework is developed. Finally, using high-resolution UAV imagery as the reference, and original, resampled, and model-inverted Sentinel-2 imagery as experimental values, accuracy is assessed and analyzed with Mean Absolute Percentage Error (MAPE) as the metric. Results demonstrate that the stacked learning model, combined with cubic convolution resampling, reduces the MAPE of NDVI values between Sentinel-2 and UAV imagery from 54.31 to 10.01%, markedly improving accuracy. This study further uncovers the synergistic effect of resampling techniques and model architecture, offering reliable data support for small-scale, long-term environmental monitoring in mining areas.}, }
@article {pmid40715152, year = {2025}, author = {Aubouin, L and Genoud, D and Givord-Coupeau, B and Tercerie, S and Gargominy, O and Geslin, B and Schatz, B}, title = {BeeFunc, a comprehensive trait database for French bees.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1302}, pmid = {40715152}, issn = {2052-4463}, mesh = {Bees/classification/anatomy &amp; histology ; Animals ; France ; *Databases, Factual ; }, abstract = {Given pollinator's reported decline, it is of utmost importance to better understand the vulnerability of wild bees to human pressures. One way to achieve this goal is to explore how their traits are associated with exposure to anthropogenic perturbations. To date, there is no database synthesizing traits of bees at the species level in France, limiting the functional interpretation of inventories. We present BeeFunc 1.0, the first database on traits for the entire fauna of French wild bees. Based on extensive literature research and expert knowledge, the database is structured according to the French taxonomic register (TAXREF) and its associated knowledge base. The base gathers 26,176 trait information from 483 sources, describing 932 species for 20 features related to morphology, ecology, biogeography, and conservation. BeeFunc is intended to be collaborative and regularly updated. Bees can finally be better considered from a functional perspective. We expect this database to be widely used by researchers, conservationists, naturalists, and stakeholders, stimulating future research on wild bees.}, }
@article {pmid40713811, year = {2025}, author = {Sun, B and Yuan, J and Zhang, X and Ma, X and Hao, Z and Wang, L and Li, Y and Zhang, L and Li, L}, title = {Metaproteomics Reveals Community Coalescence Outcomes in Co-Cultured Human Gut Microbiota.}, journal = {Proteomics}, volume = {25}, number = {17-18}, pages = {6-18}, doi = {10.1002/pmic.70009}, pmid = {40713811}, issn = {1615-9861}, support = {32370050//National Natural Science Foundation of China/ ; 82371559//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Proteomics/methods ; Coculture Techniques ; Feces/microbiology ; *Proteome/analysis ; }, abstract = {The human gut microbiome exhibits characteristics of complex ecosystems, including the ability to resist and compete with exogenous species or communities. Understanding the microbiome response that emerges from such competitive interactions is crucial, particularly for applications like fecal microbiota transplantation (FMT), where the success of treatment largely depends on the outcome of these microbial competitions. During these processes, microbial communities undergo coalescence, a phenomenon where distinct microbial communities combine and interact, leading to complex ecological outcomes that are still being uncovered. In this study, we examined the coalescent dynamics of 10 different pairs of human gut microbiota by co-culturing the plateau-phase communities of individual samples in vitro, and highlighted the critical role of metaproteomics in elucidating the competitive dynamics of co-cultured human fecal samples. Results showed that microbiome changes observed after coalescent co-culture were not straightforwardly an approximate average of the initial taxonomic or functional compositions of the two samples. Instead, both coalescent microbiotas behaved as cohesive structures, influencing the competitive outcome toward one of them. Although co-cultured communities usually exhibited high degrees of taxonomic similarities to one of its parental samples, we found that 23% of the observed proteins still showed differential expression or abundance at the metaproteomic level. Interestingly, and somewhat counterintuitively, no specific microbial ecological characteristic could linearly determine which of the two initial microbiotas would act as the driving microbiota. Instead, we observed that the outcomes of the microbial co-cultures resembled a "rock-paper-scissors"-like dynamic. Through an analysis of co-colonizing species in such "rock-paper-scissors"-like triangle, we discovered that co-colonizing species that contributed to winning each between-community competition differed from one community pair to another. This suggests that no single species or function consistently dominates across all situations; instead, this involves more complex mechanisms, which require further in-depth investigation in future studies. Our findings demonstrate that the complex competitive interactions between microbial communities make predicting success through a single parameter challenging, whereas pre-co-culturing shows promise as an effective method for predicting outcomes in ecological therapies such as FMT. SUMMARY: This study underscores the critical importance of integrating metaproteomics with microbial systems ecology to gain a functional understanding of microbial coalescence. By addressing the ecological question of how two communities compete when they are brought into contact, we investigated the metaproteomic responses of pairs of coalescent co-cultured human gut microbiotas. Our results revealed significant insights: post-co-culture microbiota changes were not merely a simple average of the initial compositions but instead exhibited distinct shifts toward one of the original samples. Notably, due to the observed rock-paper-scissors-like cycle of winning, we argue that no single microbial ecological characteristic could straightforwardly predict which of the two samples would dominate as the driving microbiota. Overall, our findings suggest that during coalescence, microbial communities behave as cohesive structures both taxonomically and functionally, influencing competitive dynamics and ecosystem complexity, indicating that an in vitro coalescence pretest may help predict the success of therapies like FMT.}, }
@article {pmid40706521, year = {2025}, author = {Liu, X and Zhai, WH and Liu, R and Liu, BL and Gao, RJ and Li, YW and Xiang, L and Cai, QY and Zhao, HM and Mo, CH}, title = {Integrated multi-omics analyses of molecular pathways underlying microcystin-LR toxicity in the earthworm Eisenia fetida.}, journal = {Ecotoxicology and environmental safety}, volume = {302}, number = {}, pages = {118724}, doi = {10.1016/j.ecoenv.2025.118724}, pmid = {40706521}, issn = {1090-2414}, mesh = {Animals ; *Microcystins/toxicity ; *Oligochaeta/drug effects/metabolism ; Marine Toxins ; *Soil Pollutants/toxicity ; Proteomics ; Metabolomics ; Multiomics ; }, abstract = {Contamination of soil with microcystin-LR (MC-LR) has emerged as a significant environmental concern, but its toxicological impacts and underlying mechanisms on soil-dwelling invertebrates are not yet fully elucidated. Here we employed a comprehensive strategy integrating histopathological, ultrastructural, biochemical, and multi-omics (metabolomics and proteomics) analyses to investigate the effects of MC-LR on Eisenia fetida, a model soil organism. MC-LR exposure induced dose-dependent structural damage to the epidermal and intestinal tissues, disrupting antioxidant systems while elevating detoxification enzyme activity. Metabolomic profiling identified 93 significantly altered metabolites in the earthworms following exposure to MC-LR at a concentration of 0.6 mg/kg, implicating pathways such as amino acid biosynthesis, protein digestion and absorption, ATP-binding cassette transporters, and aminoacyl-tRNA biosynthesis. Proteomic analysis showed that MC-LR affected distinct pathways, particularly those associated with nucleotide binding, calcium ion binding, ATP binding, cytoskeleton, and actin filament binding. Correlations between differentially expressed metabolites and differentially expressed proteins highlighted critical roles of amino acid biosynthesis, thiamine metabolism, glutathione metabolism, and longevity regulating in earthworms' defense against MC-LR toxicity. This study advances the understanding of molecular pathways underlying MC-LR-induced toxicity in soil invertebrates, providing valuable insights into its ecological impact and potential risks.}, }
@article {pmid40705801, year = {2025}, author = {Solowiej-Wedderburn, J and Pentz, JT and Lizana, L and Schroeder, BO and Lind, PA and Libby, E}, title = {Competition and cooperation: The plasticity of bacterial interactions across environments.}, journal = {PLoS computational biology}, volume = {21}, number = {7}, pages = {e1013213}, pmid = {40705801}, issn = {1553-7358}, mesh = {*Microbial Interactions/physiology ; *Models, Biological ; *Bacteria/genetics/metabolism ; Computational Biology ; Computer Simulation ; *Bacterial Physiological Phenomena ; Metabolic Networks and Pathways/genetics ; Ecosystem ; Environment ; }, abstract = {Bacteria live in diverse communities, forming complex networks of interacting species. A central question in bacterial ecology is whether species engage in cooperative or competitive interactions. But this question often neglects the role of the environment. Here, we use genome-scale metabolic networks from two different open-access collections (AGORA and CarveMe) to assess pairwise interactions of different microbes in varying environmental conditions (provision of different environmental compounds). By computationally simulating thousands of environments for 10,000 pairs of bacteria from each collection, we found that most pairs were able to both compete and cooperate depending on the availability of environmental resources. This modeling approach allowed us to determine commonalities between environments that could facilitate the potential for cooperation or competition between a pair of species. Namely, cooperative interactions, especially obligate, were most common in less diverse environments. Further, as compounds were removed from the environment, we found interactions tended to degrade towards obligacy. However, we also found that on average at least one compound could be removed from an environment to switch the interaction from competition to facultative cooperation or vice versa. Together our approach indicates a high degree of plasticity in microbial interactions in response to the availability of environmental resources.}, }
@article {pmid40705402, year = {2025}, author = {Oba, T and Takano, K and Sugawara, D and Kimura, K}, title = {Just-in-Time Delivery of Cognitive Behavioral Therapy-Based Exercises: Single-Case Experimental Design With Random Multiple Baselines.}, journal = {JMIR formative research}, volume = {9}, number = {}, pages = {e69556}, pmid = {40705402}, issn = {2561-326X}, mesh = {Humans ; *Cognitive Behavioral Therapy/methods ; Female ; Adult ; Male ; Middle Aged ; *Stress, Psychological/therapy/psychology ; *Mobile Applications ; Smartphone ; Single-Case Studies as Topic ; Feasibility Studies ; Japan ; }, abstract = {BACKGROUND: Just-in-time adaptive interventions (JITAIs) are a promising approach in mental health care given the potential scalability (ie, interventions are offered automatically and remotely) and preciseness (ie, the right interventions are offered at the right moments). Typically, a smartphone app is programmed to assess users' psychological states in daily life; when a particular state is detected, the app prompts users to engage in specific behaviors. Conceptually, JITAIs hold significant potential for precision health, although there is currently limited evidence in the literature.<br><br>OBJECTIVE: We implemented this scheme as a smartphone intervention for daily stress management, based on cognitive behavioral therapy (CBT), and evaluated its feasibility and efficacy using a single-case experimental design.<br><br>METHODS: A total of 8 Japanese adults (community sample: 4 women; mean 37.6, SD 13.1 y) were recruited. An AB phase design with multiple random baselines was used, where "A" represents the baseline phase and "B" represents the intervention phase. Throughout the study period (28 d), participants were prompted to indicate their momentary levels of stress (range 0-100) using a smartphone thrice a day. The baseline phase duration was randomly varied among participants, lasting between 7 and 14 days. The remaining period was used as the intervention phase (14-21 d), where 6 CBT-based exercises (ie, breath control, mindfulness, relaxation, self-talk, cognitive defusion, and cognitive restructuring) were offered depending on the reported levels of stress.<br><br>RESULTS: Approximately 70% (6/8) of the participants perceived the intervention to be useful and helpful. A randomization test detected a statistically significant decrease in reported stress levels after the intervention began (P=.005), though this effect was less pronounced when analyzed individually for each participant. Multilevel model analysis detected a significant acute reduction in the momentary level of stress right after completing a CBT-based exercise (pre-exercise: mean 47.98, SD 21.65; post exercise: mean 42.13, SD 19.88; P=.03; Cohen dz=0.58). Also, a significant reduction in depressive rumination was observed in the postintervention assessment (preintervention: mean 13.00, SD 3.21; post intervention: mean 9.25, SD 2.60; P=.01, Cohen dz=1.17).<br><br>CONCLUSIONS: The intervention was feasible and effective in reducing subjective stress (and rumination) in the study sample. The small sample size and the nonclinical nature of the sample may limit the generalizability and implications of the study findings for clinical practice. More evidence should be collected to draw solid conclusions for technical and technological as well as clinical aspects of mobile interventions. Accumulating exemplars with different implementations will clarify how a JITAI can be designed and developed on a mobile platform and how the program can be delivered in the prevention and treatment of mental ill health.}, }
@article {pmid40703330, year = {2025}, author = {Boyes, D and Crowley, LM and Adewumi, T and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Small Dotted Buff moth, Photedes minima Haworth, 1809.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {299}, pmid = {40703330}, issn = {2398-502X}, abstract = {We present a genome assembly from a male specimen of Photedes minima (Small Dotted Buff; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 694.66 megabases. Most of the assembly (99.95%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 15.38 kilobases.}, }
@article {pmid40702785, year = {2025}, author = {Lee, TY and Chen, CH and Liu, CM and Chen, IM and Chen, HC and Wu, SI and Hsiao, CK and Kuo, PH}, title = {Fourier Transform Analysis of GPS-Derived Mobility Patterns for Diagnosis and Mood Monitoring of Bipolar and Major Depressive Disorders: Prospective Study.}, journal = {Journal of medical Internet research}, volume = {27}, number = {}, pages = {e71658}, pmid = {40702785}, issn = {1438-8871}, mesh = {Humans ; *Major Depressive Disorder/diagnosis ; *Bipolar Disorder/diagnosis ; *Geographic Information Systems ; Female ; Male ; Adult ; Prospective Studies ; *Fourier Analysis ; Middle Aged ; Affect ; }, abstract = {BACKGROUND: Mood disorders, including bipolar disorder (BP) and major depressive disorder (MDD), are characterized by significant psychological and behavioral fluctuations, with mobility patterns serving as potential markers of emotional states.<br><br>OBJECTIVE: This study explores the diagnostic and monitoring capabilities of Fourier transform, a frequency-domain analysis method, in mood disorders by leveraging GPS data as an objective measure.<br><br>METHODS: A total of 62 participants (BP: n=20, MDD: n=27, and healthy controls: n=15) contributed 5177 person-days of data over observation periods ranging from 5 days to 6 months. Key GPS indicators-location variance (LV), transition time (TT), and entropy-were identified as reflective of mood fluctuations and diagnostic differences between BP and MDD.<br><br>RESULTS: Fourier transform analysis revealed that the maximum power spectra of LV and entropy differed significantly between BP and MDD groups, with patients with BP exhibiting greater periodicity and intensity in mobility patterns. Notably, participants with BP demonstrated consistent periodic waves (eg, 1-d, 4-d, and 9-d cycles), while such patterns were absent in those with MDD. In addition, after adjusting for age, gender, and employment status, only the power spectrum of LV remained a significant predictor of depressed mood (odds ratio [OR] 0.9976, 95% CI 0.9956-0.9996; P=.02). Daily GPS data showed stronger correlations with ecological momentary assessment (EMA)-reported mood states compared to weekly or monthly aggregations, emphasizing the importance of day-to-day monitoring. Depressive states were associated with reduced LV (OR 0.975, 95% CI 0.957-0.993; P=.008) and TT (OR 0.048, 95% CI 0.012-0.200; P<.001) on weekdays, and lower entropy (OR 0.662, 95% CI 0.520-0.842; P=.001) on weekends, indicating that mobility features vary with social and temporal contexts.<br><br>CONCLUSIONS: This study underscores the potential of GPS-derived mobility data, analyzed through Fourier transform, as a noninvasive and real-time diagnostic and monitoring tool for mood disorders. The findings suggest that the intensity of mobility patterns, rather than their frequency, may better differentiate BP from MDD. Integrating GPS data with EMAs could enhance the precision of clinical assessments, provide early warnings for mood episodes, and support personalized interventions, ultimately improving mental health outcomes. This approach represents a promising step toward digital phenotyping and advanced mental health monitoring strategies.}, }
@article {pmid40702703, year = {2025}, author = {Liu, X and Kong, J and Shan, Y and Yang, Z and Miao, J and Pan, Y and Luo, T and Shi, Z and Wang, Y and Gou, Q and Yang, C and Li, H and Li, C and Li, S and Zhang, X and Sun, Y and Holmes, EC and Guo, D and Shi, M}, title = {SegFinder: an automated tool for identifying complete RNA virus genome segments through co-occurrence in multiple sequenced samples.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {4}, pages = {}, pmid = {40702703}, issn = {1477-4054}, support = {82341118//National Natural Science Foundation of China/ ; KQTD20200820145822023//Shenzhen Science and Technology Program/ ; MRP/071/20X//Hong Kong Innovation and Technology Fund/ ; GZNL2023A01001//Major Project of Guangzhou National Laboratory/ ; GZNL2023A01008//Major Project of Guangzhou National Laboratory/ ; 2019ZT08Y464//Guangdong Province 'Pearl River Talent Plan' Innovation, Entrepreneurship Team Project/ ; ZDSYS20220606100803007//Fund of Shenzhen Key Laboratory/ ; GNT2017197//NHMRC Investigator Award/ ; //Innovation and Technology Commission, Hong Kong Special Administrative Region, China/ ; }, mesh = {*Genome, Viral ; *RNA Viruses/genetics ; Animals ; *Computational Biology/methods ; Metagenomics/methods ; *Software ; RNA, Viral/genetics ; }, abstract = {Metagenomic sequencing has expanded the ribonucleic acid (RNA) virosphere, but many identified viral genomes remain incomplete, especially for segmented viruses. Traditional methods relying on sequence homology struggle to identify highly divergent segments and group them confidently within a single virus species. To address this, we developed a new bioinformatic tool-SegFinder-that identifies virus genome segments based on their common co-occurrence at similar abundance within segmented viruses. SegFinder successfully re-discovered all segments from a test data set of individual mosquito transcriptomes, which was also used to establish parameter thresholds for reliable segment identification. Using these optimal parameters, we applied SegFinder to 858 libraries from eight metagenomic sequencing projects, including vertebrates, invertebrates, plants, and environmental samples. Excluding the RdRP segment, we identified 106 unique viral genome segments from these samples. Among them, 53 were novel, including 30 segments that showed no recognizable sequence homology to any known viruses. However, the viral origin of these highly divergent segment was supported by the presence of conserved terminal sequences. SegFinder identifies segmented genome structures in viruses previously considered to be predominantly unsegmented, and in doing so expanded the number of known families and orders of segmented RNA viruses, making it a valuable tool in an era of large-scale parallel sequencing.}, }
@article {pmid40700599, year = {2025}, author = {Mofidifar, S and Tefagh, M}, title = {Reducing redundancy and enhancing accuracy through a phylogenetically-informed microbial community metabolic modeling approach.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {7}, pages = {}, pmid = {40700599}, issn = {1367-4811}, mesh = {*Phylogeny ; *Models, Biological ; *Microbiota ; *Metagenomics/methods ; *Computational Biology/methods ; Computer Simulation ; }, abstract = {MOTIVATION: Metabolic modeling has emerged as a powerful tool for predicting community functions. However, current modeling approaches face significant challenges in balancing the metabolic trade-offs between individual and community-level growth. In this study, we investigated the effect of metabolic relatedness among taxa on growth rate calculations by merging related taxa based on their metabolic similarity, introducing this approach as PhyloCOBRA.<br><br>RESULTS: This approach enhanced the accuracy and efficiency of microbial community simulations by combining genome-scale metabolic models (GEMs) of closely related organisms, aligning with the concepts of niche differentiation and nestedness theory. To validate our approach, we implemented PhyloCOBRA within the MICOM and OptCom package (creating PhyloMICOM and PhyloOptCom, respectively), and applied it to metagenomic data from 186 individuals and four-species synthetic community (SynCom). Our results demonstrated significant improvement in the accuracy and reliability of growth rate predictions compared to the standard methods. Sensitivity analysis revealed that PhyloMICOM models were more robust to random noise, while Jaccard index calculations showed a reduction in redundancy, highlighting the enhanced specificity of the generated community models. Furthermore, PhyloMICOM reduced the computational complexity, addressing a key concern in microbial community simulations. This approach marks a significant advancement in community-scale metabolic modeling, offering a more stable, efficient, and ecologically relevant tool for simulating and understanding the intricate dynamics of microbial ecosystems.<br><br>PhyloCOBRA implementations are available as extensions to the MICOM packages and can be accessed at https://github.com/sepideh-mofidifar/PhyloCOBRA.}, }
@article {pmid40699651, year = {2025}, author = {Wang, H and Zhou, H and Yao, X}, title = {Different Species of Bats: Genomics, Transcriptome, and Immune Repertoire.}, journal = {Current issues in molecular biology}, volume = {47}, number = {4}, pages = {}, pmid = {40699651}, issn = {1467-3045}, support = {82160279//National Natural Science Foundation of China/ ; No. (2018)5637//Guizhou Provincial Hundred level Talent Fund/ ; }, abstract = {Bats are the only mammals with the ability to fly and are the second largest order after rodents, with 20 families and 1213 species (over 3000 subspecies) and are widely distributed in regions around the world except for Antarctica. What makes bats unique are their biological traits: a tolerance to zoonotic infections without getting clinical symptoms, long lifespans, a low incidence of tumors, and a high metabolism. As a result, they are receiving increasing attention in the field of life sciences, particularly in medical research. The rapid advancements in sequencing technology have made it feasible to comprehensively analyze the diverse biological characteristics of bats. This review comprehensively discusses the following: (1) The assembly and annotation overview of 77 assemblies from 54 species across 11 families and the transcriptome sequencing overview of 42 species from 7 families, focused on a comparative analysis of genomic architecture, sensory adaptations (auditory, visual, and olfactory), and immune functions. Key findings encompass marked interspecies divergence in genome size, lineage-specific expansions/contractions of immune-related gene families (APOBEC, IFN, and PYHIN), and sensory gene adaptations linked to ecological niches. Notably, echolocating bats exhibited convergent evolution in auditory genes (SLC26A5 and FOXP2), while fruit-eating bats displayed a degeneration of vision-associated genes (RHO), reflecting trade-offs between sensory specialization and ecological demands. (2) The annotation of the V (variable), D (diversity), J (joining), and C (constant) gene families in the TR and IG loci of 12 species from five families, with a focus on a comparative analysis of the differences in TR and IG genes and CDR3 repertoires between different bats and between bats and other mammals, provides us with a deeper understanding of the development and function of the immune system in organisms. Integrated genomic, transcriptomic, and immune repertoire analyses reveal that bats employ distinct antiviral strategies, primarily mediated by enhanced immune tolerance and suppressed inflammatory responses. This review provides foundational information, collaboration directions, and new perspectives for various laboratories conducting basic and applied research on the vast array of bat biology.}, }
@article {pmid40698863, year = {2025}, author = {Woo, H and Eyun, SI}, title = {Applications and techniques of single-cell RNA sequencing across diverse species.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {4}, pages = {}, pmid = {40698863}, issn = {1477-4054}, support = {RS-2022-KS221676//Korea Institute of Marine Science &amp; Technology Promotion/ ; RS-2025-02215227//Korea Institute of Marine Science &amp; Technology Promotion/ ; 2022R1A2C4002058//National Research Foundation of Korea/ ; }, mesh = {*Single-Cell Analysis/methods ; Humans ; *Sequence Analysis, RNA/methods ; Animals ; Gene Expression Profiling/methods ; Transcriptome ; Computational Biology/methods ; }, abstract = {Single-cell ribonucleic acid sequencing (scRNA-seq) is an important tool in molecular biology, allowing transcriptomic profiling at the single-cell level. This transformative technology has provided unprecedented insights into cellular heterogeneity, lineage differentiation, and cell-type-specific gene expression patterns, significantly advancing our understanding of complex biological systems. scRNA-seq is broadly applied across various fields, including oncology, where it sheds light on intratumoral heterogeneity and precision medicine strategies, and developmental biology, where it uncovers cellular trajectories in both model and non-model organisms. Additionally, scRNA-seq has been instrumental in ecological genomics, which can help elucidate cellular responses to environmental perturbations and species interactions. Despite these advancements, several challenges remain, particularly technical and financial barriers, limiting its application to non-model organisms and tissues with complex cellular compositions. Addressing these issues will require continued innovation in single-cell isolation methods, cost-effective sequencing technologies, and sophisticated bioinformatics tools. As scRNA-seq advances, it can deepen our understanding of biological systems, with broad implications for personalized medicine, evolutionary biology, and ecological research.}, }
@article {pmid40697421, year = {2025}, author = {Boyes, D and Boyes, C and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Dark Umber moth, Philereme transversata (Hufnagel, 1767).}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {300}, pmid = {40697421}, issn = {2398-502X}, abstract = {We present a genome assembly from a male specimen of Philereme transversata (Dark Umber; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 591.75 megabases. Most of the assembly (99.1%) is scaffolded into 20 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 16.07 kilobases. Gene annotation of this assembly on Ensembl identified 12,207 protein-coding genes.}, }
@article {pmid40694591, year = {2025}, author = {Gong, R and Feng, Z and Zhang, Y}, title = {Using homologous network to identify reassortment risk in H5Nx avian influenza viruses.}, journal = {PLoS computational biology}, volume = {21}, number = {7}, pages = {e1013301}, pmid = {40694591}, issn = {1553-7358}, mesh = {Animals ; *Influenza in Birds/virology/epidemiology ; *Reassortant Viruses/genetics ; *Influenza A virus/genetics ; Birds/virology ; Computational Biology ; Poultry/virology ; Phylogeny ; }, abstract = {The resurgence of H5Nx reassortment has caused multiple epidemics resulting in severe disease even death in wild birds and poultry. Assessing H5Nx reassortment risk is crucial for designing targeted interventions and enhancing preparedness efforts to manage H5Nx outbreaks effectively. However, the complexity in H5Nx reassortment, driven by the diversity of influenza A viruses (IAVs) and wide range of hosts, has hindered the effective quantification of reassortment risk. In this study, we utilized a network approach to explore the reassortment history using a large-scale dataset. By inferring genomic homogeneity among IAVs, we constructed an IAVs homologous network with reassortment history embedded within it. We estimated the communities within the IAVs homologous network to represent the reassortment risk of various viruses, revealing diverse reassortment risks across different H5Nx viruses. Our analysis also identified the primary hosts contributing to reassortment: domestic poultry in China, and wild birds in North America and Europe. These primary hosts are critical targets for future H5Nx reassortment interventions. Our study provides a framework for quantifying and ranking H5Nx reassortment risk, contributing to enhanced preparedness and prevention efforts.}, }
@article {pmid40693914, year = {2026}, author = {Burger, J and Gochfeld, M and Brown, KG and Cortes, M and Ng, K and Kosson, DS}, title = {Using National Land Cover Database as an indicator of successful remediation: the Department of Energy's Rocky Flats (Colorado) as a case study.}, journal = {Journal of toxicology and environmental health. Part A}, volume = {89}, number = {1}, pages = {1-17}, doi = {10.1080/15287394.2025.2534616}, pmid = {40693914}, issn = {2381-3504}, mesh = {*Environmental Restoration and Remediation ; Colorado ; Ecosystem ; *Conservation of Natural Resources ; Databases, Factual ; United States ; Environmental Monitoring/methods ; }, abstract = {Missions for federal facilities, such as the Department of Defense (DOD) and the Department of Energy (DOE), include protecting human health and the environment. The public is interested in whether ecological resources are protected on such lands, especially following remediation of legacy wastes remaining from World War II, Cold War, and industrial activities. Many DOE sites are remediated for future uses depending upon potential for exposure to residual contamination. This study: (1) examined the % ecological resources remaining on Rocky Flats following completion of cleanup, (2) compared the ecological resources (i.e. plant cover) of Rocky Flats (RF) with the surrounding 10-km and 30-km bands of land, and (3) measured % natural vegetation on RF with comparable % on three other large DOE facilities that are still undergoing remediation. Rocky Flats contains significantly more grassland than the surrounding region, with less development, and is mostly a National Wildlife Refuge open to the public. Agriculture and grazing do not occur on RF. The three sites undergoing remediation have significantly more natural habitat (climax vegetation) than their surrounding buffer areas. The aim of this study was to examine the implications of ecological protection of climax vegetation upon these sites and the importance of consistently examining regional ecologies.}, }
@article {pmid40692109, year = {2025}, author = {Chiolerio, A and Konkoli, Z and Adamatzky, A}, title = {Ecosystem-based reservoir computing. Hypothesis paper.}, journal = {Bio Systems}, volume = {255}, number = {}, pages = {105525}, doi = {10.1016/j.biosystems.2025.105525}, pmid = {40692109}, issn = {1872-8324}, mesh = {*Ecosystem ; Computer Simulation ; *Ecology/methods ; Humans ; *Computational Biology/methods ; }, abstract = {Reservoir computing (RC) has emerged as a powerful computational paradigm, leveraging the intrinsic dynamics of complex systems to process temporal data efficiently. Here we propose to extend RC into ecological domains, where the ecosystems themselves can function as computational reservoirs, exploiting their complexity and extreme degree of interconnectedness. This position paper explores the concept of ecosystem-based reservoir computing (ERC), examining its theoretical foundations, empirical evidence, and potential applications. We argue that ERC not only offers a novel approach to computation, but also provides insights into the computational capabilities inherent in ecological systems and offers a new paradigm for remote sensing applications.}, }
@article {pmid40691457, year = {2025}, author = {Steckler, MR and Kumar, J and Breen, AL and Zhang, T and Hoffman, FM and Hargrove, WW and Walker, DA and Wells, AF and Droghini, A and Nawrocki, TW and Wullschleger, SD and Macander, MJ and Frost, GV and Salmon, VG and Barnett, DT and Iversen, CM}, title = {PAVC: The foundation for a Pan-Arctic Vegetation Cover database.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1271}, pmid = {40691457}, issn = {2052-4463}, mesh = {Arctic Regions ; *Plants/classification ; *Databases, Factual ; Remote Sensing Technology ; Ecosystem ; Trees ; }, abstract = {Field-measured Arctic vegetation cover data is essential for creating accurate, high-quality vegetation structure and composition maps. Extrapolating field data into high-resolution cover maps provides detailed, function-specific information for use in Earth System Models, vegetation classifications, and monitoring vegetation change over time and space. However, field campaigns that collect plant cover vary substantially in scope, method, and purpose, which makes them difficult to unify across data stores, and they are often not designed to meet remote sensing needs. In this work, we synthesized and harmonized field-based fractional cover data from various data stores to create a high-quality, consistent repository schema for remote sensing-based vegetation cover mapping applications. We developed a reproducible workflow for synthesizing visual estimate and point-intercept fractional cover data. The resultant Pan-Arctic Vegetation Cover (PAVC) database contains synthesized fractional cover at both the species and plant functional type levels. The latter includes absolute foliar cover for deciduous shrubs and trees, evergreen shrubs and trees, forbs, graminoids, lichen, bryophytes, and "other" vegetation, as well as absolute cover for litter and top cover for water and bare ground.}, }
@article {pmid40689909, year = {2025}, author = {Culbreth, AJ and Barch, DM and Nepal, S and Ben-Zeev, D and Campbell, A and Moran, EK}, title = {Passive sensing of anhedonia and amotivation in a transdiagnostic sample.}, journal = {Journal of psychopathology and clinical science}, volume = {134}, number = {8}, pages = {893-901}, pmid = {40689909}, issn = {2769-755X}, support = {R37 MH066031/MH/NIMH NIH HHS/United States ; /MH/NIMH NIH HHS/United States ; }, mesh = {*Anhedonia/physiology ; Humans ; Male ; *Ecological Momentary Assessment ; Adult ; Female ; Middle Aged ; *Major Depressive Disorder/physiopathology/diagnosis ; *Bipolar Disorder/physiopathology/diagnosis ; *Schizophrenia/physiopathology/diagnosis ; *Motivation/physiology ; Actigraphy ; Geographic Information Systems ; }, abstract = {Anhedonia and avolition are core clinical features of schizophrenia, bipolar disorder, and major depressive disorder, which have been traditionally assessed using clinical rating scales. However, recent developments in mobile technology allow for measurement of anhedonia and amotivation using passive sensors (e.g., global positioning system and actigraphy) and surveys completed in daily life (i.e., ecological momentary assessment [EMA]). The current study examined associations between clinical rating scales assessing anhedonia and amotivation and passive sensing measures. We aimed to determine the added value of passive sensing measures in explaining variability in clinical interviews, compared to models using EMA alone. We recruited a transdiagnostic sample (schizophrenia = 41, bipolar disorder = 47, and major depressive disorder = 48) to complete an in-person assessment session, as well as a 2-week EMA and passive sensing protocol. Passive sensing measures included physical distance traveled, number of phone calls sent/received, and number of texts sent/received. EMA included the assessment of interest and enjoyment in daily activities. We found that reports of interest/enjoyment in daily activities significantly predicted gold standard, clinical rating scales of anhedonia and avolition across diagnostic groups (standardized β = -0.208, p = .015, model R2 = .04). Including participant distance traveled into this model aided our ability to explain variance (standardized β = -0.280, p < .001, model R[2] = .12). Finally, adding call (standardized β = -0.170, p = .039) and text (standardized β = -0.198, p = .022) data further improved variance explained (model R[2] = .18). These data suggest that passive sensor streams strengthen the associations between assessments in daily life and gold standard ratings of anhedonia and avolition, suggesting "added value" in using these approaches to understand motivational experience in people with psychotic and mood pathology. (PsycInfo Database Record (c) 2025 APA, all rights reserved).}, }
@article {pmid40688383, year = {2025}, author = {Liu, S and Rodriguez, JS and Munteanu, V and Ronkowski, C and Sharma, NK and Alser, M and Andreace, F and Blekhman, R and Błaszczyk, D and Chikhi, R and Crandall, KA and Della Libera, K and Francis, D and Frolova, A and Gancz, AS and Huntley, NE and Jaiswal, P and Kosciolek, T and Łabaj, PP and Łabaj, W and Luan, T and Mason, C and Moustafa, AM and Muralidharan, HS and Mutlu, O and Mansouri Ghiasi, N and Rahnavard, A and Sun, F and Tian, S and Tierney, BT and Van Syoc, E and Vicedomini, R and Zackular, JP and Zelikovsky, A and Zielińska, K and Ganda, E and Davenport, ER and Pop, M and Koslicki, D and Mangul, S}, title = {Analysis of metagenomic data.}, journal = {Nature reviews. Methods primers}, volume = {5}, number = {}, pages = {}, pmid = {40688383}, issn = {2662-8449}, support = {U01 DA053941/DA/NIDA NIH HHS/United States ; R01 AI125416/AI/NIAID NIH HHS/United States ; U19 AI174998/AI/NIAID NIH HHS/United States ; U54 AG089334/AG/NIA NIH HHS/United States ; R35 GM146980/GM/NIGMS NIH HHS/United States ; R01 GM146462/GM/NIGMS NIH HHS/United States ; R01 AI173172/AI/NIAID NIH HHS/United States ; R01 AI100947/AI/NIAID NIH HHS/United States ; R21 EB031466/EB/NIBIB NIH HHS/United States ; R01 AI151059/AI/NIAID NIH HHS/United States ; R21 AI129851/AI/NIAID NIH HHS/United States ; R35 GM138369/GM/NIGMS NIH HHS/United States ; }, abstract = {Metagenomics has revolutionized our understanding of microbial communities, offering unprecedented insights into their genetic and functional diversity across Earth's diverse ecosystems. Beyond their roles as environmental constituents, microbiomes act as symbionts, profoundly influencing the health and function of their host organisms. Given the inherent complexity of these communities and the diverse environments where they reside, the components of a metagenomics study must be carefully tailored to yield accurate results that are representative of the populations of interest. This Primer article examines the methodological advancements and current practices that have shaped the field, from initial stages of sample collection and DNA extraction to the advanced bioinformatics tools employed for data analysis, with a particular focus on the profound impact of next-generation sequencing (NGS) on the scale and accuracy of metagenomics studies. We critically assess the challenges and limitations inherent in metagenomics experimentation, available technologies and computational analysis methods. Beyond technical methodologies, we explore the application of metagenomics across various domains, including human health, agriculture and environmental monitoring. Looking ahead, we advocate for the development of more robust computational frameworks and enhanced interdisciplinary collaborations. This Primer serves as a comprehensive guide for advancing the precision and applicability of metagenomic studies, positioning them to address the complexities of microbial ecology and their broader implications for human health and environmental sustainability.}, }
@article {pmid40687154, year = {2025}, author = {Filippova, NV and Zvyagina, EA and Bolshakov, SY and Arefyev, SP and Bulyonkova, TM and Filippov, IV and Rebriev, YA and Shiryaev, AG and Stavishenko, IV and Svetasheva, TY}, title = {Occurrence dataset of protected fungal species for the Red Data Book in Yugra Region, Western Siberia.}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e155657}, pmid = {40687154}, issn = {1314-2828}, abstract = {BACKGROUND: The data paper describes a dataset of occurrences of fungal species listed in the Red Data Book of Yugra Region (Western Siberia, Russia). The dataset is based on all digitised records of fungal occurrences in the region. The authors conducted an assessment of the conservation status of fungal species for the revised third edition of the Red Data Book of Yugra. The third edition of the Red Data Book of Yugra includes a total of 61 fungal species (excluding lichens). Of these, nine species are listed on the IUCN Red List and six are included in the Red Data Book of Russia. At the time of publication, the dataset comprises 1180 records of protected species, including human observations, preserved specimens and material citations from literature.<br><br>NEW INFORMATION: The paper provides the first overview of the history of fungal conservation in Yugra (Khanty-Mansi Autonomous Okrug-Yugra, KhMAO-Yugra). For the first time, open-source data are used for the assessment of the occurrence of rare species and evaluation of their conservation status for the revised third edition of the Red Data Book of Yugra. An integrated occurrence dataset for the species included in the new edition of the Red Data Book is presented.}, }
@article {pmid40683291, year = {2025}, author = {Winkler, AS and Brux, CM and Carabin, H and das Neves, CG and Häsler, B and Zinsstag, J and Fèvre, EM and Okello, A and Laing, G and Harrison, WE and Pöntinen, AK and Huber, A and Ruckert, A and Natterson-Horowitz, B and Abela, B and Aenishaenslin, C and Heymann, DL and Rødland, EK and Berthe, FCJ and Capua, I and Sejvar, J and Lubroth, J and Corander, J and May, J and Roth, LF and Thomas, LF and Blumberg, L and Lapinski, MK and Stone, M and Agbogbatey, MK and Xiao, N and Hassan, OA and Dar, O and Daszak, P and Guinto, RR and Senturk, S and Sahay, S and Samuels, TA and Wasteson, Y and Amuasi, JH}, title = {The Lancet One Health Commission: harnessing our interconnectedness for equitable, sustainable, and healthy socioecological systems.}, journal = {Lancet (London, England)}, volume = {406}, number = {10502}, pages = {501-570}, doi = {10.1016/S0140-6736(25)00627-0}, pmid = {40683291}, issn = {1474-547X}, support = {001/WHO_/World Health Organization/International ; }, }
@article {pmid40681316, year = {2025}, author = {Nekrakalaya, B and Kotimoole, CN and Arefian, M and Prasad, TSK and Palliyath, GK and Veerappa Hanumanthappa, P and Pandian Ramasubramania, TP and Bangalore Jayaseelan, NK and Muddumadiah, C and Santhappan, P and Muliyar Krishna, R}, title = {A Gel-Free Genome Annotation Provides Insights into the Proteome of the Oomycete Phytophthora meadii, a Disease-Causing Pathogen in Economically Important Crops.}, journal = {Omics : a journal of integrative biology}, volume = {29}, number = {8}, pages = {384-393}, doi = {10.1177/15578100251359566}, pmid = {40681316}, issn = {1557-8100}, mesh = {*Phytophthora/genetics/metabolism/pathogenicity ; *Proteome/genetics/metabolism ; *Plant Diseases/microbiology/parasitology ; Molecular Sequence Annotation ; *Crops, Agricultural/microbiology/parasitology ; Proteomics/methods ; Computational Biology/methods ; Tandem Mass Spectrometry ; Gene Ontology ; Chromatography, Liquid ; }, abstract = {Phytophthora meadii is a polyphagous oomycete causing fatal diseases in economically important cash crops such as rubber, arecanut, cardamom, and other crops and plants of economic significance. Although information on the proteogenomic and proteomic analysis is available for several Phytophthora species, no information on the proteome repertoire of P. meadii is available. In the present study, a gel-free protein annotation was performed using liquid chromatography with tandem mass spectrometry analysis of the P. meadii hyphae, followed by bioinformatics analysis. The results were compared with a global Phytophthora proteome database-based search and an in-house P. meadii genome database, along with RefSeq proteome databases of other selected species of Phytophthora. A total of 7725 and 3979 proteins were exclusively matched with global and in-house databases, respectively. Basic Local Alignment Search Tool analysis showed 209 unique peptide sequences belonging to 85 proteins of P. meadii. Gene Ontology-based functional analysis of the P. meadii mycelial proteome categorized the proteins based on their role in cellular components, molecular functions, and biological processes. Kyoto Encyclopedia of Genes and Genomes pathway and protein-protein network analysis further revealed the role of these proteins in growth and development functions. In addition, proteins potentially involved in virulence, infections in the host system, and several signaling mechanisms were deduced. The current study is the first report on the P. meadii mycelial proteins under optimum growth conditions. These omics data also have socioeconomic implications since Phytophthora causes disease in a wide range of economically noteworthy crops and forest ecosystems.}, }
@article {pmid40680476, year = {2025}, author = {Roel Lesur, M and Longo, MR and Tajadura-Jiménez, A}, title = {Linking spatial metaphors to body size perception: Different roles of top-down associations and multisensory contributions when mapping auditory cues to finger length.}, journal = {Cortex; a journal devoted to the study of the nervous system and behavior}, volume = {190}, number = {}, pages = {178-191}, doi = {10.1016/j.cortex.2025.06.014}, pmid = {40680476}, issn = {1973-8102}, mesh = {Humans ; Male ; *Fingers/physiology ; Female ; Adult ; Cues ; Young Adult ; *Space Perception/physiology ; *Auditory Perception/physiology ; *Size Perception/physiology ; Illusions/physiology ; *Body Size/physiology ; Attention/physiology ; *Metaphor ; Judgment/physiology ; Acoustic Stimulation ; Pitch Perception/physiology ; }, abstract = {Temporospatial and semantic multisensory aspects contribute to bodily and spatial perception. An informative paradigm to study this is the Auditory Pinocchio Illusion, in which participants perceive an elongation of their finger upon vertically pulling their finger and hearing a concurrent upward pitch glissando. This arguably relies on anchoring (i.e., associating) the ecologically unrelated upward pitch glissando to the finger and allows to separately assess the role of semantic and multisensory contributions. However, what is needed for this anchoring to occur is unknown. In a first Experiment, we manipulated top-down attention to the finger upon which either an ascending or descending sound would be produced. In a second experiment, we compared how different bottom-up multisensory cues (arising from actions performed on the finger) concurrent to the ascending or descending pitch affected finger length perception. Participants either pulled, touched or stretched their finger. Through a perceptual judgment task of finger landmark localization and questionnaire ratings, we measured participants' perceived finger length in both studies and separately assessed their sensory imagery skills. Our results show that attention alters finger length perception according to questionnaire ratings but not perceptual judgements, while concurrent multisensory signals similarly affect both measures. No relationship between these effects and participants' sensory imagery was found. We suggest that while top-down associations between pitch and verticality are necessary and affect questionnaire ratings, they are not sufficient to affect perceptual judgements. Bottom-up somatosensory cues seem to be additionally needed to impact such judgements in this illusion.}, }
@article {pmid40680084, year = {2025}, author = {Laplane, L and Lamoureux, A and Richker, HI and Marquez Alcaraz, G and Fortunato, A and Shaffer, Z and Aktipis, A and Mischel, PS and Plutynski, A and Townsend, JP and Maley, CC}, title = {Applying multilevel selection to understand cancer evolution and progression.}, journal = {PLoS biology}, volume = {23}, number = {7}, pages = {e3003290}, pmid = {40680084}, issn = {1545-7885}, support = {OT2 CA278688/CA/NCI NIH HHS/United States ; R01 CA140657/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Humans ; Biological Evolution ; Cell Proliferation ; Disease Progression ; *Neoplasms/genetics/pathology ; *Selection, Genetic ; }, abstract = {Natural selection occurs at multiple levels of organization in cancer. At an organismal level, natural selection has led to the evolution of diverse tumor suppression mechanisms, while at a cellular level, it favors traits that promote cellular proliferation, survival and cancer. Natural selection also occurs at a subcellular level, among collections of cells and even among collections of organisms; selection at these levels could influence the evolution of cancer and cancer suppression mechanisms, affecting cancer risk and treatment strategies. There may also be cancer-like processes happening at different levels of organization, in which uncontrolled proliferation at lower levels may disrupt a higher level of organization. This Essay examines how selection operates across levels, highlighting how we might leverage this understanding to improve cancer research, prevention and treatment.}, }
@article {pmid40678991, year = {2025}, author = {Miller-Ter Kuile, A and Bui, A and Apigo, A and Lamm, S and Swan, M and Sanderlin, JS and Ogle, K}, title = {If You're Rare, Should I Care? How Imperfect Detection Changes Relationships Between Biodiversity and Global Change Drivers.}, journal = {Global change biology}, volume = {31}, number = {7}, pages = {e70362}, doi = {10.1111/gcb.70362}, pmid = {40678991}, issn = {1365-2486}, support = {Challenge Cost Share 21-CS-11221635-194//Rocky Mountain Research Station/ ; }, mesh = {*Biodiversity ; Animals ; Birds ; Plants ; Insecta ; *Climate Change ; Uncertainty ; Conservation of Natural Resources ; }, abstract = {Across ecosystems and biomes, most species in biological communities are rare. Many studies discount rare species when examining biodiversity patterns, assuming that common species are most influential for ecosystem functioning. There is growing evidence, however, that rare species contribute unique functions in many ecosystems; thus, discounting them produces misleading conclusions about how biodiversity is changing in the face of natural and anthropogenic forces. Rare species are more likely to be missed by multi-species sampling designs and are thus particularly vulnerable to detection error. Best practice in biodiversity assessments should include rare species and account for error in the detection process. We outline a general approach that accounts for detection error in sampling designs using multi-species occupancy and abundance models (MSOM/MSAM). We then show how uncertainty in detection can be propagated from MSOM/MSAM results to derive more accurate estimates of alpha and beta diversity metrics. Finally, we show how uncertainty in these diversity metrics can be accounted for in follow-up regression models to evaluate relationships between biodiversity and global change covariates. Using three case studies across diverse taxa (birds, insects, and plants), we demonstrate how accounting for the detection process alters the relationships between biodiversity and global change drivers in ways that are important for understanding and predicting ongoing change in these communities. Our generalizable analysis approach can aid in accounting for rare species in studies of global biodiversity.}, }
@article {pmid40677746, year = {2025}, author = {Zhou, Y and Trujillo-González, A and Nicol, S and Huerlimann, R and Sarre, SD and Gleeson, D}, title = {Evaluation of DNA barcoding reference databases for marine species in the western and central Pacific Ocean.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19674}, pmid = {40677746}, issn = {2167-8359}, mesh = {*DNA Barcoding, Taxonomic/methods/standards ; Pacific Ocean ; Animals ; *Aquatic Organisms/genetics/classification ; Biodiversity ; Electron Transport Complex IV/genetics ; *Databases, Nucleic Acid/standards ; *Databases, Genetic ; }, abstract = {DNA barcoding is a widely used tool for species identification, with its reliability heavily dependent on reference databases. While the quality of these databases has long been debated, a critical knowledge gap remains in their comprehensive evaluation and comparison at regional scales. Marine metazoan species in the western and central Pacific Ocean (WCPO), a region characterized by high biodiversity and limited sequencing efforts, are an example of this gap. This study developed a systematic workflow to assess mitochondrial cytochrome c oxidase subunit I (COI) barcode coverage and sequence quality in two commonly used reference databases for DNA barcoding: the nucleotide reference database from the National Center for Biotechnology Information (NCBI); and from the Barcode of Life Data System (BOLD). Comparative analyses across marine phyla and WCPO regions identified significant barcode gaps and quality problems, providing insights to guide future barcoding efforts. NCBI exhibited higher barcode coverage, but lower sequence quality compared to BOLD. Quality issues, including over- or under-represented species, short sequences, ambiguous nucleotides, incomplete taxonomic information, conflict records, high intraspecific distances, and low inter-specific distances were identified in both databases, likely resulting from contamination, cryptic species, sequencing errors, or inconsistent taxonomic assignment. The barcode identification number (BIN) system in BOLD demonstrated potential for identifying and addressing problematic records, highlighting the benefits of curated databases. Significant barcode deficiencies and quality issues were observed in the south temperate region of WCPO and phyla such as Porifera, Bryozoa, and Platyhelminthes. Additionally, the COI barcode showed limited species-level resolution for certain taxa, including Scombridae and Lutjanidae. Addressing barcode coverage gaps, improving taxonomic representation, and enhancing sequence quality will be essential for strengthening future barcoding initiatives and advancing biodiversity monitoring and conservation in the WCPO and beyond. This study highlights the need for standardized database curation and sequencing practices to improve the global reliability and applicability of DNA barcoding.}, }
@article {pmid40674907, year = {2025}, author = {Fan, Q and Hu, Y and Huang, S and Guo, Y and Guo, J and Liu, F and Qi, W and Liu, H and Qu, J}, title = {Anti-epidemic pharmaceuticals predominantly contributed to PPCPs flux in the Yangtze River during 2020.}, journal = {Water research}, volume = {286}, number = {}, pages = {124228}, doi = {10.1016/j.watres.2025.124228}, pmid = {40674907}, issn = {1879-2448}, mesh = {*Rivers/chemistry ; *Water Pollutants, Chemical/analysis ; China ; COVID-19 ; Pharmaceutical Preparations/analysis ; Environmental Monitoring ; SARS-CoV-2 ; *Cosmetics/analysis ; }, abstract = {The COVID-19 pandemic triggered a surge in pharmaceutical consumption, yet its impact on large-scale riverine systems remains poorly quantified. This study investigated the spatiotemporal distribution, sources and transport flux of 58 pharmaceuticals and personal care products (PPCPs) across the Yangtze River Basin (3400 km mainstream and 8 tributaries) during 2020. The mean concentration of PPCPs was 200.2 ± 205.7 ng/L in 2020, with caffeine (28.2 %), carbamazepine (13.2 %), and metronidazole (9.2 %) as dominant compounds. It was estimated that 449.8 tons of PPCPs were discharged into the sea via the Yangtze River in 2020, of which 48 % (216.0 tons) originated from COVID-19-related pharmaceuticals (e.g., metronidazole, diclofenac). Compared to pre-pandemic levels (2018), the river experienced additional pollution pressure from 209.6 tons of COVID-19 related pharmaceutical emissions. Source apportionment identified post-consumer anthropogenic activities (domestic discharges, clinical effluent outflows, and veterinary applications) as primary contributors (p < 0.05), while industrial sources associated with pharmaceutical production contributed little. Low ecological risks were observed in the study area, likely attributable to high wastewater treatment rates (>90 % in most cities) and the high efficacy of centralized wastewater management. This study provided the first basin-scale quantitative evidence of pandemic-driven PPCP pollution, offering critical insights for balancing public health emergencies with sustainable water resource governance.}, }
@article {pmid40671367, year = {2025}, author = {Venegas-Quiñones, HL and Garcia-Chevesich, PA and Guillen, M and Alejo, F and McCray, JE}, title = {Addressing the Problem of Hard-to-Reach Unpublished Data from Theses in University Repositories.}, journal = {Ground water}, volume = {63}, number = {6}, pages = {922-925}, doi = {10.1111/gwat.70007}, pmid = {40671367}, issn = {1745-6584}, support = {470266//Center for Mining Sustainability/ ; }, mesh = {Universities ; *Groundwater ; Peru ; *Databases, Factual ; Hydrology ; }, abstract = {Researchers frequently encounter challenges in accessing valuable data encapsulated within university theses, which are predominantly archived in PDF format and remain unpublished in repositories. These documents often encompass original research, including vital environmental and hydrological data, yet they pose difficulties for searching or analysis due to inconsistent formatting and inefficient repository search tools such as keyword searches, which lead to an overwhelming list of documents. Our research team, engaged in developing a groundwater database for the Arequipa region of Peru, encountered this issue directly, with numerous relevant theses dispersed across local university repositories. The manual review process proved excessively time-consuming, necessitating the development of an innovative, automated solution. Our multi-step methodology commenced with optical character recognition (OCR) and Python scripts for keyword scoring, followed by the employment of Large Language Models (LLMs), notably Google's Gemini and the locally hosted Ollama, to semantically analyze content. This facilitated the identification and extraction of pertinent data (e.g., water quality parameters, well locations) and its organization into usable formats such as Excel spreadsheets; subsequent manual checks confirmed a high level of accuracy. The final system enables users to query an extensive number of documents swiftly and contextually, effectively overcoming traditional keyword search limitations. The tool is presently being disseminated among local researchers and institutions, offering a robust solution for accessing and managing regional groundwater data. This methodology possesses the potential for global scaling and adaptation, thereby enhancing access to gray literature and expediting scientific discovery across various disciplines.}, }
@article {pmid40670386, year = {2025}, author = {McDaniel, JH and Patel, V and Olson, ND and He, HJ and He, Z and Cole, KD and Gooden, AA and Schmitt, A and Sikkink, K and Sedlazeck, FJ and Doddapaneni, H and Jhangiani, SN and Muzny, DM and Gingras, MC and Mehta, H and Behera, S and Paulin, LF and Hastie, AR and Yu, HC and Weigman, V and Rojas, A and Kennedy, K and Remington, J and Salas-González, I and Sudkamp, M and Wiseman, K and Lajoie, BR and Levy, S and Jain, M and Akeson, S and Narzisi, G and Steinsnyder, Z and Reeves, C and Shelton, J and Kingan, SB and Lambert, C and Baybayan, P and Wenger, AM and McLaughlin, IJ and Adamson, A and Kingsley, C and Wescott, M and Kim, Y and Paten, B and Park, J and Violich, I and Miga, KH and Gardner, J and McNulty, B and Rosen, GL and McCoy, R and Brundu, F and Sayyari, E and Scheffler, K and Truong, S and Catreux, S and Hannah, LC and Lipson, D and Benjamin, H and Iremadze, N and Soifer, I and Krieger, G and Eacker, S and Wood, M and Cross, E and Husar, G and Gross, S and Vernich, M and Kolmogorov, M and Ahmad, T and Keskus, AG and Bryant, A and Thibaud-Nissen, F and Trow, J and Proszynski, J and Hirschberg, JW and Ryon, K and Mason, CE and Bhakta, MS and Sanborn, JZ and Munding, EM and Wagner, J and Xiao, C and Liss, AS and Zook, JM}, title = {Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1195}, pmid = {40670386}, issn = {2052-4463}, support = {R35 GM133747/GM/NIGMS NIH HHS/United States ; OT2OD034190//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01HG011274//U.S. Department of Health &amp; Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; OT2 OD034190/OD/NIH HHS/United States ; 60NANB20D166//United States Department of Commerce | National Institute of Standards and Technology (NIST)/ ; P01 CA272295/CA/NCI NIH HHS/United States ; S10 OD028587/OD/NIH HHS/United States ; U24 HG011853/HG/NHGRI NIH HHS/United States ; R35GM133747//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; 1936791//National Science Foundation (NSF)/ ; U01CA253405//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; U54 AG089334/AG/NIA NIH HHS/United States ; R01 CA266279/CA/NCI NIH HHS/United States ; U01 CA253405/CA/NCI NIH HHS/United States ; 1919691//National Science Foundation (NSF)/ ; R01 HG011274/HG/NHGRI NIH HHS/United States ; U24HG011853//U.S. Department of Health &amp; Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; }, mesh = {Humans ; Whole Genome Sequencing ; *Genome, Human ; *Pancreatic Neoplasms/genetics ; *Carcinoma, Pancreatic Ductal/genetics ; Cell Line, Tumor ; }, abstract = {The Genome in a Bottle Consortium (GIAB), hosted by the National Institute of Standards and Technology (NIST), is developing new matched tumor-normal samples, the first explicitly consented for public dissemination of genomic data and cell lines. Here, we describe a comprehensive genomic dataset from the first individual, HG008, including DNA from an adherent, epithelial-like pancreatic ductal adenocarcinoma (PDAC) tumor cell line and matched normal cells from duodenal and pancreatic tissues. Data for the tumor-normal matched samples comes from seventeen distinct state-of-the-art whole genome measurement technologies, including high depth short and long-read bulk whole genome sequencing (WGS), single cell WGS, Hi-C, and karyotyping. These data will be used by the GIAB Consortium to develop matched tumor-normal benchmarks for somatic variant detection. We expect these data to facilitate innovation for whole genome measurement technologies, de novo assembly of tumor and normal genomes, and bioinformatic tools to identify small and structural somatic variants. This first-of-its-kind broadly consented open-access resource will facilitate further understanding of sequencing methods used for cancer biology.}, }
@article {pmid40669920, year = {2025}, author = {Piedboeuf-Potyka, K and Hering, R and Schulz, M and Mackowiak, M and Brinks, R and Kuß, O and Hoyer, A and Tönnies, T}, title = {Incidence of type 2 diabetes by socioeconomic deprivation in Germany between 2014 and 2019: an ecological study.}, journal = {BMJ open}, volume = {15}, number = {7}, pages = {e094824}, pmid = {40669920}, issn = {2044-6055}, mesh = {Humans ; *Diabetes Mellitus, Type 2/epidemiology ; Germany/epidemiology ; Female ; Male ; Incidence ; Middle Aged ; Aged ; Adult ; *Social Deprivation ; Socioeconomic Factors ; }, abstract = {OBJECTIVE: To estimate type 2 diabetes incidence trends by sex and socioeconomic position (SEP) and evaluate trends in SEP-related inequalities in incidence.<br><br>DESIGN: Ecological study using ambulatory claims data and regression-based modelling.<br><br>SETTING: All 401 counties in Germany, covering the entire country.<br><br>PARTICIPANTS: All individuals with statutory health insurance (~85% of the population). Incident cases of type 2 diabetes were identified annually from 2014 to 2019 using the International Statistical Classification of Diseases and Related Health Problems, 10th revision codes.<br><br>Incident type 2 diabetes at the county level, adjusted for age and modelled using a mixed negative binomial regression. SEP was measured using the German Index of Socioeconomic Deprivation, and a random intercept accounted for county-level heterogeneity.<br><br>RESULTS: The incidence of type 2 diabetes decreased between 2014 and 2017 and plateaued thereafter. Trends were similar between sexes and deprivation levels. The greatest difference was observed between high and low deprivation, with an incidence rate ratio of 1.20 (95% CI: 1.14 to 1.27) among men and 1.21 (95% CI: 1.14 to 1.27) among women in 2014.<br><br>CONCLUSIONS: There was a positive trend in the decline in age-adjusted type 2 diabetes incidence between 2014 and 2019. However, social inequality persisted with deprived groups at higher risk of type 2 diabetes. The level of inequality was comparable between men and women. Continued monitoring is essential to assess whether these short-term trends persist over time.}, }
@article {pmid40664368, year = {2025}, author = {Li, P and Zhu, B and Fu, J and Liu, X and Huang, K and Pan, W and Xue, Q and Zhang, H and Zhang, A and Fu, J and Jiang, G}, title = {Nontarget Screening Analysis Combined with Computational Toxicology: A Promising Solution for Identification and Risk Assessment of Environmental Pollutants in the Big Data Era.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {29}, pages = {14842-14852}, doi = {10.1021/acs.est.4c13225}, pmid = {40664368}, issn = {1520-5851}, mesh = {Risk Assessment ; *Environmental Pollutants ; *Big Data ; *Toxicology ; }, abstract = {Synthetic chemicals are intensively utilized in modern societies, and their mixtures pose significant health and ecological threats. Nontarget screening (NTS) analysis allows for the simultaneous chemical identification and quantitative reporting of tens of thousands of chemicals in complex environmental matrices, whereas the computational toxicology (CT) serves as another high-throughput means of rapidly and comprehensively screening chemicals for toxicity. To date, there has been a lack of guidance on how to combine NTS experiments and CT for the risk assessment of chemical mixtures and the prioritization of pollutants. In this perspective, the combination of two "big data" approaches in field studies is systematically proposed. The basic principles of performing NTS and CT in environmental studies are briefly outlined. The "top-down" and "bottom-up" strategies are proposed to summarize the two technologies during the experimental design stage, in accordance with research objectives and available information and tools. Following this, a universal framework combining NTS and CT is thoroughly explored. Six recommendations for future research are highlighted to enhance the utilization of this paradigm, involving multistep combination, multidisciplinary database, application platform, multilayered functionality, effect validation, and standardization.}, }
@article {pmid40663905, year = {2025}, author = {Errea, P and Lasanta, T and Zabalza-Martínez, J and Cortijos-López, M and Nadal-Romero, E}, title = {Rethinking extensive livestock grazing to revive Mediterranean mountain landscapes.}, journal = {Journal of environmental management}, volume = {391}, number = {}, pages = {126541}, doi = {10.1016/j.jenvman.2025.126541}, pmid = {40663905}, issn = {1095-8630}, mesh = {Mediterranean Region ; Altitude ; *Herbivory ; Ecosystem ; *Livestock ; Anthropogenic Effects ; *Animal Husbandry/methods ; Conservation of Natural Resources ; Geographic Information Systems ; Public Policy ; Agroecology/methods ; Climate ; Animals ; Animal Migration ; }, abstract = {Extensive livestock grazing is vital for the socio-economic resilience of Mediterranean mountains, providing key environmental benefits. Grazing patterns result from complex interactions between topographical, environmental, and anthropogenic factors, requiring an understanding of these dynamics to optimise land management. This study analyses spatio-temporal patterns of extensive livestock grazing in the Iberian System (north-eastern Spain), a representative Mediterranean mountain with a history of agricultural abandonment. Using GPS tracking, spatial analysis, and statistical modelling, this research evaluates how land use and land cover, environmental variables, public policy, and human infrastructure affect livestock movement. Three hypotheses are tested: (1) grazing distribution is influenced by both environmental and anthropogenic factors; (2) silvopastoral systems are key components of grazing; and (3) shrub cleared areas display heterogeneous levels of use. Results reveal diurnal and seasonal patterns, with peak grazing during early morning and late afternoon, and a decline in cattle presence during autumn and winter. Approximately 81 % of grazing occurs on land subsidised by the Common Agricultural Policy (CAP), whereas sheep dominate silvopastoral areas (non-subsidised). Shrub pastures and pastures are most frequently grazed, though wooded pastures exhibited the highest intensity. Species-specific preferences were evident: sheep prefer higher altitudes and steeper terrains, while cattle favour areas with higher NDVI values. Multiple regression analysis reveals that proximity to water, salt, and feed points and livestock sheds are key predictors of grazing distribution. Shrub clearing enhances grazing activity. These findings highlight the need for targeted grazing management strategies to improve the ecological and economic sustainability of Mediterranean mountains.}, }
@article {pmid40661153, year = {2025}, author = {Castoe, TA and Daly, M and Jungo, F and Kirchhoff, KN and Koludarov, I and Mackessy, S and Macrander, J and Mehr, S and Modica, MV and Sanchez, EE and Zancolli, G and Holford, M}, title = {A Vision for VenomsBase: An Integrated Knowledgebase for the Study of Venoms and Their Applications.}, journal = {Integrative organismal biology (Oxford, England)}, volume = {7}, number = {1}, pages = {obaf026}, pmid = {40661153}, issn = {2517-4843}, abstract = {Venoms are complex bioactive mixtures that have independently evolved across diverse animal lineages, including snails, insects, sea anemones, spiders, scorpions, and snakes. Despite the growing interest in venom research, data is fragmented across disparate databases which lack standardization and interoperability. A vision for the proposed VenomsBase platform presented here seeks to address these challenges by using the best practices approach in creating a centralized, open-access platform adhering to FAIR principles (Findable, Accessible, Interoperable, and Reproducible). VenomsBase will unify venom datasets, standardize terminology, and enable comparative analyses across species, facilitating novel toxin discovery and functional annotation. Key features of VenomsBase include user-friendly data submission modules with built-in validation, advanced cross-species analysis tools, and integration of multidisciplinary datasets spanning genomics, transcriptomics, proteomics, functional assays, and ecological metadata. A modular, cloud-based design will ensure scalability, while heuristic scoring systems will guide users toward high-confidence data entries. To promote accessibility, the envisioned VenomsBase will provide tutorials, regular training sessions, case studies, and feedback loops, supporting researchers at all levels. By harmonizing venom research and addressing the limitations of outdated or nonstandardized methods, VenomsBase aims to revolutionize the field, while being continuously improved and refined by venom experts. This initiative will unlock venoms' potential to make groundbreaking discoveries, address global health challenges, and foster collaboration and innovation across the scientific community.}, }
@article {pmid40660705, year = {2025}, author = {Fernando Devasahayam, BR and Uthe, H and Poeschl, Y and Deising, HB}, title = {Confrontations of the Pathogenic Fungus Colletotrichum graminicola With a Biocontrol Bacterium or a Ubiquitous Fungus Trigger Synthesis of Secondary Metabolites With Lead Structures of Synthetic Fungicides.}, journal = {Environmental microbiology}, volume = {27}, number = {7}, pages = {e70145}, pmid = {40660705}, issn = {1462-2920}, support = {//Deutsches Zentrum f&#xfc;r integrative Biodiversit&#xe4;tsforschung Halle-Jena-Leipzig/ ; }, mesh = {*Colletotrichum/metabolism/genetics/physiology ; *Fungicides, Industrial/metabolism/chemistry ; Secondary Metabolism ; *Aspergillus nidulans/metabolism/genetics/physiology ; *Bacillus amyloliquefaciens/metabolism/physiology/genetics ; Zea mays/microbiology ; Plant Diseases/microbiology ; Biological Control Agents ; Multigene Family ; }, abstract = {Microbial biological control agents are increasingly used as an alternative to synthetic pesticides. The application of these microorganisms massively affects all members of plant-colonising microbial communities, including pathogenic fungi. In the majority of cases, the resulting competition for ecological niches is decided by the toxicity of microbial secondary metabolites (SMs) formed. In this study, we devised confrontation experiments employing the fungal maize pathogen Colletotrichum graminicola and antagonistic partners, that is the biocontrol bacterium Bacillus amyloliquefaciens and the ubiquitous ascomycete Aspergillus nidulans. Transcriptome studies uncovered strong de-regulation of the vast majority of the C. graminicola secondary metabolite biosynthetic gene clusters (SMBGCs), with 69% and 86% of these clusters de-regulated at confrontation sites with B. amyloliquefaciens or A. nidulans, respectively. In the biocontrol bacterium and in A. nidulans confronting the maize pathogen, 100% and 74% of the SMBGCs were transcriptionally de-regulated, respectively. Correspondingly, non-targeted high-resolution LC-MS/MS revealed a large repertoire of 1738 and 1466 novel features formed in the fungus-bacterium and fungus-fungus confrontation, respectively. Surprisingly, several of these belong to chemical classes with lead structures of synthetic fungicides.}, }
@article {pmid40659674, year = {2025}, author = {Ren, M and You, B and Gong, X and Zhang, P and Wang, J}, title = {Microbial genomic database of the Yangtze River, the third-longest river on Earth.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1222}, pmid = {40659674}, issn = {2052-4463}, support = {42372353, 42225708, 92251304, 92351303, 42002304//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Rivers/microbiology ; China ; *Archaea/genetics/classification ; *Bacteria/genetics/classification ; *Microbiota ; Metagenomics ; *Genome, Archaeal ; Databases, Genetic ; *Genome, Bacterial ; }, abstract = {Microbes play an important role in mediating the nutrient cycling in the river ecosystem as a hotspot for biogeochemical processes. Due to scattered sampling efforts, however, there is a lack of a systematic study of the diversity of prokaryotic genomes in the Yangtze River, the third longest river on Earth. Here, we collected 602 metagenomic datasets of water, sediment and riparian soil samples spanning the Upper, Middle, and Lower basins of the Yangtze River over a 6,300 km continuum. We reconstructed 8,110 qualified genomes represented by 927 species-level genomes at the 95% ANI threshold, spanning 31 bacterial and five archaeal phyla. We further showed that more than half of these species (61.3% ~ 82.4%) were novel according to the genomic comparison against the curated databases, greatly expanding the known diversity of river prokaryotes. This dataset depicts an overview of microbial genomic diversity in the Yangtze River and provides a resource for in-depth investigation of metabolic potential, ecology, and evolution of riverine microbiomes.}, }
@article {pmid40659395, year = {2025}, author = {Ka, MM and Gaye, ND and Tukakira, J and Kyem, D and Gary-Webb, T and Sattler, L and Jobe, M and Gaye, B}, title = {Trends over time in age-standardised prevalence of cardiometabolic risk factors in Senegal between 1975 and 2021 by sex: an ecological study from the WHO Inequality Data Repository.}, journal = {BMJ open}, volume = {15}, number = {7}, pages = {e101323}, pmid = {40659395}, issn = {2044-6055}, mesh = {Humans ; Senegal/epidemiology ; Male ; Female ; Prevalence ; Middle Aged ; *Diabetes Mellitus/epidemiology ; Adult ; *Hypertension/epidemiology ; *Obesity/epidemiology ; *Cardiometabolic Risk Factors ; Sex Factors ; World Health Organization ; Aged ; *Cardiovascular Diseases/epidemiology ; *Tobacco Use/epidemiology/trends ; Young Adult ; Overweight/epidemiology ; Risk Factors ; Adolescent ; Sex Distribution ; }, abstract = {OBJECTIVE: We aimed to analyse the time trends of cardiometabolic risk factors in Senegal from 1975 to 2021.<br><br>DESIGN: Ecological study of publicly available data from the WHO Health Inequality Data Repository.<br><br>SETTING: Disaggregated datasets from publicly available sources.<br><br>PRIMARY OUTCOME: Trends of age-standardised prevalence rates, stratified by sex for tobacco use, obesity, diabetes and hypertension, were analysed for significance.<br><br>PARTICIPANTS: Only data from Senegal were included in this study.<br><br>RESULTS: Tobacco use decreased in both sexes between 2000 and 2021, from 1.7% to 0.7% (p value 0.04) in females and from 28.1% to 12.8% (p value 0.04) in males. Obesity and overweight increased in both sexes between 1975 and 2016, from 14.2% to 35.9% (p value <0.001) in females and from 7.2% to 19.5% (p value<0.001) in males. Diabetes increased in both sexes between 1980 and 2014, from 4% to 7.3% (p value <0.001) in females and from 3.6% to 7.5% (p value <0.001) in males. Between 1990 and 2019, hypertension increased in females from 39.1% to 42.9% (p value <0.001). The prevalence of hypertension in males first rose from 37.5% to 40.0% (p value <0.001), then decreased to 37.3% (p value 0.013).<br><br>CONCLUSION: Our findings highlight changes in cardiometabolic risk factors in Senegal between 1975 and 2020 by sex. While tobacco use declined, rates of obesity, diabetes and hypertension increased. These findings underscore the need for strategies to mitigate this increase in cardiometabolic risk factors and a consequential rise in non-communicable diseases.}, }
@article {pmid40658737, year = {2025}, author = {Lundberg, DS and Kersten, S and Mehmetoğlu Boz, E and Pramoj Na Ayutthaya, P and Zhu, W and Poersch, K and Yuan, W and Swartz, S and Müller, D and Bezrukov, I and ,  and Weigel, D}, title = {A major trade-off between growth and defense in Arabidopsis thaliana can vanish in field conditions.}, journal = {PLoS biology}, volume = {23}, number = {7}, pages = {e3003237}, pmid = {40658737}, issn = {1545-7885}, mesh = {*Arabidopsis/growth &amp; development/genetics/microbiology/immunology/metabolism ; *Arabidopsis Proteins/genetics/metabolism ; Plant Diseases/microbiology/genetics/immunology ; Plant Leaves/microbiology/growth &amp; development/genetics/metabolism ; Salicylic Acid/metabolism ; Gene Expression Regulation, Plant ; Disease Resistance/genetics ; Alleles ; Microbiota ; }, abstract = {When wild plants defend themselves from pathogens, this often comes with a trade-off: the same genes that protect a plant from disease can also reduce its growth and fecundity in the absence of pathogens. One protein implicated in a major growth-defense trade-off is ACCELERATED CELL DEATH 6 (ACD6), an ion channel that modulates salicylic acid (SA) synthesis to potentiate a wide range of defenses. Wild Arabidopsis thaliana populations maintain significant functional variation at the ACD6 locus, with some alleles making the protein hyperactive. In the greenhouse, plants with hyperactive ACD6 alleles are resistant to diverse pathogens, yet they are of smaller stature, their leaves senesce earlier, and they set fewer seeds compared to plants with the standard allele. We hypothesized that ACD6 hyperactivity would not only affect the growth of microbial pathogens but also more generally change leaf microbiome assembly. To test this in an ecologically meaningful context, we compared plants with hyperactive, standard, and defective ACD6 alleles in the same field-collected soil, both outdoors and in naturally lit and climate-controlled indoor conditions, taking advantage of near-isogenic lines as well as a natural accession and a CRISPR-edited derivative. We surveyed visual phenotypes, gene expression, hormone levels, seed production, and the microbiome in each environment. The genetic precision of CRISPR-edited plants allowed us to conclude that ACD6 genotype had no effect on mature field plants in our setting, despite reproducibly dramatic effects on greenhouse plants. We conclude that additional abiotic and/or microbial signals present outdoors-but not in the greenhouse-greatly modulate ACD6 activity. This raises the possibility that the fitness costs of other commonly studied immune system genes may be grossly misjudged without field studies.}, }
@article {pmid40656455, year = {2025}, author = {Komosar, M and Tamburro, G and Graichen, U and Comani, S and Haueisen, J}, title = {Combination of spatial and temporal de-noising and artifact reduction techniques in multi-channel dry EEG.}, journal = {Frontiers in neuroscience}, volume = {19}, number = {}, pages = {1576954}, pmid = {40656455}, issn = {1662-4548}, abstract = {INTRODUCTION: Dry electroencephalography (EEG) allows for recording cortical activity in ecological scenarios with a high channel count, but it is often more prone to artifacts as compared to gel-based EEG. Spatial harmonic analysis (SPHARA) and ICA-based methods (Fingerprint and ARCI) have been separately used in previous studies for dry EEG de-noising and physiological artifact reduction. Here, we investigate if the combination of these techniques further improves EEG signal quality. For this purpose, we also introduced an improved version of SPHARA.<br><br>METHODS: Dry 64-channel EEG was recorded from 11 healthy volunteers during a motor performance paradigm (left and right hand, feet, and tongue movements). EEG signals were denoised separately using Fingerprint + ARCI, SPHARA, a combination of these two methods, and a combination of these two methods including an improved SPHARA version. The improved version of SPHARA includes an additional zeroing of artifactual jumps in single channels before application of SPHARA. The EEG signal quality after application of each denoising method was calculated by means of standard deviation (SD), signal to noise ratio (SNR), and root mean square deviation (RMSD), and a generalized linear mixed effects (GLME) model was used to identify significant changes of these parameters and quantify the changes in the EEG signal quality.<br><br>RESULTS: The grand average values of SD improved from 9.76 (reference preprocessed EEG) to 8.28, 7.91, 6.72, and 6.15 &#x3bc;V for Fingerprint + ARCI, SPHARA, Fingerprint + ARCI + SPHARA, and Fingerprint + ARCI + improved SPHARA, respectively. Similarly, the RMSD values improved from 4.65 to 4.82, 6.32, and 6.90 &#x3bc;V, and the SNR values changed from 2.31 to 1.55, 4.08, and 5.56 dB.<br><br>DISCUSSION: Our results demonstrate the different performance aspects of Fingerprint + ARCI and SPHARA, artifact reduction and de-noising techniques that complement each other. We also demonstrated that a combination of these techniques yields superior performance in the reduction of artifacts and noise in dry EEG recordings, which can be extended to infant EEG and adult MEG applications.}, }
@article {pmid40651964, year = {2025}, author = {Onofri, S and Moeller, R and Billi, D and Balsamo, M and Becker, A and Benvenuto, E and Cassaro, A and Catanzaro, I and Cockell, CS and Desiderio, A and Ellis, T and Gonzáles-Pastor, JE and Hahn, C and Leys, N and Leo, P and Maurel, MC and Pacelli, C and Pavletic, B and Ripa, C and Rothschild, LJ and Surdo, L}, title = {Synthetic biology for space exploration.}, journal = {NPJ microgravity}, volume = {11}, number = {1}, pages = {41}, pmid = {40651964}, issn = {2373-8065}, support = {4000132667/20/NL/CLR/pt//European Space Agency (ESA)/ ; }, abstract = {Human space exploration faces different challenges. Topics like Bioregenerative Life Support Systems, In Situ Resource Utilization, and radiation protection, still require for more suitable solutions to be applied in long-term space exploration. Synthetic biology could be a powerful tool for enabling human exploration of space and planets. This paper explores key topics including resource utilization, life support systems, radiation protection, and human health, providing recommendations for short-, mid-, and long-term advancements in space exploration.}, }
@article {pmid40650520, year = {2025}, author = {Talavera, A and Palmada-Flores, M and Martínez-Freiría, F and Mochales-Riaño, G and Burriel-Carranza, B and Estarellas, M and Fernández-Guiberteau, D and Camina, &#xc1; and Ursenbacher, S and Vörös, J and Halpern, B and Pla, D and Calvete, JJ and Mikheyev, AS and Marquès-Bonet, T and Carranza, S}, title = {Unveiling the Evolutionary History of European Vipers and Their Venoms From a Multi-Omic Approach.}, journal = {Molecular ecology}, volume = {34}, number = {21}, pages = {e70019}, pmid = {40650520}, issn = {1365-294X}, support = {PID2021-128901NB-I00//MCIN/AEI/10.13039/501100011033/ ; LCF/BQ/DR20/11790007//"la Caixa" doctoral fellowship programme/ ; LCF/BQ/DR20/11790032//"la Caixa" doctoral fellowship programme/ ; DL57/2016/CP1440/CT0010//FCT - Funda&#xe7;&#xe3;o para a Ciencia e Tecnologia de Portugal/ ; FPU18/04742//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; PRE2019-088729//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; PRE2022-101473//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; }, mesh = {Animals ; *Viperidae/genetics/classification ; Phylogeny ; Phylogeography ; *Evolution, Molecular ; *Viper Venoms/genetics ; Europe ; Genome ; *Biological Evolution ; Genomics ; Genetics, Population ; Multiomics ; }, abstract = {Snake genomes attract significant attention from multiple disciplines, including medicine, drug bioprospection, and evolutionary biology. However, genomic research within the Viperidae family has mostly focused on the subfamily Crotalinae, while the true vipers (Viperinae) have largely been overlooked. European vipers (Vipera) have been the subject of extensive research due to their phylogeographic and ecological diversification, as well as their venoms. Nevertheless, phylogeography and systematics in this genus have primarily relied on biased information from mitochondrial genes, which fail to capture the likely effects of introgression and are prone to biases. On the other hand, venom research in this group has been conducted predominantly through proteomics alone. In this study, we generated chromosome-level genome assemblies for three Vipera species and whole-genome sequencing data for 94 samples representing 15 Vipera lineages. This comprehensive dataset allowed us to disentangle the phylogenomic relationships of this genus, affected by mito-nuclear discordance and pervaded by ancestral introgression. Population-level analyses in the Iberian Peninsula, where the three oldest lineages within Vipera meet, revealed signals of recent adaptive introgression between old-diverged and ecologically dissimilar species, whereas chromosomal rearrangements isolate species occupying similar niches. Finally, using transcriptomic and proteomic data, we characterised the Vipera toxin-encoding genes, in which opposing selective forces were unveiled as common drivers of the evolution of venom as an integrated phenotype.}, }
@article {pmid40650501, year = {2025}, author = {Davies, H and Smyth, S and Pinchbeck, G and Pirmohamed, M and Savory, R and Noble, PJ and Killick, D}, title = {An e-Reporting Tool for Facilitating Submission of Veterinary Adverse Drug Reaction Reports.}, journal = {Journal of veterinary internal medicine}, volume = {39}, number = {4}, pages = {e70173}, pmid = {40650501}, issn = {1939-1676}, support = {204822/z/16/z/WT_/Wellcome Trust/United Kingdom ; VM0541//Veterinary Medicines Directorate/ ; }, mesh = {Animals ; *Adverse Drug Reaction Reporting Systems ; Electronic Health Records ; United Kingdom ; *Veterinary Drugs/adverse effects ; *Veterinary Medicine ; }, abstract = {BACKGROUND: Adverse events (AEs) are under-reported in veterinary medicine. The ability to report AEs directly from the practice management system (PMS) has been suggested to facilitate reporting. The Small Animal Veterinary Surveillance Network (SAVSNET) informatics system provides an opportunity to integrate reporting into the workflow such that reports can be submitted directly to the National Competent Authority, the Veterinary Medicines Directorate (VMD).<br><br>OBJECTIVES: Develop an AE reporting form linked to the PMS allowing for pre-population of some fields from the electronic health record (EHR). Analyze the quality of submitted reports.<br><br>ANIMALS: Animals attending United Kingdom (UK) first-opinion veterinary practices participating in SAVSNET.<br><br>METHODS: An AE "reporting button" was developed and available in the normal clinical workflow for SAVSNET enrolled practices using the Robovet PMS. The button facilitated capture of pertinent information relating to AEs, including the ability to append clinical notes from the associated EHR. After submission, reports were automatically submitted daily to the VMD. Report quality was assessed using an adapted version of the vigiGrade scoring system, which was used to compare the quality of reports submitted to the VMD via standard routes to those submitted via SAVSNET. Assessment of reports submitted via SAVSNET, was conducted twice. First, considering only information contained in the report and second, considering information contained in both the report and associated clinical notes.<br><br>RESULTS: Sixty reports were submitted during the first 18&#x2009;months by 42 different veterinary practices. The quality of SAVSNET reports was significantly improved by information contained within the clinical notes. These reports were more likely to be well-documented than those submitted via standard routes.<br><br>Adverse event reports populated using EHR data are well documented and can support efficient reporting of AEs in veterinary medicine.}, }
@article {pmid40648098, year = {2025}, author = {Quisbert-Trujillo, E and Vuillerme, N}, title = {Towards the Operationalization of Health Technology Sustainability Assessment and the Early Eco Design of the Internet of Medical Things.}, journal = {Sensors (Basel, Switzerland)}, volume = {25}, number = {13}, pages = {}, pmid = {40648098}, issn = {1424-8220}, support = {ANR-23-IACL-0006//National Research Agency (ANR), France/ ; ANR-10-AIRT-05//Investissements d'avenir, French program/ ; ANR-15-IDEX-02//Investissements d'avenir, French program/ ; }, mesh = {*Digital Health/economics/ethics ; *Sustainable Development/economics ; Humans ; *Internet of Things/economics/ethics ; }, abstract = {An increasing number of scholars are raising concerns about the sustainability of digital health, calling for action to prevent its harmful effects on the environment. At this point, however, the comprehensive appraisal of emerging technology in the health sector remains theoretically challenging, and highly difficult to implement in practice and in ecological design. Indeed, background factors such as the rapid evolution of technology or effectiveness-efficiency tradeoffs complicate the task of distinguishing the benefits of digital health from its drawbacks, rendering early Health Technology Sustainability Assessment (HTSA) extremely complex. Within this context, the aim of this article is to draw attention to the pragmatism that should be adopted when anticipating the sustainability of technological innovation in the medical field, while simultaneously proposing an assessment framework grounded in a structural and conceptual dissection of the fundamental purpose of smart technologies and the Internet of Medical Things (IoMT). Building on this, we demonstrate how our framework can be strategically applied through a rapid back-of-the-envelope assessment of the economic and ecological balance when introducing IoMT prototypes for treating a specific condition, based on a preliminary simulation of a defined clinical outcome. In this manner, the article presents evidence that challenges two primary hypotheses, and also encourages reflection on the central role of information and its interpretation when addressing key barriers in the HTSA of digital health. Thereby, it contributes to advancing cost-benefit and cost-effectiveness evaluation tools that support eco design strategies and guide informed decision-making regarding the integration of sustainable IoMT systems into healthcare.}, }
@article {pmid40646719, year = {2025}, author = {Tong, X and Kobayashi, Y and Ikeda, M and Wen, H and Akimoto, S-i and Shigenobu, S}, title = {Draft genome sequences of Buchnera aphidicola from three aphid species (Hemiptera: Aphididae: Eriosomatinae) associated with gall formation on elm trees.}, journal = {Microbiology resource announcements}, volume = {14}, number = {7}, pages = {e0033625}, pmid = {40646719}, issn = {2576-098X}, support = {Special Postdoctoral Researcher Fellowship//RIKEN/ ; 22K20588//Japan Society for the Promotion of Science/ ; 24-IMS-C279//National Institute for Basic Biology/ ; }, abstract = {The Buchnera aphidicola genomes from eriosomatine gall-forming aphids Tetraneura sorini, Tetraneura akinire, and Eriosoma harunire were sequenced, with genome sizes of 533,871, 530,863, and 627,315 bp, respectively. These genomes shed light on Buchnera's role in aphid symbiosis and adaptation.}, }
@article {pmid40646401, year = {2025}, author = {Cobos, ME and Dunnum, JL and Armién, B and González, P and Juárez, E and Salazar, JR and Cook, JA and Colella, JP}, title = {Selecting Sites for Strategic Surveillance of Zoonotic Pathogens: A Case Study in Panamá.}, journal = {EcoHealth}, volume = {22}, number = {3}, pages = {469-485}, pmid = {40646401}, issn = {1612-9210}, support = {ftd06-089//PICANTE (Pathogen Informatics Center for Analysis, Networking, Translation, and Education, US National Science Foundation)/ ; 347998861//Climate Change Capacity Building Program: Research and Public Health Action Award from the Centers for Infectious Diseases/ ; 111130150.501.274//Ministry of Economy and Finance of Panama/ ; FPI-MEF-056//Ministry of Economy and Finance of Panama/ ; PHoEZyTV I-II//Ministry of Economy and Finance of Panama/ ; ftd06-089//Gorgas Memorial Institute of Studies of Health, Secretaria Nacional de Ciencia y Tecnolog&#xed;a/ ; }, mesh = {Animals ; *Zoonoses/epidemiology ; Panama/epidemiology ; Humans ; Disease Reservoirs/virology ; *Mammals/virology ; *Environmental Monitoring/methods ; }, abstract = {Surveillance and monitoring of zoonotic pathogens is key to identifying and mitigating emerging public health threats. Surveillance is often designed to be taxonomically targeted or systematically dispersed across geography; however, those approaches may not represent the breadth of environments inhabited by a host, vector, or pathogen, leaving significant gaps in our understanding of pathogen dynamics in their natural reservoirs and environments. As a case study on the design of pathogen surveillance programs, we assess how well 20 years of small mammal surveys in Panamá sampled available environments and propose a multistep approach to selecting survey localities in the future. We use > 8000 georeferenced mammal specimen records, collected as part of a long-term hantavirus surveillance program, to test the completeness of country-wide environmental sampling. Despite 20 years of surveillance, our analyses identify a few key environmental sampling gaps. To refine surveillance strategies, we select a series of "core" historically sampled localities for continued surveillance, supplemented with additional environmentally distinct sites to more completely represent available environments in Panamá. Based on lessons learned through decades of surveillance, we propose a series of recommendations to improve strategic sampling of wildlife for zoonotic pathogen surveillance.}, }
@article {pmid40646315, year = {2025}, author = {Tsimpida, D and Piroddi, R and Daras, K and Melis, G}, title = {Assessing hearing health inequalities using routine health information systems.}, journal = {Journal of public health policy}, volume = {46}, number = {3}, pages = {630-644}, pmid = {40646315}, issn = {1745-655X}, support = {MHF106//National Institute for Health and Care Research/ ; NIHR200182//National Institute for Health Research Collaboration for Leadership in Applied Health Research and Care North West Coast/ ; 177946//Research England/ ; }, mesh = {Humans ; *Hearing Loss/epidemiology ; England/epidemiology ; Male ; Middle Aged ; Female ; *Health Status Disparities ; Adult ; Aged ; *Health Information Systems/statistics &amp; numerical data ; Prevalence ; Adolescent ; Young Adult ; Primary Health Care/statistics &amp; numerical data ; Socioeconomic Factors ; Child ; }, abstract = {Hearing loss is a significant public health challenge, with prevalence estimates based on projected age demographics rather than actual public health needs. This study aimed to quantify hearing loss using real-world data from primary care and explore local patterns and trends from 2013 to 2022 in Cheshire and Merseyside counties of Northwest England. Annual hearing loss prevalence was measured using an ecological space-time analysis of 2.7 million primary care records from Cheshire and Merseyside Integrated Care System. We applied cluster and outlier analysis with geographically weighted regression to examine local deprivation effects. We detected spatial clusters of high prevalence of hearing loss in Cheshire and an increasing trend in hearing loss prevalence in Halton. Deprivation accounted for up to 35% of hearing loss variance in 2020. Monitoring spatial patterns of hearing loss is crucial for addressing health inequalities and guiding targeted prevention and intervention strategies.}, }
@article {pmid40643351, year = {2025}, author = {Wang, ZR and Yu, H and Yang, ZL}, title = {Cystinarius: phylogeny and species diversity in China.}, journal = {Mycologia}, volume = {117}, number = {5}, pages = {983-999}, doi = {10.1080/00275514.2025.2518029}, pmid = {40643351}, issn = {1557-2536}, mesh = {China ; *Phylogeny ; *Agaricales/cytology/genetics ; Databases, Genetic ; }, abstract = {Cystinarius is a small genus belonging to the family Cortinariaceae, distinguished by its distinctive combination of small basidiospores and presence of both cheilo- and pleurocystidia, a combination that is rarely found in other genera within the Cortinariaceae. To date, this genus consists of only two subgenera and includes seven recognized species. Previously, only a single specimen of Cy. crassus was reported from China. Based on the analysis of 17 newly collected specimens, supported by morphological evidence and two-locus phylogenetic inference, five species, namely, Cy. fulvellus, Cy. longipes, Cy. shennongensis, Cy. crassus, and Cy. paurigarhwalensis, were recognized. Among them, the former three species are new to science, whereas the last one is new to China. This study provides comprehensive taxonomic descriptions and a detailed identification key to the Cystinarius species discovered in China.}, }
@article {pmid40642868, year = {2025}, author = {Lopez, MLD and Warren, RL and Allison, MJ and Coombe, L and Imbery, JJ and Birol, I and Helbing, CC}, title = {Conserved Sequence Identification Within Large Genomic Datasets Using 'Unikseq2': Application in Environmental DNA Assay Development.}, journal = {Molecular ecology resources}, volume = {25}, number = {7}, pages = {e70014}, pmid = {40642868}, issn = {1755-0998}, support = {//Genome Quebec/ ; //Natural Sciences and Engineering Research Council of Canada/ ; //Genome British Columbia/ ; //Digital Research Alliance of Canada/ ; //Genome Canada/ ; //Liber Ero Foundation/ ; }, mesh = {Animals ; *DNA, Environmental/genetics ; *Conserved Sequence ; *Computational Biology/methods ; Fishes/genetics/classification ; Sequence Analysis, DNA/methods ; *Genomics/methods ; }, abstract = {Identification of conserved genomic sequences and their utilisation as anchor points for clade detection and/or characterisation is a mainstay in ecological studies. For environmental DNA (eDNA) assays, effective processing of large genomic datasets is crucial for reliable species detection in biodiversity monitoring. While considerable focus has been on developing robust species-targeted assays, eDNA assays with broader taxonomic coverage (e.g., detecting any species within a taxonomic group such as fish), can significantly streamline environmental monitoring, especially when detecting individual species' DNA proves challenging. Designing such assays requires identifying conserved regions representing the target taxonomic group, a chiefly manual task that is often labor-intensive and error-prone, particularly when working with large sequence datasets. To address these challenges, we present unikseq2, an enhanced, alignment-free, k-mer-based tool for identifying unique and conserved sequences. It introduces a new functionality to identify sequence conservation among target species, enabling more informed marker selection for applications such as universal primer design. This automates sequence selection in large-scale mitochondrial genome datasets eliminating the need for manual inspection of computationally costly multiple sequence alignments. Herein, we demonstrate unikseq2's capabilities by developing and validating eDNA assays for various taxa, including Osteichthyes (bony fishes), the Salmonidae family (salmon and trout), Myotis bats and Cervus deer. Unikseq2-based eDNA assays allow for accurate detection across multiple taxonomic levels, from genus to class, enhancing the flexibility, scalability and reliability of eDNA tools in environmental monitoring. By leveraging genomic data from public repositories, unikseq2 supports efficient, reproducible assay design, making it an invaluable tool for a wide range of ecological and biodiversity research applications.}, }
@article {pmid40642517, year = {2025}, author = {Zapata-Bedoya, S and Velandia-González, M and Contreras, M and Ortiz, C and Neira, Y and La Torre, L and García, S and Salas, D and Carrizales, CJ and Echazú Torres, CD and Ojeda Ocampo, JR and Cox, A and Villalta Coro, MG and Hernándes Rocha, TA}, title = {[Validation of satellite estimates for health interventions: use of microcensus data in Bolivia, 2024Validação de estimativas por satélite para intervenções de saúde: o uso de microcensos na Bolívia, 2024].}, journal = {Revista panamericana de salud publica = Pan American journal of public health}, volume = {49}, number = {}, pages = {e71}, pmid = {40642517}, issn = {1680-5348}, abstract = {OBJECTIVE: To provide more accurate population estimates to support the operation of Bolivia's immunization program.<br><br>METHODS: This cross-sectional ecological study calculated population estimates using geospatial covariates extracted from Meta Data for Good and WorldPop satellite imagery, and validated them with the results of a microcensus conducted in five Bolivian municipalities.<br><br>RESULTS: Of the 6077 buildings identified in satellite images, 4505 residential buildings were found to be occupied. Of these, 3087 (68.52%) agreed to participate in the survey. A total of 17 617 people were expected and 13 397 were enumerated. Field enumeration identified fewer people under 30 years of age and more people over 60 years of age than expected. The Meta images provided excellent matches when analyzing population estimates by sex. Meta matched best with enumeration in rural areas, and WorldPop matched best with enumeration in urban areas.<br><br>CONCLUSIONS: This study demonstrates that combining geospatial analysis with microcensus validation can significantly improve health planning, enabling equitable resource distribution and more effective immunization coverage.}, }
@article {pmid40642052, year = {2025}, author = {Temmerman, M and Peeters, E and Delacroix, C and Arunda, M and Khalid, S and Hanson, C and Ojong, SA}, title = {The impact of implementing the women's reproductive rights agenda on climate change.}, journal = {Frontiers in global women's health}, volume = {6}, number = {}, pages = {1594066}, pmid = {40642052}, issn = {2673-5059}, abstract = {The 1994 International Conference on Population and Development (ICPD) established sexual and reproductive health and rights (SRHR) as foundational to sustainable development. Thirty years later, advancing women's reproductive rights (WRR), encompassing agency, decision-making autonomy, and universal access to family planning-remains critical not only for health and gender equity but also for mitigating environmental degradation. By reducing unintended pregnancies and empowering women to align childbearing with personal and ecological capacity, WRR alleviates ecological stressors such as deforestation while enhancing health resilience in climate-vulnerable communities. Yet, despite well-documented linkages between population dynamics and environmental change, contemporary climate policies and funding mechanisms persistently exclude WRR. This oversight undermines the potential of reproductive justice to enhance climate resilience. Additionally, claims that integrating WRR into climate agendas covertly promotes population control or represses women in low- and middle-income countries are fundamentally misleading. Crucially, research is needed to quantify the specific environmental impacts of WRR, underscoring the urgent need for robust global models to predict and validate these co-benefits. Strengthening this evidence base is imperative to inform policies that integrate WRR indicators into climate financing frameworks, ensuring gender-responsive programming. Bridging this gap requires interdisciplinary collaboration to develop metrics that capture WRR's role in reducing resource consumption and enhancing adaptive capacity. Embedding WRR within climate agendas would harmonize reproductive justice with environmental action, unlocking synergies between gender equity, health resilience, and sustainability. Fulfilling the ICPD's vision demands centering WRR in global climate strategies, thereby advancing a just and livable future for all.}, }
@article {pmid40641609, year = {2025}, author = {O'Connor, L and Behar, S and Tarrant, S and Stamegna, P and Pretz, C and Wang, B and Savage, B and Scornavacca, T and Shirshac, J and Wilkie, T and Hyder, M and Zai, A and Toomey, S and Mullen, M and Fisher, K and Tigas, E and Wong, S and McManus, DD and Alper, E and Lindenauer, PK and Dickson, E and Broach, JP and Kheterpal, V and Soni, A}, title = {Healthy at Home for COPD: An Integrated Digital Monitoring, Treatment, and Pulmonary Rehabilitation Intervention.}, journal = {BMC digital health}, volume = {3}, number = {}, pages = {}, pmid = {40641609}, issn = {2731-684X}, support = {KL2 TR001455/TR/NCATS NIH HHS/United States ; TL1 TR000145/TR/NCATS NIH HHS/United States ; U54 HL143541/HL/NHLBI NIH HHS/United States ; UL1 TR001453/TR/NCATS NIH HHS/United States ; }, abstract = {BACKGROUND: Chronic Obstructive Pulmonary Disease (COPD) is a leading cause of morbidity and mortality in the United States. Frequent exacerbations result in higher use of emergency services and hospitalizations, leading to poor patient outcomes and high costs. The objective of this study is to demonstrate the feasibility of a multimodal, community-based intervention in treating acute COPD exacerbations.<br><br>RESULTS: Over 18 months, 1,333 patients were approached and 100 (7.5%) were enrolled (mean age 66, 52% female). Ninety-six participants (96%) remained in the study for the full enrollment period. Fifty-five (55%) participated in tele-pulmonary-rehabilitation. Participants wore the smartwatch for a median of 114 days (IQR 30-210) and 18.9 hours/day (IQR16-20) resulting in a median of 1034 minutes/day (IQR 939-1133). The rate at which participants completed scheduled survey instruments ranged from 78-93%. Nearly all participants (85%) performed COPD ecological momentary assessment at least once with a median of 4.85 recordings during study participation. On average, a 2.48-point improvement (p=0.03) in COPD Assessment Test Score was observed from baseline to study completion. The adherence and symptom improvement metrics were not associated with baseline patient activation measures.<br><br>CONCLUSIONS: A multimodal intervention combining preventative care, symptom and biometric monitoring, and MIH services was feasible in adults living with COPD. Participants demonstrated high protocol fidelity and engagement and reported improved quality of life.}, }
@article {pmid40641182, year = {2025}, author = {Sung, HM and Kim, SH and Kwon, EJ and Jeong, SH and Lee, HM and Kim, YH and Oh, CK}, title = {Single-Cell Transcriptomic Analysis Reveals Hair Cell-Specific Molecular Responses to Polystyrene Nanoplastics in a Zebrafish Embryo Model.}, journal = {Biotechnology and applied biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1002/bab.70028}, pmid = {40641182}, issn = {1470-8744}, support = {RS-2023-00301938//NRF/ ; 30-2023003//Pusan National University Yangsan Hospital/ ; }, abstract = {Polystyrene nanoplastics (PSNPs) have emerged as pervasive environmental pollutants with potential toxicological effects on aquatic ecosystems. Their small size, hydrophobicity, and structural stability enable penetration into biological tissues, inducing diverse toxic responses. This study investigates the physiological and molecular impacts of PSNPs on zebrafish embryos using single-cell RNA sequencing and phenotypic analyses. While PS-NP exposure at environmentally relevant concentrations caused no significant changes in survival or overt phenotypes, it led to alterations in cell type proportions and gene expression. Differentially expressed gene (DEG) analysis revealed the upregulation of genes such as col1a1a, fgfbp2b, cytl1, and fstl1a, which were validated in vivo. These genes are associated with extracellular matrix remodeling, immune regulation, and tissue repair, suggesting that PSNPs activate defensive and reparative mechanisms in response to environmental stress. These findings highlight the molecular and cellular responses to PSNP exposure in zebrafish embryos and underscore the importance of evaluating the ecological risks posed by nanoplastics.}, }
@article {pmid40640514, year = {2025}, author = {Jaman, T and Bhaskar, S and Saikhom, V and Gogoi, RB and Sarma, KK and Aggarwal, SP}, title = {GeoAI-based soil erosion risk assessment in the Brahmaputra River Basin: a synergistic approach using RUSLE and advanced machine learning.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {8}, pages = {901}, doi = {10.1007/s10661-025-14314-w}, pmid = {40640514}, issn = {1573-2959}, mesh = {*Environmental Monitoring/methods ; *Machine Learning ; Rivers ; Risk Assessment ; Geographic Information Systems ; *Soil Erosion/statistics &amp; numerical data ; Remote Sensing Technology ; Soil/chemistry ; India ; }, abstract = {Soil erosion is a critical environmental issue in the Brahmaputra River Basin, threatening agricultural productivity, water resources, and ecological balance. This study employs the revised universal soil loss equation (RUSLE) alongside remote sensing, geographic information systems (GIS), and advanced machine learning models like random forest (RF) and gradient boosting (GB) to analyze soil erosion patterns from 2005 to 2024. The analysis revealed that average annual soil loss increased from 15.8 tons/ha/year in 2005 to 25.4 tons/ha/year in 2024, marking a 60.76% rise over two decades. Peak erosion rates were observed in 2020, with localized hotspots recording up to 32,130 tons/ha/year. Spatial analysis from 2005 to 2024 indicated substantial variability, with soil loss values ranging from - 7.024 to 9034 tons/ha in 2005. Topographic influence, quantified using the LS factor, revealed that 47.2% of the basin area has slopes steeper than 16°, significantly contributing to elevated erosion risk. The rainfall erosivity (R-factor) fluctuated throughout the period, peaking at 2305.73 MJ mm/ha h year in 2015 but declining to 799.21 MJ mm/ha h year by 2024, indicating a temporal shift in rainfall patterns. Vegetation cover improvements during this time reduced the mean C-factor from 0.52 to 0.34, though 13.8% of the basin (approximately 3.05 million ha) still falls under high to very high erosion risk zones. RF model predictions achieved an R[2] of 0.915 and RMSE of 4.82, while GB attained an R[2] of 0.952 with RMSE of 3.97, indicating superior predictive performance. These findings underscore the urgent need for targeted soil conservation measures, afforestation programs, and sustainable watershed management. The integration of AI-driven modeling with remote sensing and GIS provides a robust framework for long-term soil erosion monitoring, enabling informed decision-making for climate adaptation in the region.}, }
@article {pmid40638618, year = {2025}, author = {Nagel, CL and Chen, S and Allore, HG and Botoseneanu, A and Newsom, JT and Bishop, N and Dorr, DA and Kaye, J and Quiñones, AR}, title = {Longitudinal sequencing of cardiometabolic multimorbidity among older adults and association with subsequent dementia onset.}, journal = {PloS one}, volume = {20}, number = {7}, pages = {e0326309}, pmid = {40638618}, issn = {1932-6203}, mesh = {Humans ; Aged ; Female ; Male ; *Dementia/epidemiology/etiology ; *Multimorbidity ; Longitudinal Studies ; Aged, 80 and over ; *Cardiovascular Diseases/epidemiology/complications ; Cluster Analysis ; }, abstract = {BACKGROUND: Patterns of development of cardiometabolic multimorbidity (CMM) and the impact of specific cardiometabolic disease combinations on cognitive function are not well understood. This study utilizes sequence analysis to describe the ordering and timing of cardiometabolic disease accumulation over a five-year period and to assess both sociodemographic predictors and cognitive outcomes of typical cardiometabolic disease sequences.<br><br>METHODS: We analyzed data from the National Health and Aging Trends Study (2011-2022), including respondents aged &#x2265;65 years without CMM or cognitive impairment at baseline (N&#x2009;=&#x2009;4956). We used sequence analysis with optimal matching and hierarchical cluster analysis to describe temporal patterns of cardiometabolic disease accumulation and to construct a typology by clustering similar sequences. Sociodemographic predictors of CMM cluster membership were assessed using multinomial logistic regression and discrete time survival analysis was used to examine the association of CMM clusters with subsequent dementia development.<br><br>RESULTS: 11.8% of respondents developed CMM within 5-years. From a total of 366 distinct cardiometabolic disease sequences, we identified eight cardiometabolic sequence clusters. The first five clusters, "No Cardiometabolic Disease" (N&#x2009;=&#x2009;2283, 46.1%); "Diabetes Only" (N=642, 13.0%); Heart Disease Only" (N&#x2009;=&#x2009;297, 6.0%); "MI Only" (N&#x2009;=&#x2009;145, 2.9%); "Stroke Only" (N&#x2009;=&#x2009;132, 2.7%), were composed of persons who did not develop CMM over the observation period. The sixth cluster, "Incident CVD with Multimorbidity" (N&#x2009;=&#x2009;656, 13.2%), was largely composed of persons with no conditions at baseline who developed incident cardiometabolic disease and/or CMM during the observation period (N&#x2009;=&#x2009;477, 72.7%) and the seventh cluster, "Diabetes Multimorbidity" (N&#x2009;=&#x2009;333, 6.7%), primarily consisted of persons with diabetes who developed incident CMM. Finally, the eight cluster (N&#x2009;=&#x2009;468, 9.4%) was characterized by mortality early in the observation period with minimal CMM development during the observation period. Black and Hispanic race/ethnicity, lower wealth, and obesity were associated with increased likelihood of membership in one or both of the clusters characterized by CMM development. We observed increased dementia risk among persons in the Incident CVD with Multimorbidity cluster (HR&#x2009;=&#x2009;1.32, 95% CI&#x2009;=&#x2009;1.04-1.67) and the Diabetes MM cluster (HR&#x2009;=&#x2009;1.88, 95% CI&#x2009;=&#x2009;1.44,2.44).<br><br>CONCLUSIONS: Development of cardiometabolic multimorbidity is more likely among minoritized and/or low-income older adults and is associated with increased risk of subsequent dementia. Targeted approaches to cardiometabolic disease prevention and risk reduction may be an effective means of slowing or preventing the onset of cognitive decline among these groups.}, }
@article {pmid40638150, year = {2025}, author = {Fujioka, E and Yoshimura, K and Ujino, T and Yoda, K and Fukui, D and Hiryu, S}, title = {High-Resolution GPS Tracking of Perch-Hunting Bats, Rhinolophus nippon, during Nightly Foraging Behavior.}, journal = {Zoological science}, volume = {42}, number = {3}, pages = {249-259}, doi = {10.2108/zs240033}, pmid = {40638150}, issn = {0289-0003}, mesh = {Animals ; *Chiroptera/physiology ; *Feeding Behavior/physiology ; *Geographic Information Systems ; Echolocation ; Flight, Animal ; Male ; }, abstract = {While the echolocation behavior and specialized adaptive auditory system of the greater horseshoe bat (Rhinolophus ferrumequinum) are well documented, comprehensive insights into its wild ecology, especially its detailed nocturnal movements for foraging behavior, remain scarce. Therefore, our objective was to obtain information on the spatiotemporal features of the movements of the Japanese greater horseshoe bat (Rhinolophus nippon), a close relative of R. ferrumequinum, during foraging. Hence, we investigated the nightly flight paths of R. nippon using high-resolution GPS data loggers. Initially, hidden Markov modeling analysis classified bat flight paths into two behavioral patterns: commuting and area-restricted behavior, the latter primarily corresponding to foraging activities. Focusing on foraging behavior along their trajectory, we observed that R. nippon repeatedly foraged with brief stops lasting only a few minutes and an average distance of approximately 300 m between any two foraging sites. Notably, one individual covered a considerable distance (23.6 km) from its roost, possibly because of irregular social behavior during the mating season. Furthermore, for commuting, bats occasionally used forest roads, which were located along the middle of relatively steep slopes. In cases of echolocations with limited detection distances, echoes from the ground and adjacent tree lines offered crucial navigation cues, underscoring the significance of forest roads as nightly movement routes for echolocating bats. Overall, our findings highlight the importance and urgency of ongoing research on bat movement ecology in Japan.}, }
@article {pmid40634743, year = {2025}, author = {Zheng, H and Wu, D and Wang, S and Li, X and Jin, LN and Zhao, B and Li, S and Sun, Y and Dong, Z and Wu, Q and Chen, X and Liu, Y and Chen, J and Tian, H and Liu, Q and Jiang, J and Kan, H and He, K and He, H and Chen, C and Zhao, J and Weichenthal, S and Ji, JS and Cohen, AJ and Hao, J and Li, Q}, title = {Control of toxicity of fine particulate matter emissions in China.}, journal = {Nature}, volume = {643}, number = {8071}, pages = {404-411}, pmid = {40634743}, issn = {1476-4687}, mesh = {China ; *Particulate Matter/toxicity/analysis ; Humans ; *Air Pollution/prevention &amp; control/analysis/legislation &amp; jurisprudence/statistics &amp; numerical data/adverse effects ; *Air Pollutants/toxicity/analysis ; Vehicle Emissions/analysis ; Particle Size ; Environmental Exposure/analysis ; }, abstract = {Fine particulate matter (particulate matter with a diameter of 2.5 μm or less; PM2.5) causes millions of premature deaths globally[1], but not all particles are equally harmful[2-4]. Current air-pollution control strategies, prioritizing PM2.5 mass reduction, have provided considerable health benefits but further refinements based on differences in the toxicity of various emission sources may provide greater benefits[5-7]. Here we integrated field measurements with air-quality modelling to assess the unequal toxicities of PM2.5 from various anthropogenic sources. Our findings revealed that the toxicity per unit of PM2.5 mass differed substantially between major sources, differing by up to two orders of magnitude. PM2.5 from solid fuel combustion in residential stoves had the highest toxicity, followed by those from the metallurgy industry, brake wear, diesel vehicles, petrol vehicles, the cement industry and power plants. We further analysed the source contributions of toxicity-adjusted PM2.5 emissions and population exposures in China. From 2005 to 2021, both the PM2.5 mass and relative-potency-adjusted emissions substantially decreased. Although industrial sources contributed 57.5% to the reduction in PM2.5 mass emissions, the reduction in relative potency-adjusted emissions was driven by residential combustion (approximately 80%). Clean-air policies should consider the differing toxicities of PM2.5 when formulating source-specific emission control regulations. This study proposes a cellular toxicity-based framework for PM2.5 reduction that could address the specific health risks in diverse regions, but further epidemiological studies will be required to confirm their relevance to human health outcomes and their application to public policy.}, }
@article {pmid40632788, year = {2025}, author = {Wang, L and Wang, T and Zhang, XW and Lin, XF and Li, J and Liao, JB and Wang, RW}, title = {Evolution of foraging behaviour induces variable complexity-stability relationships in mutualist-exploiter-predator communities.}, journal = {PLoS computational biology}, volume = {21}, number = {7}, pages = {e1013245}, pmid = {40632788}, issn = {1553-7358}, mesh = {Animals ; *Predatory Behavior/physiology ; *Models, Biological ; *Biological Evolution ; Population Dynamics ; Ecosystem ; Computational Biology ; *Feeding Behavior/physiology ; *Symbiosis/physiology ; Computer Simulation ; Food Chain ; }, abstract = {Early ecological theory predicts that complex ecological networks are unstable and are unlikely to persist, despite many empirical studies of such complexity in nature. This inconsistency has fascinated ecologists for decades. To resolve the complexity-stability debate, coupling population dynamics and trait dynamics is considered to be an important way to understand the long-term stability of ecological community assemblages. However, we still do not know how eco-evolutionary feedbacks affect the relationship between complexity and stability in ecologically realistic networks with both antagonistic and mutualistic interactions. Here, we explored an adaptive network model to evaluate how the evolution of foraging preference to determine the relationship between network complexity (i.e., connectance) and stability (i.e., community persistence at steady state) in mutualist-exploiter-predator communities (MEST). Our theoretical results showed: (i) adaptive foraging of the top predator contributes to the stability of mutualism and intermediate intensity of foraging adaptations can lead to chaotic dynamics in a four-species MEST community; (ii) the complexity-stability relationship may show positive monotonic, negative monotonic, peaked and double-peaked patterns in general MEST communities, while the double-peaked pattern is only obtained when both the adaptation intensity and interspecific competition are high. Furthermore, model predictions may be consistent with both the negative monotonic pattern revealed in freshwater communities and the peaked pattern revealed in marine communities. Finally, we infer that foraging adaptations of the top predator may alter positive or/and negative feedback loops (trait-mediated indirect effects) to affect the stability of general MEST communities. Our adaptive network framework may provide an effective way to address the complexity-stability debate in real ecosystems.}, }
@article {pmid40631490, year = {2025}, author = {Ogle, K and Barber, JJ and Strange, BM and Boone, RD and Formanack, AM and Peltier, DMP}, title = {Identifying the Climate Conditions Associated With Extreme Growth States in Trees Across the Western United States.}, journal = {Global change biology}, volume = {31}, number = {7}, pages = {e70317}, doi = {10.1111/gcb.70317}, pmid = {40631490}, issn = {1365-2486}, support = {2213599//US National Science Foundation Macrosystems Biology and NEON-Enabled Science/ ; //USGS-Southwest Climate Adaptation Science Center/ ; }, mesh = {*Trees/growth &amp; development ; *Climate Change ; United States ; Droughts ; *Cycadopsida/growth &amp; development ; *Magnoliopsida/growth &amp; development ; *Climate ; Seasons ; }, abstract = {Climate extremes-e.g., drought, atmospheric rivers, heat waves-are increasing in severity and frequency across the western United States of America (USA). Tree-ring widths reflect the concurrent and legacy effects of such climate extremes, yet our ability to predict extreme tree growth is often poor. Could tree-ring data themselves identify the most important climate variables driving extreme low- and high-growth states? How does the importance of these climate drivers differ across species and time? To address these questions, we explored the spatial synchrony of extreme low- and high-growth years, the symmetry of climate effects on the probability of low- and high-growth years, and how climate drivers of extreme growth vary across tree species. We compiled ring widths for seven species (four gymnosperms and three angiosperms) from 604 sites in the western USA and classified each annual ring as representing extreme low, extreme high, or nominal growth. We used classification random forest (RF) models to evaluate the importance of 30 seasonal climate variables for predicting extreme growth, including precipitation, temperature, and vapor pressure deficit (VPD) during and up to four years prior to ring formation. For four species (three gymnosperms, one angiosperm) for which climate was predictive of growth, the RF models correctly classified 89%-98% and 80%-95% of low- and high-growth years, respectively. For these species, asymmetric climate responses dominated. Current-year winter hydroclimate (precipitation and VPD) was most important for predicting low growth, but prediction of high growth required multiple years of favorable moisture conditions, and the occurrence of low-growth years was more synchronous across space than high-growth years. Summer climate and temperature (regardless of season) were only weakly predictive of growth extremes. Our results motivate ecologically relevant definitions of drought such that current winter moisture stress exerts a dominant role in governing growth reductions in multiple tree species broadly distributed across the western USA.}, }
@article {pmid40628867, year = {2025}, author = {Lee, CT and Ng, CH and Tnah, LH and Ng, KKS and Diway, B and Khoo, E and Lee, SL}, title = {DNA profile database of Koompassia malaccensis in Malaysia and its application in forensic investigation.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {24504}, pmid = {40628867}, issn = {2045-2322}, support = {05-03-10-SF1033//Ministry of Agriculture and Food Security Malaysia/ ; 05-03-10-SF1033//Ministry of Agriculture and Food Security Malaysia/ ; 05-03-10-SF1033//Ministry of Agriculture and Food Security Malaysia/ ; 05-03-10-SF1033//Ministry of Agriculture and Food Security Malaysia/ ; 05-03-10-SF1033//Ministry of Agriculture and Food Security Malaysia/ ; }, mesh = {Malaysia ; Microsatellite Repeats/genetics ; *Forensic Genetics/methods ; *Databases, Nucleic Acid ; Humans ; Gene Frequency ; *DNA Fingerprinting/methods ; Databases, Genetic ; Genotype ; }, abstract = {DNA profiling has been an important tool in human forensic for almost four decades, revolutionising criminal investigations. In recent years, it has also been utilised in timber identification and geographical traceability of stolen logs, with notable increase in forensic DNA analysis related to forest crimes, driven by the growing concerns over illegal logging and forest conservation. In this study, DNA profile database for a tropical timber species, Koompassia malaccensis was established, with a total of 1465 samples from 56 locations across Malaysia genotyped using nine short tandem repeat (STR) markers. Based on the results of cluster analyses, the STR database was partitioned into WM (West Malaysia), EM (East Malaysia) and PS (Peat Swamp) Database. Thereafter, each regional/ecological database was characterised for forensic parameters and allele frequencies. Due to weak population differentiation, the percentage of individuals correctly assigned to the population of origin was low. However, the assignment tests to the region of origin were highly accurate (mean = 99.6%). The STR database is robust and has been used to assist the enforcement agencies in the investigation of forest crimes involving K. malaccensis. A case study is presented to demonstrate its application for individual identification in forensic context.}, }
@article {pmid40626351, year = {2025}, author = {Shirakawa, T and Ide, H and Ikehata, Y and Lu, Y and Kinouchi, R and Iwasa, T and Koga, K and Tateishi, S and Fujino, Y and Yasui, T and Horie, S}, title = {Impact of Symptoms of Late-Onset Hypogonadism as a Potential Driver of Presenteeism.}, journal = {American journal of men's health}, volume = {19}, number = {4}, pages = {15579883251343972}, pmid = {40626351}, issn = {1557-9891}, mesh = {Humans ; Male ; *Hypogonadism/epidemiology/diagnosis ; *Presenteeism/statistics &amp; numerical data ; Middle Aged ; Aged ; Adult ; Fatigue/etiology ; Testosterone/blood ; Surveys and Questionnaires ; Erectile Dysfunction ; Age of Onset ; }, abstract = {Presenteeism, defined as attending work despite physical or mental health issues that impair full productivity, is a prevalent concern with significant implications for workplace efficiency and employee well-being. Testosterone, the primary male sex hormone, plays a vital role in sustaining physical energy, cognitive function, and emotional stability-key factors for optimal work performance. This study explores the association between late-onset hypogonadism (LOH) and presenteeism, emphasizing how LOH-related symptoms such as fatigue, reduced libido, erectile dysfunction, and mood disturbances may contribute to reduced workplace productivity. Data from 96 male patients aged 27 to 76 years, who sought treatment at a university hospital for LOH-related symptoms, were analyzed using blood tests and validated questionnaires, including the Aging Males' Symptoms (AMS) scale, Work Functioning Impairment Scale (WFun), and Sexual Health Inventory for Men. Significant correlations were observed between AMS scores and both work functioning impairment and erectile dysfunction, indicating a strong link between LOH symptoms and presenteeism. In addition, symptoms such as fatigue, diminished motivation, and poor sleep quality were identified as exacerbating factors for work-related impairments. The greatest strength of this study lies in its focus on clinically diagnosed LOH patients, a factor that significantly distinguishes it from prior research on presenteeism in general working populations. This study underscores the potential benefits of testosterone replacement therapy, lifestyle modifications, and workplace wellness programs in addressing presenteeism among employees with LOH. Further research is necessary to assess the efficacy of these interventions in mitigating presenteeism and improving employee well-being.}, }
@article {pmid40623431, year = {2025}, author = {Wang, L and Liu, N and Zhou, Y and Zheng, F and Jian, S and Liu, X}, title = {Multi-omics analyses provide insights into the molecular basis for salt tolerance of Phyla nodiflora.}, journal = {The Plant journal : for cell and molecular biology}, volume = {123}, number = {1}, pages = {e70325}, doi = {10.1111/tpj.70325}, pmid = {40623431}, issn = {1365-313X}, support = {2021-400//National Key R&amp;D Program of China (Key Special Project for Marine Environmental Security and Sustainable Development of Coral Reefs)/ ; 32371326//National Natural Science Foundation of China/ ; 32070551//National Natural Science Foundation of China/ ; 2023B1212060046//Science and Technology Planning Project of Guangdong Province/ ; E3330900-01//Science and Technology Projects in Guangzhou/ ; }, mesh = {*Salt Tolerance/genetics ; Genome, Plant/genetics ; Gene Expression Regulation, Plant ; Abscisic Acid/metabolism ; Transcriptome ; Plant Proteins/genetics/metabolism ; Salt Stress ; Salt-Tolerant Plants/genetics ; Genomics ; Multiomics ; }, abstract = {The perennial herbaceous plant, Phyla nodiflora (Verbenaceae), which possesses natural resistance to multiple abiotic stresses, is widely used as a pioneer species in island ecological restoration. Due to the lack of information about its genome, the mechanism underlying its tolerance to environmental stresses, such as salinity, is almost entirely unknown. Here, we report on the high-quality genome of P. nodiflora that is 403.07 Mb in size, and which was assembled and anchored onto 18 pseudo-chromosomes. Genomic synteny revealed that P. nodiflora underwent two whole genome duplication events, which promoted the expansion of genes related to environmental adaptation and the biosynthesis of secondary metabolites. An integrated genomic and transcriptomic analysis suggested that salt stress tolerance in P. nodiflora is associated with the expansion and activated expression of genes related to abscisic acid (ABA) homeostasis and signaling. The expansion of ZEP family genes may contribute to the consistent increase in ABA levels under salt stress. Lysine acetylomic analysis revealed that exposure to salt led to widespread protein deacetylation, with these proteins primarily involved in signal transduction, carbohydrate transport and metabolism, and transcription regulation. Deacetylation of glutathione S-transferase increased enzymatic activities in response to salt-induced oxidative stress. Collectively, the genomic, transcriptomic, and lysine acetylomic analyses provide profound insight into the molecular basis of the adaptation of P. nodiflora to salt stress, and will be helpful to engineer salt-tolerant plants for ecological restoration.}, }
@article {pmid40623094, year = {2025}, author = {Morison, C and Stark, D and Huang, W}, title = {Single-cell mutational burden distributions in birth-death processes.}, journal = {PLoS computational biology}, volume = {21}, number = {7}, pages = {e1013241}, pmid = {40623094}, issn = {1553-7358}, mesh = {*Single-Cell Analysis/methods ; Humans ; *Neoplasms/genetics ; *Mutation/genetics ; Computational Biology ; *Models, Genetic ; Cell Division/genetics ; }, abstract = {Genetic mutations are footprints of cancer evolution and reveal critical dynamic parameters of tumour growth, which otherwise are hard to measure in vivo. The mutation accumulation in tumour cell populations has been described by various statistics, such as site frequency spectra (SFS), single-cell division distributions (DD) and mutational burden distributions (MBD). While DD and SFS have been intensively studied in phylogenetics especially after the development of whole genome sequencing technology of bulk samples, MBD has drawn attention more recently with the single-cell sequencing data. Although those statistics all arise from the same somatic evolutionary process, an integrated understanding of these distributions is missing and requires novel mathematical tools to better inform the ecological and evolutionary dynamics of tumours. Here we introduce dynamical matrices to analyse and unite the SFS, DD and MBD and derive recurrence relations for the expectations of these three distributions. While we successfully recover classic exact results in pure-birth cases for the SFS and the DD through our new framework, we derive a new expression for the MBD and approximate all three distributions when death is introduced. We demonstrate a natural link between the SFS and the single-cell MBD, and show that the MBD can be regenerated through the DD. Counter-intuitively, the single-cell MBD is mainly driven by the stochasticity arising in the DD, rather than the extra stochasticity in the number of mutations at each cell division.}, }
@article {pmid40622159, year = {2025}, author = {Hernandez, JB and Hayer, SS and Alvarez, S and Fischer, A and Hassenstab, HR and Cooper, K and Alsafwani, ZW and Benson, AK and Suhr Van Haute, MJ and Izard, J and Song, H-S and Clayton, JB}, title = {Microbiome and metabolome association network analysis identifies Clostridium_sensu_stricto_1 as a stronger keystone genus candidate than Bifidobacterium in the gut of common marmosets.}, journal = {mSystems}, volume = {10}, number = {8}, pages = {e0021425}, pmid = {40622159}, issn = {2379-5077}, support = {K01 OD030514/OD/NIH HHS/United States ; R25 GM141506/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Callithrix/microbiology ; *Gastrointestinal Microbiome ; *Metabolome ; *Bifidobacterium/metabolism/genetics/isolation &amp; purification ; *Clostridium/metabolism/genetics/classification ; Metabolomics/methods ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The common marmoset (Callithrix jacchus), a nonhuman primate species, is a model organism of great interest due to its translational value in a variety of research settings, including the field of microbiomics. While the composition of the marmoset's gut microbiome has been somewhat described in captivity, little is known about how gut microbiota interact with each other over time and how they relate to metabolite production. To help answer this, we characterized interactions in the gut microbiome of the common marmoset by calculating the Spearman correlation coefficient between 16S rDNA-derived relative genera abundance data and targeted metabolomics data collected longitudinally from 10 captive marmosets. Association network graphs were used to visualize significant correlations and identify genera and metabolites that have high degree centrality, marking them as more influential within the microbiome. The genus Clostridium_sensu_stricto_1 engaged in the most metabolomic associations, indicating that it potentially plays a gatekeeping role over metabolites involved in microbial growth and signaling. Its associations with downregulated taurine and bile acids further suggest Clostridium_sensu_stricto_1 modifies bile acids to exert its influence. Flavonifractor and several Bacteroidales members had the most bacterial associations and were negatively associated with Bifidobacterium, indicating a potential competitive relationship. To further characterize microbiome interactions, we performed hierarchical clustering on significant within-dataset associations and developed a new "Keystone Candidate Score" metric that identified Clostridium_sensu_stricto_1 and Alloprevotella as the most influential bacteria (so-called candidate keystone genera) in the marmoset gut microbiome.IMPORTANCEPrevious studies have identified significant individuality within the gut microbiome of common marmosets. The reasons for this inter-subject variability and how it relates to health in captivity are poorly understood, owing to a lack of knowledge regarding dynamic interactions between specific microbiota. To that end, this study characterized significant temporal associations between the gut microbiome and metabolome of healthy captive marmosets. Our findings suggest that certain microbial taxa exert a stronger influence within the gut than others. Specifically, Bifidobacterium was the most abundant genus and primary driving force behind subject-specific microbiome differences, while Clostridium_sensu_stricto_1 and bacteria from the order Bacteroidales were the main sources, respectively, for significant bacteria-metabolite and bacteria-bacteria associations. Together, this suggests that Bifidobacterium may compete with the other taxa for resources and a metabolic niche in the marmoset microbiome.}, }
@article {pmid40622136, year = {2025}, author = {Fukuta, M and Fukano, S and Maekawa, N and Kobayashi, S and Okamoto, S and Hirano, M and Nio-Kobayashi, J and Kariwa, H and Kawakami, S and Konnai, S and Yoshii, K}, title = {Development of blood-brain barrier-penetrating antibodies for neutralizing tick-borne encephalitis virus in the brain.}, journal = {mSphere}, volume = {10}, number = {7}, pages = {e0018425}, pmid = {40622136}, issn = {2379-5042}, support = {20H03136,21KK0123,21K19191,23K27079//Japan Society for the Promotion of Science/ ; 21K20761,22K15012//Japan Society for the Promotion of Science/ ; 23KJ1760//Japan Society for the Promotion of Science/ ; JP24fm0208101,JP23fk0108614,JP23wm0325059//Japan Agency for Medical Research and Development/ ; }, mesh = {*Blood-Brain Barrier/virology/immunology ; Animals ; *Encephalitis Viruses, Tick-Borne/immunology ; *Encephalitis, Tick-Borne/therapy/virology ; Mice ; *Antibodies, Viral/immunology/administration &amp; dosage/genetics ; *Brain/virology ; Humans ; *Antibodies, Neutralizing/immunology/administration &amp; dosage ; Cell Line ; Viral Proteins/genetics/immunology ; Mice, Inbred BALB C ; Endothelial Cells/virology ; Recombinant Fusion Proteins/genetics/immunology ; Female ; Glycoproteins ; Peptide Fragments ; }, abstract = {UNLABELLED: Tick-borne encephalitis virus (TBEV) belongs to the genus Flavivirus and causes tick-borne encephalitis (TBE), a disease characterized by severe neurological symptoms with a high mortality rate. Currently, no specific antiviral treatments have been developed for TBE. The blood-brain barrier (BBB) restricts drug delivery to the central nervous system, posing a major challenge in developing effective therapies targeting TBEV in the brain. In this study, we developed recombinant anti-TBEV antibodies fused with BBB-penetrating rabies virus glycoprotein (RVG) peptides to facilitate their transport across the BBB. The fusion of RVG peptides to the C-terminus of the heavy chain of whole antibodies or single-chain variable fragment had minimal impact on their neutralizing ability against TBEV. The RVG fusion enhanced antibody binding to the surface of a human brain endothelial cell line and increased permeability in an in vitro BBB model. The RVG-fused antibodies exhibited a higher transport efficiency to the brain than the non-fused antibodies following peripheral injection in mice. Notably, the peripheral administration of the RVG-fused whole antibody after viral invasion into the brain significantly neutralized TBEV in the brains of infected mice. These findings suggest that RVG-fused antibodies represent a promising therapeutic strategy for treating TBE once the virus has entered the brain.<br><br>IMPORTANCE: Tick-borne encephalitis virus is a neuroinvasive pathogen that causes severe neurologic disease, significantly affecting patients' quality of life. No specific antiviral treatment is available for tick-borne encephalitis caused by virus multiplication in the brain. The delivery of drugs to the brain via peripheral administration is often obstructed by the blood-brain barrier. To develop targeted antiviral therapies for brain infections, we engineered recombinant antibodies capable of crossing the blood-brain barrier via brain-targeted ligands. These antibodies exhibited permeability across the blood-brain barrier in both in vitro and in vivo models and notably effectively neutralized the virus within the brain following peripheral administration. This study is the first to highlight the therapeutic potential of brain-targeted recombinant antibodies after viral entry into the brain, offering a promising pathway for the development of effective antiviral treatments for tick-borne encephalitis.}, }
@article {pmid40620901, year = {2025}, author = {Schrama, N and Tilman, AR and Vasconcelos, VV}, title = {Majority illusion drives the spontaneous emergence of alternative states in common-pool resource games with network-based information.}, journal = {iScience}, volume = {28}, number = {7}, pages = {112831}, pmid = {40620901}, issn = {2589-0042}, abstract = {Common-pool resources (CPRs), including fisheries and the atmosphere, are critical for ecological, social, and economic sustainability but are easily overused. We use an agent-based model to investigate how social networks shape resource extraction outcomes. Networks with highly visible nodes can create a "majority illusion" in which most users believe high-intensity extraction is dominant, even if it is not. This misperception can push the entire population toward one of two possible states: an abundant, high-welfare resource or a depleted, low-welfare one. Aligning users' environmental impact with their visibility can mitigate this effect and steer the system toward a single, predictable outcome. These results suggest that network-based policies, such as reshaping information flows, particularly targeting high-impact hubs, could help stabilize cooperative behaviors and encourage sustainable management of CPRs, reducing the risk of tragedy-of-the-commons scenarios.}, }
@article {pmid40619084, year = {2025}, author = {Liu, X and Hu, Z and Gao, J}, title = {Assessment of soil and groundwater pollution risks from coal gangue backfilling: A case study in Inner Mongolia mining areas.}, journal = {Environmental research}, volume = {285}, number = {Pt 1}, pages = {122303}, doi = {10.1016/j.envres.2025.122303}, pmid = {40619084}, issn = {1096-0953}, mesh = {*Groundwater/chemistry/analysis ; *Soil Pollutants/analysis ; *Water Pollutants, Chemical/analysis ; China ; *Coal Mining ; Environmental Monitoring ; Risk Assessment ; Coal ; Metals, Heavy/analysis ; Soil/chemistry ; }, abstract = {This study evaluates the environmental risks of coal gangue (CG) filling through leaching experiments and numerical simulation methods. The results show that under acidic conditions, the leaching concentration of heavy metals in CG is relatively high, with copper concentration reaching 0.80 mg/L, exceeding Class I discharge standards. Under neutral conditions, the leachate indicators meet national standards. Although the reclaimed soil meets the agricultural land standards, its fertility level is relatively low (soil quality index 0.416), and cadmium, due to its high toxicity coefficient, becomes the primary ecological risk factor. The use of a layered compaction process can effectively control the migration of leachate. Numerical simulations indicate that the maximum migration depth of pollutants is 17 m, with concentrations stabilizing after 2500 days. The high mineralization of groundwater is primarily influenced by the geological background values, and the fluoride contamination plume has a diffusion range of less than 204 m. The study suggests that engineered CG filling reclamation presents controllable environmental risks and resource utilization potential. However, it is important to note that the study has limitations, such as a short monitoring period and uncertainties in the model predictions. It is recommended to conduct long-term field monitoring to comprehensively assess the environmental impact.}, }
@article {pmid40617847, year = {2025}, author = {Kindt, R and Siddique, I and Dawson, I and John, I and Pedercini, F and Lillesø, JP and Graudal, L}, title = {The Agroforestry Species Switchboard, a global resource to explore information for 107,269 plant species.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1150}, pmid = {40617847}, issn = {2052-4463}, mesh = {*Plants/classification ; *Databases, Factual ; Biodiversity ; Forestry ; }, abstract = {The Agroforestry Species Switchboard is a comprehensive vascular plant database that guides users to information for a particular taxon from a global but fragmented set of resources. Via standardized species names, a user can rapidly determine which among the 59 contributing databases contain information for a species of interest, and understand how this information can be accessed. By providing taxonomic identifiers to World Flora Online, it is straightforward to check for changes in taxonomy. Among the 59 databases referenced, ten covered over 10,000 species, 20 between 1,000 and 10,000 species, and 22 between 100 and 1,000 species. The top ten plant families for species richness across covered databases were the Fabaceae (9,537 species), Asteraceae (6,041), Rubiaceae (4,812), Poaceae (3,947), Myrtaceae (3,544), Euphorbiaceae (2,689), Malvaceae (2,478), Rosaceae (2,374), Lauraceae (2,334) and Lamiaceae (2,107). Information included in the Switchboard distinguishes 54,812 tree-like species, covering most known tree species globally. Among its applications, the Switchboard can assist species selection for ecological restoration projects to synergize biodiversity and human well-being objectives.}, }
@article {pmid40617215, year = {2026}, author = {Jiao, Y and Miao, X and Liu, X and Gao, Y and Guo, J and Liu, C and Wang, L and Qian, T and Wang, X and Hong, S}, title = {Innovative engineering of red-emissive carbon dots for profoundly sensitive and recyclable determination of malachite green in fish tissue.}, journal = {Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy}, volume = {344}, number = {Pt 1}, pages = {126631}, doi = {10.1016/j.saa.2025.126631}, pmid = {40617215}, issn = {1873-3557}, mesh = {Animals ; *Rosaniline Dyes/analysis ; *Carbon/chemistry ; *Quantum Dots/chemistry ; *Fishes/metabolism ; Limit of Detection ; Spectrometry, Fluorescence/methods ; Fluorescent Dyes/chemistry ; Reproducibility of Results ; }, abstract = {Accurate measurement of hazardous synthetic dye is highly attractive for environmental and food safety inspection. Herein, red fluorescent carbon dots (R-CDs) are meticulously engineered by employing Azure A as a fluorophore to optimize the optical characteristics, thereby promoting high-efficiency fluorescence emission at 648 nm. The constructed R-CDs demonstrate excitation-independent characteristics remarkable photostability and superior water solubility. It is encouraging that the developed R-CDs demonstrate a specific response to MG, effectively differentiating it from other substances. The engineered R-CDs demonstrate concentration-responsive fluorescence quenching towards MG, exhibiting rapid response time with a well-defined linear detection range of 0.09-8.21 μM and ultralow detection limit of 24.2 nM. Furthermore, the spike recovery analysis of MG in fish tissue demonstrated robust performance with recoveries of 97.63-106.0 % (RSD <6.37 %), highlighting the analytical reliability for MG identification in aquatic products. The aforementioned results underscore the significant potential of the developed R-CDs for MG detection in aquatic products and bolster their application in food safety inspections.}, }
@article {pmid40616287, year = {2025}, author = {Matz, MV and Black, KL}, title = {RDAforest: Identifying Environmental Drivers of Polygenic Adaptation.}, journal = {Molecular ecology resources}, volume = {25}, number = {8}, pages = {e70002}, pmid = {40616287}, issn = {1755-0998}, support = {OCE-2318775//Directorate for Biological Sciences/ ; //Nature Conservancy, NatureNet Science Fellowship/ ; }, mesh = {Animals ; *Multifactorial Inheritance ; Wolves/genetics/physiology ; *Adaptation, Biological ; *Computational Biology/methods ; *Adaptation, Physiological/genetics ; *Environment ; }, abstract = {Identifying environmental gradients driving genetic adaptation is one of the major goals of ecological genomics. We present RDAforest, a methodology that leverages the predominantly polygenic nature of adaptation and harnesses the versatility of random forest regression to solve this problem. Instead of computing individual SNP-environment associations, RDAforest seeks to explain the overall genetic covariance structure based on multiple environmental predictors. By relying on random forest instead of linear regression, this method can detect non-linear and non-monotonous dependencies as well as all possible interactions between predictors. It also incorporates a novel procedure to select the best predictor out of several correlated ones, and uses jackknifing to model uncertainty of genetic structure determination. Lastly, our methodology incorporates delineation and plotting of "adaptive neighbourhoods"-areas on the landscape that are predicted to harbour differentially adapted individuals. Such maps can be used as a guide for planning conservation and ecological restoration efforts. We demonstrate the use of RDAforest in two simulated scenarios and one real dataset (North American grey wolves).}, }
@article {pmid40612400, year = {2025}, author = {Te, TT and Boland, MR and Ghadimi, S and Dzierzewski, JM and Alessi, C and Martin, JL and Kremen, S and Bui, AAT and Naeim, A and Fung, CH}, title = {Predicting subjective sleepiness during auditory cognitive testing using voice signaling analysis.}, journal = {Sleep science and practice}, volume = {9}, number = {1}, pages = {19}, pmid = {40612400}, issn = {2398-2683}, abstract = {BACKGROUND: To determine whether objective markers of sleepiness can be collected passively using voice data to detect sleepiness in individuals undergoing testing in situations where sleepiness is not the focal point of assessment. We assessed verbal reaction time (VRT) as a vocalic marker of subjective sleepiness in middle aged and older adults with history of insomnia and benzodiazepine-receptor-agonist (BZRA) use.<br><br>METHODS: Adults aged &#x2265;55 without a diagnosis of dementia were recruited from a BZRA deprescribing clinical trial and enrolled in the present study that tested the feasibility of cognitive testing using out-of-office, self-directed mobile apps. Participants' working/episodic memory were assessed through recorded verbal responses to Verbal Paired Associates (VPA) tests, and ecological momentary assessments (EMA) of self-reported sleepiness (1[not at all] to 4[more prominent]). Using a generalized additive model, we examined the association between VRT during VPA testing and self-reported sleepiness, adjusting for demographic, test parameters, caffeine intake, cognition, mood, and BZRA-use (p&#x2264;0.05 was considered significant). A stratified k-fold cross-validation/random forest (SKCV/RF) was performed to classify sleepiness levels, adjusting for other variables.<br><br>RESULTS: We analyzed 1,513 observations from 16 patients. VRT was operationalized as the time duration between recording start time and first speech epoch. Longer VRTs were positively associated with greater EMA sleepiness (p&#x2264;0.05). The SKCV/RF model yielded a mean F1-score of 0.80 &#xb1; 0.08 across folds.<br><br>CONCLUSIONS: Longer VRTs correlated with greater self-reported sleepiness, indicating that voice data can be used as a marker of sleepiness in patients undergoing cognitive testing in out-of-office settings.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s41606-025-00141-y.}, }
@article {pmid40609068, year = {2025}, author = {Sura, SA and Lloyd-Smith, JO and Fong, P}, title = {Herbivore community function shapes resilience and bistability of coral reefs.}, journal = {PLoS computational biology}, volume = {21}, number = {7}, pages = {e1013221}, pmid = {40609068}, issn = {1553-7358}, mesh = {*Coral Reefs ; *Herbivory/physiology ; Animals ; *Fishes/physiology ; *Models, Biological ; Ecosystem ; Seaweed/physiology ; Humans ; Computational Biology ; Conservation of Natural Resources ; }, abstract = {Ecological communities globally are shifting to degraded states, motivating research into attributes supporting resilience or leading to alternative stable states. Coral reef communities are particularly vulnerable as they are facing myriad anthropogenic impacts that contribute to shifts away from coral dominance, motivating much research on whether these shifts are gradual and reversible transitions versus alternative stable states. Empirical studies demonstrate functionally-diverse herbivorous fish communities support coral reef resilience to anthropogenic impacts. However, few coral reef models incorporate herbivore and algal functional groups and quantify their effects on reef resilience and alternative stable states. We built a coral reef model that includes herbivorous fish functional groups and their algal targets and explored how this expansion affects predictions of resilience and alternative stable states under different scenarios of human impacts. We found evenness across the functional groups of herbivores is increasingly important for reef recovery as fishing pressure increases, and recovery is promoted when algal communities begin with more turf than macroalgae. Our findings also highlight that models omitting functional groups that comprise real communities will miss crucial phenomena, such as loss of alternative stable states for browser-dominated communities, or continued presence of alternative stable states in grazer-dominated communities even when fishing pressure is removed entirely. This work advances our ability to understand and predict coral reef resilience and alternative stable states in the Anthropocene, and provides guidance for conservation policy on fishing practices.}, }
@article {pmid40608756, year = {2025}, author = {Ma, J and Yang, S and Wu, Q and Hao, X and Cui, B and Su, Z}, title = {Study on the synergies and trade-offs of sectoral water use and their relationship with economic development.}, journal = {PloS one}, volume = {20}, number = {7}, pages = {e0327626}, pmid = {40608756}, issn = {1932-6203}, mesh = {*Economic Development ; China ; *Water Supply/economics ; Agriculture/economics ; *Water Resources/supply &amp; distribution ; *Conservation of Water Resources/economics ; Conservation of Natural Resources ; Industry ; }, abstract = {Water scarcity is dynamic and complex, beyond geophysical stressors and responses, it is critical to also consider how multi-sector, multiscale economic teleconnections mitigate or exacerbate water shortages. This study analyzes the spatial and temporal characteristics of Water Footprint (WF) in China from 2005 to 2022 and their relationship with economic development. The findings reveal an overall increase in China's WF, with the fastest growth observed in the Northwest and Northeast regions. Notably, Heilongjiang, Inner Mongolia, and Xinjiang experienced significant increases, while Zhejiang, Beijing, and Chongqing saw declines. Agricultural water footprint (WFargi) account for the largest share, while industrial water footprint (WFindu) show a decreasing trend, indicating improved water-use efficiency in industry. However, the rise in contamination water footprint (WFcont) and significant spatial disparities in import water footprint (WFimport) and export water footprint (WFexport) highlight the challenges in water resources management. Across different regions, there is a strong synergy between agricultural and ecological water use, while a notable trade-offs exists between industrial and agricultural water use, particularly in the Northeast. The relationship between WF consumption and economic development in China exhibits a phased pattern. From 2011 to 2016, most regions achieved strong decoupling, but from 2017 to 2022, all regions reverted to weak decoupling. This study provides new insights into the relationship between sectoral water use and economic development at regional and provincial levels, contributing to efforts to alleviate water scarcity, enhance water resources management, and promote sustainable economic development.}, }
@article {pmid40607556, year = {2025}, author = {Wu, HW and Gong, CA and Gong, ZN and Zhao, YX and Qiu, HC and Chen, AK}, title = {Monitoring of salt marsh vegetation community succession process in Yellow River Delta supported by multidimensional long time-series feature dataset.}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {36}, number = {6}, pages = {1759-1769}, doi = {10.13287/j.1001-9332.202506.029}, pmid = {40607556}, issn = {1001-9332}, mesh = {Chenopodiaceae/growth &amp; development ; China ; Conservation of Natural Resources ; *Environmental Monitoring/methods ; *Poaceae/growth &amp; development ; Population Dynamics ; Rivers ; *Wetlands ; Datasets as Topic ; }, abstract = {The spatial distribution of salt marsh vegetation in Yellow River Delta are highly heterogeneous. Accurate information on the historical distribution of salt marsh is of great significance for regional ecological stability and sustainable development. We constructed a long-series temporal-spatial-spectral multidimensional elicitation based on multi-source data, and accurately extracted information on the spatial distribution of typical salt marsh in the Yellow River Delta from 1996 to 2022 using a random forest (RF) model with recursive feature elimination, and further analyzed the succession of the native/invasive salt marsh communities since the diversion of the Yellow River in 1996. Compared to the single temporal spectral feature, the use of a temporal-spatial-spectral multidimensional feature set for extraction improved the overall accuracy of salt marsh vegetation classification by 8.4%. The classification effect of the sparse Suaeda salsa and the mixed area of Phragmites australis and Spartina alterniflora was optimized based on the temporal and spatial features of optical and SAR images. The distribution of salt marsh on the tidal flats after the Yellow River was diverted was obvious. The cover area of S. salsa communities decreased from 91.67 km[2] in 1996 to 38.11 km[2] in 2022, with the successional trend being influenced by the invasion of S. alterniflora. S. alterniflora was rapidly expanded and then distributed in large areas on the tidal flats on both sides of the current river channel since 2008. The area of the community reached the maximum (51.25 km[2]) in 2020. The invasion and expansion of S. alterniflora had a certain impact on the habitat pattern of the tidal flats.}, }
@article {pmid40605677, year = {2025}, author = {Tian, Y and Pang, J}, title = {Revealing the Coupling Coordination Mechanisms between Carbon Efficiency and Carbon Equity: The Evidence in China's Interprovincial Trade.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {27}, pages = {13705-13718}, doi = {10.1021/acs.est.4c13889}, pmid = {40605677}, issn = {1520-5851}, mesh = {China ; *Carbon ; }, abstract = {Effectively balancing carbon efficiency and carbon equity is vital for China's carbon peaking and carbon neutrality goals; however, the relationship between them remains unclear. This study first reveals the coupling coordination mechanisms between carbon efficiency and carbon equity based on Chinese provincial data from 2012 to 2017. We demonstrated that the carbon efficiency and carbon equity exhibited a strong coupling coordination relation (CCR). Carbon efficiency significantly promoted carbon equity and was a major driver of the CCR. With every 1 unit increase in carbon efficiency, carbon equity and the CCR increased by 3.766 to 5.694 units and approximately 1-2 units, respectively, and the positive impact of carbon efficiency on the CCR was approximately 6 to 8 times that of carbon equity. Carbon efficiency, carbon equity, and the CCR worsened between 2012 and 2017, and the bottom 50% of them were mainly concentrated in central and western provinces with abundant natural resources and net inflow of embodied carbon emission. Additionally, we demonstrated that resource dependence hindered carbon efficiency, carbon equity, and the CCR, and the potential transmission pathways were the crowding-out effect on the technology innovation, digital informatization, and advancement of industrial structure.}, }
@article {pmid40605266, year = {2025}, author = {Herman, C and Barker, BM and Bartelli, TF and Chandra, V and Krajmalnik-Brown, R and Jewell, M and Li, L and Liao, C and McAllister, F and Nirmalkar, K and Xavier, JB and Caporaso, JG}, title = {A review of engraftment assessments following fecal microbiota transplant.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2525478}, pmid = {40605266}, issn = {1949-0984}, support = {K99 AI175599/AI/NIAID NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; U24 CA248454/CA/NCI NIH HHS/United States ; }, mesh = {*Fecal Microbiota Transplantation ; Humans ; *Gastrointestinal Microbiome ; *Clostridium Infections/therapy/microbiology ; Clostridioides difficile/physiology ; Animals ; Feces/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {Fecal Microbiota Transplant (FMT) is a treatment for recurrent Clostridium difficile infections and is being explored for other clinical applications, from alleviating digestive and neurological disorders, to restoring microbiomes impacted by cancer treatment. Quantifying the extent of engraftment following an FMT is important in understanding a recipient's response to treatment. Engraftment and clinical response need to be investigated independently to evaluate an FMT's role (or lack thereof) in achieving a clinical response. Standardized bioinformatics methodologies for quantifying engraftment extent would not only improve assessment and understanding of FMT outcomes, but also facilitate comparison of FMT results and protocols across studies. Here we review FMT studies, integrating three concepts from microbial ecology as framework to discuss how these studies approached assessing engraftment extent: 1) Community Coalescence investigates microbiome shifts following FMT engraftment, 2) Indicator Features tracks specific microbiome features as a signal of engraftment, and 3) Resilience examines how resistant post-FMT recipients' microbiomes are to reverting back to baseline. These concepts explore subtly different questions about the microbiome following FMT. Taken together, they provide holistic insight into how an FMT alters a recipient's microbiome composition and provide a clear framework for quantifying and communicating about microbiome engraftment.}, }
@article {pmid40603442, year = {2025}, author = {Prokop, P and Balcerčík, J and Bonin, P and Thiebaut, G and Provazník, Z and Zvarík, M and Zvaríková, M and Fedor, P}, title = {The effect of fear and compassion on human willingness to protect predators and prey.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {23278}, pmid = {40603442}, issn = {2045-2322}, support = {1/0211/25//Slovak Grant Agency VEGA/ ; 1/0211/25//Slovak Grant Agency VEGA/ ; 1/0211/25//Slovak Grant Agency VEGA/ ; 1/0211/25//Slovak Grant Agency VEGA/ ; 1/0211/25//Slovak Grant Agency VEGA/ ; 1/0211/25//Slovak Grant Agency VEGA/ ; }, mesh = {Humans ; *Fear/psychology ; Female ; Male ; *Empathy ; *Predatory Behavior ; Animals ; Adult ; Young Adult ; Snakes ; Slovakia ; Conservation of Natural Resources ; }, abstract = {Human perception of predators is extremely important because the decline in biodiversity requires greater involvement from the public in species conservation. We conducted an online study in Slovakia with 225 adult participants (151 women; mean age = 24 years), who viewed a series of short videos depicting predator-prey interactions in which the predator either won or lost the encounter. Most of the predators depicted were large mammals (e.g., leopards, lions), one of which was a snake. We examined participants' compassion towards both the predator and prey and their willingness to protect these species. Participants exhibited greater compassion towards predators when they lost, whereas prey received higher compassion scores when they lost than when they won. Prey generally received higher compassion scores than predators. Fear of perceived animals was negatively correlated with compassion for predators and prey. Perceived fear and compassion for both predators and prey were positively correlated with the willingness to protect them (WTP), although these correlations were negative for the majority of predator species. WTP was not significantly influenced by the outcome of the encounter. Snakes, often considered prototypical stimuli for human fear, elicited less compassion and lower WTP compared to mammalian predators. We conclude that human sensitivity to physical interactions between predators and prey does not necessarily translate into a willingness to protect these animals. Conservation strategies need to consider the emotional and cognitive biases people hold toward different species. By acknowledging these biases, especially fear and perceived charisma, conservation campaigns may more effectively foster public support for protecting a broader range of species.}, }
@article {pmid40600126, year = {2025}, author = {Boyes, D and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Dotted Ermel moth, Ethmia dodecea (Haworth, 1828).}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {93}, pmid = {40600126}, issn = {2398-502X}, abstract = {We present a genome assembly from a male Ethmia dodecea (Dotted Ermel; Arthropoda; Insecta; Lepidoptera; Depressariidae). The genome sequence has a total length of 457.55 megabases. Most of the assembly (99.87%) is scaffolded into 29 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.34 kilobases in length.}, }
@article {pmid40598319, year = {2025}, author = {Maeke, MD and Yin, X and Wunder, LC and Vanni, C and Richter-Heitmann, T and Miravet-Verde, S and Ruscheweyh, HJ and Sunagawa, S and Fabian, J and Piontek, J and Friedrich, MW and Hassenrück, C}, title = {Extensive data mining uncovers novel diversity among members of the rare biosphere within the Thermoplasmatota.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {155}, pmid = {40598319}, issn = {2049-2618}, support = {EXC-2077-390741603//Deutsche Forschungsgemeinschaft/ ; EXC-2077-390741603//Deutsche Forschungsgemeinschaft/ ; XJ2300006031//Start-up research fund of Hainan University, China/ ; LT0050/2023-L//Human Frontier Science Program/ ; 205320_215395//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 03F0814//German Federal Ministry of Education and Research (BMBF)/ ; 03F0848A//German Federal Ministry of Education and Research (BMBF)/ ; }, mesh = {Phylogeny ; *Geologic Sediments/microbiology ; *Archaea/classification/genetics/isolation &amp; purification ; Metagenomics/methods ; *Data Mining/methods ; Metagenome ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Rare species, especially of the marine sedimentary biosphere, have long been overlooked owing to the complexity of sediment microbial communities, their sporadic temporal and patchy spatial abundance, and challenges in cultivating environmental microorganisms. In this study, we combined enrichments, targeted metagenomic sequencing, and extensive data mining to uncover uncultivated members of the archaeal rare biosphere in marine sediments.<br><br>RESULTS: In protein-amended enrichments, we detected the ecologically and metabolically uncharacterized class Candidatus Penumbrarchaeia within the phylum Thermoplasmatota. By screening more than 8000 metagenomic runs and 11,479 published genome assemblies, we expanded the phylogeny of Ca. Penumbrarchaeia by 3 novel orders. All six identified families of this class show low abundance in environmental samples characteristic of rare biosphere members. Members of the class Ca. Penumbrarchaeia were predicted to be involved in organic matter degradation in anoxic, carbon-rich habitats. All Ca. Penumbrarchaeia families contain high numbers of taxon-specific orthologous genes, highlighting their environmental adaptations and habitat specificity. Besides, members of this group exhibit the highest proportion of unknown genes within the entire phylum Thermoplasmatota, suggesting a high degree of functional novelty in this class.<br><br>CONCLUSIONS: In this study, we emphasize the necessity of targeted, data-integrative approaches to deepen our understanding of the rare biosphere and uncover the functions and metabolic potential hidden within these understudied taxa. Video Abstract.}, }
@article {pmid40594873, year = {2025}, author = {Ahammad, AKS and Abid, MB and Ahmed, I and Mariom,  and Khan, MGQ and Haque, MM and Wong, LL and Alam, MA and Bashar, MA}, title = {Transcriptomic profiling to unravel the underlying causes of early gonadal development of hilsa (Tenualosa ilisha) in Bangladesh.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {22543}, pmid = {40594873}, issn = {2045-2322}, support = {5200//Bangladesh Fisheries Research Institute/ ; }, mesh = {Female ; *Gene Expression Profiling ; Bangladesh ; *Transcriptome ; Animals ; *Ovary/growth &amp; development/metabolism ; Gene Expression Regulation, Developmental ; Gene Ontology ; }, abstract = {Hilsa (Tenualosa ilisha) is crucial to Bangladesh's economy and ecology, but recent trends show early maturation in small-sized hilsa, with unclear causes. This study aimed to identify differentially expressed genes (DEGs) between the ovaries of large and small hilsa using RNA-sequencing. Samples from both sizes were collected from the Meghna River in Chandpur District, and four ovary libraries were sequenced via the Illumina platform. A total of 908 DEGs were detected, of which 453 were up-regulated and 455 were down-regulated. Transcriptome analysis revealed significant differences in Gene Ontology terms such as extracellular region (GO:0005576), innate immune response (GO:0045087), and protein ubiquitination (GO:0016567), peptide antigen binding (GO:0042605), KEGG pathways including MAPK signaling pathway (ko04010), endocytosis (ko04144), and spliceosome (ko03040), as well as COG terms like signal transduction, between the ovary of large and small hilsa shad. These findings suggest that differentially expressed genes may play a role in regulating the ovarian development of T. ilisha. However, the entire process, from sampling to final annotation, is described here, along with the workflow. This study will offer a valuable resource for current and upcoming Hilsa transcriptome-based expression profiling studies.}, }
@article {pmid40594150, year = {2025}, author = {Lin, Y and Zhou, J and Wang, J and Xu, H and Li, Y and Chen, F and Liu, Y}, title = {Spatiotemporal evolution and driving forces of landscape ecological risk in the lower reaches of the Yellow River from 2000 to 2020.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {21375}, pmid = {40594150}, issn = {2045-2322}, support = {0031504//Shandong Top Talent Special Foundation/ ; 42201077//National Natural Science Foundation of China/ ; ZR2021QD074//Shandong Provincial Natural Science Foundation/ ; 2023M732105//China Postdoctoral Science Foundation/ ; SDMTKCY-2022-17//Open Subject of Institute of Coal Geology Planning Survey of Shandong Province/ ; 2024KJH087//the Youth Innovation Team Project of Higher School in Shandong Province, China/ ; }, mesh = {*Rivers ; China ; *Ecosystem ; Humans ; Spatio-Temporal Analysis ; *Conservation of Natural Resources ; Environmental Monitoring ; Human Activities ; Urbanization ; }, abstract = {Rapid urban development and human activities have led to drastic changes in land use, resulting to heightened ecological pressures and risks to ecosystems, especially in cities along the lower reaches of the Yellow River (CLRYR), China. However, the landscape pattern and associated ecological risks in the CLRYR in the past twenty years remain unclear. In this study, we employed the land use data to identify the primary landscape types and their transformations, providing an in-depth analysis of the prevailing landscape pattern and the landscape ecological risk (LER) in the CLRYR. Additionally, we explored the spatial distribution of LER and investigated the underlying driving forces behind these changes. The results reveal that: (1) Cropland is the main landscape type in the CLRYR region; however, the area of cropland decreases with the transition to impervious. (2) Due to human activities, landscape fragmentation and diversity have gradually increased in CLRYR, while aggregation has gradually decreased, until there was some improvement between 2015 and 2020. (3) The LER in the CLRYR region exhibits instability, with values of 0.1761, 0.1751, 0.1760, 0.1773, and 0.1751 displaying a fluctuating downward trend. Directional distribution analysis indicates a movement of the LER center of gravity towards the mouth of the Yellow River, accompanied by an increasing dispersion pattern. Analysis of driving forces suggests that natural factors hold greater explanatory power compared to social factors. Moreover, interaction detection results reveal that the combined effect of any two factors surpasses that of a single factor. The findings offer a theoretical foundation for enhancing planning policies aimed at striking a balance between environmental preservation and social advancement within the CLRYR region.}, }
@article {pmid40593040, year = {2025}, author = {Liu, S and Li, J and Xia, L and Li, R and Wang, J and Namkha, N}, title = {An integrated GIS-pXRF approach assesses ecological and human health risks from heavy metals in county level soils.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {22834}, pmid = {40593040}, issn = {2045-2322}, support = {2024WHZ0237//Technology Innovation Center for Land Engineering and Human Settlements, Shaanxi Land Engineering Construction Group Co., Ltd and Xi'an Jiaotong University/ ; 2024WHZ0237//Technology Innovation Center for Land Engineering and Human Settlements, Shaanxi Land Engineering Construction Group Co., Ltd and Xi'an Jiaotong University/ ; 2024WHZ0237//Technology Innovation Center for Land Engineering and Human Settlements, Shaanxi Land Engineering Construction Group Co., Ltd and Xi'an Jiaotong University/ ; 2023-CX-RKX-102//Innovation Capability Support Program of Shaanxi Province, China/ ; 2023-CX-RKX-102//Innovation Capability Support Program of Shaanxi Province, China/ ; 2023-CX-RKX-102//Innovation Capability Support Program of Shaanxi Province, China/ ; 2024WZ-YBXM-19//Shaanxi Province Foreign Expert Service Project/ ; 300102352502//Open Fund of Shaanxi Key Laboratory of Land Consolidation, China/ ; DJNY-YB-2023-20//Project of Shaanxi Province Land Engineering Construction Group/ ; DJNY-YB-2023-20//Project of Shaanxi Province Land Engineering Construction Group/ ; 2024JC-YBQN-0541//Natural Science Basic Research Program of Shaanxi Province/ ; }, mesh = {*Metals, Heavy/analysis ; Humans ; *Geographic Information Systems ; *Soil Pollutants/analysis ; China ; *Environmental Monitoring/methods ; *Soil/chemistry ; Risk Assessment ; Spectrometry, X-Ray Emission/methods ; }, abstract = {Counties in China are the primary components of small and mid-sized city (SMC), and at the core of China's future urbanization and industrialization development. Land is an essential nature resource providing the basis for urban-rural development, which is directly influenced by anthropogenic processes and in turn has impacts on human health. Clarifying the distribution characteristics and causes of heavy metals (HMs) pollution in soils is key to ensuring human health, as well as promoting land sustainability at county-level. In order to efficiently identify high risk regions of HMs pollution, this study proposed a geographic information system (GIS)-portable X-ray fluorescence (pXRF)-based approach to measure local soil background of HMs and to screen high risk regions in Shangzhou, China. ICP-MS and pXRF results showed a good agreement of Cr, Ni, Cu, Zn, Pb and As with R[2] ranging from 0.757 to 0.966. Soil background of Ni, Cu, Zn, As and Pb had increased by 33.34-129.74% compared to 1990 levels. HMs concentrations in soils of urban-rural fringe were generally larger than those of urban and rural area. Particularly, soil background of Zn and Pb in urban-rural fringe exceeded 28.90% and 19.93% of urban area, 46.33% and 41.91% of rural area, respectively. In high soil background regions, 25% of sampling points were considered as moderate risk or above, with ecological risk index (RI) greater than 150. As, Cr and Ni were identified as major contributors to human health risk, and children were more vulnerable than adults with considerably total non-carcinogenic risk (THI = 1.46) and carcinogenic health risk (TCR = 1.52 × 10[- 4]). Anthropogenic process including industrial manufacturing, agricultural practice, urban expansion and land conversion brought about the HMs accumulation in soils. This study indicated industrial zone in urban-rural fringe should be priority-controlled, and provided scientific basis for urban-rural environmental management and human health risk protection.}, }
@article {pmid40589590, year = {2025}, author = {Richards, CS and Vera Cruz, D and Shapiro, JW and Wootton, JT and Pfister, CA}, title = {Spatially Varying Selection Amplifies Intrapopulation Differentiation Among Phenotypic Traits in the Rocky-Shore Mussel, Mytilus californianus.}, journal = {Ecology and evolution}, volume = {15}, number = {7}, pages = {e71641}, pmid = {40589590}, issn = {2045-7758}, support = {T32 GM139782/GM/NIGMS NIH HHS/United States ; }, abstract = {Strong ecological gradients along heterogeneous environments play an important role in shaping population differentiation across species ranges. Thus, the selective pressure of environmental variation on phenotypic variation strongly affects an organism's ability to persist across diverse or new environments. We investigated the spatial variability of biological responses in the intertidal bivalve Mytilus californianus to highlight the costs and trade-offs of local adaptation and phenotypic plasticity across various functional traits in a dynamic environment, the marine intertidal. To test this, we performed a reciprocal transplant experiment with M. californianus individuals originating from the upper and lower intertidal measuring relevant phenotypic traits, followed by whole genome sequencing (WGS). We determined that morphological traits in individuals demonstrated phenotypic plasticity when moved to new environments, whereas physiological traits such as metabolism exhibited constraints in plasticity. Additionally, mussels from high intertidal zones, which experience greater heat and aerial exposure stress, maintained lower metabolic rates and showed increased frequencies of non-synonymous mutations in functionally relevant heat shock proteins when compared to low intertidal mussels. These results suggest that morphological and physiological traits responded differently to spatially varying selection within the marine intertidal.}, }
@article {pmid40588733, year = {2025}, author = {Zhang, H and Fu, Y and Cao, C and Jiang, H and Tang, R and Dai, Z and Zhang, W}, title = {Identification and characterization of novel CRESS-DNA viruses in the human respiratory tract.}, journal = {Virology journal}, volume = {22}, number = {1}, pages = {211}, pmid = {40588733}, issn = {1743-422X}, support = {82341106//National Natural Science Foundation of China/ ; 2023YFD1801301 and 2022YFC2603801//National Key Research and Development Programs of China/ ; JLY2021151//Clinical Medicine Science and Technology Development Foundation of Jiangsu University/ ; }, mesh = {Humans ; Phylogeny ; *DNA Viruses/classification/genetics/isolation &amp; purification ; Metagenomics ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; *Respiratory System/virology ; Computational Biology ; *Nasopharynx/virology ; DNA, Viral/genetics ; Female ; Male ; Adult ; }, abstract = {CRESS-DNA viruses are small, circular, single-stranded DNA viruses that have been identified in diverse environments and hosts, including vertebrates, invertebrates, and environmental samples. However, their diversity and role in the human respiratory tract remain poorly understood. In this study, we employed viral metagenomics to analyze 140 nasopharyngeal swab samples from asymptomatic individuals. High-throughput sequencing and bioinformatics analyses were used to identify and characterize novel CRESS-DNA viruses. Phylogenetic relationships were inferred based on Rep protein sequences using maximum likelihood analysis. We identified and characterized eight novel CRESS-DNA viruses, which were classified into the families Endolinaviridae and Naryaviridae, with one potentially representing a novel viral family. These viruses exhibited typical circular genomic structures encoding Rep and Cap proteins, with conserved motifs associated with rolling circle replication. Phylogenetic analysis showed that some viruses were closely related to sequences from vertebrate hosts or environmental samples, suggesting a diverse ecological distribution. Our findings expand the known diversity of CRESS-DNA viruses in the human respiratory tract and highlight their potential ecological and evolutionary significance. Further studies are needed to explore their host specificity, replication mechanisms, and potential roles in human health and disease.}, }
@article {pmid40588154, year = {2025}, author = {Wang, Y and Li, H and Tan, F and Jin, LN and Su, J and Luo, C}, title = {Root and foliar uptake, bidirectional translocation, subcellular distribution, and metabolism of tire wear particle-derived p-phenylenediamines and their quinones in Chinese cabbage and bok choy.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {382}, number = {}, pages = {126737}, doi = {10.1016/j.envpol.2025.126737}, pmid = {40588154}, issn = {1873-6424}, mesh = {*Plant Roots/chemistry/metabolism ; *Plant Leaves/chemistry/metabolism ; *Phenylenediamines/analysis/metabolism ; *Quinones/analysis/metabolism ; *Soil Pollutants/metabolism ; Microplastics/analysis/metabolism ; Motor Vehicles/statistics &amp; numerical data ; Hydroponics ; *Brassica/metabolism ; Agriculture/methods ; }, abstract = {Tire wear particles (TWPs) and TWP-derived compounds have caused global concern for their toxicity, but their impacts on vegetables, particularly through foliar absorption, remain largely unknown. We investigated the absorption, translocation, accumulation, and metabolism of TWP-derived p-phenylenediamines (PPDs) and PPD-quinones (PPDQs) in hydroponic and soil-cultured leafy vegetables by exposing them to TWPs through roots and leaves. PPDs and PPDQs can be absorbed by vegetables through both roots and leaves, with subsequent bidirectional translocation within vegetables. TWPs with smaller particle sizes and higher aging degrees can release more PPDs and PPDQs, resulting in increased absorptions by the vegetables. Leaves with higher wax secretion, lipid content, and trichome abundance exhibit greater uptake capabilities. PPDs and PPDQs absorbed by leaves can be released back into the environment through roots. The subcellular distribution and translocation of PPDs and PPDQs in vegetables are mainly controlled by their octanol-water partition coefficients with highly hydrophobic congeners primarily accumulating in cell walls and organelles. We screened the 6PPD and 6PPDQ metabolites in leafy vegetables and found that their metabolic processes are influenced by their exposure medium and tissue specificity. The results highlight the risks posed by vegetables absorbing, accumulating, and metabolizing airborne TWP-derived chemicals through their leaves.}, }
@article {pmid40586834, year = {2025}, author = {Moisa, MB and Roba, ZR and Purohit, S and Deribew, KT and Gemeda, DO}, title = {Evaluating the impact of land use and land cover change on soil moisture variability using GIS and remote sensing technology in southwestern Ethiopia.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {7}, pages = {824}, doi = {10.1007/s10661-025-14301-1}, pmid = {40586834}, issn = {1573-2959}, mesh = {Ethiopia ; *Soil/chemistry ; *Remote Sensing Technology ; *Environmental Monitoring/methods ; Geographic Information Systems ; Agriculture ; Climate Change ; Conservation of Natural Resources ; Water/analysis ; Ecosystem ; Forests ; }, abstract = {Soil moisture dynamics are critical for agriculture, water resources, and climate resilience in Ethiopia, influencing crop yields, water availability, and ecosystem health. Assessing soil moisture variability in relation to land use and cover (LULC) changes is essential for effective ecosystem conservation and climate change adaptation, ensuring sustainable development and resilience to environmental challenges. This study examines the impact of LULC changes on soil moisture variability in Southwestern Ethiopia over 30 years (1994-2024). Utilizing Landsat Thematic Mapper (1994), Enhanced Thematic Mapper Plus (2004), and Operational Land Imager/Thermal Infrared Sensor (2024) data, LULC changes were analyzed using supervised classification approach with the Maximum Likelihood Algorithm. The classification process was conducted using ERDAS Imagine 2015 software. In addition, vegetation health and soil moisture dynamics were assessed through the Normalized Difference Vegetation Index (NDVI) and the Normalized Difference Moisture Index (NDMI). Results reveal a significant increase in cultivated land from 3595.2 km[2] (42.0%) to 6183.3 km[2] (72.2%), with a corresponding decrease in forest cover from 3119.2 km[2] (36.4%) to 2030.4 km[2] (23.7%).This significant shift indicates intensive agricultural expansion at the expense of forest cover, highlighting increased land conversion pressures. NDVI values dropped from 0.71 in 1994 to 0.52 in 2024, this decline in NDVI values signifies a substantial reduction in vegetation cover and density over the 30-year period. The NDMI results indicated a decrease in peak moisture levels and average soil moisture, emphasizing a growing trend of intensified dryness. This soil moisture decline is attributed to factors such as reduced precipitation, increased evaporation, and changes in LULC. The conversion of forest land to cultivation led to a significant decrease in NDMI values, reflecting a reduction in soil moisture due to the loss of forest cover and increased evapotranspiration from agricultural activities. A strong correlation (R[2] = 0.98) between NDVI and NDMI highlights that higher vegetation cover is associated with higher soil moisture. Therefore, the study highlights the profound impact of land use and land cover changes on soil moisture, underscoring the urgent need for sustainable land management practices. These practices are critical to combat environmental degradation, improve soil moisture retention, and bolster ecosystem resilience, ensuring a sustainable and climate-resilient future.}, }
@article {pmid40585004, year = {2025}, author = {Boyes, D and Crowley, LM and Boyes, C and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Uncertain moth, Hoplodrina octogenaria (Goeze, 1781).}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {201}, pmid = {40585004}, issn = {2398-502X}, abstract = {We present a genome assembly from a male specimen of Hoplodrina octogenaria (Uncertain moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 476.65 megabases. Most of the assembly (99.98%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 15.93 kilobases.}, }
@article {pmid40583840, year = {2025}, author = {Zhou, H and Tang, J and Cheng, Z and Mei, Y}, title = {InsectTFDB: A Comprehensive Database and Analysis Platform for Insect Transcription Factors.}, journal = {Molecular ecology resources}, volume = {25}, number = {7}, pages = {e70006}, doi = {10.1111/1755-0998.70006}, pmid = {40583840}, issn = {1755-0998}, support = {2021YFD1400100//National Key Research and Development Program of China/ ; 2021YFD1400101//National Key Research and Development Program of China/ ; 32102271//National Natural Science Foundation of China/ ; 2022T150579//China Postdoctoral Science Foundation/ ; }, mesh = {*Insecta/genetics ; *Transcription Factors/genetics/metabolism ; Databases as Topic ; *Databases, Genetic ; Gene Expression Regulation ; Animals ; Gene Regulatory Networks ; Classification ; Insect Proteins/genetics/metabolism ; Genes, Insect/genetics ; Genome, Insect/physiology ; }, abstract = {Transcription factors (TFs) are key regulators of gene expression, driving diverse biological processes in insects. Despite their importance, a dedicated and comprehensive database for insect TFs has been lacking. To address this gap, we developed InsectTFDB (http://www.insecttfdb.com/), a specialised resource encompassing 1796 insect species across 21 orders, 258 families and 1034 genera. From 59,491,033 predicted proteins, we identified 1,570,627 TFs, systematically classified into six structural groups and annotated using multiple approaches. Approximately 87% of these TFs were successfully annotated to known proteins, enhancing their functional interpretability. InsectTFDB offers a user-friendly interface with four functional modules, including tools for species retrieval, TF exploration, sequence alignment and predictive analysis of novel sequences. These features make it a versatile platform for diverse research applications, from evolutionary studies to functional genomics and pest management. By providing unprecedented taxonomic coverage and reliable annotations, InsectTFDB serves as a critical resource for advancing our understanding of transcriptional regulation and gene regulatory networks across the insects.}, }
@article {pmid40583524, year = {2025}, author = {Kanamori, S and Imamura, K and Inagawa, Y and Yamauchi, T and Ikeda, H and Okuyama, T and Muto, G and Kato, R and Iida, M and Asaoka, H and Inoue, A and Watanabe, K and Tsuno, K and Sasaki, N and Kobayashi, Y and Sakuraya, A and Komase, Y and Otsuka, Y and Iwanaga, M and Inoue, R and Kuribayashi, K and Hino, A and Shimazu, A and Tsutsumi, A and Kawakami, N and Tani, N and Eguchi, H and Kojimahara, N and Ebara, T}, title = {Physical activity interventions delivered through digital health technology for improving workers' mental health symptoms: a systematic review and meta-analysis.}, journal = {Journal of occupational health}, volume = {67}, number = {1}, pages = {}, pmid = {40583524}, issn = {1348-9585}, support = {//Japan Agency for Medical Research and Development/ ; }, mesh = {Humans ; *Exercise ; Randomized Controlled Trials as Topic ; *Occupational Health ; *Mental Health ; *Digital Technology ; Depression/prevention &amp; control ; *Health Promotion/methods ; Digital Health ; }, abstract = {OBJECTIVES: This study aimed to clarify the primary preventive effects of physical activity interventions delivered through digital health technology (DHT) on workers' mental health symptoms, and to examine the conditions of attrition and adherence in these interventions.<br><br>METHODS: We examined randomized controlled trials (RCTs) that analyzed the effects of physical activity interventions delivered through DHT on workers' health outcomes. We included RCTs published in English or Japanese since 2010 and excluded studies that targeted specific diseases or secondary and tertiary prevention. We conducted the search on July 25, 2023, using Cochrane CENTRAL, Embase, PsycINFO, PubMed, and Ichushi-Web, and citation searches. We assessed risk of bias using the Cochrane Risk of Bias Tool version 2, and data were integrated using a random-effects model. Attrition rates were averaged, and adherence was qualitatively reviewed.<br><br>RESULTS: Eight studies were included in the systematic review, and 5 in the meta-analysis. Pooled effect sizes immediately after intervention were as follows: Cohen d&#x2009;=&#x2009;-0.51 (95% CI, -0.75 to -0.27) for depression and negative affect, and -0.36 (95% CI, -0.60 to -0.05) for perceived stress. The attrition rate was 16.8% and 12.4% for the control and intervention groups, with only 2 studies providing details on adherence.<br><br>CONCLUSIONS: Physical activity interventions delivered through DHT may moderately improve depression and negative affect, and slightly reduce perceived stress among workers. However, these findings should be interpreted with caution due to the limited number of studies and low evidence certainty. Future studies should explore long-term effects, additional mental health outcomes, and factors affecting adherence.}, }
@article {pmid40578867, year = {2025}, author = {Topalian, N and Fagherazzi, G and Perchoux, C}, title = {Daily mobility, activity and environmental determinants of stress in ecological momentary assessment (EMA) and GPS studies: a scoping review protocol.}, journal = {BMJ open}, volume = {15}, number = {6}, pages = {e091509}, pmid = {40578867}, issn = {2044-6055}, mesh = {Humans ; Scoping Reviews as Topic ; *Ecological Momentary Assessment ; *Geographic Information Systems ; *Stress, Psychological ; Research Design ; *Activities of Daily Living ; Environment ; }, abstract = {INTRODUCTION: Stress is omnipresent in our everyday lives and a key risk factor for our physical and mental health. Yet little is known about the impact of geographic life environments, linked to our daily activities and mobility patterns, on our momentary and daily stress levels.We propose this review to gather evidence on the spatio-temporal determinants of momentary or daily stress in studies using ecological momentary assessment (EMA) or experience sampling methods (ESM) in addition to global positioning systems (GPS) tracking. We will focus on the spatio-temporal definition and modelling of environmental exposures accounting for participant daily activities and mobility patterns and their association with stress.<br><br>METHODS AND ANALYSIS: This scoping review will follow the Preferred Reporting Items for Systematic Reviews and Meta-Analyses framework for scoping reviews (2018). We will search the PubMed/Medline, Web of Science, PsycInfo and Scopus databases. We will include papers using EMA or ESM and GPS measuring chronic, daily or momentary stress as an outcome; these methods are also referred to as geographically-explicit ecological momentary assessment.Articles published from January 2000-June 2025 will be screened. Two independent reviewers will screen titles and abstracts to agree on the inclusion of articles. No geographical or population limitation will be imposed.<br><br>ETHICS AND DISSEMINATION: This study is a scoping review based on previously published and publicly available literature. It does not involve the collection of primary data, human participants, or the processing of personal or sensitive information. Therefore, ethical approval is not required in accordance with institutional and international research ethics guidelines. The results will be submitted in peer-reviewed journals and presented at international conferences.}, }
@article {pmid40578340, year = {2025}, author = {Wang, M and Hu, Q and Tu, Z and Kong, L and Yu, T and Jia, Z and Wang, Y and Yao, J and Xiang, R and Chen, Z and Zhao, Y and Zhou, Y and Ye, Q and Ouyang, K and Wang, X and Bai, Y and Yang, Z and Wang, H and Wang, Y and Jiang, H and Yang, T and Chen, J and Huang, Y and Yin, N and Mo, W and Liang, W and Liu, C and Lin, X and Liu, C and Gu, Y and Chen, W and Liu, L and Xu, X and Hu, Y}, title = {A Drosophila single-cell 3D spatiotemporal multi-omics atlas unveils panoramic key regulators of cell-type differentiation.}, journal = {Cell}, volume = {188}, number = {17}, pages = {4734-4753.e31}, doi = {10.1016/j.cell.2025.05.047}, pmid = {40578340}, issn = {1097-4172}, mesh = {Animals ; *Single-Cell Analysis/methods ; *Cell Differentiation/genetics ; *Drosophila melanogaster/genetics/cytology/growth &amp; development/metabolism ; Drosophila Proteins/metabolism/genetics ; Gene Expression Regulation, Developmental ; Transcriptome/genetics ; Transcription Factors/metabolism ; Chromatin/metabolism ; Spatio-Temporal Analysis ; Multiomics ; }, abstract = {The development of a multicellular organism is a highly intricate process tightly regulated by numerous genes and pathways in both spatial and temporal manners. Here, we present Flysta3D-v2, a comprehensive multi-omics atlas of the model organism Drosophila spanning its developmental lifespan from embryo to pupa. Our datasets encompass 3D single-cell spatial transcriptomic, single-cell transcriptomic, and single-cell chromatin accessibility information. Through the integration of multimodal data, we generated developmentally continuous in silico 3D models of the entire organism. We further constructed tissue development trajectories that uncover the detailed profiles of cell-type differentiation. With a focus on the midgut, we identified transcription factors involved in midgut cell-type regulation and validated exex as a key regulator of copper cell development. This extensive atlas provides a rich resource and serves as a systematic platform for studying Drosophila development with integrated single-cell data at ultra-high spatiotemporal resolution.}, }
@article {pmid40578201, year = {2025}, author = {Son, HF and Hwang, S and Kim, Y and Ahn, JH and Ko, JK and Gong, G and Um, Y and Park, JH and Park, HJ and Lee, SM}, title = {Enzymatic depolymerization of polyethylene using a small laccase and its potential for bio-upcycling.}, journal = {Journal of hazardous materials}, volume = {495}, number = {}, pages = {139021}, doi = {10.1016/j.jhazmat.2025.139021}, pmid = {40578201}, issn = {1873-3336}, mesh = {*Laccase/metabolism/chemistry/genetics ; *Polyethylene/metabolism/chemistry ; Biodegradation, Environmental ; Molecular Docking Simulation ; Polymerization ; Phylogeny ; Actinobacteria/enzymology ; }, abstract = {Polyethylene (PE) plastics present significant environmental challenges due to their recalcitrant nature and widespread usage. This study explores the biological degradation of PE using a novel enzyme, small laccase from Amycolatopsis sp. ATCC 39116 (ASLAC). Among four selected laccases, ASLAC demonstrated the highest biomass production using PE as a carbon source when expressed by Yarrowia lipolytica. Surface analysis of PE films treated with purified ASLAC, using scanning electron microscopy (SEM) and atomic force microscopy (AFM), revealed substantial degradation of the material. The degradation products were successfully utilized by Y. lipolytica, underscoring its potential for converting PE into bioenergy. Structural analysis and molecular docking simulations revealed that the substrate binding site of ASLAC, characterized by a hydrophobic planner configuration, is highly optimized for binding and cleaving PE polymers. This unique structure distinguishes it from other laccases with narrower or obstructed binding sites. Phylogenetic analysis of 311 small laccase sequences classified ASLAC into the Type-Ia subgroup, which exhibited superior potential for PE degradation. This study establishes ASLAC as a promising biocatalyst for sustainable PE management, providing a foundation for future applications in bioremediation and polymer upcycling.}, }
@article {pmid40577926, year = {2025}, author = {Ding, TT and Du, SL and Liang, HY and Zhang, YH and Tao, Y and Li, MX and Zhang, J and Liu, SS}, title = {Data mining-based screening of prevalent mixture systems in aquatic environments: A case study of antibiotics in the Yangtze River Basin.}, journal = {Ecotoxicology and environmental safety}, volume = {302}, number = {}, pages = {118568}, doi = {10.1016/j.ecoenv.2025.118568}, pmid = {40577926}, issn = {1090-2414}, mesh = {*Rivers/chemistry ; *Water Pollutants, Chemical/analysis/toxicity ; *Anti-Bacterial Agents/analysis/toxicity ; China ; *Data Mining/methods ; *Environmental Monitoring/methods ; Risk Assessment ; Geologic Sediments/chemistry ; }, abstract = {Chemical pollution in real-world environment often involves exposure to combinations of thousands of chemicals. However, due to the vast number of possible combinations, it is nearly impossible to conduct comprehensive mixture toxicity tests and risk assessments for all of them. This study applied frequent itemset mining, a technique traditionally used in market basket analysis, to develop a prevalent mixture system screening (PMSS) method for identifying combinations that frequently co-occur in the environment. PMSS enables efficient data mining of chemical concentrations, allowing for the identification of a small number of prevalent mixture systems from numerous theoretical possibilities. In this study, 16 antibiotics were detected in the Linjiang River and the Xuebu River. Using the PMSS method, 48 prevalent antibiotic combinations (PACs), primarily ranging from binary to septenary combinations, were identified in the Xuebu River and the Linjiang River. The PACs in the surface water presented acceptable ecological risks, whereas the PACs in the sediments exhibited moderate to even high ecological risks. Therefore, targeted risk management measures should be developed for the sediments to reduce the potential harm to benthic organisms. Additionally, a case study demonstrates the application of identified PACs in mixture design. This study provides essential methodological and material support for advancing research on mixture toxicity evaluation and risk assessment.}, }
@article {pmid40577234, year = {2025}, author = {Roberts, T and Hanan, NP}, title = {Sapflow Database Reveals Density-Dependent Competition Among Woody Plants at Global Scale.}, journal = {Ecology letters}, volume = {28}, number = {6}, pages = {e70167}, pmid = {40577234}, issn = {1461-0248}, support = {DEB 2025166//National Science Foundation/ ; //New Mexico Space Consortium/ ; }, mesh = {Databases, Factual ; Ecosystem ; *Trees/physiology ; *Water/metabolism ; }, abstract = {Though limiting resources differ among systems, water is limiting in most arid and many mesic systems, potentially allowing for direct measurement of competition by measurement of water uptake. Sapflow measurements provide a direct measure of water movement through plant stems, but, to our knowledge, sapflow has never been used to study density dependence and competition at large (regional or global) scales. Here, we examine a global database of sapflow measurements, the SapFluxNet database, for signs of density-dependent competition for water. We find that plant-level water uptake decreases with increasing competition from neighbours (specifically, neighbourhood basal area). Further analysis demonstrates that global-scale variability in annual sapflow can be largely explained (R[2] = 0.522) by the combination of average vapour pressure and neighbourhood summed basal area. This analysis provides a rare quantification of plant competition for a limiting resource inferred directly via measurements of resource acquisition (i.e., sapflow).}, }
@article {pmid40573089, year = {2025}, author = {Suarez, C and Adibi, S}, title = {Integrating Traditional Nutritional Wisdom into Digital Nutrition Platforms: Toward Culturally Adaptive and Inclusive Health Technologies.}, journal = {Nutrients}, volume = {17}, number = {12}, pages = {}, pmid = {40573089}, issn = {2072-6643}, mesh = {Humans ; *Biomedical Technology/methods ; Culture ; *Digital Technology ; Health Knowledge, Attitudes, Practice ; *Nutritional Sciences ; }, abstract = {Background/Objectives: Traditional nutritional knowledge, shaped by centuries of cultural and ecological adaptation, offers holistic and sustainable dietary frameworks that remain highly relevant to modern health challenges. However, current digital nutrition platforms often fail to reflect this diversity, relying instead on standardized models with limited cultural sensitivity. This paper aims to explore how traditional nutritional wisdom can be integrated into digital health platforms to promote more inclusive and effective approaches to personalized nutrition. Methods: This perspective paper employs a cultural adaptation framework to analyze the integration of traditional food knowledge into digital contexts. Drawing from interdisciplinary research across nutrition science, anthropology, digital health and implementation science, we utilize the Knowledge-to-Action (KTA) Framework and the PEN-3 Cultural Model to structure our analysis. A systematic scoping review of literature published between 2010 and 2025 was conducted to identify integration challenges and opportunities. Additionally, we analyzed case studies of three traditional dietary systems (Argentina, Italy and Japan) and evaluated five leading digital nutrition platforms for their degree of cultural inclusivity, using qualitative comparative methods. Results: The analysis highlights significant challenges in adapting traditional knowledge to digital formats, including standardization barriers, contextual loss and technological limitations. However, successful integration initiatives demonstrate that through participatory design, flexible data architectures and culturally-informed algorithms, traditional food systems can be meaningfully represented. Our proposed four-phase integration framework-documentation, digital adaptation, implementation and evaluation-provides a structured approach for developers and researchers. Conclusions: Bridging traditional nutrition with digital platforms represents a vital opportunity to enhance personalization and preserve food heritage while improving health outcomes for diverse populations. This integration requires interdisciplinary collaboration, user-centered design processes and ethical approaches that respect cultural ownership and context.}, }
@article {pmid40571921, year = {2025}, author = {Demsash, AW and Abebe, R and Gezimu, W and Kitil, GW and Tizazu, MA and Lambebo, A and Bekele, F and Alemu, SS and Jarso, MH and Dube, GN and Wedajo, LF and Purohit, S and Kalayou, MH}, title = {Correction: Data-driven machine learning algorithm model for pneumonia prediction and determinant factor stratification among children aged 6-23 months in Ethiopia.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {808}, pmid = {40571921}, issn = {1471-2334}, }
@article {pmid40571725, year = {2025}, author = {Li, X and Liu, W and Shi, R and Ge, Y and Wang, Q and Yin, C and Liu, J and Shi, X and Mo, F and Chen, C and An, J}, title = {6PPD and 6PPD-Q Inhibit Macrophyte Photosynthesis by Targeting Photosynthetic Antenna: Multiomics and Computational Modeling Insights.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {26}, pages = {13216-13226}, doi = {10.1021/acs.est.5c03958}, pmid = {40571725}, issn = {1520-5851}, mesh = {*Photosynthesis/drug effects ; Molecular Docking Simulation ; *Phenylenediamines/toxicity ; Multiomics ; Benzoquinones ; }, abstract = {Emerging evidence indicates that N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine (6PPD) and its derivative 6PPD-quinone (6PPD-Q) exert photosynthetic toxicity on aquatic macrophytes. However, their precise inhibitory mechanisms and toxic targets within the photosynthetic pathways remain poorly understood. Through a combination of physio-biochemical indicators, multiomics analysis, and molecular docking simulation, this study systematically explored the photosynthetic toxic effects of 6PPD and 6PPD-Q on Ceratophyllum demersum L. (C. demersum). Transcriptomic data identified photosynthetic antenna proteins as primary molecular targets, with both contaminants perturbing the transcriptional regulation of genes and impairing the structural plasticity of associated proteins. These molecular perturbations consequently disrupted the photosynthetic electron transport efficiency. Metabolomic evidence revealed subsequent carbohydrate metabolism imbalances, suggesting compromised carbon fixation capacity of C. demersum. Additionally, molecular docking simulations demonstrated superior binding affinities for both compounds with antenna proteins, particularly emphasizing the enhanced interactions mediated by 6PPD-Q's quinone structure. Comparative analysis indicated that 6PPD-Q's structural modifications may confer greater photosynthetic toxicity compared to the parent compound 6PPD. This multiomics investigation reveals the mechanistic basis of 6PPD and 6PPD-Q-driven photosynthetic toxicity and underscores their potential to destabilize aquatic ecosystems by disrupting primary productivity.}, }
@article {pmid40571080, year = {2025}, author = {Han, H and Zhang, JM and Li, K and Amankwah, JF and Zeng, XB and Shen, ZQ and Jin, XC and Chen, TY and Liu, JW and Liu, LP}, title = {Multi-omics and random forest reveal lipid metabolism disruption and biomarkers in grass carp (Ctenopharyngodon idellus) exposed to 2-methylisoborneol.}, journal = {Environmental research}, volume = {284}, number = {}, pages = {122226}, doi = {10.1016/j.envres.2025.122226}, pmid = {40571080}, issn = {1096-0953}, mesh = {Animals ; *Carps/metabolism ; *Lipid Metabolism/drug effects ; Biomarkers/metabolism ; *Water Pollutants, Chemical/toxicity ; *Camphanes/toxicity ; Liver/metabolism/drug effects ; Lipidomics ; Random Forest ; Multiomics ; }, abstract = {The lipophilic nature of 2-methylisoborneol (2-MIB), a prevalent off-flavor compound in aquatic systems, raises concerns about its bioaccumulation potential and metabolic interference in fish. Most studies have focused on removing this compound from water and fish. However, the effect of lipid metabolism in fish exposed to 2-MIB remains poorly defined. This study investigated lipid metabolism disruption in grass carp (Ctenopharyngodon idellus) induced by 96 h of exposure to 5 and 20 μg/L of 2-MIB through integrated serum biochemistry, hepatic lipidomics, and multi-omics analysis. Grass carp exhibited varying degrees of oxidative stress, immune response, and lipid metabolism disruption. Non-targeted lipidomic analysis reveals that 2-MIB alters the levels of phosphatidylcholine (PC), sphingomyelin (SM), and phosphatidylmethanol (PMeOH) in the liver, potentially affecting the structure and function of cell membranes. Multi-omics analysis suggests that pathways related to carbohydrate metabolism, lipid metabolism, and amino acid biosynthesis may be crucial in regulating the physiological status of grass carp. Additionally, random forest and correlation analysis identified pregnenolone and 1-cyano-2-methyl-2-propen-1-yl docosanoate as potential biomarkers for 2-MIB exposure. Collectively, this study highlights the lipid characteristics and mechanisms of grass carp under 2-MIB exposure, contributing to the evaluation of its impact on fish health and improving aquaculture management.}, }
@article {pmid40563242, year = {2025}, author = {Arhami, O and Rohani, P}, title = {Topolow: a mapping algorithm for antigenic cross-reactivity and binding affinity assays.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {7}, pages = {}, pmid = {40563242}, issn = {1367-4811}, support = {75N93021C00018/AI/NIAID NIH HHS/United States ; //NIAID Centers of Excellence for Influenza Research and Response, CEIRR/ ; }, mesh = {*Algorithms ; Cross Reactions ; Influenza A Virus, H3N2 Subtype/immunology ; *Antigens, Viral/immunology/chemistry ; Dengue Virus/immunology ; HIV/immunology ; Humans ; *Computational Biology/methods ; *Antigens/immunology/chemistry ; }, abstract = {MOTIVATION: Understanding antigenic evolution through cross-reactivity assays is crucial for tracking rapidly evolving pathogens requiring regular vaccine updates. However, existing cartography methods, commonly based on multidimensional scaling (MDS), face significant challenges with sparse and complex data, producing incomplete and inconsistent maps. There is an urgent need for robust computational methods that can accurately map antigenic relationships from incomplete experimental data while maintaining biological relevance, especially given that more than 95% of possible measurements could be missing in large-scale studies.<br><br>RESULTS: We present Topolow, an algorithm that transforms cross-reactivity and binding affinity measurements into accurate positions in a phenotype space. Using a physics-inspired model, Topolow achieved comparable prediction accuracy to MDS for H3N2 influenza and 56% and 41% improved accuracy for dengue and HIV, while maintaining complete positioning of all antigens. The method effectively reduces experimental noise and bias, determines optimal dimensionality through likelihood-based estimation, avoiding distortions due to insufficient dimensions, and demonstrates orders of magnitude better stability across multiple runs. We also introduce antigenic velocity vectors, which measure the rate of antigenic advancement of each isolate per unit of time against its temporal and evolutionary related background, revealing the underlying antigenic relationships and cluster transitions.<br><br>Topolow is implemented in R and freely available at https://doi.org/10.5281/zenodo.15620983 and https://github.com/omid-arhami/topolow.}, }
@article {pmid40562960, year = {2025}, author = {Habibie, MI and Hariyanto,  and Arifandri, R and Qonita, Z and Kricella, P and Khoirudin, MH and Fuadi, NMR and Shabrina, N and Gutami, NI and Sadiah, S and Kartikasari, D and Widodo, MMA and Waluyo,  and Binaruno, FA and Ismoyo, K}, title = {A comparative study of fully automatic and semi-automatic methods for oil spill detection using Sentinel-1 data.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {7}, pages = {808}, doi = {10.1007/s10661-025-14222-z}, pmid = {40562960}, issn = {1573-2959}, mesh = {*Petroleum Pollution/analysis/statistics &amp; numerical data ; *Environmental Monitoring/methods ; *Water Pollutants, Chemical/analysis ; Machine Learning ; Indonesia ; Geographic Information Systems ; Neural Networks, Computer ; }, abstract = {The oil spill detection and assessment study conducted in the Banten Province of Indonesia involves the application of Sentinel-1 satellite data and machine learning tools in the year 2024. Synthetic Aperture Radar (SAR) data were used with VV polarization to observe the surface characteristics, using an oil spill threshold of - 25 dB to differentiate clean water from the oil spill based on low backscatter intensity. After desiring image processing and binary masking applications on the data that improve visibility of the oil spill-affected zones, vectorization was conducted for integration into geographic information systems (GIS). A temporal analysis indicated high variability across the spill sizes with an extreme peak on May 16 (79.686 km[2]) and July 3 (41.593 km[2]), which are likely dictated by the weather and oceanographic conditions plus the ship traffic of that time. Wind pattern analysis via ERA5 reanalysis data presented more insight into spill dispersion dynamics. Three machine learning classifiers were applied toward oil spill detection, namely Artificial Neural Networks (ANN), Random Forest (RF), and Extreme Gradient Boosting (XGBoost). Performance metrics indicate the ANN outperformed in discriminative ability (AUC = 0.92), while RF was highly accurate (99.01%) and precise (99.02%). This clearly demonstrates the viability of using an integrated approach of remote sensing, advanced image processing, and supervised learning for environmental monitoring and provides important information for minimizing ecological impacts and optimizing disaster response plans for maritime areas. Such an integrated scheme calls for advanced technology to combat ecological threats in maritime areas and provides crucial evidence toward ongoing interventions to protect and manage marine ecosystems and the associated local communities.}, }
@article {pmid40561147, year = {2025}, author = {Impalli, I and Bergland, E and Saad-Roy, CM and Grenfell, BT and Levin, SA and Larsson, DGJ and Laxminarayan, R}, title = {Optimal sampling frequency and site selection for wastewater and environmental surveillance of infectious pathogens: A value of information assessment.}, journal = {PLoS computational biology}, volume = {21}, number = {6}, pages = {e1013190}, pmid = {40561147}, issn = {1553-7358}, mesh = {Humans ; *Wastewater/microbiology ; *Environmental Monitoring/methods ; Animals ; Computational Biology ; *Communicable Diseases/epidemiology ; Computer Simulation ; Disease Outbreaks ; Sensitivity and Specificity ; }, abstract = {Wastewater and environmental surveillance (WES) is a promising method of detecting infectious diseases in human and animal populations and offers significant advantages over traditional surveillance methods in the early detection of outbreaks. However, WES involves financial and human resources, and public policy decisions must determine whether the benefits of WES outweigh the costs, particularly in low-resource areas. The selection of surveillance sites, sampling frequency, and test sensitivity and specificity are crucial determinants of WES effectiveness and cost-efficiency. We created an analytical model and numerical simulations of disease arrival, spread, and WES strategies to determine the optimal sampling frequency for two interacting patches, each represented by a different sampling site. We show that it is optimal to test in one patch more frequently than it is to test in both patches less frequently if the patches are sufficiently interactive, surveillance is of sufficient sensitivity and specificity, and setup costs are substantial. In our value of information (VOI) assessment, the net value of surveillance information for both patches is non-monotonic with respect to the degree of patch interaction. Increased mixing between the patches allows for quicker surveillance detection but is worse for overall infection burden. Overall, optimizing the value of surveillance information for all patches being surveilled requires coordination and deliberate selection of surveillance sites and sampling frequencies. This paper provides a VOI assessment of WES to determine the optimal number of sites and sampling frequency at a high level of abstraction, leaving opportunity to adapt the model to specific pathogens and populations as needed. Our findings can inform the cost-efficient implementation of WES for infectious diseases, particularly in resource-constrained settings.}, }
@article {pmid40561027, year = {2025}, author = {Otte, A and Wohlrab, S and Moritz, F and Müller, C and Janouškovec, J and Michálek, J and Cembella, A and Voss, D and Wang, X and Tebben, J and Larsen, TO and Edvardsen, B and Schmitt-Kopplin, P and John, U}, title = {High-resolution multiomics links nutrients and mixotrophy to toxicity in a harmful bloom of the haptophyte Chrysochromulina leadbeateri.}, journal = {Science advances}, volume = {11}, number = {26}, pages = {eadv3390}, pmid = {40561027}, issn = {2375-2548}, mesh = {*Harmful Algal Bloom ; *Haptophyta/metabolism/genetics/growth &amp; development ; *Nutrients/metabolism ; Polyketide Synthases/metabolism/genetics ; Multiomics ; }, abstract = {Harmful algal blooms (HABs) of the toxigenic haptophyte Chrysochromulina are known to cause fish mortalities and collateral ecosystem damage. The ichthyotoxic mechanisms are poorly understood but likely dependent on toxigenesis by polyketide synthases (PKSs). We hypothesize that induction of PKS activity facilitates mixotrophic behavior during nutrient-depleted bloom conditions. To identify potential in situ stimuli for growth, toxigenicity, and bloom persistence, we compared environmental factors and biological processes identified by metaomics to Chrysochromulina leadbeateri HABs between two fjords in northern Norway. We identified the polyketide ichthyotoxin leadbeaterin-1 from the C. leadbeateri bloom and found potentially associated candidate PKS genes of which most were higher expressed at bloom stations. A relative depletion of inorganic nitrogen and phosphate during the bloom was correlated with higher expression of genes involved in endocytosis, autophagy, and lysosomal activity. Mixotrophy is evidently a compensatory nutritional strategy coupled to induction of toxigenesis and other metabolomic processes as biotic factors linked to Chrysochromulina bloom dynamics.}, }
@article {pmid40559311, year = {2025}, author = {Liang, X and Yu, S and Meng, B and Ju, Y and Wang, S and Wang, Y}, title = {Machine-Learning-Guided Design of Nanostructured Metal Oxide Photoanodes for Photoelectrochemical Water Splitting: From Material Discovery to Performance Optimization.}, journal = {Nanomaterials (Basel, Switzerland)}, volume = {15}, number = {12}, pages = {}, pmid = {40559311}, issn = {2079-4991}, support = {LH2022B019//Heilongjiang Provincial Natural Science Foundation of China/ ; }, abstract = {The rational design of photoanode materials is pivotal for advancing photoelectrochemical (PEC) water splitting toward sustainable hydrogen production. This review highlights recent progress in the machine learning (ML)-assisted development of nanostructured metal oxide photoanodes, focusing on bridging materials discovery and device-level performance optimization. We first delineate the fundamental physicochemical criteria for efficient photoanodes, including suitable band alignment, visible-light absorption, charge carrier mobility, and electrochemical stability. Conventional strategies such as nanostructuring, elemental doping, and surface/interface engineering are critically evaluated. We then discuss the integration of ML techniques-ranging from high-throughput density functional theory (DFT)-based screening to experimental data-driven modeling-for accelerating the identification of promising oxides (e.g., BiVO4, Fe2O3, WO3) and optimizing key parameters such as dopant selection, morphology, and catalyst interfaces. Particular attention is given to surrogate modeling, Bayesian optimization, convolutional neural networks, and explainable AI approaches that enable closed-loop synthesis-experiment-ML frameworks. ML-assisted performance prediction and tandem device design are also addressed. Finally, current challenges in data standardization, model generalizability, and experimental validation are outlined, and future perspectives are proposed for integrating ML with automated platforms and physics-informed modeling to facilitate scalable PEC material development for clean energy applications.}, }
@article {pmid40558602, year = {2025}, author = {Mpuhua, CAM and Souza, OF and Daboin, BEG and Bezerra, IMP and Na Blei, M and Sarti, TD and Silva, VEBD and Abreu, LC}, title = {Proportional Stroke Mortality in Espírito Santo, Brazil: A 20-Year Joinpoint Regression Study.}, journal = {Epidemiologia (Basel, Switzerland)}, volume = {6}, number = {2}, pages = {}, pmid = {40558602}, issn = {2673-3986}, support = {001/2025//Fapes. Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado do Esp&#xed;rito Santo, Brazil./ ; }, abstract = {Introduction: Stroke is one of the leading causes of death and disability worldwide. In Brazil, it remains the primary cause of mortality among adults. Although overall stroke mortality rates have declined, the absolute number of stroke incidents, deaths, and years of life loss continues to rise, particularly in developing and underdeveloped countries. Objective: The aim of this study was to analyze trends in stroke mortality across different age groups and both sexes in Espírito Santo, Brazil, from 2000 to 2021. Methods: This ecological time series study utilized secondary data from Espírito Santo, Brazil, from 2000 to 2021. Mortality data, categorized by sex and age group, were obtained from the Department of Informatics of the Unified Health System (DATASUS) database. Stroke-related mortality included deaths recorded under the International Classification of Diseases, 10th Revision (ICD-10) codes for subarachnoid hemorrhage (I60), intracerebral hemorrhage (I61), cerebral infarction (I63), and stroke not specified as hemorrhagic or ischemic (I64). Temporal trends in stroke mortality were assessed using joinpoint regression analysis. Results: From 2000 to 2021, there was a significant reduction in proportional mortality from stroke, with an overall decrease of -3.7% (p < 0.001). When analyzed by sex, the decline was -3.0% (p < 0.001) for males and -3.9% (p < 0.001) for females. The most significant decrease in proportional mortality was observed in the 50 to 59 age group, with an average annual percentage change of -4.9% (p < 0.001). The 30 to 39 age group exhibited the smallest decline, with an average annual percentage change of -2.4% (p < 0.001). No significant segments were observed in the 40 to 49, 60 to 69, and 70 to 79 age groups during the study period. Conclusions: This study identified a notable decline in stroke-related proportional mortality in the adult population of Espírito Santo between 2000 and 2021. While males had a higher absolute number of deaths, females exhibited a higher proportional mortality rate, underscoring the need for targeted preventive measures and effective acute stroke treatment, particularly among men.}, }
@article {pmid40556364, year = {2025}, author = {Peat, GM and Hill, JC and Yu, D and Wathall, S and Parry, E and Bailey, J and Stevenson, K and Thompson, C and Wilkie, R and Dziedzic, K and Jordan, KP and , }, title = {Local variation in musculoskeletal pain consultation rates in primary care: findings from an ecologic study in Staffordshire.}, journal = {Primary health care research &amp; development}, volume = {26}, number = {}, pages = {e52}, pmid = {40556364}, issn = {1477-1128}, mesh = {Humans ; *Musculoskeletal Pain/epidemiology/therapy ; Male ; Female ; *Primary Health Care/statistics &amp; numerical data ; Middle Aged ; Adult ; England/epidemiology ; *Referral and Consultation/statistics &amp; numerical data ; Aged ; Prevalence ; Chronic Pain/epidemiology ; Self Report ; Young Adult ; Adolescent ; }, abstract = {Variation between general practices in the rate of consultations for musculoskeletal pain conditions may signal important differences in access to primary care, perceived usefulness, or available alternative sources of care; however, it might also just reflect differences in underlying 'need' between practices' registered populations. In a study of 30 general practices in Staffordshire, we calculated the proportion of adults consulting for a musculoskeletal pain condition, then examined this in relation to selected practice and population characteristics, including the estimated prevalence of self-reported musculoskeletal problems and chronic pain in each practices' registered population. Between September 2021 and July 2022, 18,388 adults were consulted for a musculoskeletal pain condition. After controlling for length of recruitment, time of year, and age-sex structure, the proportion consulting varied up to two-fold between practices but was not strongly associated with the prevalence of self-reported long-term musculoskeletal problems, chronic pain, and high-impact chronic pain.}, }
@article {pmid40554807, year = {2025}, author = {Poulin-Laprade, D and Broadbent, J and Biot-Pelletier, D and Kraemer, S and Griffiths, E and Kumar, A and Li, X and Carrillo, C and Zaheer, R and McAllister, T and Kullik, S and Liebana, E and Ricker, N and Langlois, A and Reid-Smith, R and Faucher, S and Flores-Vargas, G and Bédard, E and Summers, J and Jarocki, V and Thongthum, T and Carson, C}, title = {Requirements and considerations for effective implementation of integrated One Health antimicrobial resistance research.}, journal = {Canadian journal of microbiology}, volume = {71}, number = {}, pages = {1-17}, doi = {10.1139/cjm-2024-0194}, pmid = {40554807}, issn = {1480-3275}, mesh = {*One Health ; Humans ; Animals ; *Anti-Bacterial Agents/pharmacology ; *Research ; *Drug Resistance, Bacterial ; *Drug Resistance, Microbial ; }, abstract = {The One Health (OH) approach recognizes the interconnectedness of the health of people, animals, plants/crops and ecosystems, and is central to addressing antimicrobial resistance (AMR). The 7th Environmental Dimension of Antimicrobial Resistance Conference (EDAR7), held in Montreal in May 2024, exemplified this approach by convening international experts and stakeholders to discuss AMR research and policy progress. EDAR7 workshop #8 focused on (1) barriers to establishing effective OH AMR research programs, (2) gaps in OH AMR research priorities, and (3) potential solutions/approaches or "tools" to ensure programs develop in accordance with OH principles and generate insightful data that maximizes limited resources. Key workshop outcomes included identifying critical principles for OH AMR research programs and highlighting the pivotal role of sustainable data management strategies. Additionally, the importance of considering AMR policy and risk assessment needs when planning and designing research was emphasized. Discussions explored specific tools and approaches that support the standardized and harmonized collection and analysis of data, and associated challenges of integrating genomics data into current risk assessments and models. Synthesis of the workshop's discussions outlined critical considerations that interdisciplinary OH AMR research programs and networks should prioritize to enhance the impact of their outputs.}, }
@article {pmid40552042, year = {2025}, author = {Mu, YQ and Song, JB and Zhao, M and Ren, P and Liu, HY and Huang, X}, title = {Integrative omics analysis of plant-microbe synergies in petroleum pollution remediation.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19396}, pmid = {40552042}, issn = {2167-8359}, mesh = {Biodegradation, Environmental ; *Medicago sativa/microbiology/metabolism/genetics ; Metabolomics ; *Petroleum Pollution ; *Petroleum/metabolism ; *Soil Pollutants/metabolism ; Rhizosphere ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Hydrocarbons/metabolism ; Plant Roots/microbiology/metabolism ; Transcriptome ; Multiomics ; }, abstract = {As the petrochemical industry continues to advance, the exacerbation of ecological imbalance and environmental degradation due to petroleum pollution is increasingly pronounced. The synergistic interaction between plants and microorganisms are pivotal in the degradation of petroleum hydrocarbons; however, the underlying degradation mechanisms are not yet fully understood. This study aims to contribute to understanding these mechanisms by employing a multi-omics approach, integrating transcriptomics, 16S rRNA gene sequencing, and metabolomics, to analyze key differential genes, dominant microbial strains, and root-secreted metabolites involved in petroleum hydrocarbon degradation in alfalfa. Our findings revealed that several stress-related genes are upregulated in alfalfa contaminated with petroleum hydrocarbon. Moreover, Pseudomonas, Rhodococcus, and Brevundimonas were identified as dominant species in the rhizosphere microbiome. Metabolomics analysis identified pantothenic acid, malic acid, and ascorbic acid as critical metabolites that enhance hydrocarbon degradation. Application of pantothenic acid in oil-contaminated soil increased the degradation rate by approximately 10% compared to other treatments. These results highlight the potential of alfalfa-based phytoremediation strategies and offer a novel perspective for improving the efficiency of soil decontamination. Further research is needed to validate the scalability of these strategies for practical applications.}, }
@article {pmid40550119, year = {2025}, author = {Kang, B and Park, MK and Kim, JI and Yoon, S and Heo, SJ and Kang, C and Lee, S and Choi, Y and Hong, D}, title = {Exploring Factors Related to Social Isolation Among Older Adults in the Predementia Stage Using Ecological Momentary Assessments and Actigraphy: Machine Learning Approach.}, journal = {Journal of medical Internet research}, volume = {27}, number = {}, pages = {e69379}, pmid = {40550119}, issn = {1438-8871}, mesh = {Humans ; *Machine Learning ; Aged ; *Social Isolation ; Female ; Male ; *Actigraphy ; Loneliness ; *Ecological Momentary Assessment ; Aged, 80 and over ; *Dementia ; Cognitive Dysfunction ; }, abstract = {BACKGROUND: As the global population ages, the economic burden of dementia continues to rise. Social isolation-which includes limited social interaction and feelings of loneliness-negatively affects cognitive function and is a significant risk factor for dementia. Individuals with subjective cognitive decline and mild cognitive impairment represent predementia stages in which functional decline may still be reversible. Therefore, identifying factors related to social isolation in these at-risk groups is crucial, as early detection and intervention can help mitigate the risk of further cognitive decline.<br><br>OBJECTIVE: This study aims to develop and validate machine learning models to identify and explore factors related to social interaction frequency and loneliness levels among older adults in the predementia stage.<br><br>METHODS: The study included 99 community-dwelling older adults aged 65 years and above in the predementia stage. Social interaction frequency and loneliness levels were assessed 4 times daily using mobile ecological momentary assessment over a 2-week period. Actigraphy data were categorized into 4 domains: sleep quantity, sleep quality, physical movement, and sedentary behavior. Demographic and health-related survey data collected at baseline were also included in the analysis. Machine learning models, including logistic regression, random forest, Gradient Boosting Machine, and Extreme Gradient Boosting, were used to explore factors associated with low social interaction frequency and high levels of loneliness.<br><br>RESULTS: Of the 99 participants, 43 were classified into the low social interaction frequency group, and 37 were classified into the high loneliness level group. The random forest model was the most suitable for exploring factors associated with low social interaction frequency (accuracy 0.849; precision 0.837; specificity 0.857; and area under the receiver operating characteristic curve 0.935). The Gradient Boosting Machine model performed best for identifying factors related to high loneliness levels (accuracy 0.838; precision 0.871; specificity 0.784; and area under the receiver operating characteristic curve 0.887).<br><br>CONCLUSIONS: This study demonstrated the potential of machine learning-based exploratory models, using data collected from mobile ecological momentary assessment and wearable actigraphy, to detect vulnerable groups in terms of social interaction frequency and loneliness levels among older adults with subjective cognitive decline and mild cognitive impairment. Our findings highlight physical movement as a key factor associated with low social interaction frequency, and sleep quality as a key factor related to loneliness. These results suggest that social interaction frequency and loneliness may operate through distinct mechanisms. Ultimately, this approach may contribute to preventing cognitive and physical decline in older adults at high risk of dementia.<br><br>RR2-10.1177/20552076241269555.}, }
@article {pmid40548332, year = {2025}, author = {Pita, L and Maldonado, M and Koutsouveli, V and Riesgo, A and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and ,  and ,  and ,  and ,  and , }, title = {The chromosomal genome sequence of the kidney sponge, Chondrosia reniformis Nardo, 1847, and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {283}, pmid = {40548332}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from a specimen of Chondrosia reniformis (kidney sponge; Porifera; Demospongiae; Chondrillida; Chondrillidae). The genome sequence has a total length of 117.37 megabases. Most of the assembly (99.98%) is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 17.45 kilobases in length. Several symbiotic bacterial genomes were assembled as MAGs. Gene annotation of the host organism assembly on Ensembl identified 17,340 protein-coding genes. The metagenome of the specimen was also assembled and 53 binned bacterial genomes were identified, including 40 high-quality MAGs that were representative of a typical high microbial abundance sponge and included three candiate phyla (Poribacteria, Latescibacteria, Binatota).}, }
@article {pmid40545607, year = {2025}, author = {Yu, Z and Lei, T and Yi, X and Hao, Y and Wu, S and Xiao, Z and Qu, J and Li, S and Wang, L and Li, Y and Zhang, L and Pan, Y and Wang, Y and Gou, L and Jiao, Y and Wang, J}, title = {LGRPv2: A high-value platform for the advancement of Fabaceae genomics.}, journal = {Plant biotechnology journal}, volume = {23}, number = {9}, pages = {4057-4075}, pmid = {40545607}, issn = {1467-7652}, support = {32470676//National Natural Science Foundation of China/ ; 32170236//National Natural Science Foundation of China/ ; 31501333//National Natural Science Foundation of China/ ; C2020209064//Hebei Natural Science Foundation/ ; C2024209014//Hebei Natural Science Foundation/ ; H2023209084//Hebei Natural Science Foundation/ ; 246Z2508G//Central Guiding Local Science and Technology Development Fund Project/ ; ZD-YG-202313-23//Key Research Project of North China University of Science and Technology/ ; }, mesh = {*Fabaceae/genetics ; *Genome, Plant/genetics ; *Genomics/methods ; Synteny ; Databases, Genetic ; }, abstract = {Fabaceae, as one of the most diverse angiosperm families, plays a crucial role in maintaining global ecosystems and advancing human civilization. With the rapid accumulation of legume genomes, we developed LGRPv2 (https://fabaceae.cgrpoee.top), an updated version of the Legume Genomics Research Platform. LGRPv2 integrates 414 genomes, covering all published legume genomes and containing our latest deciphered Tamarindus indica genome from early-diverging legumes and three outgroup genomes (Euscaphis pleiosperma, Vitis vinifera, and Platycodon tenuifolia). It features user-friendly interactive interfaces for studying functional annotations, gene duplications, regulatory proteins, N[6]-methyladenosine modifications, and transposable elements. For easily exploring genome evolution associated with polyploidizations, we incorporated DotView, SynView, and DecoBrowse with genome synteny (GenS) to establish a central GenS database for legumes. Specialized web services for ancestral legume genomes enable scientists to analyse the role of paleogenome reshuffling in shaping genomic diversity. The platform offers 184 511 synteny-based orthogroups and 1 086 836 genes from 139 families, and tools to explore agronomic trait origins. LGRPv2 integrates 40 550 transcriptomes, 5091 pan-genomes, 12 136 metabolomes, species encyclopaedias, ecological resources, and literature for exploring legume genomics comprehensively. Furthermore, LGRPv2 implemented 58 window-based operating tools (31 new) to efficiently support new mining, especially in advancing assembling pipelines for polyploidization identification, ancestral genome reconstruction, and gene family evolution. Finally, we provided detailed usage guides and community support to empower LGRPv2 with user-friendly and continuously updated features.}, }
@article {pmid40544059, year = {2025}, author = {Moloney, ME and Moga, DC and Grandner, M and Schoenberg, N}, title = {"No rest for me tonight": A social-ecological exploration of insomnia in rural Appalachian women.}, journal = {Sleep health}, volume = {11}, number = {5}, pages = {717-723}, pmid = {40544059}, issn = {2352-7226}, support = {R01 HL152453/HL/NHLBI NIH HHS/United States ; K12 DA035150/DA/NIDA NIH HHS/United States ; UL1 TR001998/TR/NCATS NIH HHS/United States ; R01 MD016236/MD/NIMHD NIH HHS/United States ; L60 MD017858/MD/NIMHD NIH HHS/United States ; }, mesh = {Humans ; Female ; *Rural Population/statistics &amp; numerical data ; Middle Aged ; *Sleep Initiation and Maintenance Disorders/epidemiology/psychology ; Appalachian Region/epidemiology ; Adult ; Aged ; Interviews as Topic ; Risk Factors ; Sex Factors ; }, abstract = {OBJECTIVES: Insomnia disproportionally affects women and is prevalent among rural Appalachian adults at higher rates than in the general US population. Given the strong, bi-directional relationship between sleep and health, a better understanding of insomnia in this health-disparate population is critical. The present study focused on the sex (females), gender (women), and age group (45+) at highest insomnia risk and explores the social determinants of sleep that contributed to insomnia.<br><br>METHODS: Semistructured telephone interviews were conducted to understand factors associated with insomnia among rural Appalachian women who self-reported insomnia symptoms &#x2265;3 nights per week for &#x2265;3months. Interviews were recorded with permission and transcribed. We used a multistage, inductive and deductive coding process aided by NVIVO 12.0 software.<br><br>RESULTS: Participants were 46 cisgender women in rural Appalachia who met the criteria for insomnia. The social-ecological model was our interpretative framework. Findings illuminate individual (e.g., rumination, menopause, pain, depression), social (e.g., family roles, grief, caregiving, financial concerns), and societal (e.g., gender norms, technology use) factors that likely contribute to insomnia among middle-aged rural Appalachian women.<br><br>CONCLUSIONS: Across levels of the social-ecological model, factors of female sex (e.g., menopause) and gendered behaviors, roles, and norms (e.g., caregiving close and extended kin) played a central role in the precipitation and perpetuation of insomnia in this population. Attending to the regional cultural norms of heightened self-sufficiency, domestic work, and inter-generational familial care may aid healthcare providers and policy makers aiming to address insomnia among rural Appalachian women as well as other rural populations.}, }
@article {pmid40541223, year = {2025}, author = {Kamgno, J and Adeleke, M and Basáñez, MG and Coulibaly, Y and de Souza, DK and Debrah, LB and Debrah, AY and Diggle, PJ and Nana-Djeunga, HC and Domché, A and Gass, K and Hoerauf, A and Hopkins, A and Klion, A and Mackenzie, CD and Mwingira, U and Njenga, SM and Nutman, TB and Nwane, P and Stolk, WA and Unnasch, TR and Kelly-Hope, LA}, title = {Vector-borne helminthiases: a road map for current and future research to support control and elimination in sub-Saharan Africa.}, journal = {The Lancet. Infectious diseases}, volume = {25}, number = {10}, pages = {e555-e604}, doi = {10.1016/S1473-3099(25)00084-2}, pmid = {40541223}, issn = {1474-4457}, }
@article {pmid40537580, year = {2025}, author = {Sahana, S and Sarkar, J and Mandal, S and Chatterjee, I and Dhar, S and Datta, S and Mondal, S}, title = {Multi-omics approaches: transforming the landscape of natural product isolation.}, journal = {Functional &amp; integrative genomics}, volume = {25}, number = {1}, pages = {132}, pmid = {40537580}, issn = {1438-7948}, mesh = {*Biological Products/isolation &amp; purification/metabolism ; *Proteomics/methods ; *Genomics/methods ; *Metabolomics/methods ; Transcriptome ; Drug Discovery/methods ; Humans ; Multiomics ; }, abstract = {The field of natural product (NPs) discovery has significantly evolved with the advent of multi-omics approaches, encompassing genomics, transcriptomics, proteomics, and metabolomics. This review highlighting targeted isolation strategies and the comprehensive applications of omics in investigating natural products. Omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, have emerged as powerful tools that revolutionize the traditional methods of natural product discovery. This review delves into the integration of multi-omics technology in the isolation and discovery of natural product. Omics applications in natural product investigation have revolutionized the field by enabling high-throughput screening, rapid identification of novel compounds, and understanding the complex interactions within biological systems. For instance, metabolomics gives insights into the metabolic profiles of organisms under different conditions, aiding in the discovery of unique NPs with potential therapeutic applications. Genomics has facilitated the mining of microbial genomes for biosynthetic gene clusters, leading to the discovery of new antibiotics and carcinopreventive agents. Transcriptomics and proteomics provide insights into gene expression and protein synthesis, revealing the dynamics of NPs biosynthesis under various conditions. Despite these limitations, the future prospects of multi-omics in natural product discovery are promising. Advances in omics technologies, coupled with machine learning and artificial intelligence, are expected to enhance data integration and predictive modeling, accelerating the discovery and development of innovative drugs. Furthermore, the continuous improvement in analytical techniques and the establishment of comprehensive databases will facilitate the identification and characterization of NPs, ultimately contributing to the development of new therapeutic agents. Collaborative efforts across disciplines and the integration of environmental and ecological data will further enhance our understanding of NP biosynthesis and lead to more effective and sustainable drug discovery strategies.}, }
@article {pmid40536912, year = {2025}, author = {Vilela-Estrada, AL and Villarreal-Zegarra, D and Mayo-Puchoc, N and Holt, N and Flórez-Varela, &#xc1; and Fung, C and Ariza-Salazar, K and Carbonetti, FL and Flores, S and Carbonel, A and Olivar, N and Gomez-Restrepo, C and Brusco, LI and Priebe, S and Diez-Canseco, F}, title = {Fluctuations in Daily Happiness and Nervousness Based on Depressive and Anxious Symptoms in Adolescents or Young Adults Across 3 Latin American Cities: Experience Sampling Study.}, journal = {JMIR formative research}, volume = {9}, number = {}, pages = {e65732}, pmid = {40536912}, issn = {2561-326X}, mesh = {Humans ; Male ; Adolescent ; Female ; *Happiness ; Young Adult ; *Anxiety/psychology/epidemiology ; *Depression/psychology/epidemiology ; Quality of Life/psychology ; Latin America/epidemiology ; Argentina ; Cities ; Ecological Momentary Assessment ; }, abstract = {BACKGROUND: Experience sampling methods (ESMs) have been used in clinical research to collect data on emotional and behavioral states in real-life contexts among different populations. Although the use of ESMs in mental health has increased, it has not been applied to larger samples of young people in disadvantaged urban settings.<br><br>OBJECTIVE: This study aimed to determine the extent to which mood status scores (happiness and nervousness) vary during a week, as a function of having or not having symptoms of depression or anxiety, in a sample of adolescents and young adults in the cities of Buenos Aires, Bogot&#xe1;, and Lima. A secondary objective was to identify factors associated with mood scores, including sociodemographics, quality of life, and daily activities.<br><br>METHODS: This study was part of the Building Resilience and Resources to Reduce Mental Distress in Young People in Latin America research program, which focuses on mental health resources for young people. Participants (n=143) aged 15-24 years completed daily ESM assessments over a week using the mobile app, resulting in 5246 reports. Data were analyzed using descriptive analyses with 2-tailed t tests and chi-square tests, and multilevel linear regression was used to examine associations between depressive or anxiety symptoms, mood variability, and factors influencing mean mood. Finally, Spearman correlation assessed the relationship between happiness and nervousness.<br><br>RESULTS: The analysis revealed that depressive or anxiety symptoms were not significantly associated with increased variability in mood scores (happiness P=.40 and nervousness P=.84). However, males exhibited greater variability in happiness and nervousness scores (P<.001) than females. Additionally, young people showed higher variability in nervousness than adolescents (P=.02). Regarding average happiness scores, young adults reported higher average happiness than adolescents (&#x3b2;=.604; P=.003). Engaging in structured activities (eg, sports, music lessons, and dance classes) was associated with increased happiness (&#x3b2;=.266; P=.01). In contrast, instrumental activities (eg, cleaning, shopping, meal preparation, or taking medication; &#x3b2;=-.144; P=.02) and work-related tasks (&#x3b2;=-.205; P=.01) were linked to lower happiness and higher nervousness (&#x3b2;=.387; P<.001). Quality of life was positively correlated with happiness (&#x3b2;=.486; P<.001) and negatively correlated with nervousness (&#x3b2;=-.273; P=.005). Finally, as for average scores, a strong negative correlation was found between happiness and nervousness (rs=-0.92; P<.001). The simple multilevel analysis showed that for each point of happiness, nervousness decreased by 0.45 points (95% CI -0.48 to -0.42; t3=-41.7; P<.001; SE 0.01).<br><br>CONCLUSIONS: Our study reveals that depressive and anxiety symptoms do not significantly affect the variability in predicted happiness and nervousness scores. However, we observed that demographic factors, such as gender and age, play a role in emotional variability.}, }
@article {pmid40531985, year = {2025}, author = {Priorelli, M and Stoianov, IP and Pezzulo, G}, title = {Embodied decisions as active inference.}, journal = {PLoS computational biology}, volume = {21}, number = {6}, pages = {e1013180}, pmid = {40531985}, issn = {1553-7358}, mesh = {*Decision Making/physiology ; Humans ; Computational Biology ; Choice Behavior/physiology ; }, abstract = {Decision-making is often conceptualized as a serial process, during which sensory evidence is accumulated for the choice alternatives until a certain threshold is reached, at which point a decision is made and an action is executed. This decide-then-act perspective has successfully explained various facets of perceptual and economic decisions in the laboratory, in which action dynamics are usually irrelevant to the choice. However, living organisms often face another class of decisions-called embodied decisions-that require selecting between potential courses of actions to be executed timely in a dynamic environment, e.g., for a lion, deciding which gazelle to chase and how fast to do so. Studies of embodied decisions reveal two aspects of goal-directed behavior in stark contrast to the serial view. First, that decision and action processes can unfold in parallel; second, that action-related components, such as the motor costs associated with selecting a particular choice alternative or required to "change mind" between choice alternatives, exert a feedback effect on the decision taken. Here, we show that these signatures of embodied decisions emerge naturally in active inference-a framework that simultaneously optimizes perception and action, according to the same (free energy minimization) imperative. We show that optimizing embodied choices requires a continuous feedback loop between motor planning (where beliefs about choice alternatives guide action dynamics) and motor inference (where action dynamics finesse beliefs about choice alternatives). Furthermore, our active inference simulations reveal the normative character of embodied decisions in ecological settings - namely, achieving an effective balance between a high accuracy and a low risk of missing valid opportunities.}, }
@article {pmid40527958, year = {2025}, author = {Jendrusch, MA and Yang, ALJ and Cacace, E and Bobonis, J and Voogdt, CGP and Kaspar, S and Schweimer, K and Perez-Borrajero, C and Lapouge, K and Scheurich, J and Remans, K and Hennig, J and Typas, A and Korbel, JO and Sadiq, SK}, title = {AlphaDesign: a de novo protein design framework based on AlphaFold.}, journal = {Molecular systems biology}, volume = {21}, number = {9}, pages = {1166-1189}, pmid = {40527958}, issn = {1744-4292}, support = {de.NBI project: 031A537B//Bundesministerium f&#xfc;r Bildung und Forschung (BMBF)/ ; contract 95826//Volkswagen Foundation (VolkswagenStiftung)/ ; 93874-1//Volkswagen Foundation (VolkswagenStiftung)/ ; COFUND grant nr. 847543//EC | Horizon Europe | Excellent Science | HORIZON EUROPE Marie Sklodowska-Curie Actions (MSCA)/ ; }, mesh = {*Protein Engineering/methods ; Synthetic Biology/methods ; *Proteins/chemistry/genetics ; Models, Molecular ; *Computational Biology/methods ; Protein Folding ; Protein Conformation ; Algorithms ; }, abstract = {De novo protein design is of fundamental interest to synthetic biology, with a plethora of computational methods of various degrees of generality developed in recent years. Here, we introduce AlphaDesign, a hallucination-based computational framework for de novo protein design developed with maximum generality and usability in mind, which combines AlphaFold with autoregressive diffusion models to enable rapid generation and computational validation of proteins with controllable interactions, conformations and oligomeric state without the requirement for class-dependent model re-training or fine-tuning. We apply our framework to design and systematically validate in vivo active inhibitors of a family of bacterial phage defense systems with toxic effectors called retrons, paving the way towards efficient, rational design of novel proteins as biologics.}, }
@article {pmid40527897, year = {2025}, author = {Basava, K and Alam, MNU and Roberts, L and Martinet, K and Cherry, P and García-Verdugo, H and Román-Palacios, C}, title = {Mapping nonhuman cultures with the Animal Culture Database.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1019}, pmid = {40527897}, issn = {2052-4463}, mesh = {Animals ; *Databases, Factual ; *Behavior, Animal ; *Social Behavior ; }, abstract = {Socially transmitted behaviors are widespread across the animal kingdom, yet there is a lack of comprehensive datasets documenting their distribution and ecological significance. Knowledge of animal behavioral traditions could be essential for understanding many species' responses to anthropogenic disturbances and further enhancing conservation efforts. Here, we introduce the first open-access database that synthesizes data on animal cultural behaviors and traditions. The Animal Culture Database (ACDB) contains descriptions of 128 behaviors including forms of vocal communication, migration, predator defense, foraging practices, habitat alteration, play, mating displays, and other social behaviors for an initial sample of 61 species. In addition to offering an open-access resource for researchers, educators, and conservationists, the ACDB represents a step toward recognizing the role of social learning in animal populations.}, }
@article {pmid40524951, year = {2025}, author = {Jánošíková, R and Tulis, F and Baláž, I and Eccard, JA and Mazza, V}, title = {Range expansion during recolonization: what does animal personality have to do with it?.}, journal = {Behavioral ecology : official journal of the International Society for Behavioral Ecology}, volume = {36}, number = {4}, pages = {araf053}, pmid = {40524951}, issn = {1045-2249}, abstract = {At the edge of an ongoing expansion, pioneer individuals encounter novel ecological and evolutionary pressures that may not be experienced by conspecifics settled in long-colonized areas. Consistent behavioral differences among conspecifics (animal personality) may be important determinants of individuals' successful colonization of novel environments and range expansion. By enhancing an individual's ability to find food and shelter as well as increasing its capacity to navigate novel environments, behavioral traits such as exploration and risk-taking are thus expected to be more highly expressed in populations undergoing expansion than in established populations. We investigated among-individual variation in behaviors associated to risk-taking and exploratory tendencies in populations of small mammals during different stages of the colonization process. Using a standardized behavioral test in the field, we quantified exploration and boldness of striped field mice (Apodemus agrarius, N = 95) from six subpopulations from Germany, where they are established, and in Slovakia, where a recolonization of the area is currently in progress, and in control species bank voles (Myodes glareolus, N = 76) that shared the same habitats but were long-established at all sites. Striped field mice in the expanding populations were significantly slower in exploring the open field arena, while showing comparable levels of risk taking compared to conspecifics from established populations. No difference in behavior was detected between the populations of bank voles. Our results suggest that a slow exploration strategy might play an advantageous role in expansion processes of small mammal populations.}, }
@article {pmid40524188, year = {2025}, author = {Perillo, VL and Nute, M and Sapoval, N and Curry, KD and Golia, L and Yin, Y and Ogilvie, HA and Nakhleh, L and Segarra, S and Bhaya, D and Cuadrado, DG and Treangen, TJ}, title = {A survey of computational approaches for characterizing microbial interactions in microbial mats.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {168}, pmid = {40524188}, issn = {1474-760X}, support = {EF-2126387//National Science Foundation/ ; BBSRC-NSF/BIO #1921429//National Science Foundation/ ; NSF#2125965//National Science Foundation/ ; PICT 2020-302//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; Pampa Azul A8 Programa "Investigaci&#xf3;n//Ministerio de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n/ ; Desarrollo e Innovaci&#xf3;n en Ciencias del Mar"//Ministerio de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n/ ; Proposal 503441//Joint Genome Institute/ ; proposal: 10.46936/10.25585/60001132//Joint Genome Institute/ ; }, mesh = {*Microbial Interactions ; *Computational Biology/methods ; *Microbiota ; Ecosystem ; Bacteria/genetics/metabolism ; }, abstract = {In this review, we use microbial mat communities as a general model system to highlight the strengths and limitations of current computational methods for analyzing interactions between members of microbial ecosystems. We describe the factors that make this environment have such a high degree of interaction, and we explore different categories of both laboratory and computational tools for studying these interactions. For each tool, we describe efforts to apply them to microbial mats in the past and, in the process, argue that genome-scale metabolic models have breakthrough potential for modeling microbial interactions in microbial mats.}, }
@article {pmid40523168, year = {2025}, author = {Barfuss, W and Flack, J and Gokhale, CS and Hammond, L and Hilbe, C and Hughes, E and Leibo, JZ and Lenaerts, T and Leonard, N and Levin, S and Madhushani Sehwag, U and McAvoy, A and Meylahn, JM and Santos, FP}, title = {Collective cooperative intelligence.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {25}, pages = {e2319948121}, pmid = {40523168}, issn = {1091-6490}, abstract = {Cooperation at scale is critical for achieving a sustainable future for humanity. However, achieving collective, cooperative behavior-in which intelligent actors in complex environments jointly improve their well-being-remains poorly understood. Complex systems science (CSS) provides a rich understanding of collective phenomena, the evolution of cooperation, and the institutions that can sustain both. Yet, much of the theory in this area fails to fully consider individual-level complexity and environmental context-largely for the sake of tractability and because it has not been clear how to do so rigorously. These elements are well captured in multiagent reinforcement learning (MARL), which has recently put focus on cooperative (artificial) intelligence. However, typical MARL simulations can be computationally expensive and challenging to interpret. In this perspective, we propose that bridging CSS and MARL affords new directions forward. Both fields can complement each other in their goals, methods, and scope. MARL offers CSS concrete ways to formalize cognitive processes in dynamic environments. CSS offers MARL improved qualitative insight into emergent collective phenomena. We see this approach as providing the necessary foundations for a proper science of collective, cooperative intelligence. We highlight work that is already heading in this direction and discuss concrete steps for future research.}, }
@article {pmid40522165, year = {2025}, author = {Huang, JN and Wen, B and Wang, ZN and Gao, JZ and Chen, ZZ}, title = {Microplastics Change the Food Utilization of Filter-Feeding Fish via Gut Microbiota.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {29}, pages = {15353-15363}, doi = {10.1021/acs.est.5c02067}, pmid = {40522165}, issn = {1520-5851}, mesh = {Animals ; *Carps/growth &amp; development/microbiology/parasitology ; *Environmental Pollutants/toxicity ; Fecal Microbiota Transplantation ; *Feeding Behavior/drug effects ; *Gastrointestinal Microbiome/drug effects ; *Microplastics/toxicity ; Multiomics ; Zebrafish ; Phytoplankton ; Zooplankton ; Food Chain ; }, abstract = {Microplastics (MPs) are ubiquitous in aquatic environments, while their effects on filter-feeding fish are poorly understood. This study aims to explore how MPs change the feeding of planktivorous silver carp. After exposure to MPs, the utilization efficiency of zooplankton by carp increased from 28.45% to 38.63-40.20%, while that of phytoplankton decreased from 50.64% to 40.47-43.32%. MPs did not cause changes in the phytoplankton and zooplankton communities that carp consumed but altered its gut microbiota, leading to increased abundance of genes encoding proteases but decreased carbohydrase genes. Gut metabolomics further showed corresponding metabolic changes especially with increased levels of l-tyrosine, citrulline, succinic acid, and propionic acid, which are significantly correlated with the isotopic signatures of carp utilizing zooplankton. Germ-free zebrafish transplanted with feces of MPs-exposed carp showed metabolic changes like those of carp, verifying that the gut microbiota mediated the effects induced by MPs, while silver carp transplanted with feces of MPs-exposed carp exhibited increased protease activity and enhanced zooplankton utilization efficiency, confirming that MPs could alter its food utilization via gut microbiota. Our findings fill a knowledge gap regarding the ecological risk of MPs to the feeding of planktivorous fish, with potential cascading effects on aquatic ecosystems.}, }
@article {pmid40520149, year = {2025}, author = {Maldonado, M and Pita, L and Hentschel, U and Erpenbeck, D and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and ,  and ,  and ,  and ,  and , }, title = {The chromosomal genome sequence of the sponge Crambe crambe (Schmidt, 1862) and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {275}, pmid = {40520149}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual Crambe crambe (Porifera; Demospongiae; Poecilosclerida; Crambeidae). The host genome sequence is 143.20 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.53 kilobases in length. Several symbiotic prokaryotic genomes were assembled as MAGs, including two relevant sponge symbionts, the Candidatus Beroebacter blanensis/ AqS2 clade (Tethybacterales, Gammaproteobacteria) of LMA sponges, and the widely distributed archaeal Nitrosopumilus sp. clade.}, }
@article {pmid40519052, year = {2025}, author = {Hilbert, A and Klotz, U and Sadeghi, S and Juarascio, AS and Kirsten, T}, title = {Smartphone-Supported Cognitive-Behavioral Therapy in Binge-Eating Disorder: An Exploratory Randomized Trial.}, journal = {The International journal of eating disorders}, volume = {58}, number = {9}, pages = {1793-1805}, pmid = {40519052}, issn = {1098-108X}, support = {3/2019//Roland Ernst Foundation for Healthcare/ ; }, mesh = {Humans ; *Cognitive Behavioral Therapy/methods ; Adult ; Female ; Male ; *Smartphone ; Middle Aged ; Feasibility Studies ; *Binge-Eating Disorder/therapy ; *Mobile Applications ; Adolescent ; Young Adult ; Treatment Outcome ; Aged ; }, abstract = {OBJECTIVE: To assess the feasibility of a smartphone app delivering just-in-time adaptive interventions as an adjunct to cognitive-behavioral therapy (CBT) adapted to binge-eating disorder (BED), estimate its effects assuming superiority over CBT alone, and document safety and target engagement.<br><br>METHOD: A single-center, assessor-blinded, parallel feasibility study randomized adults aged 18-65&#x2009;years with full-syndrome or subthreshold BED to smartphone-supported CBT (SmartCBT) or standard CBT (DRKS00024597). Both arms received 16 individual 50-min CBT sessions over 4&#x2009;months. Assessments were conducted at baseline (T0), midtreatment (T1), posttreatment (T2), and 3-month follow-up (T3). Feasibility was determined regarding recruitment, attrition, dropout, adherence, assessment completion, app use, and acceptance. Further, eating disorder symptoms, mental and physical health, weight management behavior, safety, and target engagement (i.e., skill use) were assessed.<br><br>RESULTS: Over a 7-month recruitment period, 28 of 50 eligible volunteers were included and randomized 1:1 to SmartCBT or CBT. In the modified intent-to-treat sample (N&#x2009;=&#x2009;25; SmartCBT: 13, CBT: 12), the feasibility of SmartCBT was further supported regarding attrition, dropout, adherence, treatment completion, app use, and acceptance; however, assessment completion was moderate. Clinical improvements were found in both arms, but differential results were affected by baseline differences and moderate assessment completion in the SmartCBT arm. Safety was documented, and support for target engagement was found.<br><br>CONCLUSIONS: This exploratory study provides evidence for the feasibility of app-supported CBT for BED. With few procedural refinements, the protocol can be used in a confirmatory randomized-controlled trial with long-term follow-up to evaluate efficacy and determine treatment mechanisms.<br><br>TRIAL REGISTRATION: German Clinical Trials Register, https://www.drks.de, DRKS00024597.}, }
@article {pmid40518659, year = {2025}, author = {Gurung, S and Lee, CM and Weon, HY and Han, SR and Oh, TJ}, title = {Comparative Genome Analysis of Three Halobacillus Strains Isolated From Saline Environments Reveal Potential Salt Tolerance and Algicidal Mechanisms.}, journal = {Environmental microbiology reports}, volume = {17}, number = {3}, pages = {e70121}, pmid = {40518659}, issn = {1758-2229}, support = {RS-2024-00441423//The Bio &amp; Medical Technology Development Program of the National Research Foundation (NRF) funded by the Korean government (MSIT)/ ; }, mesh = {*Salt Tolerance/genetics ; *Genome, Bacterial ; Harmful Algal Bloom ; Phylogeny ; *Bacillaceae/genetics/isolation &amp; purification/physiology/classification ; Computational Biology ; Genomics ; }, abstract = {Harmful algal blooms (HABs) pose a significant global threat to water ecosystems, prompting extensive research into their inhibition and control strategies. This study presents genomic and bioinformatic analyses to investigate the algicidal potential and elucidate the survival mechanisms in harsh conditions of newly identified Halobacillus species three strains (SSTM10-2[T], SSBR10-3[T], and SSHM10-5[T]) isolated from saline environments. Moreover, genomic and bioinformatic analyses were conducted to elucidate their survival mechanisms in harsh conditions. Moreover, comparative genomic analysis revealed a diverse set of orthologous genes, with a core genome primarily associated with metabolism and information processing. Pangenome analysis highlighted accessory and unique genes potentially involved in environmental adaptation and stress response. Functional annotation using KEGG pathways identified genes linked to xenobiotic compound degradation, stress tolerance, and salt adaptation. Additionally, the study elucidated potential mechanisms underlying algicidal activity, implicating Carbohydrate-Active enZYmes (CAZymes), cytochrome P450 oxidases (CYP), and quorum sensing (QS) systems. Finally, analysis of KEGG pathways related to microcystin degradation suggested the strains' capacity to mitigate HABs. Thus, this research enhances understanding of the genomic diversity, phylogeny, and functional characteristics of Halobacillus species, offering insights into their ecological roles and potential applications in biotechnology and environmental management.}, }
@article {pmid40517927, year = {2025}, author = {Liu, M and Xie, L and Pan, Y and Li, Y and Zhang, X and Yan, W}, title = {Size-induced toxic effect of plastic particles on earthworms characterized by gut multi-omics analysis.}, journal = {Environmental research}, volume = {283}, number = {}, pages = {122133}, doi = {10.1016/j.envres.2025.122133}, pmid = {40517927}, issn = {1096-0953}, mesh = {Animals ; *Oligochaeta/drug effects ; *Soil Pollutants/toxicity ; Particle Size ; *Plastics/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Polystyrenes/toxicity ; Metabolomics ; Nanoparticles/toxicity ; Multiomics ; }, abstract = {The emission and accumulation of plastic particles in soil have raised concerns about their impact on soil organisms. As key components of soil fauna, earthworms (Eisenia fetida) are prone to ingesting plastic particles and experiencing associated health effects. However, the size-dependent toxicological mechanisms of these particles in earthworms remain unclear. In this study, earthworms were exposed to polystyrene particles of different sizes (50 nm, 200 nm, and 250 μm), and their biological responses were evaluated through morphological analysis, gut microbiota profiling, and metabolomics. Micro-sized particles (250 μm, 200 mg kg[-1]) caused mechanical damage to intestinal tissues and reduced survival rates after 28 days. Nano-sized particles (50 nm, 200 nm) disrupted gut microbial diversity and altered metabolic profiles, including reductions in amino acids involved in the TCA cycle. All particle sizes affected metabolite levels and key metabolic pathways. These results indicate that micro-sized particles primarily induce acute physical damage, while nano-sized particles exert long-term biochemical effects. This study highlights the size-specific ecological impacts of plastic particles on soil invertebrates.}, }
@article {pmid40512727, year = {2025}, author = {Clauss, M and Roller, M and Bertelsen, MF and Rudolf von Rohr, C and Müller, DWH and Schiffmann, C and Kummrow, M and Encke, D and Ferreira, S and Duvall, ES and Maré, C and Abraham, AJ}, title = {Reply to Ferraro et al.: Breed-and-feed reflects inevitable trade-offs between individual longevity and population sustainability.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {26}, pages = {e2509145122}, pmid = {40512727}, issn = {1091-6490}, }
@article {pmid40508665, year = {2025}, author = {Jiao, Y and Miao, X and Wang, L and Hong, S and Gao, Y and Wang, X}, title = {The Engineered Synthesis and Enhancement of Nitrogen and Chlorine Co-Doped Fluorescent Carbon Dots for the Sensitive Detection of Quercetin.}, journal = {Materials (Basel, Switzerland)}, volume = {18}, number = {11}, pages = {}, pmid = {40508665}, issn = {1996-1944}, support = {202303021221041, 202203021212443//Fundamental Research Program of Shanxi Province/ ; 22408259//Young Scientists Fund of the National Natural Science Foundation of China/ ; 2023M743771//China Postdoctoral Science Foundation/ ; SXBYKY2022076//Shanxi Province doctoral graduates and postdoctoral researchers come to work in Shanxi Province to reward the fund scientific research project/ ; 2021L029//Science and technology innovation project of colleges and universities in Shanxi Province/ ; }, abstract = {Flavonoid alcohols, particularly quercetin, as emerging antioxidants, demand advanced detection methodologies to comprehensively explore and evaluate their potential environmental and health risks. In this study, nitrogen-chlorine co-doped carbon dots (N, Cl-CDs), featuring an extended wavelength emission at 625 nm, were synthesized via the reaction of 4-chloro-1,2-phenylenediamine with polyethyleneimine. The engineered N, Cl-CDs exhibit superior photostability, exceptional aqueous dispersibility, and anti-interference capability in complex matrices. Leveraging static electron transfer mechanisms, the N, Cl-CDs demonstrate selective fluorescence quenching toward quercetin with an ultralow detection limit of 60.42 nM. Validation through rigorous spiked recovery assays in apple peel and red wine has been proficiently performed with satisfactory accuracy, highlighting the significant prospect of the constructed N, Cl-CDs for quercetin identification in real samples. This study provides valuable insights into the analytical determination of flavonoid compounds in complex environmental matrices, highlighting the potential of N, Cl-CDs for environmental and food safety monitoring.}, }
@article {pmid40505944, year = {2025}, author = {Liu, F and Lorenz, C and Zhao, G}, title = {From land to sea: Hydrological source tracking of microplastics in coastal sediments.}, journal = {Environmental research}, volume = {283}, number = {}, pages = {122132}, doi = {10.1016/j.envres.2025.122132}, pmid = {40505944}, issn = {1096-0953}, mesh = {*Microplastics/analysis ; *Environmental Monitoring/methods ; *Geologic Sediments/analysis/chemistry ; Denmark ; *Water Pollutants, Chemical/analysis ; Hydrology ; Geographic Information Systems ; }, abstract = {Land-based sources are the predominant contributors to marine microplastic pollution; however, identifying specific inland origins and their correspondence transport paths remain challenging at large-scale. In Denmark, terrestrial-marine connectivity is largely mediated by a complex network of streams, that further complicates hydrological connections between diverse inland discharges and the final coastal receptor. This study presents a GIS-based hydrological source tracking approach to identify the relevant inland discharges and further delineating their transportation paths for microplastics (≥10 μm) sampled from coastal sediments. After analyzed with Focal Plane Array-based Fourier Transform Infrared (FPA-μFTIR) imaging, samples from 13 Danish coastal monitoring stations were tested for souce tracking operations. The tracking tool first screened the stream network across Denmark to identify both point and non-point inland sources-stormwater runoff, wastewater effluent, and combined sewer overflow (CSO)-contributing microplastics to the selected coastal zones. Microplastics were detected at all stations, with variations in abundance, polymer composition, particle shape, and size. Significant positive correlations (p < 0.05) were observed between discharge volume and the composition of certain microplastics: wastewater effluent positively correlates with fiber and polyvinylchloride (PVC), while stormwater-associated discharges (including CSOs) correlated with polypropylene (PP). However, total microplastic concentration was not significantly linked to the discharges. Nevertheless, the GIS-based hydrological tool demonstrated an early-screening tool to identify inland source of marine microplastics. The results underscored the significant role of inland discharges in transporting distinct microplastics to coastal environment, offering valuable insights for authorities to further implement more targeted hydrodynamic modelling, source-specific mitigation strategies, as well as optimised station deployment strategies in future.}, }
@article {pmid40505380, year = {2025}, author = {Borics, G and Lerf, V and Falucskai, J and B-Béres, V and Kisantal, T and Tóth, I and T-Krasznai, E and Stanković, I and Görgényi, J and Lukács, &#xc1; and Várbíró, G}, title = {Projected area calculation for microalgae using three-dimensional models.}, journal = {Water research}, volume = {284}, number = {}, pages = {123951}, doi = {10.1016/j.watres.2025.123951}, pmid = {40505380}, issn = {1879-2448}, mesh = {*Microalgae ; Computer Simulation ; Species Specificity ; }, abstract = {Light acquisition and sinking properties of microalgae fundamentally affect how species perform in aquatic environments. Both properties are the function of their projected area (Ā), a crucial morphological trait of microalgae. Despite their importance, species-specific Ā values have not been computed for microalgae. The reason for this is that although using an analytical approach Ā can be calculated for every convex shape, a vast majority of planktic algae are concave and currently not known how to calculate the projected area of concave shapes. Applying shape-realistic 3D models of microalgae and a novel numerical approach combined with computer simulation, we calculated the projected area for more than 800 microalgae. Validating this approach using convex shapes and the analytical Ā = surface area/4 formula we found, that the proposed method achieves less than 5 % estimation bias. We also studied how Ā values of species can be predicted by easy-to-measure morphological metrics (such as Gald/width ratio, compactness, relative surface area extension, relative elongation, surface area constant, volume constant). We have found that the metrics do not show a sufficiently close relationship with the projected area to allow us to estimate species-specific Ā values. We demonstrated that the morphological differences among species can result in up to 6-fold differences in Ā values for the same volume. Spindle-form, filamentous species and loosely packed coenobia are the most efficient adaptations to maximize Ā. This study provides an innovative methodology and a huge dataset containing Ā values of 844 planktic freshwater microalgae. Although the dataset contains species only for the Pannonian and Dinaric ecoregions, because of the cosmopolitan nature of planktic algae it can be used for other ecoregions. Species-specific projected area values multiplied by cell counts give a new metric that characterizes the shading property of the given phytoplankton assemblage and enables us to better understand the changes in light availability and study the vertical processes in the water.}, }
@article {pmid40505009, year = {2025}, author = {Yang, S and Zhang, X and Jin, LN and Fang, M and Gu, AZ and Li, D and Chen, J}, title = {Unveiling Phase-Dependent Genotoxicity of Organic Pollutants in Gaseous and Aqueous Forms.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {24}, pages = {12048-12059}, doi = {10.1021/acs.est.5c01852}, pmid = {40505009}, issn = {1520-5851}, mesh = {Gases ; *Organic Chemicals/toxicity ; *tert-Butylhydroperoxide/toxicity ; Water ; }, abstract = {Organic pollutants exist in various physical states within the natural environment, yet it remains unclear how their physical states influence their toxicity characteristics. This study investigated the phase-dependent genotoxicity and combined effects of two organic compounds, tert-butyl hydroperoxide (TBHP) and dimethyl sulfate (DES), in both gaseous and aqueous phases. Given the substantial differences in concentrations for the same compound in gaseous and aqueous environments, we constructed the complete multitoxic and dose-response curves for gene induction in both phases, covering environmentally relevant concentrations. Under the same stress conditions, the genotoxicity of gaseous TBHP was 158.21 ± 33.17% of that of its aqueous form, while gaseous DES exhibited 260.56 ± 12.63% of the genotoxicity of its aqueous form. Notably, while no formation of new reaction products were observed, aqueous-phase mixtures exhibited greater complexity and higher toxicity compared to their gaseous counterparts. These differences were attributed to variations in molecular energy states, free radical generation and diffusion, molecular interaction pathways, and chemical reactivity between the two phases. By elucidating the mechanisms underlying these disparities, this study highlights the critical role of physical states in evaluating the toxicity and risks associated with gaseous organic chemicals.}, }
@article {pmid40504830, year = {2025}, author = {Negeri, BG and Xiuguang, B and Moisa, MB}, title = {Assessment of potential land suitability for rainfed wheat production using GIS and multi criteria decision analysis in the Southwestern parts of Ethiopia.}, journal = {PloS one}, volume = {20}, number = {6}, pages = {e0324540}, pmid = {40504830}, issn = {1932-6203}, mesh = {*Triticum/growth &amp; development ; Ethiopia ; *Geographic Information Systems ; Rain ; Soil/chemistry ; *Decision Support Techniques ; *Agriculture/methods ; Crops, Agricultural/growth &amp; development ; }, abstract = {Wheat production in Ethiopia is vital for improving food security, boosting the national economy, and achieving self-sufficiency in food consumption. The present study aims to assess the potential land suitability for rainfed wheat (Triticum aestivum L.) production by using Geographic Information System and multi criteria decision analysis in southwestern parts of Ethiopia. Biophysical data, including land use and land cover (LULC), soil drainage, soil texture, soil depth, proximity to markets and roads, land surface temperature, slope, rainfall, and elevation, were used. In addition, different software tools, such as ArcGIS 10.3, ERDAS Imagine 2015, IDRISI Selva 17, and ArcSWAT were applied. The results revealed that approximately 177.1 km[2] (1.3%) of the study area was classified as highly suitable, 5375.2 km[2] (38.2%) as moderately suitable, 7,246.0 km[2] (51.5%) as marginally suitable, and 1235.1 km[2] (8.8%) as currently not suitable for rainfed wheat cultivation. Furthermore, out of the 23 districts analyzed, Sayo Nole and Bedelle Zuriya were identified as highly suitable for wheat production, with an area of 32.7km2 and 23.3km2 respectively. Therefore, the study recommends that future study research investigate additional other ecological parameters, such as soil PH, lime, gypsum, salinity, alkalinity and socio-economic data, which were not included in the present study.}, }
@article {pmid40504771, year = {2025}, author = {Augustijn, HE and Reitz, ZL and Zhang, L and Boot, JA and Elsayed, SS and Challis, GL and Medema, MH and van Wezel, GP}, title = {Genome mining based on transcriptional regulatory networks uncovers a novel locus involved in desferrioxamine biosynthesis.}, journal = {PLoS biology}, volume = {23}, number = {6}, pages = {e3003183}, pmid = {40504771}, issn = {1545-7885}, mesh = {*Deferoxamine ; *Gene Regulatory Networks ; Gene Expression Regulation, Bacterial ; *Streptomyces coelicolor/genetics/metabolism ; *Genome, Bacterial ; Multigene Family ; Bacterial Proteins/genetics/metabolism ; Operon ; Computational Biology ; Iron/metabolism ; Data Mining ; }, abstract = {Bacteria produce a plethora of natural products that are in clinical, agricultural and biotechnological use. Genome mining has uncovered millions of biosynthetic gene clusters (BGCs) that encode their biosynthesis, the vast majority of them lacking a clear product or function. Thus, a major challenge is to predict the bioactivities of the molecules these BGCs specify, and how to elicit their expression. Here, we present an innovative strategy whereby we harness the power of regulatory networks combined with global gene expression patterns to predict BGC functions. Bioinformatic analysis of all genes predicted to be controlled by the iron master regulator DmdR1 combined with co-expression data, led to identification of the novel operon desJGH that plays a key role in the biosynthesis of the iron overload drug desferrioxamine (DFO) B in Streptomyces coelicolor. Deletion of either desG or desH strongly reduces the biosynthesis of DFO B, while that of DFO E is enhanced. DesJGH most likely act by changing the balance between the DFO precursors. Our work shows the power of harnessing regulation-based genome mining to functionally prioritize BGCs, accelerating the discovery of novel bioactive molecules.}, }
@article {pmid40504102, year = {2025}, author = {Roces, V and Cañal, MJ and Mateo, JL and Valledor, L}, title = {Pra-GE-ATLAS: Empowering Pinus radiata stress and breeding research through a multi-omics database.}, journal = {Journal of integrative plant biology}, volume = {67}, number = {8}, pages = {2028-2043}, pmid = {40504102}, issn = {1744-7909}, support = {FPU18/02953//Ministerio de Universidades/ ; PID2019-107107GB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; }, mesh = {*Pinus/genetics/physiology ; *Stress, Physiological/genetics ; *Proteomics/methods ; *Plant Breeding ; Gene Expression Regulation, Plant ; *Databases, Genetic ; Transcriptome/genetics ; Multiomics ; }, abstract = {In recent decades, research on model organisms has significantly increased our understanding of core biological processes in plant science. However, this focus has created a substantial knowledge bottleneck due to the limited phylogenetic and ecological spectrum covered. Gymnosperms, especially conifers, represent a molecular and ecological diversity hotspot among seed plants. Despite their importance, research on these species is notably underrepresented, primarily due to a slower pace of investigation resulting from a lack of community-based resources and databases. To fill this gap, we developed the P(inus)ra(diata)-G(ene)E(xpression) (Pra-GE)-ATLAS, which consists of several tools and two main modules: transcriptomics and proteomics, presented in this work for the forestry commercial and stress-sensitive species Pinus radiata. We have summarized and centralized all the available information to provide a comprehensive view of the gene expression landscape. To illustrate how applications of the database lead to new biological insights, we have integrated multiple regulatory layers across tissues and stressors. While stress favors the retention of small introns, harmonized alternative splicing analyses reveal that genes with conifers' iconic large introns tend to be under constitutive regulation. Furthermore, the degree of convergence between stressors differed between regulatory layers, with proteomic responses remaining highly distinctive even through intergenerational memory tolerance. Overall, the Pra-GE-ATLAS aims to narrow the distance between angiosperms and gymnosperms resources, deepening our understanding of how characteristic pine features have evolved. Pra-GE-ATLAS DB is available at: http://pra-ge-atlas.valmei.es.}, }
@article {pmid40502560, year = {2025}, author = {Gontjes, KJ and Singh, A and Sansom, SE and Boyko, JD and Smith, SA and Lautenbach, E and Snitkin, E}, title = {Phylogenetic context of antibiotic resistance provides insights into the dynamics of resistance emergence and spread.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {40502560}, support = {F31 AI186288/AI/NIAID NIH HHS/United States ; R01 AI148259/AI/NIAID NIH HHS/United States ; T32 HG000040/HG/NHGRI NIH HHS/United States ; U19 AI181767/AI/NIAID NIH HHS/United States ; }, abstract = {BACKGROUND: To ameliorate the antibiotic resistance crisis, the drivers of resistance emergence (i.e., de novo evolution) and resistance spread (i.e., cross-transmission) must be better understood.<br><br>METHODS: Whole-genome sequencing and susceptibility testing were performed on clinical carbapenem-resistant Klebsiella pneumoniae isolates collected from August 2014 to July 2015 across 12 hospitals. Ancestral state reconstruction partitioned patients with resistant strains into those that likely acquired resistance via de novo evolution or cross-transmission. Logistic regression was used to evaluate the associations between patient characteristics/exposures and these two pathways: resistance due to predicted within-host emergence of resistance, and resistance due to predicted cross-transmission. This framework is available in the user-friendly R package, phyloAMR (https://github.com/kylegontjes/phyloAMR).<br><br>RESULTS: Phylogenetic analysis of 386 epidemic lineage carbapenem-resistant Klebsiella pneumoniae sequence type 258 isolates revealed differences in the relative contribution of de novo evolution and cross-transmission to the burden of resistance to five antibiotics. Clade-specific variations in rates of resistance emergence and their frequency and magnitude of spread were detected for each antibiotic. Phylogenetically-informed regression modeling identified distinct clinical risk factors associated with each pathway. Exposure to the cognate antibiotic was an independent risk factor for resistance emergence (trimethoprim-sulfamethoxazole, colistin, and beta-lactam/beta-lactamase inhibitors) and resistance spread (trimethoprim-sulfamethoxazole, amikacin, and colistin). In addition to antibiotic exposures, comorbidities (e.g., stage IV+ decubitus ulcers) and indwelling devices (e.g., gastrostomy tubes) were detected as unique risk factors for resistance spread.<br><br>CONCLUSIONS: Phylogenetic contextualization generated insights and hypotheses into how bacterial genetic background, patient characteristics, and clinical practices influence the emergence and spread of antibiotic resistance.}, }
@article {pmid40502073, year = {2025}, author = {Chen, H and Shu, J and Mudappathi, R and Li, E and Wang, P and Bergsagel, L and Yang, P and Sun, Z and Zhao, L and Shi, C and Townsend, JP and Maley, C and Liu, L}, title = {Competing Subclones and Fitness Diversity Shape Tumor Evolution Across Cancer Types.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40502073}, issn = {2692-8205}, support = {R01 LM013438/LM/NLM NIH HHS/United States ; }, abstract = {Intratumor heterogeneity arises from ongoing somatic evolution complicating cancer diagnosis, prognosis, and treatment. Here we present TEATIME (estimating evolutionary events through single-timepoint sequencing), a novel computational framework that models tumors as mixtures of two competing cell populations: an ancestral clone with baseline fitness and a derived subclone with elevated fitness. Using cross-sectional bulk sequencing data, TEATIME estimates mutation rates, timing of subclone emergence, relative fitness, and number of generations of growth. To quantify intratumor fitness asymmetries, we introduce a novel metric-fitness diversity-which captures the imbalance between competing cell populations and serves as a measure of functional intratumor heterogeneity. Applying TEATIME to 33 tumor types from The Cancer Genome Atlas, we revealed divergent as well as convergent evolutionary patterns. Notably, we found that immune-hot microenvironments constraint subclonal expansion and limit fitness diversity. Moreover, we detected temporal dependencies in mutation acquisition, where early driver mutations in ancestral clones epistatically shape the fitness landscape, predisposing specific subclones to selective advantages. These findings underscore the importance of intratumor competition and tumor-microenvironment interactions in shaping evolutionary trajectories, driving intratumor heterogeneity. Lastly, we demonstrate that TEATIME-derived evolutionary parameters and fitness diversity offer novel prognostic insights across multiple cancer types.}, }
@article {pmid40498870, year = {2025}, author = {Wu, X and Liu, J and Hou, Y}, title = {Data and methods for assessing urban green infrastructure using GIS: A systematic review.}, journal = {PloS one}, volume = {20}, number = {6}, pages = {e0324906}, pmid = {40498870}, issn = {1932-6203}, mesh = {*Geographic Information Systems ; Humans ; Sustainable Development ; Cities ; *City Planning/methods ; Ecosystem ; *Conservation of Natural Resources/methods ; }, abstract = {Comprehensive and visual assessments utilizing Geographic Information Systems (GIS) offer an empirical foundation for the planning, construction, and optimization of Urban Green Infrastructure (UGI), effectively promoting its sustainable development. A comprehensive review of this field clarifies the research methods, application scope, trends, and challenges associated with using GIS to advance UGI development. This study synthesizes research findings from the Science Citation Index (SCI) and Social Science Citation Index (SSCI) within the Web of Science (WOS) database, as well as from the Scopus database, for the period from January 1, 2020, to June 30, 2024. The initial dataset included 640 articles from WOS and 952 articles from Scopus. After removing 1,572 duplicates and irrelevant studies, the final selection consisted of 20 articles. The integration of both WOS and Scopus databases ensures a comprehensive capture of current trends and limitations in GIS-based UGI assessments. This study centers on the scope, data sources, theoretical models, analyses, and objectives of GIS-based UGI assessments. The research indicates that over the past five years, GIS-based UGI assessments have primarily focused on areas such as accessibility, ecosystem service potential, resilience, and environmental justice, in addition to non-ecological aspects such as social benefits and aesthetics. While the integration of diverse data and analytical indicators into GIS has enhanced assessment comprehensiveness, and AI technologies have deepened data analysis, field research with urban residents remains crucial, underscoring the importance of inclusiveness in the study. This study also reveals a significant increase in interdisciplinarity in GIS-based assessments of UGI. The integration of assessment methods from ecology, computer science, urban planning, sociology, aesthetics, and other disciplines demonstrates that research in this field has fully considered ecological, social, economic, and humanistic factors, thereby more comprehensively reflecting the integrated needs of sustainable urban development.}, }
@article {pmid40498755, year = {2025}, author = {Morrison, ES and Pandolfi, GP and Aguillon, SM and Ali, JR and Archard, O and Baldassarre, DT and Baquero, I and Bennett, KFP and Bonney, KM and Bryant, R and Catanach, RM and Catanach, TA and Chavoshan, I and Davis, SN and Goodman, BD and Gulson-Castillo, ER and Hack, M and Hudon, J and Leighton, GM and Long, KM and Ma, Z and McCoy, DE and McLaughlin, JF and Rueda Moreno, G and Mota, TM and Noguchi, L and Nwigwe, U and Pegan, T and Provost, KL and Rasband, SA and Salter, JF and Silvernail, LC and Simard, JA and Skeen, HR and Soto-Patiño, J and Suh, YH and Wang, Q and Warshauer, ME and Yan, S and Zalinski, B and Zhao, Z and Shultz, AJ}, title = {AvianLexiconAtlas: A database of descriptive categories of English-language bird names around the world.}, journal = {PloS one}, volume = {20}, number = {6}, pages = {e0325890}, pmid = {40498755}, issn = {1932-6203}, mesh = {*Birds/classification ; Animals ; *Language ; *Terminology as Topic ; *Databases, Factual ; Humans ; }, abstract = {Common names of species are important for communicating with the general public. In principle, these names should provide an accessible way to engage with and identify species. The common names of species have historically been labile without standard guidelines, even within a language. Currently, there is no systematic assessment of how often common names communicate identifiable and biologically relevant characteristics about species. This is a salient issue in ornithology, where common names are used more often than scientific names for species of birds in written and spoken English, even by professional researchers. To gain a better understanding of the types of terminology used in the English-language common names of bird species, a group of 85 professional ornithologists and non-professional contributors classified unique descriptors in the common names of all recognized species of birds. In the AvianLexiconAtlas database produced by this work, each species' common name is assigned to one of ten categories associated with aspects of avian biology, ecology, or human culture. Across 10,906 species of birds, 89% have names describing the biology of the species, while the remaining 11% of species have names derived from human cultural references, human names, or local non-English languages. Species with common names based on features of avian biology are more likely to be related to each other or be from the same geographic region. The crowdsourced data collection also revealed that many common names contain specialized or historic terminology unknown to many of the data collectors, and we include these terms in a glossary and gazetteer alongside the dataset. The AvianLexiconAtlas can be used as a quantitative resource to assess the state of terminology in English-language common names of birds. Future research using the database can shed light on historical approaches to nomenclature and how people engage with species through their names.}, }
@article {pmid40497295, year = {2025}, author = {Taylor, BA and Slater, GP and Stolle, E and Dorey, J and Buchmann, G and Oldroyd, BP and Gloag, R and Harpur, BA}, title = {Multi-Omic Analysis Reveals Population Differentiation and Signatures of Social Evolution in Tetragonula Stingless Bees.}, journal = {Molecular ecology}, volume = {34}, number = {13}, pages = {e17823}, pmid = {40497295}, issn = {1365-294X}, support = {DE220100466//Australian Research Council/ ; LT0056/2022-L//Human Frontier Science Program/ ; }, mesh = {Animals ; Bees/genetics ; *Genetics, Population ; *Social Evolution ; Male ; Genome, Insect ; Selection, Genetic ; Australia ; Female ; Social Behavior ; Multiomics ; }, abstract = {Stingless bees in the genus Tetragonula are social insects with a fully sterile worker caste, and are therefore well-placed to provide insights into the genomic changes associated with 'superorganismal' life histories. Here we assemble the genome of Tetragonula carbonaria and characterise the population structure and divergence of both T. carbonaria and its cryptic congener T. hockingsi in eastern Australia, revealing three distinct populations for T. carbonaria and two partially differentiated subpopulations for T. hockingsi. We then combine our genomic results with RNA-seq data from different T. carbonaria castes (queens, males, workers) to test two hypotheses about genomic adaptations in social insects: the 'Relaxed Constraint' hypothesis, which predicts indirect, and therefore relaxed, selection on worker-biased genes; and the 'Adapted Worker' hypothesis, which predicts intensified positive selection on worker genes due to their evolutionarily novel functions. Although we do not find a direct signal of either weaker purifying selection or elevated positive selection in worker-biased genes based on deviations from neutral expectations of nucleotide change between the two species, other evidence does support a model of relaxed selection on worker-biased genes: such genes show higher nucleotide diversity and greater interspecies divergence than queen-biased genes. We also find that differentially caste-biased genes exhibit distinct patterns of length, GC content and evolutionary origin. These findings, which converge with patterns found in other social insects, support the hypothesis that social evolution produces distinct signatures in the genome. Overall, Tetragonula bees emerge as a valuable model for studying the genomic basis of social complexity in insects.}, }
@article {pmid40494636, year = {2025}, author = {Yaling, H and Shasha, C and Mengyao, L and Wenhui, L and Yan, G and Mengjiao, L and Qian, Z and Siyuan, Z and Diao, Z and Xinhui, L and Lei, Z and Qiong, Z and Ziqiang, Y and Yandong, X and Gaihua, Z and Yin, J}, title = {Phosphate-solubilizing function of Pediococcus pentosaceus PSM16 and its underlying mechanism.}, journal = {Microbiology spectrum}, volume = {13}, number = {7}, pages = {e0049125}, pmid = {40494636}, issn = {2165-0497}, mesh = {Soil Microbiology ; *Phosphates/metabolism ; Phosphorus/metabolism ; *Pediococcus pentosaceus/metabolism/genetics/enzymology ; Soil/chemistry ; Bacterial Proteins/genetics/metabolism ; Acid Phosphatase/metabolism/genetics ; Phytic Acid/metabolism ; Solubility ; Whole Genome Sequencing ; Hydrogen-Ion Concentration ; }, abstract = {Phosphorus is a crucial nutrient for plant growth, but only a limited quantity is typically accessible in the soil for plants to absorb directly. Phosphate-solubilizing bacteria (PSB) can convert inorganic phosphorus compounds into forms that are more readily usable for plant nutrition. Our previous research has verified the function of Pediococcus pentosaceus PSM16 in degrading phytic acid. On this basis, we further explored the phosphorus-solubilizing capacity of PSM16 and evaluated its potential for practical application in this study. The results indicated that PSM16 significantly enhanced phosphorus utilization, not only enriching the environment with bioavailable phosphorus but also lowering the environmental pH and conductivity. These changes are instrumental in enhancing soil fertility, providing favorable conditions for plant growth, and stimulating seed germination. Through whole-genome sequencing of PSM16, we have identified key genes associated with the production of acid phosphatase. Specifically, the genes of GM000834, GM000917, GM000925, and GM000974 are implicated in PSM16's phosphorus solubilization function, likely through the production of phosphatase enzymes. Moreover, we have discovered that the phosphatases T.fus-QOS58989.1, A.cae-WP_156200763, M.the-SNW17984, N.gly-GGP12115, T.chr-SDQ48339.1, and T.chr-SDQ90039.1 are homologous to the aforementioned proteins and are present in compost, as confirmed by our informatics analysis. This presence in compost suggests their potential for real-world agricultural applications. This research presents promising candidate strains for the development of phosphorus-degrading bacterial agents, which could increase the efficiency of phosphorus fertilizers and contribute to sustainable agricultural practices. This strategy is not only effective but also environmentally benign and cost-effective, offering a valuable contribution to the field of agricultural biotechnology.IMPORTANCEThis study sheds light on the transformative power of the PSM16 strain, a paragon of phosphorus solubilization that adeptly converts inert phosphorus into a form that is readily absorbed by plants. In this way, it not only elevates the levels of available phosphorus in the environment but also enriches the soil fertility, supporting the healthy growth of plants. The strategic application of PSM16 in tandem with phosphorus fertilizers promises to enhance the utilization rates of these fertilizers, reinforcing sustainable agricultural initiatives and alleviating the environmental pressures caused by excessive application. In addition, the study has uncovered a trove of strains that hold promise for the development of safe dephosphorylating bacterial agents. These agents are poised to deliver an economical, efficient, and eco-friendly alternative, encapsulating a commitment to agricultural advancement that is both responsible and resourceful.}, }
@article {pmid40493719, year = {2025}, author = {Campbell, AM and Kula, AC and Jabaily, RS and Oberle, B and Sidoti, B and Capaldi, A and Bodine, EN}, title = {Predicting potential recovery of the endangered bromeliad Tillandsia utriculata: An agent-based modeling approach.}, journal = {PLoS computational biology}, volume = {21}, number = {6}, pages = {e1013157}, pmid = {40493719}, issn = {1553-7358}, mesh = {Animals ; *Endangered Species ; *Weevils/physiology ; *Models, Biological ; *Bromeliaceae/physiology/parasitology ; Predatory Behavior ; Florida ; Female ; Computational Biology ; Computer Simulation ; Population Dynamics ; Introduced Species ; }, abstract = {Invasive pests and pathogens are a major driver of biodiversity loss. Some rare species may persist through rapid evolution to tolerate or escape new threats, but representing the underlying ecological and evolutionary processes at the appropriate scale is analytically and computationally challenging. Tillandsia utriculata has been classified as endangered in Florida where its population has decreased significantly due to predation by the invasive Mexican weevil Metamasius callizona. Adult female weevils deposit their eggs in leaves of epiphytic bromeliads, preferentially ovipositing in the largest rosettes. Once the eggs hatch, the larvae consume the core of the rosette, often leading to pre-reproductive death. During the past three decades of predation, the T. utriculata population has shifted to initiating the production of inflorescences (to commence its single attempt at sexual reproduction) at smaller rosette sizes. Importantly, the rosette size at induction is correlated with the number of seeds produced. We have constructed an agent-based model to simulate the dynamics of a Florida T. utriculata population over many generations where the minimum rosettes size required to initiate inflorescence production (minimum size of induction or MSI), is an inherited trait. We use the model to explore how predation may have shifted the population's genetic composition and the impact this has on population viability. Our results show that larger germination rates are required for population viability when weevils are present. Parameter uncertainty analysis revealed that in the presence of weevil predation, only a population with a very high germination rate and a short period of predation would sustain its population for 100 years with sizes similar to simulations without weevil predation. Furthermore, uncertainty analysis showed that the mean MSI of the population decreased over a 100-year period without weevil predation, and this trend was exacerbated by the presence of weevil predation.}, }
@article {pmid40491419, year = {2026}, author = {Tuerlinckx, F and Kuppens, P and Ariens, S and Cloos, L and Dejonckheere, E and Lafit, G and Niemeijer, K and Revol, J and Schat, E and Schreuder, M and Vanhasbroeck, N and Ceulemans, E}, title = {New developments in experience sampling methodology.}, journal = {The British journal of mathematical and statistical psychology}, volume = {79}, number = {1}, pages = {46-65}, doi = {10.1111/bmsp.12398}, pmid = {40491419}, issn = {2044-8317}, support = {//Fonds Wetenschappelijk Onderzoek/ ; //Onderzoeksraad, KU Leuven/ ; C14/23/062//KU Leuven Research Council/ ; IBOF/21/090//IBOF/ ; EOS 4000528/G0I2422N//EOS excellence of science program/ ; }, mesh = {Humans ; Reproducibility of Results ; *Research Design ; Data Interpretation, Statistical ; *Ecological Momentary Assessment/statistics &amp; numerical data ; Models, Statistical ; Self Report ; Sample Size ; Smartphone ; }, abstract = {Experience Sampling Methodology (ESM) has been widely used over the past decades to study feelings, behaviour and thoughts as they occur in daily life. Typically, participants complete several assessments per day via a smartphone for multiple days. The growing adoption of ESM has spurred a number of methodological advancements. In this paper, we provide an overview of recent developments in ESM design, statistical analysis and implementation. In terms of design, we discuss considerations around what to measure-including the reliability and validity of self-report measures as well as mobile sensing-as well as when to measure, where we focus on the pros and cons of burst designs and advances in sample size planning methodology. Regarding statistical analysis, we highlight non-linear models, survival analysis for understanding time-to-event data and real-time monitoring of ESM time series. At the implementation level, we address open science practices and advances in data preprocessing. Although most of the topics discussed in this paper are generic, many of the examples are focused on the study of affect in daily life.}, }
@article {pmid40489655, year = {2025}, author = {Kruse, PM and Ring, CL}, title = {A cheminformatics workflow for higher-throughput modeling of chemical exposures from biosolids.}, journal = {Toxicological sciences : an official journal of the Society of Toxicology}, volume = {207}, number = {1}, pages = {126-138}, doi = {10.1093/toxsci/kfaf081}, pmid = {40489655}, issn = {1096-0929}, support = {/EPA/EPA/United States ; //Oak Ridge Institute for Science and Education/ ; //Department of Energy/ ; /EPA/EPA/United States ; DE-SC0014664//Oak Ridge Associated Universities/ ; //Center for Computational Toxicology and Exposure/ ; //Office of Research and Development/ ; /EPA/EPA/United States ; }, mesh = {Workflow ; Humans ; *Sewage/chemistry ; *Cheminformatics/methods ; United States Environmental Protection Agency ; *High-Throughput Screening Assays ; United States ; *Environmental Exposure ; Risk Assessment ; Software ; }, abstract = {The U.S. Environmental Protection Agency's Biosolids Screening Tool can predict potential human and ecological exposures to chemical contaminants in treated sewage sludge biosolids, but large quantities of chemical-specific physico-chemical data are required to parameterize the model. Here, an R workflow is presented that leverages publicly available databases of chemical information, particularly the U.S. EPA's CompTox Chemicals Dashboard, to prepare data for model simulations using the Biosolids Screening Tool. The workflow is publicly available at https://github.com/USEPA/CompTox-ExpoCast-autoBST. The automated Biosolids Screening Tool workflow (autoBST) reduces the time to gather data necessary to screen hundreds of chemicals from days to just a few minutes. autoBST is a practical example of the utility of leveraging the US EPA CompTox Chemicals Dashboard. autoBST provides transparent and reproducible data retrieval and input into existing models, allowing assessors to defensibly prioritize chemicals in biosolids that may pose a risk to human health or the environment.}, }
@article {pmid40489617, year = {2025}, author = {van Ittersum, MK and Alimagham, S and Silva, JV and Adjei-Nsiah, S and Baijukya, FP and Bala, A and Chikowo, R and Grassini, P and de Groot, HLE and Nshizirungu, A and Mahamane Soulé, A and Sulser, TB and Taulya, G and Amor Tenorio, F and Tesfaye, K and Yuan, S and van Loon, MP}, title = {Prospects for cereal self-sufficiency in sub-Saharan Africa.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {24}, pages = {e2423669122}, pmid = {40489617}, issn = {1091-6490}, support = {INV-005431/GATES/Gates Foundation/United States ; INV-018444//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)/ ; INV-030103/GATES/Gates Foundation/United States ; INV-030103/GATES/Gates Foundation/United States ; INV-005431/GATES/Gates Foundation/United States ; }, mesh = {Africa South of the Sahara ; *Edible Grain/growth &amp; development ; *Food Supply ; Humans ; *Agriculture/methods/trends ; Climate Change ; *Crops, Agricultural/growth &amp; development ; Zea mays/growth &amp; development ; Millets/growth &amp; development ; }, abstract = {Sub-Saharan Africa (SSA) has the world's largest projected increase in demand for food. Increased dependence on imports makes SSA vulnerable to geopolitical and economic risks, while further expansion of agricultural land is environmentally harmful. Cereals, in particular, maize, millet, rice, sorghum, and wheat, take nearly 50% of the cropland and 43% of the calories and proteins consumed in the region. Demand is projected to double until 2050. Here, we assess recent developments in cereal self-sufficiency and provide outlooks until 2050 under different intensification, area expansion, and climate change scenarios. We use detailed data for ten countries. Cereal self-sufficiency increased between 2010 and 2020 from 84 to 92% despite the 29% population increase. The production increase was achieved by increased yields per hectare (44%), area expansion (34%), and a shift from millet to the higher yielding maize (22%). Outlooks for 2050 are less pessimistic than earlier assessments because of the larger 2020 baseline area, higher shares of maize and somewhat less steep projected population increase. Yet, to halt further area expansion, a drastic trend change in annual yield increase from the present 20 to 58 kg ha[-1] y[-1] is needed to achieve cereal self-sufficiency. While such yield increases have been achieved elsewhere and are feasible given the yield potentials in SSA, they require structural changes and substantial agronomic, socioeconomic, and political investments. We estimate that amounts of added nitrogen need to at least triple to achieve such yield improvements, but it is essential that this comes with improved context-specific agronomy.}, }
@article {pmid40489355, year = {2025}, author = {Valverde, S and Vidiella, B and Martínez-Redondo, GI and Duran-Nebreda, S and Fernández, R and Bombarely, A and Rojas, AM and Bentley, RA}, title = {Structural Changes in Gene Ontology Reveal Modular and Complex Representations of Biological Function.}, journal = {Molecular biology and evolution}, volume = {42}, number = {6}, pages = {}, pmid = {40489355}, issn = {1537-1719}, support = {PID2020-117822GB-I00//AEI/ ; PID2021-127503OB-I00//AEI/ ; PCI2022-132936//Swedish Environmental Protection Agency/ ; }, mesh = {*Gene Ontology/trends ; Computational Biology/methods ; }, abstract = {The Gene Ontology is a central resource for representing biological knowledge, yet its internal structure is often treated as static-or as a black box-in computational analyses. Here, we examine 15 years of Gene Ontology evolution using network-based methods, revealing that Gene Ontology changes not only through incremental growth but also through punctuated, curator-driven restructuring. In particular, we document a major reorganization of the Cellular Component branch in 2019, where broad "part" terms were removed and the ontology was modularized into distinct domains for anatomical entities and protein-containing complexes. Semantic modularity aligns Gene Ontology with emerging frameworks such as the Common Anatomy Reference Ontology and Gene Ontology-Causal Activity Modeling, but also disrupts similarity metrics that rely solely on hierarchical proximity. More broadly, the restructuring of the cellular components branch consolidates a shift toward treating Gene Ontology as a multi-layer semantic network-a transformation rooted in a decade-long process of scientific and social consensus across institutions. These findings underscore the need for version-aware, multi-layer models to ensure reproducibility and interpretability-and to better represent biological function across compositional, spatial, and regulatory dimensions as ontologies continue to evolve.}, }
@article {pmid40488574, year = {2025}, author = {Débarre, F and Hensel, Z}, title = {A Critical Reexamination of Recovered SARS-CoV-2 Sequencing Data.}, journal = {Molecular biology and evolution}, volume = {42}, number = {6}, pages = {}, pmid = {40488574}, issn = {1537-1719}, support = {UIDB/04612/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDP/04612/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, mesh = {*SARS-CoV-2/genetics ; Humans ; Animals ; Chiroptera/virology ; *Genome, Viral ; Genotype ; China ; Sequence Analysis, RNA ; RNA, Viral/genetics ; Datasets as Topic ; }, abstract = {In 2021, Jesse Bloom published a study addressing why the earliest SARS-CoV-2 sequences in Wuhan from late December 2019 were not those most similar to viruses sampled in bats. The study concluded that recovered partial sequences from Wuhan and annotation of Wuhan links for other sequences increased support for one genotype as the progenitor of the SARS-CoV-2 pandemic. However, we show that the collection date for the recovered sequences was January 30, 2020, later than that of hundreds of other SARS-CoV-2 sequences. Mutations in these sequences also exhibit diversity consistent with SARS-CoV-2 sequences collected in late January 2020. Furthermore, we found that Wuhan exposure history was common for early samples, so Bloom's annotation for a single familial cluster does not support that an early genotype was undersampled in Wuhan. Both the recovered partial sequences and additional annotation align with contemporaneous data rather than increase support for a progenitor. Our findings clarify the significance of the recovered sequences and are supported by additional data and analysis published since mid-2021.}, }
@article {pmid40484397, year = {2025}, author = {Adachi, A and Dominguez, JJ and Utami, YD and Fuji, M and Kirita, S and Imai, S and Murakami, T and Hongoh, Y and Shinjo, R and Kamiya, T and Fujiwara, T and Minamisawa, K and Ono, N and Kanaya, S and Saijo, Y}, title = {Field dynamics of the root endosphere microbiome assembly in paddy rice cultivated under no fertilizer input.}, journal = {Plant &amp; cell physiology}, volume = {66}, number = {7}, pages = {1086-1101}, doi = {10.1093/pcp/pcaf045}, pmid = {40484397}, issn = {1471-9053}, support = {18H02467//Ministry of Education, Culture, Sports, Science, and Technology of Japan/ ; 24K21870//Ministry of Education, Culture, Sports, Science, and Technology of Japan/ ; JPMJTR23UJ//Japan Science and Technology Agency/ ; JPMJSP2140//JST SPRING, Japan/ ; }, mesh = {*Oryza/microbiology/growth &amp; development ; *Plant Roots/microbiology ; *Microbiota/genetics ; Fertilizers ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Metagenome ; Nitrogen Fixation ; Bacteria/genetics ; }, abstract = {Plants accommodate diverse microbial communities, termed the microbiome, which can change dynamically during plant adaptation to varying environmental conditions. However, the direction of these changes and the underlying mechanisms driving them, particularly in crops adapting to the field conditions, are not well understood. Here, we investigate the root endosphere microbiome of rice (Oryza sativa ssp. japonica) across four consecutive cultivation seasons in a high-yield, non-fertilized, and pesticide-free paddy field, compared with a neighboring fertilized and pesticide-treated field. Using 16S rRNA amplicon and metagenome sequencing, we analyzed three Japonica cultivars-Nipponbare, Hinohikari, and Kinmaze. Our findings reveal that the root endosphere microbiomes diverge based on fertilization regime and plant developmental stages, while the effects of cultivar variation are less significant. Machine learning model and metagenomic analysis of nitrogenase (nif) genes suggest enhanced nitrogen fixation activity in the non-fertilized field-grown roots, highlighting a potential role of diazotrophic, iron-reducing bacteria Telmatospirillum. These results provide valuable insights into the assembly of the rice root microbiome in nutrient-poor soil, which can aid in managing microbial homeostasis for sustainable agriculture.}, }
@article {pmid40481658, year = {2025}, author = {von Mering, S and Leachman, S and Santos, J and Meudt, HM}, title = {Wikidata for botanists: benefits of collaborating and sharing Linked Open Data.}, journal = {Annals of botany}, volume = {136}, number = {3}, pages = {491-511}, pmid = {40481658}, issn = {1095-8290}, support = {//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; }, mesh = {*Botany ; *Information Dissemination/methods ; *Internet ; Knowledge Bases ; *Databases, Factual ; }, abstract = {BACKGROUND: Wikidata is a multilingual linked open knowledge base to which anyone can contribute that contains multitudes of botany-related information. Wikidata reveals interactions between entities and connects botany-related information from multiple institutions and other sources, benefiting the botanical community in numerous ways. The aim of this article is to give an overview of Wikidata from a botany perspective and issue a call to action to the botanical community to collectively improve the quantity and quality of information related to botany, botanists and botanical collections, in Wikidata. Here, we use a broad definition of botany to include the study of many different taxa and specializations.<br><br>SCOPE: Wikidata contains botany-related data and identifiers for botanists and botanical collectors, botanical taxa, natural history institutions and collections, botany-related publications, geographical locations and research expeditions, as well as genes, genetic variants, chemical compounds, diseases, and more. As an open, collaborative and community-curated knowledge base, Wikidata enables different communities to add and link data related to botany and empowers the querying and reuse of this data via digital tools such as the Wikidata Query Service, Bionomia, Scholia, TL-2 and Expeditia.<br><br>CONCLUSIONS: Collaboration is key in botany and Wikidata, and the sharing and enriching of botany-related Linked Open Data benefits us all. Several resources, including ethical and legal guidelines, are available for botanists to edit, use, reuse, roundtrip and teach Wikidata. We call on all botanists to be active participants in Wikidata, improving the quality, quantity and linking of botany-related data. Our individual and collective actions can help harness the power of Linked Open Data to answer important queries in the field, improve accessibility of herbaria, increase visibility of botanists and their scientific contributions, integrate Wikidata into the classroom, support the Madrid Declaration strategic actions, achieve our collective goals, and ultimately make botany-related information more FAIR (Findable, Accessible, Interoperable, Reusable) and equitable.}, }
@article {pmid40478826, year = {2025}, author = {Flynn, KJ and Morozov, AY}, title = {Resource acquisition in diel cycles and the cost of growing quickly.}, journal = {PLoS computational biology}, volume = {21}, number = {6}, pages = {e1013132}, pmid = {40478826}, issn = {1553-7358}, mesh = {*Models, Biological ; *Microalgae/growth &amp; development/metabolism/physiology ; Computer Simulation ; Carbon/metabolism ; Biomass ; Computational Biology ; *Circadian Rhythm/physiology ; Carbon Cycle/physiology ; }, abstract = {Many organisms, notably phototrophs, routinely acquire resources over only a fraction of the day. They have to balance their main period of initial biosynthesis against cell cycle events. Because of their short generation times, this challenge is especially acute for the planktonic microalgae that perform 50% of global C-fixation. Empirical evidence indicates that microalgal day-average growth is a function of the ability to acquire resources rapidly when available, retaining initial products of assimilation to support growth. A fundamental question arises over the optimal physiological configuration to support such activity. Here, we applied computer simulations implementing a development of the quota concept, in which the internal limiting resource is itself C, ratioed against total organism C-biomass. The model comprises metabolite and core pools of carbon C (MC and CC, respectively), with growth modulated by MC/(MC + CC); MC supports growth of CC in the absence of concurrent resource acquisition. Dynamic feedback interactions from the relative size of MC controls resource acquisition. The model reproduces the general pattern of growth at different light:day fraction (LD), and of afternoon-depression of C-fixation. We explored the efficiency of the physiological cell configuration to locate optimal configurations at different combinations of maximum growth rates (Umax) and LD values across plausible parameter values for microalgae. While the optimum maximum resource acquisition rate deployed during the L phase scales with Umax/LD, the maximum size of the metabolite pool scales to LD/DV, where DV is division time (i.e. Umax/Ln(2)). Accordingly, we conclude that faster growing organisms carry a penalty limiting their geographic spread to latitudes and seasons where LD is high. Larger, vacuolated organisms (such as diatoms), having a bigger metabolite compartment, may be at an advantage in such situations.}, }
@article {pmid40474615, year = {2025}, author = {Amador, LG and Ramirez-Parada, TH and Park, IW and Mazer, SJ and Ellison, AM and O'Brien, M and Sokol, ER and Smith, CA and Davis, CC and Record, S}, title = {Bridging data silos to holistically model plant macrophenology.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.70249}, pmid = {40474615}, issn = {1469-8137}, support = {1556768//Division of Environmental Biology/ ; 2105903//Division of Environmental Biology/ ; 2105907//Division of Environmental Biology/ ; 2105932//Division of Environmental Biology/ ; 22425//Maine Agricultural and Forest Experiment Station/ ; 2223103//Division of Biological Infrastructure/ ; 2223104//Division of Biological Infrastructure/ ; }, abstract = {Phenological response to global climate change can impact ecosystem functions. There are various data sources from which spatiotemporal and taxonomic phenological data may be obtained: mobilized herbaria, community science initiatives, observatory networks, and remote sensing. However, analyses conducted to date have generally relied on single sources of these data. Siloed treatment of data in analyses may be due to the lack of harmonization across different data sources that offer partially nonoverlapping information and are often complementary. Such treatment precludes a deeper understanding of phenological responses at varying macroecological scales. Here, we describe a detailed vision for the harmonization of phenological data, including the direct integration of disparate sources of phenological data using a common schema. Specifically, we highlight existing methods for data harmonization that can be applied to phenological data: data design patterns, metadata standards, and ontologies. We describe how harmonized data from multiple sources can be integrated into analyses using existing methods and discuss the use of automated extraction techniques. Data harmonization is not a new concept in ecology, but the harmonization of phenological data is overdue. We aim to highlight the need for better data harmonization, providing a roadmap for how harmonized phenological data may fill gaps while simultaneously being integrated into analyses.}, }
@article {pmid40472753, year = {2025}, author = {Liu, F and Gao, H and Qin, F and Zhao, S and Zhou, B and Zhou, J and Wu, R and Luo, H and Wang, Z and Ye, H}, title = {Multi-omics reveals dynamic molecular characteristics in the ovarian development of Chinese longsnout catfish Leiocassis longirostris.}, journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics}, volume = {56}, number = {}, pages = {101551}, doi = {10.1016/j.cbd.2025.101551}, pmid = {40472753}, issn = {1878-0407}, mesh = {Animals ; Female ; *Ovary/growth &amp; development/metabolism ; *Catfishes/genetics/growth &amp; development/metabolism ; *Fish Proteins/genetics/metabolism ; Gene Expression Regulation, Developmental ; *Transcriptome ; Multiomics ; }, abstract = {Leiocassis longirostris (L. longirostris) is a significant freshwater fish species in China. Due to the decline in natural populations, its market demand is now largely met through artificial breeding. However, the complex and prolonged ovarian maturation process has rendered current artificial breeding methods limited. Additionally, the molecular mechanisms underlying ovarian development in L. longirostris remain poorly understood. In this study, we conducted RNA and protein sequencing of L. longirostris ovarian samples across five developmental stages, categorized based on histological staining results. To uncover the dynamic characteristics of ovarian development, we identified differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) by comparing gene and protein expression profiles stage-by-stage (stage I to II, II to III, III to IV, and IV to V). GO and KEGG enrichment analyses of these profiles revealed significant enrichment in terms and pathways related to the endocrine system, signal transduction, and lipid metabolism, with dynamic changes observed across stages. The nine-quadrant analysis further elucidated the regulatory characteristics of DEGs and DEPs, highlighting differences in mRNA and protein-level regulation of genes and proteins involved in fat and protein digestion and absorption. Protein-protein interaction networks were further constructed from shared DEGs and DEPs profiles to evacuate candidate proteins involved in L. longirostris ovarian development. Moreover, we clustered DEGs and DEPs into ten clusters based on their expression trend. KEGG enrichment analysis of clusters showed pathways such as FoxO and MAPK signaling pathways were significantly enriched in cluster 4, where the expression increased as ovarian development. qPCR validation confirmed differential expression of genes associated with oocyte meiosis and steroid hormone biosynthesis, consistent with RNA-seq results. This study provides a foundation for understanding yolk lipids metabolism, paracrine factors, and endocrine system regulation during ovarian development and offers insights into developing efficient artificial breeding strategies for L. longirostris.}, }
@article {pmid40468364, year = {2025}, author = {Pan, X and Shan, Z and Tian, X and Niu, Y and Liu, Y and Li, Z and Li, Y and Huang, Y and Ye, J}, title = {Evaluating conservation gaps of China's national key protected wild plants: insights from county-level distribution data.}, journal = {BMC biology}, volume = {23}, number = {1}, pages = {156}, pmid = {40468364}, issn = {1741-7007}, support = {202206193000001//Shenzhen Science and Technology Program/ ; 20220816162653003//Shenzhen Science and Technology Program/ ; 32270233//National Natural Science Foundation of China/ ; 32200177//National Natural Science Foundation of China/ ; 2022YFF0802300//National Key Research Development Program of China/ ; 2023BSZR014//Doctoral Research Foundation of Jiangxi University of Chinese Medicine/ ; Jiangxi Traditional Chinese Medicine Comprehensive Word No. 3 (2024)//Construction of National Heritage Studio for Old Medicine Workers/ ; }, mesh = {*Conservation of Natural Resources ; China ; *Endangered Species ; *Plants/classification ; Biodiversity ; Databases, Factual ; }, abstract = {BACKGROUND: The National Key Protected Wild Plants (NKPWPs) list serves as China's primary legal framework for plant diversity protection, with the species categorized into Level I (critically endangered, strictly protected) and Level II (lower risk but still requiring protection). However, the geographical distribution of these species and gaps in their conservation remain elusive due to the limited availability of data on species distribution. Thus, to address these gaps and support precise conservation, we developed a county-level distribution database for the NKPWP species using information primarily sourced from literature. Using this database, we elucidated the geographical distribution patterns of NKPWPs and identified the gaps in both in situ and ex situ conservation.<br><br>RESULTS: The NKPWPs analyzed in the study included 1,128 plant species. We compiled a county-level distribution database for these species with 30,397 records. Detailed analysis of this data revealed that these species were concentrated in the mountainous regions of southern China, including the Eastern Himalaya-Hengduan Mountains, south Yunnan, the Yunnan-Guizhou-Guangxi border, and the Wuling Mountains. Among the 1,118 embryophyte species of the checklist, 1,060 (94.81%) were found conserved in situ, 681 (60.91%) were found conserved ex situ, and 660 (59.03%) through both approaches. Besides, species with a higher threat level and limited distribution range exhibited lower conservation coverage in both ex situ and in situ approaches; 37 species received no conservation (3.31%).<br><br>CONCLUSIONS: The county-level distribution database developed in this study comprehensively depicts the geographical distribution patterns of NKPWP in China, offering valuable data for planning species conservation and providing a foundational framework for addressing the existing gaps in their conservation across China. This database will ultimately support targeted conservation and resource allocation to protect plant diversity effectively. We also suggest adopting an integrated evaluation approach for conservation strategies in other areas, globally, or for other biological groups.}, }
@article {pmid40465754, year = {2025}, author = {Duan, Z and Wang, G and Hu, J and Yu, T and Chen, S and Zhang, Y and Wang, Y and Liu, H and Zhao, X and Chen, H}, title = {Spatiotemporal dynamics of northern Caspian shorelines (1985-2023) and implications for coastal management: Lessons from the Aral Sea.}, journal = {PloS one}, volume = {20}, number = {6}, pages = {e0325546}, pmid = {40465754}, issn = {1932-6203}, mesh = {Oceans and Seas ; *Conservation of Natural Resources ; Spatio-Temporal Analysis ; Ecosystem ; Geographic Information Systems ; Biodiversity ; }, abstract = {Dynamic changes to the northern Caspian Sea shoreline have significant ecological implications, including impacts to biodiversity and the surrounding environment. This study employs Landsat datasets, historical records, and geographic information systems (GIS) to quantitatively analyze spatiotemporal variations along the northern Caspian Sea coastline from 1985 to 2023. The findings demonstrate pronounced cyclic variations in the Caspian Sea's water level. Compared to 1930, the water level decreased by 2.6 m by 2023, with 1935 marking the onset of a significant downward trend. From 1995 to 2023, a pronounced decline in the water level at a rate of 6.1 cm/year was observed. Multiscale temporal oscillations in water levels revealed periodic rises and falls with cycles ranging from 6-8 years to 10-16 years. Due to the broad and shallow morphology of the northern Caspian Sea, fluctuations in water level have resulted in significant displacements of the northern coastline. Between 1985 and 2023, the shoreline length decreased by 262 km, which is equivalent to a 17% reduction. The intensity of the coastline length index reached a critical point during from 2010 to 2015, after which it declined sharply by 3.67. By 2023, the coastline had shifted seaward by 1.33 × 10[4] km2 relative to that in 1985. This continuous retreat of the shoreline poses a severe threat to the ecological stability of the northern Caspian Sea. If the trend persists, then the disappearance of the eastern basin of the South Aral Sea may be replicated in the northern Caspian Sea by 2100. These findings provide critical insights for formulating effective coastal management strategies and conservation initiatives.}, }
@article {pmid40463795, year = {2025}, author = {Petrou, E and Davies, H and Aoun, M and Radford, AD and Singleton, D and Noble, PM and Killick, DR}, title = {First opinion practice electronic health records are a useful source of descriptions of medication errors.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1560652}, pmid = {40463795}, issn = {2297-1769}, abstract = {BACKGROUND: Medication error (MedE) is a leading global cause of harm in human healthcare with significance both in patient morbidity and mortality, and consequent legal and financial issues. Despite this, MedEs are a poorly explored area in veterinary medicine. Research has so far focussed on survey work and errors spontaneously reported to third parties, such as professional indemnity providers.<br><br>AIM: Determine if MedEs can be successfully identified in first opinion electronic health records (EHRs).<br><br>ANIMALS: EHRs pertaining to animals treated in UK first opinion practice.<br><br>MATERIALS AND METHODS: Regular expressions (REGEX) were designed (with assistance from a domain expert) to identify explicit reference to MedEs in the SAVSNET EHR dataset. Identified MedEs were then classified by the linear sequence of medication therapy, the degree of harm caused, the role of the person who made the error, and the medication type involved.<br><br>RESULTS: In total, 6,665 EHRs were identified by the REGEX, of which a random 2,847 were manually reviewed, with 1,023 (35.9%) matching the MedEs case definition. Of these MedEs, 29.5% (n&#x202f;=&#x202f;302) caused mild harm to the patient, 2.8% (n&#x202f;=&#x202f;27) moderate harm and 0.2% (n&#x202f;=&#x202f;2) severe harm. MedEs were most frequent during the "drug administered" phase (51.4%) and within this phase, "dosing errors" were most common (68.1%). The most common medication types, associated with "drug administered" phase MedEs were vaccinations (27.1%) and non-steroidal anti-inflammatory drugs (19.0%).<br><br>CONCLUSION: EHRs are a useful source of data on MedEs. MedEs are a common cause of patient harm in veterinary practice. The data provided here highlights drug classes at higher risk of problems for which mitigating action and/or education interventions are indicated.}, }
@article {pmid40463267, year = {2025}, author = {Brook, JBH and Salo, T and Luo, AC and Bagautdinova, J and Rush, S and Alexander-Bloch, AF and Baller, EB and Calkins, ME and Cieslak, M and Cooper, EC and Detre, JA and Elliot, MA and Fair, DA and Freedman, P and Gehrman, PR and Gur, RC and Gur, RE and Klein, A and Laney, N and Laumann, TO and Mehta, K and Merikangas, K and Milham, MP and Mitchell, JA and Moore, TM and Nelson, SM and Ruparel, K and Sevchik, BL and Shanmugan, S and Shou, H and Taso, M and White, LK and Wolf, DH and Tisdall, MD and Roalf, DR and Satterthwaite, TD}, title = {An open, fully-processed data resource for studying mood and sleep variability in the developing brain.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40463267}, issn = {2692-8205}, support = {R37 MH125829/MH/NIMH NIH HHS/United States ; R01 MH117014/MH/NIMH NIH HHS/United States ; K23 MH133118/MH/NIMH NIH HHS/United States ; U24 NS130411/NS/NINDS NIH HHS/United States ; R01 EB031080/EB/NIBIB NIH HHS/United States ; R01 MH113550/MH/NIMH NIH HHS/United States ; R00 MH129616/MH/NIMH NIH HHS/United States ; S10 OD023495/OD/NIH HHS/United States ; R01 MH119219/MH/NIMH NIH HHS/United States ; R01 EB022573/EB/NIBIB NIH HHS/United States ; R01 MH112847/MH/NIMH NIH HHS/United States ; F31 MH136685/MH/NIMH NIH HHS/United States ; DP5 OD036142/OD/NIH HHS/United States ; }, abstract = {Brain development during adolescence and early adulthood coincides with shifts in emotion regulation and sleep. Despite this, few existing datasets simultaneously characterize affective dynamics, sleep variation, and multimodal measures of brain development. Here, we describe the study protocol and initial release (n = 10) of an open data resource of neuroimaging paired with densely sampled behavioral measures in adolescents and young adults. All participants complete multi-echo functional MRI, compressed-sensing diffusion MRI, and advanced arterial spin-labeled MRI. Behavioral measures include ecological momentary assessment, actigraphy, extensive cognitive assessments, and detailed clinical phenotyping focused on emotion regulation. Raw and processed data are openly available without a data use agreement and will be regularly updated as accrual continues. Together, this resource will accelerate research on the links between mood, sleep, and brain development.}, }
@article {pmid40459864, year = {2025}, author = {Shilenok, VV and Shilenok, IV and Soldatov, VO and Orlov, YL and Kobzeva, KA and Deykin, AV and Bushueva, OY}, title = {Bioinformatic analysis of the regulatory potential of tagging SNPs provides evidence of the involvement of genes encoding the heat-resistant obscure (Hero) proteins in the pathogenesis of cardiovascular diseases.}, journal = {Journal of integrative bioinformatics}, volume = {22}, number = {1}, pages = {}, pmid = {40459864}, issn = {1613-4516}, mesh = {*Polymorphism, Single Nucleotide ; Humans ; *Computational Biology/methods ; *Cardiovascular Diseases/genetics/pathology/metabolism ; *Genetic Predisposition to Disease ; Quantitative Trait Loci ; }, abstract = {Although multiple aspects of molecular pathology underlying cardiovascular diseases (CVDs) have been revealed, the complete picture has yet to be elucidated. In this respect, annotation of the novel links between genes and atherosclerosis is of great importance for cardiovascular medicine. Aligning with our previous research, we aimed to analyze the cardiovascular predisposition contribution of the genes encoding Hero-proteins, polypeptides with chaperone activity. Following bioinformatic sources were utilized to annotate data regarding the cardiovascular contribution of Hero-proteins and their genes: SNPinfo Web Server, The Cardiovascular Disease Knowledge Portal, GTEx Portal, HaploReg, rSNPBase, RegulomeDB, atSNP, Gene Ontology, QTLbase, and the Blood eQTL browser. Almost all analyzed genes were characterized by a very high regulatory potential of tag SNPs (except BEX3). Multiple substantial impacts of the analyzed SNPs on histone modifications, eQTL effects on CVD-related genes, and binding to transcription factors involved in biological processes pathogenetically significant for CVDs have been discovered. Here we provide in silico evidence of the involvement of genes C9orf16 (BBLN), C11orf58, SERBP1, SERF2, and C19orf53 in CVDs and their risk factors (high blood pressure, dyslipidemia, obesity, arrhythmias, etc.), thus revealing Hero-proteins as putative actors in the pathobiology of the heart and vessels.}, }
@article {pmid40458985, year = {2025}, author = {Carné, A and Vieites, DR and van den Burg, MP}, title = {In Vouchers We (Hope to) Trust: Unveiling Hidden Errors in GenBank's Tetrapod Taxonomic Foundations.}, journal = {Molecular ecology}, volume = {34}, number = {13}, pages = {e17812}, pmid = {40458985}, issn = {1365-294X}, support = {10.13039/501100011033//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades, Agencia Estatal de Investigaci&#xf3;n./ ; }, mesh = {Animals ; *Databases, Nucleic Acid/standards ; Sequence Analysis, DNA ; Phylogeny ; DNA Barcoding, Taxonomic ; }, abstract = {Genetic repositories are invaluable resources foundational to various biological disciplines. While their data and metadata reliability are essential for robust research outcomes, numerous studies have highlighted data quality and consistency issues. Here, we detect and quantify errors at the most fundamental level by analysing the congruence of sequences derived from the same genetic marker and specimen voucher across tetrapods. Our analysis reveals that 32% of re-sequenced vouchers (with identical field or museum numbers) yield unequal sequences, ranging from a few mutations to significant divergences (0.06%-33.95%). These divergences may result from sample misidentification, labelling errors, fidelity disparities between sequencing methods, or contamination at various stages of the research process. Our findings demonstrate errors within GenBank at its most basal level and suggest that, although undetectable, a similar error rate likely exists in non-re-sequenced data. These previously overlooked errors are concerning because they arise from replicated experiments, which are uncommon, and raise serious questions about the reliability of non-re-sequenced specimens. Such errors can compromise the accuracy of biodiversity assessments (e.g., taxonomic assessment, eDNA and barcoding), phylogenetic analyses and conservation planning by artificially inflating the intraspecific divergence or misidentifying (to-be-described) species. Additionally, the accuracy of large-scale biological studies that rely on such data can be compromised. Our concerning results call for protocols ensuring sample traceability to the specimens or tissues during the whole process of data generation, analysis and deposition in a database. We propose a third-party annotation system for individual GenBank records that would allow flagging common errors and alert both the original submitter and all users to potential problems without modifying the original records.}, }
@article {pmid40455595, year = {2025}, author = {Fetters, AM and Cantalupo, PG and Robles, MTS and Pipas, JM and Ashman, TL}, title = {Sharing Pollinators and Viruses: Virus Diversity of Pollen in a Co-Flowering Community.}, journal = {Integrative and comparative biology}, volume = {65}, number = {4}, pages = {942-954}, pmid = {40455595}, issn = {1557-7023}, support = {KA2017-91786//Charles E. Kaufman Foundation/ ; //Kenneth P. Dietrich School of Arts and Sciences/ ; }, mesh = {*Pollination ; *Pollen/virology ; *Plant Viruses/physiology ; *Biodiversity ; Animals ; *Magnoliopsida/virology/physiology ; Flowers/virology ; }, abstract = {Co-flowering plant species frequently share pollinators, flower-inhabiting bacteria, and fungi, but whether pollen-associated viruses are shared is unknown. Given that pollen-associated viruses are sexually transmitted diseases, their diversity is expected to increase with pollinator sharing. We conducted a metagenomic study to identify pollen-associated viruses from 18 co-flowering plant species to determine whether (1) life history, floral traits, or pollination generalism were associated with viral richness, and (2) plants shared pollen-associated viruses. We demonstrated that pollination generalism influences pollen-associated virus richness and the extent of pollen virus sharing between plant species. We also revealed that perenniality, multiple flowers, and bilateral floral symmetry were associated with high pollen viral richness locally, confirming and extending patterns observed previously at a continental scale. Our results highlight the importance of plant-pollinator interactions as drivers of plant-viral interaction diversity.}, }
@article {pmid40450230, year = {2025}, author = {Leung, WKC and Yau, CYC and Lam, SC}, title = {Facilitators, barriers, and recommendations for mobile health applications among Chinese older populations: a scoping review.}, journal = {BMC geriatrics}, volume = {25}, number = {1}, pages = {396}, pmid = {40450230}, issn = {1471-2318}, support = {CRG2023/01//Tung Wah College/ ; CRG2023/01//Tung Wah College/ ; }, mesh = {Aged ; Aged, 80 and over ; Humans ; Middle Aged ; China ; *COVID-19/epidemiology ; *Mobile Applications ; *Telemedicine ; East Asian People ; }, abstract = {BACKGROUND: Mobile health (mHealth) applications have become indispensable in people's daily lives and are now incorporated into a multitude of healthcare services. However, due to inappropriate designs and ineffective promotional strategies, the rates of uptake and continued use of mHealth applications in older adults are usually low. Given that recent evidence has reported distinct mHealth adoption patterns between Chinese and non-Chinese populations, the aim of this scoping review was to map relevant evidence on the end-user perceptions and age-appropriate recommendations for interface design, persuasive features, and promotional strategies among Chinese older adults.<br><br>METHODS: All primary studies conducted in Chinese older people aged 60&#x2009;+&#x2009;years, including quantitative, qualitative, and mixed methods research, examining end-user perceptions (e.g., motivators, barriers, and design) of mHealth applications were considered eligible for inclusion. Four electronic databases (PubMed, CINAHL, PsycINFO, and Medline) were searched from their inceptions through 31 May 2024. A narrative approach was adopted for data analyses relevant to the study aim.<br><br>RESULTS: A total of 23 studies (n&#x2009;=&#x2009;8,203) were included. End-user perceptions (facilitators and barriers) of older people were narratively synthesized according to the socio-ecological model (individual/product, interpersonal, community, and societal). In Chinese deaf and hard-of-hearing older adults, the lack of proficiency in mastering operations of smartphone, Internet, and mHealth applications greatly jeopardized their communication with family or friends, accessibility to online medical consultations, and access to public places amidst COVID-19 pandemic. Recommended interface designs were categorized into various aspects of functional impairments (vision, manual dexterity, and cognition) of elderly users. Seven promotional strategies were also highlighted, whereas more than half of the studies recommended education measures (e.g., personalized family/peer- or health professional-led training program) and technical support (e.g., face-to-face instructions, detailed manual instructions, and timely consultation services). Other recommendations included increased publicity, co-creation, and supportive government policies.<br><br>CONCLUSION: This review synthesizes the existing relevant evidence and hence provides age-friendly recommendations for interface designs, persuasive features, and promotional strategies in Chinese older populations. Overall, this study empirically offers actionable guidelines for mHealth developers to meet the multifaceted needs of older people.}, }
@article {pmid40449428, year = {2025}, author = {Hussain, M and Ullah, K and Tayyab, M and Ullah, S and Shah, AA and Zhang, J and Tong, Z and Liu, X and Rahman, ZU}, title = {Data-driven multi-hazard susceptibility and community perceptions assessment using a mixed-methods approach.}, journal = {Journal of environmental management}, volume = {388}, number = {}, pages = {126009}, doi = {10.1016/j.jenvman.2025.126009}, pmid = {40449428}, issn = {1095-8630}, mesh = {Climate Change ; *Disaster Planning ; Floods ; Geographic Information Systems ; Landslides ; Pakistan ; Perception ; Surveys and Questionnaires ; }, abstract = {Assessing multi-hazard susceptibility and understanding community insights are important for effective disaster risk management; however, limited research has been conducted to study these aspects together. This study uses a data-driven approach to assess multi-hazard susceptibility and community perceptions, aiming to deepen climate change mitigation strategies. We employed a two-stage framework in Eastern Hindukush, Pakistan, which is based on machine learning, remote sensing, geographical information systems, and index-based methods. In the first stage, flood and landslide inventories were generated, and predictive factors were analyzed using logistic regression, resulting in an integrated multi-hazard susceptibility map. In the second stage, a survey of 410 household heads assessed community risk perception, communication, and preparedness, using a structured questionnaire with 28 Likert-scale indicators, and a composite index was calculated. The findings indicate that 25.81 % and 35.43 % of the study area are susceptible to flooding and landslides, respectively, with 15.07 % vulnerable to both hazards concurrently. On the other hand, the community is generally aware of flood and landslide risks; however, there are significant gaps in coping abilities and preparedness, including insufficient insurance coverage and training. Moreover, socioeconomic challenges, such as limited access to information and low trust in local authorities, further complicate disaster preparedness efforts. This study provides a holistic framework for identifying multi-hazard hotspots and assessing community perceptions, facilitating targeted interventions to enhance disaster preparedness and resilience in the region.}, }
@article {pmid40443799, year = {2025}, author = {Broad, GR and Lees, DC and Boyes, D and ,  and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Straw-barred Pearl moth, Pyrausta despicata Scopoli, 1763.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {151}, pmid = {40443799}, issn = {2398-502X}, abstract = {We present a genome assembly from a male specimen of Pyrausta despicata (Straw-barred Pearl; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence has a total length of 481.83 megabases. Most of the assembly (99.61%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 15.29 kilobases.}, }
@article {pmid40442647, year = {2025}, author = {Maździarz, M and Zając, S and Paukszto, &#x141; and Sawicki, J}, title = {RSCUcaller: an R package for analyzing differences in relative synonymous codon usage (RSCU).}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {141}, pmid = {40442647}, issn = {1471-2105}, support = {2024/53/N/NZ8/02829//The National Science Center Krak&#xf3;w, Poland/ ; 12.610.002-110//University of Warmia and Mazury in Olsztyn/ ; }, mesh = {*Codon Usage ; *Software ; *Codon ; *Computational Biology/methods ; }, abstract = {BACKGROUND: Synonymous codon usage bias, a significant factor in gene expression and genome evolution, was extensively studied in genomics and molecular biology. Although the genetic code is universal, significant variations in synonymous codon usage have been observed among and within organisms. This bias was linked to various factors, including gene expression levels, tRNA abundance, protein structure, and environmental adaptation. Relative Synonymous Codon Usage (RSCU), a normalized measure, was used to quantify this bias. By analyzing RSCU values, researchers uncovered patterns and trends related to the underlying mechanisms driving codon usage bias.<br><br>RESULTS: We present an R package named RSCUcaller designed for the analysis of coding nucleotide sequences at the level of relative synonymous codon usage (RSCU). The package enables both visualization of data and the performance of advanced statistical analyses. RSCUcaller accepts as input a multi-fasta file containing coding sequences (CDS) and an accompanying description table. Alternatively, the user may provide separate fasta files for each sequence along with the corresponding table. The program merges the provided sequences and calculates RSCU values for each. Implemented visualization features include creating heatmaps and dendrograms based on these heatmaps. Furthermore, the package allows for the presentation of data in the form of histograms. The calculated RSCU values can also be used to create matrices that can be subjected to further analysis by the user. RSCUcaller offers the functionality of correlation analysis between any two organisms. Additionally, to compare the frequency of amino acid occurrence between different groups of sequences, statistical&#xa0;tests have been implemented.<br><br>CONCLUSIONS: RSCUcaller enabled comparative RSCU analysis between coding sequences of different organisms or individuals of the same species. It facilitated visualization and statistical analysis among codons and user-defined groups. The RSCUcaller package is available at https://github.com/Mordziarz/RSCUcaller under the GPL-3 license.}, }
@article {pmid40442224, year = {2025}, author = {Sun, Y and Meng, W and Wang, F and Han, H and Sui, M and Jian, Z}, title = {Spatio-temporal evolution and coupling relationship between biodiversity and urbanization in the areas along the Yellow River of Shandong province.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {18876}, pmid = {40442224}, issn = {2045-2322}, support = {20221830//cultivation platform for integrating production, science, and education jointly built by Shandong Province and Peking University/ ; 42301320//National Natural Science Fund of China/ ; }, mesh = {*Biodiversity ; *Urbanization ; China ; *Rivers ; Spatio-Temporal Analysis ; Ecosystem ; Conservation of Natural Resources ; Sustainable Development ; }, abstract = {Mastering the coupling relationship and driving mechanism between urbanization and biodiversity is of great significance to ecological protection and regional sustainable development. The study took areas along the Yellow River of Shandong province (AYRSP) as the study area, which have the most rich and unique biodiversity resources in the whole basin. First, this study constructed a new indicator system of biodiversity based on remote-sensing data from species, ecosystem, and landscape to monitor and evaluate the spatial heterogeneity. The result was quantified by the proportion of key biodiversity areas, based on Sustainable Development Goal 15.1.2 from The United Nations. Then, the urbanization system was evaluated based on panel data. At last, the coordination relationship, lead-lag type between biodiversity and urbanization, and key influencing factors of coupling system at the county scale in 2015-2021 were identified by combining multiple models. The results demonstrated that the biodiversity level was gradually declining, with a distribution pattern of "low in the western, and high in mid-southern and eastern regions." The AYRSP still faced certain challenges in the sustainable development of biodiversity. The coupling coordination degree between biodiversity and urbanization showed an increasing trend with continuous improvement in the urbanization level. Only two counties were types of biodiversity-urbanization synchronous development. The results of grey relation degree model indicated that most of indicators were above 0.6 and the urbanization had a significant impact on the coupling system. This study established the evaluation system for biodiversity and urbanization at the small scale, which could provide theoretical reference for the sustainable development of county-level administrative region.}, }
@article {pmid40441709, year = {2025}, author = {Dang, T and Fuji, Y and Kumaishi, K and Usui, E and Kobori, S and Sato, T and Narukawa, M and Toda, Y and Sakurai, K and Yamasaki, Y and Tsujimoto, H and Hirai, MY and Ichihashi, Y and Iwata, H}, title = {I-SVVS: integrative stochastic variational variable selection to explore joint patterns of multi-omics microbiome data.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {3}, pages = {}, pmid = {40441709}, issn = {1477-4054}, support = {JP21J21850//JSPS KAKENHI/ ; JPMJCR1602//JST-CREST Program/ ; JPMJMI120C7//JST-Mirai Program/ ; JPMJAN23D1//JST ALCA-Next Program/ ; }, mesh = {*Microbiota ; Mice ; Animals ; Humans ; Stochastic Processes ; Bayes Theorem ; Glycine max/microbiology ; *Metabolomics/methods ; Algorithms ; *Computational Biology/methods ; Metabolome ; Cluster Analysis ; Multiomics ; }, abstract = {High-dimensional multi-omics microbiome data play an important role in elucidating microbial community interactions with their hosts and environment in critical diseases and ecological changes. Although Bayesian clustering methods have recently been used for the integrated analysis of multi-omics data, no method designed to analyze multi-omics microbiome data has been proposed. In this study, we propose a novel framework called integrative stochastic variational variable selection (I-SVVS), which is an extension of stochastic variational variable selection for high-dimensional microbiome data. The I-SVVS approach addresses a specific Bayesian mixture model for each type of omics data, such as an infinite Dirichlet multinomial mixture model for microbiome data and an infinite Gaussian mixture model for metabolomic data. This approach is expected to reduce the computational time of the clustering process and improve the accuracy of the clustering results. Additionally, I-SVVS identifies a critical set of representative variables in multi-omics microbiome data. Three datasets from soybean, mice, and humans (each set integrated microbiome and metabolome) were used to demonstrate the potential of I-SVVS. The results indicate that I-SVVS achieved improved accuracy and faster computation compared to existing methods across all test datasets. It effectively identified key microbiome species and metabolites characterizing each cluster. For instance, the computational analysis of the soybean dataset, including 377 samples with 16 943 microbiome species and 265 metabolome features, was completed in 2.18 hours using I-SVVS, compared to 2.35 days with Clusternomics and 1.12 days with iClusterPlus. The software for this analysis, written in Python, is freely available at https://github.com/tungtokyo1108/I-SVVS.}, }
@article {pmid40441315, year = {2025}, author = {Zhang, B and Yang, M and Liu, W}, title = {Integrating multi-omics analysis unveils the key mechanisms of PQS-enhanced Algicidal activity in Enterobacter hormaechei F2.}, journal = {Genomics}, volume = {117}, number = {4}, pages = {111060}, doi = {10.1016/j.ygeno.2025.111060}, pmid = {40441315}, issn = {1089-8646}, mesh = {Quorum Sensing/drug effects ; *Enterobacter/genetics/drug effects/metabolism ; *Quinolones/pharmacology/metabolism ; Proteomics ; Metabolomics ; Bacterial Proteins/metabolism/genetics ; Transcriptome ; Multiomics ; }, abstract = {Quorum sensing, as a pivotal bacterial signaling pathway, exhibits substantial potential for regulating algicidal activity. This study pioneers the integration of multi-omics analyses (transcriptomics, proteomics, metabolomics) with phenotypic profiling to systematically unravel the molecular mechanisms underlying Pseudomonas Quinolone Signal (2-heptyl-3-hydroxy-4(1H)-quinolinone, PQS)-enhanced algicidal activity in Enterobacter hormaechei F2. Co-cultivation with PQS triggered marked reductions in algal biomass and chlorophyll-a levels, outperforming traditional approaches. Fourier-transform infrared spectroscopy (FTIR) revealed PQS-induced metabolic disruption and membrane degradation in algal cells. Transcriptomic profiling identified novel regulatory hubs, including upregulated glycolysis (tktA, transketolase), fatty acid degradation (fadE, acyl-CoA dehydrogenase), and chemotaxis (malE, maltose-binding protein) pathways. Proteomics confirmed PQS-driven enrichment of terpenoid precursors, notably DXS synthase (1-deoxy-D-xylulose-5-phosphate synthase), and quorum sensing effectors. Metabolomics highlighted amino acid derivatives (e.g., L-glutamate) and heterocyclic antibiotics as dominant algicidal metabolites. Crucially, multi-omics integration delineated a core network of 46 key nodes (e.g., ribose transporter rbsB, L-glutamate) coordinating energy metabolism, motility, and algicide synthesis. Fatty acid degradation enzymes (e.g., FadE) and flagellar assembly regulators (e.g., FlgK) emerged as previously unrecognized targets, with PQS significantly enhancing bacterial swarming motility (p < 0.01) and biofilm formation. These findings establish the first mechanistic framework linking PQS signaling to algicidal process, demonstrating its role in synchronizing metabolic flux toward terpenoid synthesis while optimizing bacterial-algal interactions. Key pathways-including chemotaxis (malE) and terpenoid biosynthesis (DXS synthase)-provide actionable targets for engineering bioaugmented consortia or precision algicidal formulations. This work advances quorum sensing-driven strategies for sustainable harmful algal bloom (HAB) mitigation, offering scalable solutions for aquaculture and eutrophic water remediation with minimal ecological disruption. By bridging molecular mechanisms to field applications, the study underscores the translational potential of this approach in global water security initiatives.}, }
@article {pmid40440249, year = {2025}, author = {Guevara Rodríguez, DM and Pichihua Grandez, JD and Dianderas, FV and Del Carmen Sara, J}, title = {Incidence of cerebrovascular disease in Peru from 2015 to 2023.}, journal = {PLOS global public health}, volume = {5}, number = {5}, pages = {e0004559}, pmid = {40440249}, issn = {2767-3375}, abstract = {Cerebrovascular disease (stroke) is one of the leading causes of mortality and disability worldwide, particularly in low- and middle-income countries. This study aims to estimate the incidence of stroke in Peru between 2015 and 2023 using national hospital discharge data provided by the National Health Superintendency. We conducted a mixed ecological study using records of stroke cases reported across various healthcare systems, including the Ministry of Health, Social Security, and private entities. Hospitalizations were categorized according to ICD-10 codes (I60-I64) and stratified by age, sex, and region. Incidence rates were calculated using population projections from the National Institute of Statistics and Informatics. A total of 89,776 hospital discharges for stroke were analyzed, yielding an incidence rate of 3.11 per 10,000 persons over the study period, with a predominance in men and individuals over 60 years of age. Cerebral infarction was the most common diagnosis, particularly among those over 40 years old. Incidence varied significantly across regions, with Lima and Callao consistently exceeding the national average. The results highlight disparities in healthcare access and the need for targeted public health interventions. Our findings provide a 9-year overview of stroke in Peru, offering evidence to estimate hospital bed demand and prioritize preventive and management strategies-particularly in regions with higher vulnerability.}, }
@article {pmid40435619, year = {2025}, author = {Matuszewska, D and Kiedrzyńska, E and Jóźwik, A and Kiedrzyński, M}, title = {An analysis of catchment factors associated with heavy metal export into the Baltic Sea and nature-based solutions aimed at its limitation.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138727}, doi = {10.1016/j.jhazmat.2025.138727}, pmid = {40435619}, issn = {1873-3336}, mesh = {*Metals, Heavy/analysis ; *Water Pollutants, Chemical/analysis ; Environmental Monitoring ; Baltic States ; Oceans and Seas ; Animals ; Aquaculture ; Rivers ; }, abstract = {The aim of the article was to determine the shares of individual Baltic countries participating in the inflow of metal loads to the Baltic Sea and identify patterns of similarity between these countries regarding the causes of heavy metal load generation. The analyses used HELCOM and EUROSTAT data. The findings indicate that Finland and Sweden generate the highest total loads of heavy metals flowing in through rivers. However, Lithuania and Finland are distinguished by high metal loads calculated per km[2] of catchment area. Clustering countries in terms of their similarity in the heavy metal loads provided to the Baltic resulted in three groups. Finland and Lithuania generates the highest mean loads of cadmium, chromium, nickel and zinc per unit area [kg/km[2]/year]. Estonia and Latvia generates the highest mean annual loads of lead, mercury and copper. Poland, Germany and Sweden generates the lowest heavy metal loads. Multidimensional data analysis showed a strong correlation between aquaculture production in the Baltic Sea catchment area, the number of cattle, beef, mutton, pigs, poultry, and meat produced from them, the amount of waste, trucks, cereal production, the use of nitrogen fertilizers, and the loads of heavy metals reaching the Baltic Sea with river waters. Therefore, there is a need for continuous monitoring of the loads and transfer of heavy metals to the Baltic Sea, and for activities aimed at eliminating them from the environment. For this purpose, Nature-Based Solutions can be used, as they represent inexpensive, nature-friendly methods for removing pollutants from surface waters.}, }
@article {pmid40435606, year = {2025}, author = {Guo, J and Xie, Y and Dou, X and Qi, W and Liao, Y and Cao, X and Peng, J and Liu, H}, title = {Combining source identification and risk assessment to uncover spatial risk patterns in an agricultural lake.}, journal = {Journal of environmental management}, volume = {387}, number = {}, pages = {125966}, doi = {10.1016/j.jenvman.2025.125966}, pmid = {40435606}, issn = {1095-8630}, mesh = {*Lakes ; Agriculture ; *Environmental Monitoring/methods ; Risk Assessment ; Geologic Sediments ; Water Pollutants, Chemical/analysis ; Polycyclic Aromatic Hydrocarbons/analysis ; Metals, Heavy/analysis ; Bayes Theorem ; Water Quality ; Rivers ; }, abstract = {Pollutant source identification and risk assessment underpin environmental management, necessitating innovative methods for both pollution source identification and comprehensive evaluation to enhance management efficiency. In this study, we developed a novel integrated framework that combines Bayesian isotope mixing, positive matrix factorization (PMF), random forest, and spatial autocorrelation for multi-pollutant source identification and risk assessment. The Bayesian isotope mixing model revealed that fertilizers accounted for 61 % of the nitrate in the lake and 46 % of the nitrate in the river. Furthermore, PMF analysis indicated that polycyclic aromatic hydrocarbons (PAHs) in sediments and soil were primarily sourced from vehicular emissions (32 %), while heavy metals (40 %) were mainly from vehicular emissions and agricultural activities. Using a comprehensive pollution assessment framework for water and sediment quality, we found that water quality ranged from "medium" to "excellent", and sediment quality ranged from "good" to "excellent". Among various evaluation indices, CODMn, As, F[-], TP, Pb, and Zn were pivotal in determining comprehensive water quality. Key indices for sediment quality evaluation included Flua, BaP, BaA, Pyr, Ant, Pb, and As, primarily sourced from automobile emissions and agricultural activities. Spatial autocorrelation analysis demonstrated a spatial relationship between water quality and sediment quality, covering 43 % of the area. High-pollution areas (13 %) were concentrated around natural river inlets, while low-pollution zones (17 %) were located near ecological water replenishment river inlets. This underscores the significant influence of inflowing water quality on sediment conditions. This study highlights the development of a comprehensive pollution assessment framework to evaluate sediment and soil pollution, as well as to identify high-risk zones of compound pollution in water and sediment. Furthermore, the framework's universal applicability for agricultural lake systems enables the identification of high-risk zones through water-sediment interaction analysis.}, }
@article {pmid40435494, year = {2025}, author = {Berger, M and Ehlers, JP and Nitsche, J}, title = {Aligning With the Goals of the Planetary Health Concept Regarding Ecological Sustainability and Digital Health: Scoping Review.}, journal = {Journal of medical Internet research}, volume = {27}, number = {}, pages = {e71795}, pmid = {40435494}, issn = {1438-8871}, mesh = {*Telemedicine ; Climate Change ; Humans ; Global Health ; Delivery of Health Care ; Artificial Intelligence ; Digital Health ; }, abstract = {BACKGROUND: Climate change, driven by greenhouse gas emissions, threatens human health and biodiversity. While the digitalization of health care, including telemedicine and artificial intelligence, offers sustainability benefits, it also raises concerns about energy use and electronic waste. Balancing these factors is key to a sustainable health care future.<br><br>OBJECTIVE: The objective of this review was to examine the extent to which digitalization in the health care sector influences environmental sustainability. Specifically, it aimed to assess how digitalization can contribute to reducing the health care sector's impact on global climate change. From these findings, conclusions were drawn regarding the extent to which digitalization aligns with the objectives of the Planetary Health movement and how these 2 movements may mutually reinforce each other.<br><br>METHODS: A scoping review guided by the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) 2020 guidelines using databases such as PubMed and Scopus was conducted, and 58 quantitative studies from 2009 to 2024 were analyzed for environmental, social, and economic outcomes aligned with Planetary Health goals.<br><br>RESULTS: This review analyzed 58 studies on the environmental impact of digitalization in health care primarily focusing on telemedicine, which was examined in 91% (53/58) of the studies. Most studies (56/58, 97%) quantified transport-related emissions avoided through digitalization, with some also assessing emissions from health care facilities, medical equipment, and energy consumption. Findings indicated that telemedicine significantly reduces carbon dioxide emissions, with total avoided emissions amounting to approximately 830 million kg. A substantial proportion of the studies (36/58, 62%) focused on social aspects, highlighting factors such as patient satisfaction, time efficiency, and overall convenience. In addition, economic considerations were analyzed in 48% (28/58) of the studies, emphasizing cost reductions and resource optimization. However, only 12% (7/58) of the studies evaluated the full life cycle impact of digital technologies, highlighting the need for further research on their long-term environmental sustainability.<br><br>CONCLUSIONS: This review calls for further research beyond telemedicine, advocating for life cycle analyses and actionable strategies for a sustainable digitalization in health care systems. The Planetary Health framework is highlighted as a guide for ensuring sustainable digital transformation in health care.}, }
@article {pmid40433986, year = {2024}, author = {He, Y and Mulqueeney, JM and Watt, EC and Salili-James, A and Barber, NS and Camaiti, M and Hunt, ESE and Kippax-Chui, O and Knapp, A and Lanzetti, A and Rangel-de Lázaro, G and McMinn, JK and Minus, J and Mohan, AV and Roberts, LE and Adhami, D and Grisan, E and Gu, Q and Herridge, V and Poon, STS and West, T and Goswami, A}, title = {Opportunities and Challenges in Applying AI to Evolutionary Morphology.}, journal = {Integrative organismal biology (Oxford, England)}, volume = {6}, number = {1}, pages = {obae036}, pmid = {40433986}, issn = {2517-4843}, abstract = {Artificial intelligence (AI) is poised to revolutionize many aspects of science, including the study of evolutionary morphology. While classical AI methods such as principal component analysis and cluster analysis have been commonplace in the study of evolutionary morphology for decades, recent years have seen increasing application of deep learning to ecology and evolutionary biology. As digitized specimen databases become increasingly prevalent and openly available, AI is offering vast new potential to circumvent long-standing barriers to rapid, big data analysis of phenotypes. Here, we review the current state of AI methods available for the study of evolutionary morphology, which are most developed in the area of data acquisition and processing. We introduce the main available AI techniques, categorizing them into 3 stages based on their order of appearance: (1) machine learning, (2) deep learning, and (3) the most recent advancements in large-scale models and multimodal learning. Next, we present case studies of existing approaches using AI for evolutionary morphology, including image capture and segmentation, feature recognition, morphometrics, and phylogenetics. We then discuss the prospectus for near-term advances in specific areas of inquiry within this field, including the potential of new AI methods that have not yet been applied to the study of morphological evolution. In particular, we note key areas where AI remains underutilized and could be used to enhance studies of evolutionary morphology. This combination of current methods and potential developments has the capacity to transform the evolutionary analysis of the organismal phenotype into evolutionary phenomics, leading to an era of "big data" that aligns the study of phenotypes with genomics and other areas of bioinformatics.}, }
@article {pmid40432488, year = {2025}, author = {Min, J and Kim, B and Park, Y and Son, Y and Park, W}, title = {Bacterial cell wall synthesis and recycling: new antimicrobial targets and vaccine development.}, journal = {Critical reviews in microbiology}, volume = {51}, number = {6}, pages = {1364-1383}, doi = {10.1080/1040841X.2025.2510250}, pmid = {40432488}, issn = {1549-7828}, mesh = {*Cell Wall/metabolism/drug effects ; *Bacterial Vaccines/immunology ; Humans ; *Vaccine Development ; *Peptidoglycan/biosynthesis/metabolism ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/drug effects/metabolism ; Bacterial Proteins/metabolism ; }, abstract = {Almost all bacteria have peptidoglycan (PG) components that are essential for virulence and are absent in humans, making them a top-priority target for antibiotics and vaccines. The rise of multidrug-resistant bacteria (MRB) necessitates urgent expansion of our arsenal of inhibitors targeting the PG cell wall. This review addresses our understanding of PG biosynthesis and recycling processes, emphasizing the need to identify novel target proteins and redesign existing PG-targeted antimicrobial peptides. Building on our understanding of cell wall biochemistry and biogenesis derived from Escherichia coli, we also aim to compare and elucidate the cell wall processes in other pathogens, such as Acinetobacter baumannii and Salmonella Typhimurium, where knowledge remains incomplete. We cover in detail the distinct roles of PG-related proteins in Gram-negative bacteria, strategies to block PG biosynthesis/recycling pathways, and their potential as novel antibiotic targets to address the growing challenge of antibiotic resistance. Finally, we review the application of rigorous immuno-informatics analysis and several immune filters to construct epitope-specific vaccines displaying PG-related proteins on the surface of outer membrane vesicles (OMVs), aiming to combat MRB proliferation.}, }
@article {pmid40432231, year = {2025}, author = {Tian, XC and Nie, S and Domingues, D and Rossi Paschoal, A and Jiang, LB and Mao, JF}, title = {PlantLncBoost: key features for plant lncRNA identification and significant improvement in accuracy and generalization.}, journal = {The New phytologist}, volume = {247}, number = {3}, pages = {1538-1549}, pmid = {40432231}, issn = {1469-8137}, support = {2022YFD2200103//National Key R&amp;D Program of China/ ; 32171816//National Natural Science Foundation of China/ ; ZR2022YQ23//Natural Science Fund for Excellent Young Scholars of Shandong Province/ ; 2025A1515012969//Guangdong Basic and Applied Basic Research Foundation/ ; #440412/2022-6//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico - CNPq/ ; Project: NAPI Bioinformatica #66.2021//Funda&#xe7;&#xe3;o Arauc&#xe1;ria/ ; }, mesh = {*RNA, Long Noncoding/genetics ; *RNA, Plant/genetics ; *Computational Biology/methods ; Algorithms ; *Plants/genetics ; RNA, Messenger/genetics ; *Software ; Open Reading Frames/genetics ; }, abstract = {Long noncoding RNAs (lncRNAs) are critical regulators of numerous biological processes in plants. Nevertheless, their identification is challenging due to the low sequence conservation across various species. Existing computational methods for lncRNA identification often face difficulties in generalizing across diverse plant species, highlighting the need for more robust and versatile identification models. Here, we present PlantLncBoost, a novel computational tool designed to improve the generalization in plant lncRNA identification. By integrating advanced gradient boosting algorithms with comprehensive feature selection, our approach achieves both high accuracy and generalizability. We conducted an extensive analysis of 1662 features and identified three key features - ORF coverage, complex Fourier average, and atomic Fourier amplitude - that effectively distinguish lncRNAs from mRNAs. We assessed the performance of PlantLncBoost using comprehensive datasets from 20 plant species. The model exhibited exceptional performance, with an accuracy of 96.63%, a sensitivity of 98.42%, and a specificity of 94.93%, significantly outperforming existing tools. Further analysis revealed that the features we selected effectively capture the differences between lncRNAs and mRNAs across a variety of plant species. PlantLncBoost represents a significant advancement in plant lncRNA identification. It is freely accessible on GitHub (https://github.com/xuechantian/PlantLncBoost) and has been integrated into a comprehensive analysis pipeline, Plant-LncRNA-pipeline v.2 (https://github.com/xuechantian/Plant-LncRNA-pipeline-v2).}, }
@article {pmid40431635, year = {2025}, author = {Rodrigues, GVP and Santos, JPN and Ferreira, LYM and Conceição, LBA and Porto, JAM and Aguiar, ERGR}, title = {Theobroma cacao Virome: Exploring Public RNA-Seq Data for Viral Discovery and Surveillance.}, journal = {Viruses}, volume = {17}, number = {5}, pages = {}, pmid = {40431635}, issn = {1999-4915}, support = {Financial Code 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior (CAPES)/ ; //Conselho Nacional de Pesquisa Cient&#xed;fica (CNPq)/ ; }, mesh = {*Cacao/virology ; *Virome/genetics ; Plant Diseases/virology ; RNA-Seq ; Computational Biology/methods ; Phylogeny ; *Plant Viruses/genetics/classification/isolation &amp; purification ; Genome, Viral ; Badnavirus/genetics/isolation &amp; purification/classification ; Microbiota ; }, abstract = {Cocoa (Theobroma cacao L.) is a major agricultural commodity, essential for the global chocolate industry and the livelihoods of millions of farmers. However, viral diseases pose a significant threat to cocoa production, with Badnavirus species causing severe losses in Africa. Despite its economic importance, the overall virome of T. cacao remains poorly characterized, limiting our understanding of viral diversity and potential disease interactions. This study aims to assess the cocoa-associated virome by analyzing 109 publicly available RNA-seq libraries from nine BioProjects, covering diverse conditions and geographic regions. We implemented a comprehensive bioinformatics pipeline integrating multiple viral sequence enrichment steps, a hybrid assembly strategy using different assemblers, and sequence similarity searches against NCBI non-redundant databases. Our approach identified ten putative novel viruses associated with the cocoa microbiome and a novel Badnavirus species. These findings provide new insights into the viral landscape of T. cacao, characterizing the diversity of cacao-associated viruses and their potential ecological roles. Expanding the catalog of viruses associated with cocoa plants not only enhances our understanding of plant-virus-microbiome interactions but also contributes to the development of more effective disease surveillance and management strategies, ultimately supporting sustainable cocoa production.}, }
@article {pmid40427823, year = {2025}, author = {Santos, AFB and Nunes, M and Filipa-Silva, A and Pimentel, V and Pingarilho, M and Abrantes, P and Miranda, MNS and Crespo, MTB and Abecasis, AB and Parreira, R and Seabra, SG}, title = {Wastewater Metavirome Diversity: Exploring Replicate Inconsistencies and Bioinformatic Tool Disparities.}, journal = {International journal of environmental research and public health}, volume = {22}, number = {5}, pages = {}, pmid = {40427823}, issn = {1660-4601}, support = {PTDC/CTA AMB/29586/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia, Portugal 568 through projects AgriWWAter/ ; 706, Internalproject IBETXplore 2017//VirusFreeWater/ ; GHTM- UID/04413/2020//Internal exploratory Project WasteWaterVir/ ; LA/P/0117/2020//LA-REAL/ ; }, mesh = {*Wastewater/virology ; *Computational Biology/methods ; *Virome ; Portugal ; *Metagenomics/methods ; *Viruses/classification/isolation &amp; purification/genetics ; }, abstract = {This study investigates viral composition in wastewater through metagenomic analysis, evaluating the performance of four bioinformatic tools-Genome Detective, CZ.ID, INSaFLU-TELEVIR and Trimmomatic + Kraken2-on samples collected from four sites in each of two wastewater treatment plants (WWTPs) in Lisbon, Portugal in April 2019. From each site, we collected and processed separately three replicates and one pool of nucleic acids extracted from the replicates. A total of 32 samples were processed using sequence-independent single-primer amplification (SISPA) and sequenced on an Illumina MiSeq platform. Across the 128 sample-tool combinations, viral read counts varied widely, from 3 to 288,464. There was a lack of consistency between replicates and their pools in terms of viral abundance and diversity, revealing the heterogeneity of the wastewater matrix and the variability in sequencing effort. There was also a difference between software tools highlighting the impact of tool selection on community profiling. A positive correlation between crAssphage and human pathogens was found, supporting crAssphage as a proxy for public health surveillance. A custom Python pipeline automated viral identification report processing, taxonomic assignments and diversity calculations, streamlining analysis and ensuring reproducibility. These findings emphasize the importance of sequencing depth, software tool selection and standardized pipelines in advancing wastewater-based epidemiology.}, }
@article {pmid40426056, year = {2025}, author = {Charest, J and Loebenstein, P and Mach, RL and Mach-Aigner, AR}, title = {FunFEA: an R package for fungal functional enrichment analysis.}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {138}, pmid = {40426056}, issn = {1471-2105}, mesh = {*Genome, Fungal ; *Software ; Molecular Sequence Annotation/methods ; *Fungi/genetics ; Gene Ontology ; Databases, Genetic ; Genomics/methods ; Computational Biology/methods ; }, abstract = {BACKGROUND: The functional annotation of fungal genomes is critical for understanding their biological processes and ecological roles. While existing tools support functional enrichment analysis from publicly available annotations of well-established model organisms, few are tailored to the specific needs of the fungal research community. Furthermore, many tools struggle with processing functional annotations of novel species, for which no publicly available functional annotations are yet available.<br><br>RESULTS: FunFEA is an R package designed for functional enrichment analysis of fungal genomes. It supports COG/KOG (Clusters of Orthologous Genes), GO (Gene Ontology), and KEGG (Kyoto Encyclopedia of Genes and Genomes) annotations, and generates background frequency models from publicly available annotations for overrepresentation analysis, within a set of experimentally defined genes or proteins. Additionally, FunFEA can process eggNOG-mapper annotations, thus enabling functional enrichment analysis of novel genomes. The package offers a suite of tools for generation of background frequency models, functional enrichment analysis, as well as visualization of enriched functional categories. On release, the package includes precomputed models for 65 commonly used fungal strains in academic research and strains listed on the WHO fungal priority pathogens list.<br><br>CONCLUSIONS: FunFEA fills a critical need for a specialized tool in fungal genomics, providing valuable insights into fungal biology. Additionally, its ability to process eggNOG-mapper annotations makes it an essential resource for researchers, helping to drive further exploration of fungal functional diversity and pathways and derive biological insights from novel genomes.}, }
@article {pmid40425680, year = {2025}, author = {Péter, SA and Gallo, T and Mullinax, J and Roess, A and Palomo-Munoz, G and Anderson, T}, title = {Integrating human mobility and animal movement data reveals complex space-use between humans and white-tailed deer in urban environments.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {18588}, pmid = {40425680}, issn = {2045-2322}, support = {AP23OA000000C003//Animal and Plant Health Inspection Service/ ; AP23OA000000C003//Animal and Plant Health Inspection Service/ ; AP23OA000000C003//Animal and Plant Health Inspection Service/ ; AP23OA000000C003//Animal and Plant Health Inspection Service/ ; AP23OA000000C003//Animal and Plant Health Inspection Service/ ; AP23OA000000C003//Animal and Plant Health Inspection Service/ ; }, mesh = {Animals ; *Deer/physiology ; Humans ; Zoonoses/transmission ; Animals, Wild ; Ecosystem ; Maryland ; Cities ; Wasting Disease, Chronic/transmission ; COVID-19/transmission/epidemiology/virology ; SARS-CoV-2 ; Geographic Information Systems ; }, abstract = {Human expansion into wildlife habitats has increased the need to understand human-wildlife interactions, necessitating interdisciplinary approaches to assess zoonotic disease transmission risks and public health impacts. This study integrated fine-grained human foot traffic data with hourly GPS data from 38 white-tailed deer (Odocoileus virginianus), a species linked to SARS-CoV-2, brucella, and chronic wasting disease, in Howard County, Maryland. We explored spatial and temporal overlap between human and deer activity over 24 months (2018-2019) across a hexagonal tessellation with metrics like hourly popularity and visit counts. Negative binomial models were fitted to the visit counts of each deer and humans per tessellation area, using landscape features as predictors. A separate deer-only model included commercial human activity as another predictor. Spatial analysis showed deer and humans sharing spaces in the study area, with results indicating deer using more populated residential areas and areas with commercial activity. Temporal analysis showed deer avoiding commercial spaces during daytime but using them in late evening and early morning. These findings highlight the complex space use between species and the importance of integrating detailed human mobility and animal movement data when managing wildlife-human conflict and zoonotic disease transmission, particularly in urban areas with a high probability of deer-human interactions.}, }
@article {pmid40425424, year = {2025}, author = {Cardoso, P and Branco, V and Correia, L and Emerson, BC and Laine, VN and Lopes, M}, title = {Automated biodiversity research critically requires multidisciplinary expertise.}, journal = {Trends in ecology &amp; evolution}, volume = {40}, number = {7}, pages = {626-628}, doi = {10.1016/j.tree.2025.05.003}, pmid = {40425424}, issn = {1872-8383}, mesh = {*Biodiversity ; *Conservation of Natural Resources/methods ; *Automation ; *Ecology/methods ; *Computational Biology/methods ; }, abstract = {Data-driven computational methods in taxonomy, ecology, and conservation biology are revolutionising these disciplines, from data collection to analysis and interpretation. However, effective automation requires both critical thinking about the limitations of the data and methods, and thorough training and validation by experts, supported by strong interdisciplinary collaboration.}, }
@article {pmid40425079, year = {2025}, author = {Mambully, S and Ramesh, V and Rani, S and Khatoon, M and A, J and Patil, AV and Palavesam, A and Sengupta, PP and Patil, SS and Kp, S}, title = {Genotype patterns and evolutionary rates: uncovering Japanese encephalitis virus spread across Asia's climate regions.}, journal = {Acta tropica}, volume = {267}, number = {}, pages = {107676}, doi = {10.1016/j.actatropica.2025.107676}, pmid = {40425079}, issn = {1873-6254}, mesh = {*Encephalitis Virus, Japanese/genetics/classification/isolation &amp; purification ; *Encephalitis, Japanese/epidemiology/virology/transmission ; *Evolution, Molecular ; *Genotype ; Humans ; Asia/epidemiology ; Phylogeny ; Viral Envelope Proteins/genetics ; Climate ; Animals ; Phylogeography ; }, abstract = {Japanese Encephalitis Virus (JEV) is a highly endemic zoonotic virus, consistently found in Asia and parts of the Western Pacific, and it's a major cause of human encephalitis. JEV belongs to a family of antigenically related viruses such as West Nile Virus (WNV), Murray Valley encephalitis virus (MVEV), and Aichi Lake Fever Virus (ALFV) and is transmitted by mosquitoes. Persistent outbreaks of the disease necessitate detailed studies to understand their transmission dynamics and develop effective prevention strategies. This study explores the evolutionary dynamics and spatial transmission of JEV, concentrating on the envelope protein (E) structural gene sequences obtained from across Asia's diverse climatic regions. Evolutionary modeling of the JEV E gene revealed a higher evolutionary rate in tropical regions compared to temperate regions, with nucleotide substitution rates estimated at 1.12 × 10[-3] per site per year for tropical regions and 5.284 × 10[-4] for temperate regions. The time to the most recent common ancestor (tMRCA) was traced to 1796 from Korea for temperate regions, and 1865 from Indonesia for tropical regions. Among the five genotypes of JEV, Genotype I (GI) and III (GIII) were established all over Southeast Asia; moreover, GI revealed a higher evolutionary rate, reflecting its adaptability to diverse ecological niches. The phylogeographic analysis highlighted significant contributions to virus diffusion by China, Korea, and Japan in temperate zones and by Vietnam in tropical zones. By analyzing genetic sequences from various regions and time periods, this study delivered valuable intuitions into transmission pathways. The findings highlighted the necessity of ongoing surveillance and evolutionary monitoring to track the spread and emergence of novel variations of JEV, which are crucial not just for managing JEV outbreaks but also for guiding immunization programs and public health initiatives.}, }
@article {pmid40419494, year = {2025}, author = {Jucker, T and Fischer, FJ and Chave, J and Coomes, DA and Caspersen, J and Ali, A and Loubota Panzou, GJ and Feldpausch, TR and Falster, D and Usoltsev, VA and Jackson, TD and Adu-Bredu, S and Alves, LF and Aminpour, M and Angoboy Ilondea, B and Anten, NPR and Antin, C and Askari, Y and Ayyappan, N and Banin, LF and Barbier, N and Battles, JJ and Beeckman, H and Bocko, YE and Bond-Lamberty, B and Bongers, F and Bowers, S and van Breugel, M and Chantrain, A and Chaudhary, R and Dai, J and Dalponte, M and Dimobe, K and Domec, JC and Doucet, JL and Dupuy Rada, JM and Duursma, RA and Enríquez, M and van Ewijk, KY and Farfán-Rios, W and Fayolle, A and Ferretti, M and Forni, E and Forrester, DI and Gilani, H and Godlee, JL and Haeni, M and Hall, JS and He, JK and Hemp, A and Hernández-Stefanoni, JL and Higgins, SI and Holdaway, RJ and Hussain, K and Hutley, LB and Ichie, T and Iida, Y and Jiang, HS and Joshi, PR and Kaboli, H and Kazempour Larsary, M and Kenzo, T and Kloeppel, BD and Kohyama, TS and Kunwar, S and Kuyah, S and Kvasnica, J and Lin, S and Lines, ER and Liu, H and Lorimer, C and Loumeto, JJ and Malhi, Y and Marshall, PL and Mattsson, E and Matula, R and Meave, JA and Mensah, S and Mi, X and Momo, ST and Moncrieff, GR and Mora, F and Muñoz, R and Nissanka, SP and Nur Hajar, ZS and O'Hara, KL and Pearce, S and Pelissier, R and Peri, PL and Ploton, P and Poorter, L and Pour, MJ and Pourbabaei, H and Ribeiro, SC and Ryan, C and Sanaei, A and Sanger, J and Schlund, M and Sellan, G and Shenkin, A and Sonké, B and Sterck, FJ and Svátek, M and Takagi, K and Trugman, AT and Vadeboncoeur, MA and Valipour, A and Vanderwel, MC and Vovides, AG and Waldner, P and Wang, W and Wang, LQ and Wirth, C and Woods, M and Xiang, W and de Aquino Ximenes, F and Xu, Y and Yamada, T and Zavala, MA and Zimmermann, NE}, title = {The global spectrum of tree crown architecture.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {4876}, pmid = {40419494}, issn = {2041-1723}, support = {NE/S01537X/1//RCUK | Natural Environment Research Council (NERC)/ ; }, mesh = {*Trees/anatomy &amp; histology/physiology/classification ; Ecosystem ; *Plant Stems/anatomy &amp; histology ; Photosynthesis ; Climate ; Biological Evolution ; Phylogeny ; }, abstract = {Trees can differ enormously in their crown architectural traits, such as the scaling relationships between tree height, crown width and stem diameter. Yet despite the importance of crown architecture in shaping the structure and function of terrestrial ecosystems, we lack a complete picture of what drives this incredible diversity in crown shapes. Using data from 374,888 globally distributed trees, we explore how climate, disturbance, competition, functional traits, and evolutionary history constrain the height and crown width scaling relationships of 1914 tree species. We find that variation in height-diameter scaling relationships is primarily controlled by water availability and light competition. Conversely, crown width is predominantly shaped by exposure to wind and fire, while also covarying with functional traits related to mechanical stability and photosynthesis. Additionally, we identify several plant lineages with highly distinctive stem and crown forms, such as the exceedingly slender dipterocarps of Southeast Asia, or the extremely wide crowns of legume trees in African savannas. Our study charts the global spectrum of tree crown architecture and pinpoints the processes that shape the 3D structure of woody ecosystems.}, }
@article {pmid40417563, year = {2024}, author = {Foreman, MA and Ross, A and Burgess, APH and Myneni, S and Franklin, A}, title = {Barriers and Facilitators of Digital Health Use for Self-Management of Hypertensive Disorders by Black Pregnant Women.}, journal = {AMIA ... Annual Symposium proceedings. AMIA Symposium}, volume = {2024}, number = {}, pages = {433-442}, pmid = {40417563}, issn = {1942-597X}, mesh = {Humans ; Female ; Pregnancy ; *Self-Management ; *Black or African American ; *Hypertension, Pregnancy-Induced/therapy/ethnology ; Adult ; Interviews as Topic ; Telemedicine ; Digital Health ; }, abstract = {Although digital health tools are increasingly common for managing health conditions, these applications are often developed without consideration of differences across user populations. A reproducible framework is needed to support tailoring applications to include cultural considerations, potentially leading to better adoption and more effective use. As a first step, this study captures a snapshot of Black women's barriers and facilitators in using digital health products for self-management of hypertensive disorders of pregnancy (HDP). One-on-one semi-structured interviews were conducted with 17 Black pregnant women with HDP. We established a unique model for cultural tailoring with these experiences using Black feminist theory and the CDC's Social-Ecological Model (SEM). 38 themes across the four levels of SEM were found through grounded theory. These themes can inform the feature development of a digital health intervention. Future work will instantiate and validate a framework that provides theoretical constructs for developing culturally tailored digital health interventions.}, }
@article {pmid40416669, year = {2025}, author = {Gaievskyi, S and Delfrate, N and Ragazzoni, L and Bahattab, A}, title = {Use of multi-criteria decision analysis (MCDA) to support decision-making during health emergencies: a scoping review.}, journal = {Frontiers in public health}, volume = {13}, number = {}, pages = {1584026}, pmid = {40416669}, issn = {2296-2565}, mesh = {Humans ; *Decision Support Techniques ; *Decision Making ; *Emergencies ; }, abstract = {BACKGROUND: The mismatch between the health needs of populations affected by emergencies and resources devoted to response is projected to further increase. Making the response more effective is one of the solutions to meet the growing needs. Multi-criteria decision analysis (MCDA) has been successfully used to increase effectiveness in various fields by supporting decision-making. However, no review of its application to all-hazard health emergencies has been done to date.<br><br>METHODS: A review of peer-reviewed English-language articles published since 2004 was conducted in May 2024 using Scopus, PubMed and Web of Science databases. The review focused on the empirical application of MCDA to support decision-making during health emergencies. The review was guided by the Joanna Briggs Institute methodology for scoping reviews and adhered to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews. Quantitative data were analyzed using summary statistics and qualitative data were analyzed using content analysis.<br><br>RESULTS: Seventy-one articles were included after screening. The articles described the MCDA application to support a variety of decision problems related to health emergency management. However, the technique was mostly applied to infectious hazards management and only seldom to other hazards. The review also found a lack of standardized methodology for identifying alternatives and criteria, weighting, computation of model output, methods of dealing with uncertainty, and stakeholder engagement.<br><br>CONCLUSION: The review provides an overview of the current use of the MCDA approach to support decision-making in health emergency management and informs areas of future development. The review emphasizes that while MCDA is already used for infectious hazards, it is underutilized for other types of health emergencies. Developing tailored MCDA approaches for health emergencies, including defining evaluation criteria and stakeholder engagement, may improve uptake of the technique and benefit the efforts to meet the growing health needs of the population affected by emergencies, https://osf.io/6kd5s/.}, }
@article {pmid40415801, year = {2025}, author = {Yang, P and Wang, X and Yang, J and Yan, B and Sheng, H and Li, Y and Yang, Y and Wang, J}, title = {AI-Driven Multiscale Study on the Mechanism of Polygonati Rhizoma in Regulating Immune Function in STAD.}, journal = {ACS omega}, volume = {10}, number = {19}, pages = {19770-19796}, pmid = {40415801}, issn = {2470-1343}, abstract = {Polygonati Rhizoma, a traditional Chinese medicine, has demonstrated immunomodulatory and anticancer properties, yet its precise mechanisms in stomach adenocarcinoma (STAD) remain underexplored. This study aims to uncover the multitarget mechanisms of Polygonati Rhizoma in regulating the tumor immune microenvironment in STAD using artificial intelligence (AI)-driven network pharmacology, bioinformatics, and single-cell RNA sequencing, offering new insights into its immunotherapeutic potential. This study harnessed the power of AI to unravel the molecular mechanisms underlying Polygonati Rhizoma's effects. AI-driven methodologies screened 38 putative constituents, retaining 8 based on ADME criteria. Machine Learning algorithms predicted potential targets, which were cross-referenced with 5,569 immune-related genes from GeneCards, revealing 52 immune-associated targets. Differential expression analysis of the STAD data set identified 18 overlapping DEGs with prognostic significance and immune cell infiltration correlations. Key targets (AKT1, TP53, PTGS2 and VEGFA) emerged as central nodes in the network, with AI-assisted molecular docking confirming strong binding affinities, particularly between diosgenin and these core proteins. Molecular dynamics simulations further validated these interactions. Single-cell RNA sequencing revealed distinct target-gene expression patterns across malignant, stromal, and immune cell subsets in digestive-system tumors. In vitro, Polygonati Rhizoma extract significantly inhibited HGC-27 cell viability and increased intracellular ROS levels. These findings underscore the critical role of AI in integrating multiscale analyses, unveiling a multitarget immunomodulatory and antitumor mechanism for Polygonati Rhizoma in STAD, and providing a foundation for future preclinical and clinical studies.}, }
@article {pmid40414987, year = {2025}, author = {Jia, L and Liu, Z and Li, Y}, title = {Spatiotemporal dynamics of rural settlement evolution in Guangdong Province, China.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {18244}, pmid = {40414987}, issn = {2045-2322}, support = {23BDJ019//National Planning Office of Philosophy and Social Science/ ; 23BDJ019//National Planning Office of Philosophy and Social Science/ ; }, mesh = {China ; *Rural Population/statistics &amp; numerical data ; Humans ; *Urbanization/trends ; Spatio-Temporal Analysis ; *Population Dynamics ; Socioeconomic Factors ; Industrial Development ; Geographic Information Systems ; }, abstract = {This study analyzes the spatiotemporal dynamics of rural settlement evolution in Guangdong Province, China, examining their transformation amid rapid urbanization and industrialization over the past 20 years. Rural settlements serve as primary spatial carriers for production and living activities, embodying multiple functions including production, living, ecological, and cultural aspects. Using GIS-based analytical tools, including landscape pattern indices, average nearest neighbor index, kernel density estimation, and geographical detector methods, we examined settlement evolution patterns and their driving factors. Results show a continuous decline in settlement numbers, while patch areas exhibited a U-shaped trend of decreasing then increasing. Settlement patterns shifted from "reduction" to "integration", with intensifying spatial agglomeration over time. The Pearl River Delta and Eastern Guangdong regions followed similar trajectories, reflecting the impact of urbanization and industrialization on rural development. Multiple factors, including natural conditions, socioeconomic variables, and locational accessibility, drove these changes. The spatial distribution of rural settlements demonstrates an overall trend of agglomeration, which has gradually intensified over time, leading to significant variations in settlement density across different regions. The findings reveal significant regional disparities and temporal changes in settlement patterns, highlighting the complex interplay between rural transformation and urban development. This research contributes to understanding rural transformation processes in developing countries and emphasizes the need for differentiated approaches in spatial planning and rural revitalization strategies to address the challenges of disordered land expansion and population hollowing while promoting sustainable rural development.}, }
@article {pmid40414334, year = {2025}, author = {Dou, X and Liu, Q and Fan, Q and Guo, J and Qi, W}, title = {Comprehensive analysis of common heavy metals in the Yellow River over 20 Years: Spatiotemporal distribution, migration characteristics, traceability, and potential risk evaluation.}, journal = {Environmental research}, volume = {281}, number = {}, pages = {121931}, doi = {10.1016/j.envres.2025.121931}, pmid = {40414334}, issn = {1096-0953}, mesh = {*Metals, Heavy/analysis ; *Water Pollutants, Chemical/analysis ; *Rivers/chemistry ; China ; *Environmental Monitoring ; Risk Assessment ; Geologic Sediments/chemistry ; Spatio-Temporal Analysis ; }, abstract = {Heavy metal pollution posed a great threat to the global aquatic ecological environment, especially in the Yellow River where the utilization rate of water resources was as high as 80 %. This study addressed the spatiotemporal distribution, sources, and ecological risks of seven heavy metals (As, Cd, Cr, Cu, Ni, Pb, Zn) in the Yellow River by analyzing historical data collected from 2000 to 2020. The annual heavy metal fluxes increased from Qinghai to Henan section, then decreased from Henan to Shandong section. Similarly, concentrations of Cu, Ni, Pb, and Zn peaked in the sediments of the Henan section. These trends might be attributed to the interception effects of the Xiaolangdi and Sanmenxia Dams. The annual fluxes from 2016 to 2020 increased by an average of 162.6 % compared to that from 2011 to 2015, likely reflecting the impact of ongoing economic growth (33.36 %) and SS increase (69.68 %). The annual fluxes of SS demonstrated a significant correlation with all heavy metal fluxes, underscoring their role as a critical transport medium in aquatic ecosystem. The fluxes of Cd and Pb were most strongly influenced by human factors. While most metals in surface water present negligible risks to aquatic life, Cd in sediments presents a considerable ecological threat. Furthermore, the highest potential ecological risk index (RI) was observed in the river sections in Gansu and Inner Mongolia, mainly due to Cd, which contributed up to 85.87 %. The findings establish a fundamental framework for safeguarding the aquatic ecosystem of the Yellow River and managing its heavy metal contamination.}, }
@article {pmid40413976, year = {2025}, author = {Bai, Z and Zhang, D and Zhang, S and Li, T and Wang, G and Xu, X and Pan, X and Zhong, Q and Zhou, W and Pu, Y and Jia, Y}, title = {Integrating multi-omics and biomarkers to reveal the stress mechanisms of high fluoride on earthworms.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138706}, doi = {10.1016/j.jhazmat.2025.138706}, pmid = {40413976}, issn = {1873-3336}, mesh = {Animals ; *Oligochaeta/drug effects/metabolism/genetics ; Reactive Oxygen Species/metabolism ; Biomarkers/metabolism ; Oxidative Stress/drug effects ; *Soil Pollutants/toxicity ; *Fluorides/toxicity ; Apoptosis/drug effects ; Multiomics ; }, abstract = {Excessive fluorine accumulation poses a significant threat to soil ecology and even human health, yet its impact on soil fauna, especially earthworms, remains poorly understood. This study employed multi-omics and biomarkers to investigate high fluorine-induced biochemical changes that cause tissue damages in Eisenia fetida. The results demonstrated that earthworms exhibited obvious damage with fluorine addition exceeding 200 mg kg[-1], with stress levels escalating as fluorine contents increased. Further analysis of the underlying mechanisms revealed that fluorine could upregulate genes encoding mitochondrial respiratory chain complexes I-III and downregulate those for IV-V, leading to reactive oxygen species (ROS) accumulation despite antioxidant system activation. The resulting ROS interfered with deoxyribonucleoside triphosphate synthesis, prompting homologous recombination as the main DNA repair mechanism. Additionally, fluorine-induced ROS also attacked and disrupted protein and lipid related metabolisms ultimately causing oxidative damages. These cumulative oxidative damages from high fluorine contents subsequently triggered autophagy or apoptosis, resulting in tissue ulceration and epithelial exfoliation. Therefore, high fluorine could threaten earthworms by inducing ROS accumulation and subsequent biomolecule damages.}, }
@article {pmid40413228, year = {2025}, author = {Fan, J and Zhang, Y and Nie, X and Liu, Y and Wei, S and Peng, H and Li, H and Zhang, M and Ning, L and Wang, S and Qin, L and Zheng, Y and Xing, Y}, title = {Comprehensive curation and validation of genomic datasets for chestnut.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {860}, pmid = {40413228}, issn = {2052-4463}, mesh = {*Fagaceae/genetics ; *Genome, Plant ; Genomics ; Databases, Genetic ; Molecular Sequence Annotation ; Data Curation ; }, abstract = {The Chinese chestnut (Castanea mollissima) stands out as a plant with significant ecological and economic value, excellent nutritional quality and natural resistance to pests and diseases. Recent strides in high-throughput techniques have enabled the continuous accumulation of genomic data on chestnuts, presenting a promising future for genetic research and advancing traits in this species. To facilitate the accessibility and utility of this data, we have curated and analyzed a collection of genomic datasets for eight Castanea species, including functional annotations, 213 RNA-Seq samples, and 330 resequencing samples. These datasets are publicly available on Figshare and are also available through other platforms such as GEO and EVA, providing a valuable resource for researchers studying Castanea genetics, functional genomics, and evolutionary biology. Furthermore, the datasets are integrated into the Castanea Genome Database (CGD, http://castaneadb.net), which serves as a complementary platform, offering advanced data mining and analysis tools, including BLAST, Batch Query, GO/KEGG Enrichment Analysis, and Synteny Viewer, to enhance the usability of the curated datasets.}, }
@article {pmid40412934, year = {2025}, author = {Zhu, Q and Cai, Y and Hu, Z}, title = {Effects of bactericides and sulphate reducing bacteria addition on acidification and microbial community structure of newly produced coal gangue.}, journal = {Journal of environmental sciences (China)}, volume = {156}, number = {}, pages = {311-320}, doi = {10.1016/j.jes.2024.06.024}, pmid = {40412934}, issn = {1001-0742}, mesh = {*Coal ; Sulfates/metabolism ; *Bacteria/metabolism ; Hydrogen-Ion Concentration ; *Microbiota ; *Soil Microbiology ; }, abstract = {Microbiologically driven acidic pollution of coal gangue has become a major environmental problem in coal gangue dumps in coal mining areas. Addition of bactericides and sulphate reducing bacteria (SRB) is an effective means to control the acidic pollution of coal gangue, but their mechanism of action has not been fully investigated. By adding bactericide, SRB and bactericide-SRB to the newly produced coal gangue, respectively, the effects of these treatments on the microbial community structure were observed. Changes in pH and electrical conductivity (EC) of the gangue leaching solution, as well as the microbial community composition and functional abundance on the gangue surface were analysed by leaching simulation experiments and 16S rRNA sequencing. The results showed that (1) the addition of bactericide-SRB was the most effective treatment to elevate pH before 8 d, while the addition of SRB performed best after 22 d (2) The addition of bactericide and SRB drastically changed the microbial community structure on the gangue surface. Simultaneous addition of both had the best inhibitory effect on pathogenic bacteria and Thiobacillus. (3) All three treatments promote higher abundance of genes related to nitrogen cycling, but reflected in different gene functions. Microorganisms with sulfate respiration function in the experimental group all showed different increases. The abundance of other sulfur cycle genes decreased substantially. However, Human Pathogens All had higher abundance than control check (CK) in each treatment, which may indicate that the addition of either bactericides or SRB increases the risk of microbial pathogenicity to humans.}, }
@article {pmid40410961, year = {2025}, author = {Zhang, L and Zhang, L and Gao, S and Huang, C and Dai, Q}, title = {Structural balance and evolution of cooperation in a population with hybrid interactions.}, journal = {Physical review. E}, volume = {111}, number = {4-1}, pages = {044309}, doi = {10.1103/PhysRevE.111.044309}, pmid = {40410961}, issn = {2470-0053}, abstract = {This study explores the evolution of cooperation in populations with mixed pairwise and three-body interactions, investigating the impact of higher-order interaction density ρ and individual interaction preference α. Our results reveal that sparse higher-order interactions markedly boost cooperation, exhibiting two critical phase transitions as ρ changes. These transitions underscore the delicate equilibrium needed for optimal cooperation, as excessive higher-order interactions can diminish returns. The preference parameter α significantly influences cooperation sustainability, with intermediate values maximizing cooperative outcomes, particularly when the temptation to defect r is not strong. Crucially, our findings demonstrate that hybrid social dilemmas structurally encode emergent cooperation pathways that are unattainable within homogeneous interaction frameworks, emphasizing the importance of modeling mixed interactions to capture real-world complexity. These insights offer valuable guidance for designing systems aimed at promoting cooperative behavior across social, ecological, and artificial domains.}, }
@article {pmid40409688, year = {2025}, author = {Zaabaar, E and Zhang, Y and Kam, KW and Li, Y and Zhang, XJ and Ho, M and Liu, D and Ng, MP and Ip, P and Young, A and Pang, CP and Tham, CC and Kwan, MP and Chen, LJ and Yam, JC}, title = {Association of residential air pollution with visual impairment in adults: The UK Biobank study.}, journal = {Asia-Pacific journal of ophthalmology (Philadelphia, Pa.)}, volume = {14}, number = {6}, pages = {100209}, doi = {10.1016/j.apjo.2025.100209}, pmid = {40409688}, issn = {2162-0989}, mesh = {UK Biobank/statistics &amp; numerical data ; Visual Acuity ; *Vision Disorders/diagnosis/epidemiology/etiology ; Nitrogen Oxides/analysis/toxicity ; *Air Pollutants/analysis/toxicity ; Particulate Matter/analysis/toxicity ; Principal Component Analysis ; Ecological Parameter Monitoring/statistics &amp; numerical data ; *Air Pollution/adverse effects/statistics &amp; numerical data ; Blindness/diagnosis/epidemiology/etiology ; *Environmental Exposure/adverse effects/statistics &amp; numerical data ; United Kingdom/epidemiology ; Persons with Visual Disabilities/statistics &amp; numerical data ; Humans ; Male ; Female ; Middle Aged ; Prospective Studies ; Adult ; Aged ; }, abstract = {PURPOSE: To investigate the association of joint exposure to residential air pollutants with different severities of visual impairment (VI) in adults.<br><br>METHODS: Exposure to particulate matter and oxides of nitrogen were evaluated in 95,246 adults aged 40-70 years. Joint exposure to the pollutants was calculated using principal component analysis to create an air pollution score. Subjects were categorized by distance visual acuity into bilateral normal vision, near normal vision, unilateral VI, socially significant VI, and blindness and low vision.<br><br>RESULTS: A unit rise in air pollution score was associated with 9.2&#x202f;%, 4.1&#x202f;%, and 1.8&#x202f;% increased risks of blindness and low vision, adjusted OR (AOR) =&#x202f;1.092 (95&#x202f;% CI, 1.057-1.129); socially significant VI, AOR =&#x202f;1.041 (95&#x202f;% CI, 1.016-1.066); and unilateral VI, AOR =&#x202f;1.018 (95&#x202f;% CI, 1.007-1.029), respectively. Compared to subjects in the lowest quartile of air pollution score, those in the highest quartile had 69.2&#x202f;%, 30.5&#x202f;%, and 9.9&#x202f;% greater risks of blindness and low vision, AOR =&#x202f;1.692 (95&#x202f;% CI, 1.355-2.114), socially significant VI, AOR =&#x202f;1.305 (95&#x202f;% CI, 1.127-1.513), and unilateral VI, AOR =&#x202f;1.099 (95&#x202f;% CI, 1.035-1.167), respectively while those in the third quartile had 40.5&#x202f;% and 25.6&#x202f;% higher risks of blindness and low vision, AOR =&#x202f;1.405 (95&#x202f;% CI, 1.121-1.760) and socially significant VI, AOR =&#x202f;1.256 (95&#x202f;% CI, 1.086-1.453), respectively. There was a significant trend of increasing risk of blindness and low vision, as well as socially significant VI, as pollution levels rose.<br><br>CONCLUSION: Joint exposure to air pollutants increased the risks of poor vision and blindness, suggesting that reducing such exposure could alleviate the disease burden of VI.}, }
@article {pmid40408306, year = {2025}, author = {Bukat, A and Bukowicki, M and Bykowski, M and Kuczkowska, K and Nowakowski, S and Śliwińska, A and Kowalewska, &#x141;}, title = {GRANA: An AI-based tool for accelerating chloroplast grana nanomorphology analysis using hybrid intelligence.}, journal = {Plant physiology}, volume = {198}, number = {2}, pages = {}, pmid = {40408306}, issn = {1532-2548}, support = {2019/35/D/NZ3/03904//National Science Centre, Poland/ ; BOB-IDUB-622-523/2024//University of Warsaw/ ; }, mesh = {*Artificial Intelligence ; *Software ; *Chloroplasts/ultrastructure ; *Thylakoids/ultrastructure ; Neural Networks, Computer ; Photosynthesis ; }, abstract = {Grana are fundamental structural units of the intricate chloroplast membrane network. Investigating their nanomorphology is essential for understanding photosynthetic efficiency regulation. Here, we present GRANA (Graphical Recognition and Analysis of Nanostructural Assemblies), an artificial intelligence-enhanced, user-friendly software tool that recognizes grana on thylakoid network electron micrographs and generates a complex set of their structural parameters. GRANA employs 3 artificial neural networks of different architectures and binds them in a 1-click workflow. Its output is designed to facilitate hybrid intelligence analysis, securing fast and reliable results from large datasets. The GRANA tool is over 100 times faster compared with currently used manual approaches. As a proof of concept, we have successfully applied GRANA software to diverse grana structures across different land plant species grown under various conditions, demonstrating the wide range of potential applications for our software. GRANA tool supports large-scale analysis of grana nanomorphological features, facilitating advancements in photosynthesis-oriented studies.}, }
@article {pmid40408146, year = {2025}, author = {Fontanarrosa, P and Clare, C and Fedorec, AJH and Barnes, CP}, title = {MIMIC: a Python package for simulating, inferring, and predicting microbial community interactions and dynamics.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {5}, pages = {}, pmid = {40408146}, issn = {1367-4811}, support = {BB/W013770/1//Bioengineered Cells &amp; Systems/ ; BB/T008709/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Software ; *Microbiota ; Bayes Theorem ; *Computational Biology/methods ; *Microbial Interactions ; Machine Learning ; Computer Simulation ; }, abstract = {SUMMARY: The study of microbial communities is vital for understanding their impact on environmental, health, and technological domains. The Modelling and Inference of MICrobiomes Project (MIMIC) introduces a Python package designed to advance the simulation, inference, and prediction of microbial community interactions and dynamics. Addressing the complex nature of microbial ecosystems, MIMIC integrates a suite of mathematical models, including previously used approaches such as Generalized Lotka-Volterra (gLV), Gaussian Processes (GP), and Vector Autoregression (VAR) plus newly developed models for integrating multi-omic data, to offer a versatile framework for analyzing microbial dynamics. By leveraging Bayesian inference and machine learning techniques, MIMIC provides the ability to infer the dynamics of microbial communities from empirical data, facilitating a deeper understanding of their complex biological processes, unveiling possible unknown ecological interactions, and enabling the design of microbial communities. Such insights could help to advance microbial ecology research, optimizing biotechnological applications, and contribute to environmental sustainability and public health strategies. MIMIC is designed for flexibility and ease of use, aiming to support researchers and practitioners in microbial ecology and microbiome research.<br><br>MIMIC is freely available under the MIT License at https://github.com/ucl-cssb/MIMIC. It is implemented in Python (version 3.7 or higher) and is compatible with Windows, macOS, and Linux operating systems. MIMIC depends on standard Python libraries including NumPy, SciPy, and PyMC. Comprehensive examples and tutorials (including the main text demonstrations) are provided as Jupyter notebooks in the examples/directory and at the MIMIC Docs website, along with detailed installation instructions and real-world data use cases. The software will remain freely available for at least two years following publication. A code snapshot for this publication is also available at Zenodo: https://doi.org/10.5281/zenodo.15149003.}, }
@article {pmid40407930, year = {2025}, author = {Bate, JB and Dagamac, NHA}, title = {Wallow land suitability assessment using GIS-based multicriteria decision-making framework.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {6}, pages = {668}, pmid = {40407930}, issn = {1573-2959}, mesh = {*Geographic Information Systems ; *Conservation of Natural Resources/methods ; Animals ; *Environmental Monitoring/methods ; Ecosystem ; Philippines ; Decision Making ; Biodiversity ; }, abstract = {Protected areas are the frontlines of biodiversity conservation, featuring critical landscapes and microhabitats that are fitted for the survival of the organisms that have restricted populations. The determination of land suitability and habitat connectivity in these protected areas are important for species with specialized adaptive behavior that requires favorable conditions to survive. The Bubalus mindorensis is a critically endangered bovine of the Philippines which utilizes mud or water puddles to address heat stress through body submersion, known as wallowing. With Mts. Iglit-Baco National Park (MIBNP) harboring the largest remaining subpopulation of the tamaraw, the preservation of its natural landscapes is critical for tamaraw survival. Here, the potential wallows in MIBNP were determined using the weighted overlay analysis (WOA) assisted by the analytical hierarchy process (AHP). Using environmental variables that were influential to the creation of wallows, an equal-weighed scenario and an AHP-assisted scenario wallow suitability map was generated. Moderate and highly suitable areas were found at the north-central portion of the mountain, coinciding with the current and future conservation zones of the tamaraw, whereas low suitable areas dominate the other half, aggregating at the corners due to build areas and agriculture. The result of the study provides supplementary information in constructing future conservation strategies for an endemic species with global importance, particularly in its possible range expansion within the park. Furthermore, this study provides a framework for future conservation efforts, which helps in the management of critical landscapes for species with specialized adaptive behaviors through GIS-based multicriteria decision-making.}, }
@article {pmid40407563, year = {2025}, author = {Araujo, ACB and Souza, OF and Kersanach, BB and Mozzer, JSC and Feitosa, VL and Brandão, VA and Alencar, FEC and Oliveira, NS and Silva, AVBD and Abreu, LC}, title = {Trends in Congenital Syphilis Incidence and Mortality in Brazil's Southeast Region: A Time-Series Analysis (2008-2022).}, journal = {Epidemiologia (Basel, Switzerland)}, volume = {6}, number = {2}, pages = {}, pmid = {40407563}, issn = {2673-3986}, support = {182023//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Esp&#xed;rito Santo/ ; }, abstract = {Congenital syphilis (CS) is an important infectious cause of miscarriage, stillbirth, and neonatal morbidity and mortality. Despite the advances in diagnosis and treatment, CS continues to challenge health systems with increasing incidence and mortality rates in recent years worldwide. Given this, the present study aims to comparatively analyze the temporal trends in CS incidence and mortality in Brazil's Southeast Region from 2008 to 2022. This is an ecological time-series study using secondary data on congenital syphilis from the states of Espírito Santo, Minas Gerais, Rio de Janeiro, and São Paulo. The data was extracted from the Brazilian Health System Informatics Department. Incidence and mortality rates were calculated per 100,000 live births. Joinpoint regression models were employed to identify trends in annual percentage change and average annual percentage change with 95% confidence intervals. The temporal trend of CS incidence in Brazil's Southeast Region increased 12.8% between 2008 and 2022. Minas Gerais, São Paulo, Espírito Santo, and Rio de Janeiro showed increasing temporal trends of 21.4%, 14.1%, 14.0%, and 10.9%, respectively. The temporal trend of CS mortality in Brazil's Southeast Region rose 11.9% between 2008 and 2022. Minas Gerais, São Paulo, and Rio de Janeiro exhibited increasing mortality temporal trends of 21.9%, 20.8%, and 10.1%, respectively. In contrast, Espírito Santo showed reduced mortality, with no deaths in 2021 and 2022. The temporal trend of CS incidence increased in all states of Brazil's Southeast Region between 2008 and 2022, highlighting the need to reassess control measures. The temporal trend of CS mortality also increased during the same period, except in Espírito Santo. Considering that CS is preventable with adequate prenatal care and low-cost measures, these findings can serve as instruments to support strengthening public health policies.}, }
@article {pmid40407387, year = {2025}, author = {Wang, M and Chen, X and Liu, M and Luo, H and Zhang, S and Guo, J and Wang, J and Zhou, L and Zhang, N and Li, H and Wang, C and Li, L and Wang, Z and Wang, H and Guo, Z and Li, Y and Wang, Y}, title = {Decoding herbal combination models through systematic strategies: insights from target information and traditional Chinese medicine clinical theory.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {3}, pages = {}, pmid = {40407387}, issn = {1477-4054}, support = {2021CXGC010509//2021 Shandong Provincial Key RD Program (Major Technological Innovation Project)/ ; 2022ZDYF0410//Key RD Projects of Ningxia Hui Nationality Autonomous Region in 2022/ ; }, mesh = {*Medicine, Chinese Traditional/methods ; *Drugs, Chinese Herbal/therapeutic use/pharmacology ; Humans ; Arthritis, Rheumatoid/drug therapy ; Databases, Factual ; Animals ; }, abstract = {Traditional Chinese medicine (TCM) utilizes intricate herbal formulations that exemplify the principles of compatibility and synergy. However, the rapid proliferation of herbal data has resulted in redundant information, complicating the understanding of their potential mechanisms. To address this issue, we first established a comprehensive database that encompasses 992 herbs, 18 681 molecules, and 2168 targets. Consequently, we implemented a multi-network strategy based on a core information screening method to elucidate the highly intertwined relationships among the targets of various herbs and to refine herbal target information. Within a non-redundant network framework, separation and overlap analysis demonstrated that the networking of herbs preserves essential clinical information, including their properties, meridians, and therapeutic classifications. Furthermore, two notable trends emerged from the statistical analyses of classical TCM formulas: the separation of herbs and the overlap between herbs and diseases. This phenomenon is termed the herbal combination model (HCM), validated through statistical analyses of two representative case studies: the common cold and rheumatoid arthritis. Additionally, in vivo and in vitro experiments with the new formula YanChuanQin (YanHuSuo-Corydalis Rhizoma, ChuanWu-Aconiti Radix, and QinJiao-Gentianae Macrophyllae Radix) for acute gouty arthritis further support the HCM. Overall, this computational method provides a systematic network strategy for exploring herbal combinations in complex and poorly understood diseases from a non-redundant perspective.}, }
@article {pmid40407023, year = {2025}, author = {Pang, D and Zhu, R and Zhao, H and Wang, T}, title = {Probabilistic exponential family inverse regression and its applications.}, journal = {Biometrics}, volume = {81}, number = {2}, pages = {}, doi = {10.1093/biomtc/ujaf065}, pmid = {40407023}, issn = {1541-0420}, support = {12222111//National Natural Science Foundation of China/ ; 12331009//National Natural Science Foundation of China/ ; }, mesh = {Humans ; Algorithms ; Computer Simulation ; *Models, Statistical ; Regression Analysis ; Likelihood Functions ; *Biometry/methods ; Data Interpretation, Statistical ; }, abstract = {Rapid advances in high-throughput sequencing technologies have led to the fast accumulation of high-dimensional data, which is harnessed for understanding the implications of various factors on human disease and health. While dimension reduction plays an essential role in high-dimensional regression and classification, existing methods often require the predictors to be continuous, making them unsuitable for discrete data, such as presence-absence records of species in community ecology and sequencing reads in single-cell studies. To identify and estimate sufficient reductions in regressions with discrete predictors, we introduce probabilistic exponential family inverse regression (PrEFIR), assuming that, given the response and a set of latent factors, the predictors follow one-parameter exponential families. We show that the low-dimensional reductions result not only from the response variable but also from the latent factors. We further extend the latent factor modeling framework to the double exponential family by including an additional parameter to account for the dispersion. This versatile framework encompasses regressions with all categorical or a mixture of categorical and continuous predictors. We propose the method of maximum hierarchical likelihood for estimation, and develop a highly parallelizable algorithm for its computation. The effectiveness of PrEFIR is demonstrated through simulation studies and real data examples.}, }
@article {pmid40406849, year = {2025}, author = {Han, Y and Cai, J and Chen, Y and Zhang, Y and Jin, LN and Chen, T and Li, J and Zhang, G and Chen, J}, title = {Concurrent Formation of Low-Maturity EC and BrC in Biomass and Coal Burning: O-PAH as a Precursor.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {24}, pages = {12083-12095}, doi = {10.1021/acs.est.4c13299}, pmid = {40406849}, issn = {1520-5851}, mesh = {*Coal ; *Biomass ; *Carbon ; *Polycyclic Aromatic Hydrocarbons ; Soot ; }, abstract = {Black carbon (BC) significantly influences climate change through light absorption. Traditional emission inventories equate BC with elemental carbon (EC) and overlook the variability in its properties across sources, leading to uncertainties in climate predictions. This study shows that EC from solid fuel combustion contains substantial low-maturity EC (char), whose emissions increase alongside the light absorption of soluble organic carbon (OC) as the fuel aromaticity rises. Concurrently, the abundance of oxygenated polycyclic aromatic hydrocarbons (O-PAHs) in soluble OC also increases. This suggests that char and brown carbon (BrC) share similar formation pathways with O-PAHs as key precursors. Time-resolved analysis during combustion cycles revealed a significant positive correlation between O-PAHs, the light absorption of soluble OC, and char emissions, further supporting this shared pathway. The nonbonding orbitals in BrC and char facilitate n → π* transitions in the visible region, which are more wavelength-dependent than the π → π* transition in high-maturity EC (soot). This study highlights char as a light-absorbing intermediate, influencing light absorption of EC emitted from solid fuel combustion. These insights into the formation pathways and optical properties of carbonaceous aerosols enhance our understanding of their climate impacts and underscore the need to differentiate between char and soot in climate models to improve accuracy.}, }
@article {pmid40404926, year = {2025}, author = {Pringle, S and Dallimer, M and Goddard, MA and Le Goff, LK and Hart, E and Langdale, SJ and Fisher, JC and Abad, SA and Ancrenaz, M and Angeoletto, F and Auat Cheein, F and Austen, GE and Bailey, JJ and Baldock, KCR and Banin, LF and Banks-Leite, C and Barau, AS and Bashyal, R and Bates, AJ and Bicknell, JE and Bielby, J and Bosilj, P and Bush, ER and Butler, SJ and Carpenter, D and Clements, CF and Cully, A and Davies, KF and Deere, NJ and Dodd, M and Drinkwater, R and Driscoll, DA and Dutilleux, G and Dyrmann, M and Edwards, DP and Farhadinia, MS and Faruk, A and Field, R and Fletcher, RJ and Foster, CW and Fox, R and Francksen, RM and Franco, AMA and Gainsbury, AM and Gardner, CJ and Giorgi, I and Griffiths, RA and Hamaza, S and Hanheide, M and Hayward, MW and Hedblom, M and Helgason, T and Heon, SP and Hughes, KA and Hunt, ER and Ingram, DJ and Jackson-Mills, G and Jowett, K and Keitt, TH and Kloepper, LN and Kramer-Schadt, S and Labisko, J and Labrosse, F and Lawson, J and Lecomte, N and de Lima, RF and Littlewood, NA and Marshall, HH and Masala, GL and Maskell, LC and Matechou, E and Mazzolai, B and McConnell, A and Melbourne, BA and Miriyev, A and Nana, ED and Ossola, A and Papworth, S and Parr, CL and Payo-Payo, A and Perry, G and Pettorelli, N and Pillay, R and Potts, SG and Prendergast-Miller, MT and Qie, L and Rolley-Parnell, P and Rossiter, SJ and Rowcliffe, M and Rumble, H and Sadler, JP and Sandom, CJ and Sanyal, A and Schrodt, F and Sethi, SS and Shabrani, A and Siddall, R and Smith, SC and Snep, RPH and Soulsbury, CD and Stanley, MC and Stephens, PA and Stephenson, PJ and Struebig, MJ and Studley, M and Svátek, M and Tang, G and Taylor, NK and Umbers, KDL and Ward, RJ and White, PJC and Whittingham, MJ and Wich, S and Williams, CD and Yakubu, IB and Yoh, N and Zaidi, SAR and Zmarz, A and Zwerts, JA and Davies, ZG}, title = {Opportunities and challenges for monitoring terrestrial biodiversity in the robotics age.}, journal = {Nature ecology &amp; evolution}, volume = {9}, number = {6}, pages = {1031-1042}, pmid = {40404926}, issn = {2397-334X}, mesh = {*Biodiversity ; *Robotics/methods ; *Conservation of Natural Resources/methods ; *Environmental Monitoring/methods/instrumentation ; Delphi Technique ; }, abstract = {With biodiversity loss escalating globally, a step change is needed in our capacity to accurately monitor species populations across ecosystems. Robotic and autonomous systems (RAS) offer technological solutions that may substantially advance terrestrial biodiversity monitoring, but this potential is yet to be considered systematically. We used a modified Delphi technique to synthesize knowledge from 98 biodiversity experts and 31 RAS experts, who identified the major methodological barriers that currently hinder monitoring, and explored the opportunities and challenges that RAS offer in overcoming these barriers. Biodiversity experts identified four barrier categories: site access, species and individual identification, data handling and storage, and power and network availability. Robotics experts highlighted technologies that could overcome these barriers and identified the developments needed to facilitate RAS-based autonomous biodiversity monitoring. Some existing RAS could be optimized relatively easily to survey species but would require development to be suitable for monitoring of more 'difficult' taxa and robust enough to work under uncontrolled conditions within ecosystems. Other nascent technologies (for instance, new sensors and biodegradable robots) need accelerated research. Overall, it was felt that RAS could lead to major progress in monitoring of terrestrial biodiversity by supplementing rather than supplanting existing methods. Transdisciplinarity needs to be fostered between biodiversity and RAS experts so that future ideas and technologies can be codeveloped effectively.}, }
@article {pmid40404775, year = {2025}, author = {Wang, J and Xu, Y and Zhu, H and Chen, C and Zhao, Y and Wang, Y}, title = {CheloniansTraits: a comprehensive trait database of global turtles and tortoises.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {840}, pmid = {40404775}, issn = {2052-4463}, support = {32271734//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Turtles/anatomy &amp; histology ; Animals ; Databases, Factual ; Biological Evolution ; Life History Traits ; Conservation of Natural Resources ; }, abstract = {Turtles and tortoises (chelonians) possess a variety of ecological characteristics, including long lifespans and protective shells, which have enabled them to survive and adapt to environmental challenges since the Triassic period. However, many characteristics of chelonians have turned into disadvantages for their populations in the Anthropocene. Currently, there remains a lack of comprehensive data on the morphological, life-history, and ecological characteristics of all chelonians on a global scale. Consequently, our study aims to collect a complete trait database of global chelonians (CheloniansTraits), which may help bridge the knowledge gap regarding the identity and ecology of global chelonians and thereby aiding future conservation endeavors. We compiled 69 trait data for all 358 recognized chelonian species, utilizing ~2,000 literature sources, covering 33 morphological, 21 life-history, 7 ecological traits, and 8 conservation information. This database serves as a uniquely valuable resource for exploring evolutionary, biogeographical, and ecological inquiries related to chelonians, as well as elucidating key aspects of ecological strategy variation among species.}, }
@article {pmid40404082, year = {2025}, author = {Zhang, S and Qiang, J and Liu, H and Zhou, J and Li, J and Chen, J and Ding, Q and Qian, K}, title = {An efficient and precise (micro)plastic identification method: feature infrared spectra extraction based on EIS-VIP-CARS and ANN modeling.}, journal = {Environmental research}, volume = {279}, number = {Pt 2}, pages = {121916}, doi = {10.1016/j.envres.2025.121916}, pmid = {40404082}, issn = {1096-0953}, mesh = {*Neural Networks, Computer ; *Environmental Monitoring/methods ; *Microplastics/analysis ; Algorithms ; Spectrophotometry, Infrared/methods ; }, abstract = {Understanding microplastics' (MPs) ecological impact necessitates their precise identification. To address the issue of the competitive adaptive reweighted sampling (CARS) algorithm extracting numerous feature wavenumber points (FWPs) that often miss transmittance peaks (TPs), resulting in high computational load and low accuracy in artificial neural network (ANN) models, this study introduces a novel approach. Initially, the equal interval sampling (EIS) method is employed to capture the main information of the full spectra. Subsequently, the variable importance in projection (VIP) is innovatively integrated into the CARS to formulate the EIS-VIP-CARS method for extracting feature spectra (FS). Using 20 typical MPs as the subjects, this study compares the identification performance of ANN models using full-spectra, EIS, CARS, EIS-CARS, VIP-CARS, and EIS-VIP-CARS. The results show that VIP-CARS extracts 128 FWPs, a reduction of 49.41 % compared to CARS. Moreover, the distribution of these FWPs is more concentrated around the TPs and their vicinity. The accuracy of MPs by the ANN model based on VIP-CARS is generally higher than that of CARS. EIS-VIP-CARS extracts 55 FWPs, representing a reduction of 58.65 % and 57.03 % compared to EIS and VIP-CARS, respectively. The overall distribution of these points closely aligns with the distribution of functional groups. The ANN model based on EIS-VIP-CARS can achieve a similar accuracy for MPs as the model based on EIS, both greater than 99 %, demonstrating good generalization ability. The accuracies of the MNN and convolutional neural network (CNN) models are higher than those of the SNN model, but the modeling time is longer. The ANN model established using the EIS-VIP-CARS is an efficient and precise approach for the identification of MPs in infrared spectroscopy. This study provides technical references for the research on the environmental behavior of MPs and is also of significant importance for the classification and management of plastic waste.}, }
@article {pmid40403917, year = {2025}, author = {Wang, H and Lei, W and Wu, M and Guo, J and He, S and Shen, N and Li, C and Wang, L}, title = {Spatial distribution and ecological risks of neonicotinoids in surface waters of Eastern China.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {378}, number = {}, pages = {126507}, doi = {10.1016/j.envpol.2025.126507}, pmid = {40403917}, issn = {1873-6424}, mesh = {China ; *Water Pollutants, Chemical/analysis ; *Neonicotinoids/analysis ; *Insecticides/analysis ; *Environmental Monitoring ; Risk Assessment ; Rivers/chemistry ; Nitro Compounds/analysis ; Thiamethoxam/analysis ; Guanidines/analysis ; Animals ; }, abstract = {Over the past two decades, neonicotinoid insecticides (NNIs) have been extensively used in agricultural activities. Due to its high-water solubility, NNIs are primarily found in surface waters, contaminating them and posing significant ecological risks. However complex watershed environments pose challenges in elucidating the pollution characteristics and ecological risks of NNIs in large-scale waters. This study focused on typical surface waters in Eastern China, exploring the spatial characteristics, driving factors, and ecological risks of NNIs. The total concentration of NNIs (Σ8NNIs) ranges from 2.3 ng/L to 1377.8 ng/L. This concentration range exceeded the European water environment toxicity thresholds, with 86 of the sites surpassing the chronic toxicity threshold (8.3 ng/L) and 14 of the sites exceeding the acute toxicity threshold (200 ng/L). Thiamethoxam (THIA), imidacloprid (IMI), and dinotefuran (DIN) were detected with high rates and concentrations. Spatially, the Σ8NNIs in the Yangtze River (YZ, 140.0 ng/L) are significantly higher than in the north of Beijing-Hangzhou Grand Canal (BHN, 62.8 ng/L), Taihu Lake (TH, 36.6 ng/L), and Taihu Basin (THB, 21.9 ng/L). Moreover, Σ8NNIs in the south of Beijing-Hangzhou Grand Canal (BHS, 326.5 ng/L) are significantly higher than in BHN (62.8 ng/L). The spatial distribution of NNI components indicated that DIN and THIA dominated in YZ (37 %), THIA (34 %) and DIN (20 %) in BHN, IMI (53 %) in BHS, DIN (53 %) in TH, and THIA (49 %) and DIN (31 %) in THB. Correlation analysis and linear mixed modeling identified land use, pH, and dissolved oxygen (DO) as significant factors influencing the occurrence of NNIs, with DO emerging as a crucial element. The species sensitivity distribution (SSD) results showed the acute and chronic toxicity thresholds of NNIs for 5 % of aquatic species were 716 ng/L and 166 ng/L respectively with 19 sites exceeding the chronic toxicity threshold and 1 sites surpassing the acute toxicity threshold.}, }
@article {pmid40402004, year = {2025}, author = {Brunk, KM and Kramer, HA and Peery, MZ and Kahl, S and Wood, CM}, title = {Assessing spatial variability and efficacy of surrogate species at an ecosystem scale.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {39}, number = {5}, pages = {e70058}, pmid = {40402004}, issn = {1523-1739}, support = {//Arthur Vining Davis Foundations/ ; FKZ 01|S22072//German Federal Ministry of Education and Research/ ; //Josh Holshuh/ ; //University of Wisconsin's Office of the Vice Chancellor for Research/ ; 20-ECOF20-0017//NASA Biodiversity and Ecological Forecasting Program/ ; //National Park Service/ ; 19-RP-NEU-043//California Climate Investment Forest Health Research Program/ ; FKZ 67KI31040E//German Federal Ministry of Environment, Nature Conservation, and Nuclear Safety/ ; //USDA Forest Service Region 5/ ; }, mesh = {*Conservation of Natural Resources/methods ; Animals ; California ; *Biodiversity ; *Birds/physiology ; *Ecosystem ; Forests ; }, abstract = {Preserving biodiversity is a central goal of conservation, but, in practice, monitoring biodiversity often involves assessing population trends for one or a handful of species that are presumed proxies for biodiversity. Despite the popularity of surrogate species strategies, the links between biodiversity and surrogate species are rarely tested, especially across the broad spatial scales at which they are applied. We quantitatively evaluated a prominent surrogate species strategy across 25,000 km[2] of California's Sierra Nevada, an ecosystem undergoing substantial forest loss due to changing fire regimes and climate. We used passive acoustic monitoring and multispecies occupancy models to quantify pairwise co-occurrence among 6 indicator species and much of the avian community (63 species). We found that 95% of the sampled avian community had a positive association with at least one indicator species and that latitude played an important role in shaping co-occurrence for many species. Our work provides an important test of a long-standing conservation tool, suggests that a well-chosen suite of surrogate species can represent the occurrence patterns of a large portion of the rest of the community, and demonstrates the importance of explicitly considering the spatial scale over which surrogate species are effective.}, }
@article {pmid40401771, year = {2025}, author = {Callens, M and Le Berre, G and Van den Bulcke, L and Lolivier, M and Derycke, S}, title = {An Accessible Metagenomic Strategy Allows for Better Characterisation of Invertebrate Bulk Samples.}, journal = {Molecular ecology resources}, volume = {25}, number = {8}, pages = {e14126}, doi = {10.1111/1755-0998.14126}, pmid = {40401771}, issn = {1755-0998}, support = {RT/24/DNASense_ILVO//Belgian Federal Science Policy Office/ ; //Biodiversa+/ ; //Belgian Federal Public Service Economy/ ; BAR0159//Directorate-General for Regional Policy of the European Union/ ; }, mesh = {*Metagenomics/methods ; Animals ; *Invertebrates/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; Biodiversity ; Computational Biology/methods ; Sequence Analysis, DNA ; }, abstract = {DNA-based techniques are a popular approach for assessing biodiversity in ecological research, especially for organisms which are difficult to detect or identify morphologically. Metabarcoding, the most established method for determining species composition and relative abundance in bulk samples, can be more sensitive and time- and cost-effective than traditional morphological approaches. However, one drawback of this method is PCR bias caused by between-species variation in the amplification efficiency of a marker gene. Metagenomics, bypassing PCR amplification, has been proposed as an alternative to overcome this bias. Several studies have already shown the promising potential of metagenomics, but they all indicate the unavailability of reference genomes for most species in any ecosystem as one of the primary bottlenecks preventing its wider implementation. In this study, we present a strategy that combines unassembled reads of low-coverage whole genome sequencing and publicly available reference genomes to construct a genomic reference database, thus circumventing high sequencing costs and intensive bioinformatic processing. We show that this approach is superior to metabarcoding for approximating relative biomass of macrobenthos species from bulk samples. Furthermore, these results can be obtained with a sequencing effort comparable to metabarcoding. The strategy presented here can thus accelerate the implementation of metagenomics in biodiversity assessments, as it should be relatively easy to adopt by laboratories familiar with metabarcoding and can be used as an accessible alternative.}, }
@article {pmid40399277, year = {2025}, author = {Petit, MJ and Flory, C and Gu, Q and Fares, M and Lamont, D and Score, A and Davies, K and Bell-Sakyi, L and Scaturro, P and Brennan, B and Kohl, A}, title = {Multi-omics analysis of SFTS virus infection in Rhipicephalus microplus cells reveals antiviral tick factors.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {4732}, pmid = {40399277}, issn = {2041-1723}, support = {MC_UU_00034/5//RCUK | Medical Research Council (MRC)/ ; SC 314/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 210462/Z/18/Z//Wellcome Trust (Wellcome)/ ; TICKITS 890970//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; MC_UU_12014/8//RCUK | Medical Research Council (MRC)/ ; /WT_/Wellcome Trust/United Kingdom ; MC_UU_00034/4//RCUK | Medical Research Council (MRC)/ ; }, mesh = {Animals ; *Rhipicephalus/virology/genetics/immunology ; Cell Line ; Proteomics/methods ; Virus Replication ; *Phlebovirus/physiology/genetics ; Transcriptome ; Host-Pathogen Interactions/genetics ; RNA Helicases/metabolism/genetics ; Proteome ; *Severe Fever with Thrombocytopenia Syndrome/virology ; Gene Expression Profiling ; Multiomics ; }, abstract = {The increasing prevalence of tick-borne arboviral infections worldwide necessitates advanced control strategies, particularly those targeting vectors, to mitigate the disease burden. However, the cellular interactions between arboviruses and ticks, especially for negative-strand RNA viruses, remain largely unexplored. Here, we employ a proteomics informed by transcriptomics approach to elucidate the cellular response of the Rhipicephalus microplus-derived BME/CTVM6 cell line to severe fever with thrombocytopenia syndrome virus (SFTSV) infection. We generate the de novo transcriptomes and proteomes of SFTSV- and mock-infected tick cells, identifying key host responses and regulatory pathways. Additionally, interactome analysis of the viral nucleoprotein (N) integrated host responses with viral replication and dsRNA-mediated gene silencing screen reveals two anti-SFTSV effectors: the N interacting RNA helicases DHX9 and UPF1. Collectively, our results provide insights into the antiviral responses of R. microplus vector cells and highlight critical SFTSV restriction factors, while enriching transcriptomic and proteomic resources for future research.}, }
@article {pmid40398052, year = {2025}, author = {Guo, Z and Li, J and Hu, J and An, G and Wang, C}, title = {Deciphering the joint intracellular and extracellular regulatory strategies of toxigenic Microcystis to achieve intraspecific competitive advantage: An integrated multi-omics analysis with novel allelochemicals identified.}, journal = {Water research}, volume = {283}, number = {}, pages = {123774}, doi = {10.1016/j.watres.2025.123774}, pmid = {40398052}, issn = {1879-2448}, mesh = {*Microcystis/metabolism ; *Pheromones ; Microcystins ; Proteomics ; Metabolomics ; Multiomics ; }, abstract = {Global increase in Microcystis-dominated cyanobacterial blooms (MCBs) severely threatens ecological and human health. Intraspecific interaction between microcystin (MC)-producing (MC[+]) Microcystis and co-existing MC-free (MC[-]) Microcystis influences the relative abundance of MC[+]Microcystis, ultimately determining the toxicity and hazard of MCBs. However, specific allelochemicals driving this interaction and underlying molecular mechanisms remain unclear. This study confirmed that intraspecific interaction promoted the competitive advantage of MC[+]Microcystis over MC[-]Microcystis and unveiled the joint intracellular and extracellular regulatory strategies of MC[+]Microcystis based on proteomics-metabolomics analyses and biochemical validation. Intracellularly, MC[+]Microcystis enhanced pentose phosphate pathway and lipid and fatty acid biosynthesis to maintain cellular functions and membrane stability, but inhibited glycolysis, tricarboxylic acid cycle, and protein biosynthesis to optimize energy utilization for growth and proliferation. Extracellularly, MC[+]Microcystis released allelochemicals, including cytidine diphosphate-diacylglycerol and N-acyl-homoserine lactones, to inhibit MC[-]Microcystis growth by 13.53% and 16.39%, respectively, thereby achieving its competitive advantage. In contrast, MC[-]Microcystis exhibited the suppressed photosynthesis and oxidative phosphorylation, imbalanced anti-inflammatory responses, nucleic acid degradation, and membrane damage, resulting in its competitive disadvantage in co-culture. These findings provide new insights into the competitive dynamics between MC[+] and MC[-]Microcystis, and their involved implications for aquatic ecosystem health.}, }
@article {pmid40397662, year = {2025}, author = {Li, S and Zou, J and Wu, J and Sun, B and Zhao, M and Liu, D and Cheng, Q and Tan, H and Ma, J}, title = {New Insights into Natural Polyphenol-Enhanced Fe(III)/Peracetic Acid System under Acidic pH Conditions: The Overlooked Role of Coexisting Hydrogen Peroxide.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {21}, pages = {10608-10619}, doi = {10.1021/acs.est.5c01622}, pmid = {40397662}, issn = {1520-5851}, mesh = {Hydrogen Peroxide/chemistry ; *Polyphenols/chemistry ; Hydrogen-Ion Concentration ; *Peracetic Acid/chemistry ; Hydroxybenzoates ; Iron ; Ferric Compounds/chemistry ; }, abstract = {Natural polyphenols have been extensively utilized as reducing agents to enhance contaminant degradation in the Fe(III)/peracetic acid (PAA) system. However, the roles of coexisting hydrogen peroxide (H2O2) remain insufficiently explored. This study, using protocatechuic acid (PCA) as a representative natural polyphenol, demonstrated that contaminant removal within the PCA/Fe(III)/PAA system under acidic pH conditions exhibited two kinetic stages: an initial rapid stage driven by PAA, followed by a slower stage driven by H2O2. The presence of H2O2 facilitated the complete degradation (100%) of contaminants even at low concentrations (<1.0 μM). Interestingly, these two stages contributed differently to various contaminants' degradation. Mechanistic investigations revealed that Fe(IV) was the major reactive species (RSs) for contaminant degradation during the PAA stage, while [•]OH dominated during the H2O2 stage. In brief, H2O2 enriched the generation pathways and types of RSs. Notably, besides PCA itself, the reaction intermediates (i.e., phenoxy radicals) formed during the reaction between PCA and RSs also played a key role in reducing Fe(III), which explained why the PCA/Fe(III)/PAA system was able to maintain sufficient Fe(II) to further interact with H2O2. Overall, this study highlighted the synergistic role of coexisting H2O2 and provided valuable insights for optimizing various contaminants' degradation in actual waters using PAA-based Fenton-like systems.}, }
@article {pmid40393855, year = {2025}, author = {Zhivkoplias, E and da Silva, JM and Blasiak, R}, title = {How transdisciplinarity can help biotech-driven biodiversity research.}, journal = {Trends in biotechnology}, volume = {43}, number = {9}, pages = {2105-2116}, doi = {10.1016/j.tibtech.2025.04.008}, pmid = {40393855}, issn = {1879-3096}, mesh = {*Biodiversity ; *Biotechnology ; Conservation of Natural Resources ; Humans ; }, abstract = {The Kunming-Montreal Global Biodiversity Framework marks a significant step toward conserving genetic diversity on a global scale. Sequencing advancements have broadened biodiversity studies by enabling the mapping of species distributions, increasing understanding of ecological interactions, and monitoring genetic diversity. However, these tools are hindered by inequalities and biases, particularly in biodiversity-rich developing countries. To navigate these challenges, we propose strategies using the existing biotechnological toolbox to make biodiversity data more accessible and useful for research and development. This includes increasing funding for database curation, improving metadata standards, addressing inequalities in technological capacity, and supporting holistic capacity-building programmes. Implementing these strategies can unlock new opportunities for biodiversity research aligned with sustainable development principles and can contribute to improved conservation outcomes.}, }
@article {pmid40393297, year = {2025}, author = {Yang, H and Zhou, J and Zhou, J}, title = {Integrated multi-omics and DNA stable-isotope probing approaches to reveal soil-ryegrass response to ionic rare earth mineral ammonium-lead contamination.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138658}, doi = {10.1016/j.jhazmat.2025.138658}, pmid = {40393297}, issn = {1873-3336}, mesh = {*Lolium/drug effects/metabolism/growth &amp; development/genetics ; *Soil Pollutants/toxicity ; *Lead/toxicity ; Plant Roots/drug effects/metabolism/growth &amp; development ; Soil/chemistry ; *Ammonium Compounds/toxicity ; Oxidative Stress/drug effects ; Nitrogen/metabolism ; Nitrogen Isotopes ; Multiomics ; }, abstract = {The extensive use of ammonium (NH4[+]) sulfate in ionic rare earth mining has resulted in soil contamination with NH4[+] and lead (Pb), posing significant challenges for ecological restoration. Here, multi-omics and DNA stable-isotope probing (DNA-SIP) approaches were utilized to investigate soil nitrogen cycling and the molecular response of ryegrass (Lolium perenne L.) to NH4[+] (180-720 mg kg[-1])-Pb[2+] (207-828 mg kg[-1]) co-contamination. A synergistic interaction between NH4[+] and Pb[2+] was observed, significantly inhibited ryegrass growth, and induced oxidative stress and mitochondrial swelling. The EC50 toxicity thresholds were 383 mg kg[-1] for NH4[+] and 512 mg kg[-1] for Pb. The Integrated Biomarker Response (IBRv2) model elucidated the synergistic toxic effects. Transcriptomic and metabolomic analyses indicated that ryegrass roots enhanced carbon metabolism and antioxidant response pathways related to stress tolerance. Galactose metabolism and lysine degradation were identified as key pathways associated with stress response. Co-contamination with NH4[+] and Pb[2+] reduced ryegrass root [15]N-total nitrogen (TN) by 30 % while increasing soil [15]N-NH4[+] residue by 95 % and decreasing [15]N-microbial biomass nitrogen (MBN) by 59 %, compared to NH4[+] single contamination. DNA-SIP analysis revealed that ryegrass cultivation under NH4[+]- Pb[2+] co-contamination increased the abundance of plant growth-promoting rhizobacteria (Dyella), acid-tolerant nitrogen (Acidibacter), and sulfur-cycling taxa (Desulfosporosinus). The presence of raffinose and chlorogenic acid in ryegrass root metabolites was associated with shifts in the structure and composition of using NH4[+] active microbial taxa. These findings provide valuable insights into plant-soil-microbe interactions under multi-pollutant stress and offer practical strategies for phytoremediation and ecological restoration in areas affected by mining.}, }
@article {pmid40393068, year = {2025}, author = {Williams, CM and Scelza, BA and Slack, SD and Font-Porterias, N and Al-Hindi, DR and Mathias, RA and Watson, H and Barnes, KC and Lange, E and Johnson, RK and Gignoux, CR and Ramachandran, S and Henn, BM}, title = {A rapid accurate approach to inferring pedigrees in endogamous populations.}, journal = {Genetics}, volume = {230}, number = {4}, pages = {}, pmid = {40393068}, issn = {1943-2631}, support = {R35 GM133531/GM/NIGMS NIH HHS/United States ; BCS-1534682//NSF/ ; T32 GM128596/GF/NIH HHS/United States ; R35GM139628/GF/NIH HHS/United States ; R35 GM139628/GM/NIGMS NIH HHS/United States ; T32 GM128596/GM/NIGMS NIH HHS/United States ; R35GM133531/GF/NIH HHS/United States ; }, mesh = {*Pedigree ; Humans ; Haplotypes ; Algorithms ; Male ; *Genetics, Population/methods ; Female ; Machine Learning ; }, abstract = {Accurate reconstruction of pedigrees from genetic data remains a challenging problem. Many relationship categories (e.g. half-sibships vs avuncular) can be difficult to distinguish without external information. Pedigree inference algorithms are often trained on European-descent families in urban locations. Thus, existing methods tend to perform poorly in endogamous populations for which there may be reticulations within the pedigrees and elevated haplotype sharing. We present a simple, rapid algorithm which initially uses only high-confidence first-degree relationships to seed a machine learning step based on summary statistics of identity-by-descent sharing. One of these statistics, our "haplotype score," is novel and can be used to: (1) distinguish half-sibling pairs from avuncular or grandparent-grandchildren pairs; and (2) assign individuals to ancestor vs descendant generation. We test our approach in a sample of 700 individuals from northern Namibia, sampled from an endogamous population called the Himba. Due to a culture of concurrent relationships in the Himba, there is a high proportion of half-sibships. We accurately identify first through fourth-degree relationships and distinguish between various second-degree relationships: half-sibships, avuncular pairs, and grandparent-grandchildren. We further validate our approach in a second African-descent dataset, the Barbados Asthma Genetics Study, and a European-descent founder population from Quebec. Accurate reconstruction of relatives facilitates estimation of allele frequencies, tracing allele trajectories, improved phasing, heritability and other population genomic questions.}, }
@article {pmid40389091, year = {2025}, author = {Narita, M and Matsugaki, R and Muramatsu, K and Fushimi, K and Matsuda, S}, title = {Obesity and risk of post-operative pneumonia among older adult patients with hip fracture: An obesity paradox.}, journal = {Clinical nutrition ESPEN}, volume = {68}, number = {}, pages = {342-347}, doi = {10.1016/j.clnesp.2025.05.020}, pmid = {40389091}, issn = {2405-4577}, mesh = {Humans ; *Hip Fractures/surgery/complications ; Aged ; Male ; *Obesity/complications ; Female ; *Pneumonia/etiology/epidemiology ; Body Mass Index ; *Postoperative Complications/epidemiology/etiology ; Risk Factors ; Aged, 80 and over ; Incidence ; Obesity Paradox ; }, abstract = {BACKGROUND &amp; AIM: Hip fracture is a condition with a high incidence among older adults and is associated with a high post-operative mortality rate. Post-operative pneumonia is one of the most important risk factors for mortality, making its prevention essential. In recent years, reports on obesity paradoxes have increasingly been documented. Therefore, this study aimed to investigate the relationship between body mass index (BMI) and the risk of developing post-operative pneumonia using a large database.<br><br>METHOD: We included 407,203 patients aged 75 years or older who underwent surgery for hip fracture between 2014 and 2018 using Diagnosis Procedure Combination data, a healthcare reimbursement system. Patients were classified into six BMI categories: <16.0, 16.0-16.9, 17.0-18.4, 18.5-24.9, 25.0-29.9, and &#x2265;30 kg/m[2]. Multilevel logistic regression analysis was performed based on BMI 18.5-24.9 kg/m[2] to determine odds ratios for post-operative pneumonia.<br><br>RESULTS: The data of 332,768 patients were included in the final analysis. Those with BMI <18.5 kg/m[2] demonstrated significantly higher odds of developing post-operative pneumonia compared to those with BMI between 18.5 and 24.9 kg/m[2], BMI <16.0 kg/m[2] (adjusted odds ratio [AOR: 2.14, 95 % confidence interval [CI: 2.01-2.27 p < 0.001); BMI 16.0-16.9 kg/m[2] (AOR: 1.57, 95 % CI: 1.46-1.69, p < 0.001); and BMI 17.0-18.4 kg/m[2] (AOR: 1.31, 95 % CI: 1.24-1.39, p < 0.001). Conversely, patients with BMI 25.0-29.9 kg/m[2] showed a reduced risk of post-operative pneumonia compared to the other groups (AOR: 0.83, 95 % CI: 0.76-0.91, p < 0.001). Notably, a J-curve relationship was observed between BMI and the incidence of post-operative pneumonia.<br><br>CONCLUSION: Patients with higher BMI had a lower risk of developing post-operative pneumonia, revealing the presence of an obesity paradox between hip fracture and post-operative pneumonia. Patients with low BMI are at a higher risk and may benefit from enhanced preventive measures to mitigate the risk of pneumonia.}, }
@article {pmid40386950, year = {2025}, author = {Cordeiro, AL and Cusack, DF and Guerrero-Ramírez, N and Norby, RJ and Toro, L and Wong, MY and Wright, SJ and Cabugao, KGM and Andersen, KM and Fuchslueger, L and Iversen, CM and Soper, F and Ghimire, OP and Lugli, LF and Miron, AC and Valverde-Barrantes, O and Arnaud, M and Batterman, SA and Dietterich, LH and Lee, MY and Weemstra, M and Yaffar, D and Addo-Danso, SD and Pierick, K and Bridges, R and Easton, C and Felsing, I and Gonçalves, NB and Krudop, R and McKinzie, MR and Perbohner, J and Pozzoli-Oropeza, AN and Samaniego, M and Smilor, AW and Vargas, IS and Webb, L and Powers, JS and McCormack, ML}, title = {TropiRoot 1.0: Database of tropical root characteristics across environments.}, journal = {Ecology}, volume = {106}, number = {5}, pages = {e70074}, doi = {10.1002/ecy.70074}, pmid = {40386950}, issn = {1939-9170}, mesh = {*Plant Roots/physiology/anatomy &amp; histology ; *Tropical Climate ; *Databases, Factual ; Ecosystem ; Biodiversity ; }, abstract = {Tropical ecosystems contain the world's largest biodiversity of vascular plants. Yet, our understanding of tropical functional diversity and its contribution to global diversity patterns is constrained by data availability. This discrepancy underscores an urgent need to bridge data gaps by incorporating comprehensive tropical root data into global datasets. Here, we provide a database of tropical root characteristics. This new database, TropiRoot 1.0, will be instrumental in evaluating an array of hypotheses pertaining to root functional ecology and plant biogeography, both within the tropics and relative to other global biomes. The data compilation was conducted by the TropiRoot Initiative, in partnership with the Fine-Root Ecology Database (FRED) and the Global Root Trait (GRooT) database, Colorado State University (CSU) and the Smithsonian Tropical Research Institute (STRI). Literature search and data extraction were conducted between 2020 and 2024. Literature was identified using Web of Science, Scopus, and complemented using the expert knowledge of members of TropiRoot. To provide broad environmental and geographical distributions, literature searches included root characteristics (traits) across global change drivers, natural gradients, and from different continents. We adopted FRED standardized data columns and streamlined the format to enhance accessibility for data extraction across various user groups. This optimized framework resulted in a smaller, yet comprehensive datasheet. To make the database compatible with other global root trait initiatives, column identification was standardized following the codes provided by FRED. These efforts culminated in data extracted from 104 new sources, resulting in more than 8000 rows of data (either species or community data). Most of the data in TropiRoot 1.0 include root characteristics such as root biomass, morphology, root dynamics, mass fraction, architecture, anatomy, physiology, and root chemistry. This initiative represents a 30% increase in the currently available data for tropical roots in FRED. TropiRoot 1.0 contains root characteristics from 25 different countries, where seven are located in Asia, six in South America, five in Central America and the Caribbean, four in Africa, two in North America, and 1 in Oceania. Due to the volume of data, when ancillary data were available, including soil data, these data were either extracted and included in the database or its availability was recorded in an additional column. Multiple contributors checked the entries for outliers during the collation process to ensure data quality. For text-based observations, we examined all cells to ensure that their content relates to their specific categories. For numerical observations, we ordered each numerical value from least to greatest and plotted the values, checking apparent outliers against the data in their respective sources and correcting or removing incorrect or impossible values. Some data (soil and aboveground) have different columns for the same variable presented in different units, including originally published units, but root characteristics data had units converted to match those reported in FRED. By filling a gap from global databases, TropiRoot 1.0 expands our knowledge of otherwise so far underrepresented regions and our ability to assess global trends. This advancement can be used to improve tropical forest representation in vegetation models. The data are freely available and should be cited when used.}, }
@article {pmid40386543, year = {2025}, author = {Ramos, E and Schweizer, M and Wu, MY and Sahli, C and Latt, C and Lunak, M and Crochet, PA and Salzburger, W and Meier, J and Marques, DA and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Yellow-legged Gull, Larus michahellis Naumann, 1840.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {129}, pmid = {40386543}, issn = {2398-502X}, abstract = {We present a genome assembly from a female specimen of Larus michahellis (Yellow-legged Gull; Chordata; Aves; Charadriiformes; Laridae). The genome sequence has a total length of 1,405.56 megabases. Most of the assembly (90.55%) is scaffolded into 35 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 16.79 kilobases in length.}, }
@article {pmid40381407, year = {2025}, author = {Lei, L and Sha, W and Liu, Q and Liu, S and Zhou, Y and Li, R and Duan, Y and Fu, S and Li, H and Liao, R and Li, L and Zhou, R and Zhou, C and Liu, H}, title = {Hepatotoxic effects of exposure to different concentrations of Dibutyl phthalate (DBP) in Schizothorax prenanti: Insights from a multi-omics analysis.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {285}, number = {}, pages = {107390}, doi = {10.1016/j.aquatox.2025.107390}, pmid = {40381407}, issn = {1879-1514}, mesh = {*Dibutyl Phthalate/toxicity ; Animals ; *Liver/drug effects/pathology/metabolism ; *Water Pollutants, Chemical/toxicity ; *Cyprinidae/physiology ; Oxidative Stress/drug effects ; Multiomics ; }, abstract = {Dibutyl phthalate (DBP) is one of the most widely used phthalate esters (PAEs) that raise increasing ecotoxicological concerns due to their harmful effects on living organisms and ecosystems. Recently, while PAEs pollution in the Yangtze River has attracted significant attention, little research has been conducted on the impact of PAEs stress on S. prenanti, an endemic and valuable species in the Yangtze River. In this study, one control group (C-L) and three experimental groups: T1-L (3 µg/L), T2-L (30 µg/L), and T3-L (300 µg/L) were established with reference to the DBP concentration in the environment. For the first time, we investigated the effects of DBP stress on the liver of S. prenanti using histomorphological, physiological, and biochemical indexes, as well as a joint multi-omics analysis. The results revealed that compared to the C-L group, liver structural damage and stress were not significant in the environmental concentration group (T1-L) and the number of differential genes and differential metabolites were lower. However, as DBP stress concentration increased, the liver damage became severe, with significant vacuolation and hemolysis observed in the T2-L and T3-L groups. The TUNEL assay revealed a significant increase in the number of apoptotic cells along with a notable rise in differential genes and metabolites in the T2-L and T3-L groups. Oxidative stress markers (T-AOC, SOD, CAT, and GSH-PX) were also significantly higher in the T2-L and T3-L groups. RNA-Seq analysis showed that the protein processing in the endoplasmic reticulum pathway was most significantly -enriched differential gene pathway shared by both C-L vs T2-L and C-L vs T3-L, with most of the genes in this pathway showing significant up-regulation. This suggests that the protein processing in the endoplasmic reticulum pathway may play a key role in protecting the liver from injuries caused by high DBP stress. Interestingly, C XI, C XII, C XIII, C XIV and C XV in the chemical carcinogenesis - reactive oxygen species pathway were significantly down-regulated in the T2-L and T3-L groups based on combined transcriptomic and metabolomic analyses, suggesting that DBP causes liver injury by disrupting mitochondria. This comprehensive histomorphometric and multi-omics study demonstrated that the current DBP concentration in the habitat of S. prenanti in the upper reaches of the Yangtze River temporarily causes less liver damage. However, with increasing of DBP concentration, DBP could still cause serious liver damage to S. prenanti. This study provides a new mechanistic understanding of the liver response mechanism of S. prenanti under different concentrations of DBP stress and offers basic data for the ecological protection of the Yangtze River.}, }
@article {pmid40379663, year = {2025}, author = {Iminjili, V and Crowther, A and Fisher, MT and Kay, A and Roberts, P and Goldstein, S and Boivin, N and Fernandes, R}, title = {A dataset of scientific dates from archaeological sites in eastern Africa spanning 5000 BCE to 1800 CE.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {801}, pmid = {40379663}, issn = {2052-4463}, mesh = {*Archaeology ; Africa, Eastern ; History, Ancient ; History, 18th Century ; Humans ; }, abstract = {Large collections of archaeological spatiotemporal data can reveal past cultural and demographic trends, land use strategies, and processes of environmental adaptation. Within Africa, archaeological Big Data can contribute to the study of the spread of agriculture, domesticated species, and specific artefacts and technologies, as well as their ecological impacts. Although reviews addressing these topics are available for different parts of the continent, existing mid-late Holocene archaeology datasets have yet to be compiled into a central, open-access, standardized informatic-oriented dataset. Here we present Wanyika, a dataset of scientific dates from archaeological sites in eastern Africa spanning almost 7 millennia, from ~5000 BCE to 1800 CE. This dataset compiles published scientific dates and associated botanical, faunal, iron, and ceramic finds from sites in Kenya, Tanzania, the Comoros Islands, and Madagascar. The records also include data for megafauna extinctions in Madagascar. We describe the spatiotemporal coverage of the dataset, how the data were collected, the structure of the dataset, and the applied quality control measures.}, }
@article {pmid40378593, year = {2025}, author = {Broel, N and Daumüller, F and Ali, A and Lemanschick, J and Maibach, K and Mewe, C and Bunk, B and Spröer, C and Baschien, C and Zorn, H and Schlüter, H and Rühl, M and Janssen, S and Gand, M}, title = {Unravelling the enzymatic wood decay repertoire of Cerrena zonata: A multi-omics approach.}, journal = {Microbiological research}, volume = {298}, number = {}, pages = {128214}, doi = {10.1016/j.micres.2025.128214}, pmid = {40378593}, issn = {1618-0623}, mesh = {Lignin/metabolism ; *Wood/metabolism/microbiology ; Fungal Proteins/genetics/metabolism ; Glycoside Hydrolases/metabolism/genetics ; Peroxidases/metabolism/genetics ; Laccase/metabolism/genetics ; Biomass ; *Basidiomycota/enzymology/genetics/metabolism ; Genomics ; Gene Expression Profiling ; Genome, Fungal ; Proteomics ; Hydrolysis ; Multiomics ; }, abstract = {Lignocellulosic biomass (LCB), such as wheat straw, bagasse, or wood, is a cost-effective, sustainable carbon source but remains challenging to utilize due to the recalcitrance of lignin, which hinders efficient carbohydrate hydrolysis. Effective LCB degradation demands a wide range of enzymes, and commercial enzyme cocktails often require physical or chemical pretreatments. A fully enzymatic degradation could drastically improve the efficiency of these processes. Basidiomycota fungi naturally possess diverse enzymes suited for LCB breakdown. The white-rot fungus Cerrena zonata, a member of the phylum Basidiomycota, was analyzed for its Carbohydrate-Active Enzymes (CAZymes) using a multi-omics approach. Genomic and transcriptomic analyses of C. zonata identified 20,816 protein-encoding genes, including 487 CAZymes (2.3 %). Cultivating C. zonata with and without LCB addition revealed a total of 147 proteins, of which 36 were CAZymes (13 auxiliary activities (AA), 3 carbohydrate esterases, and 20 glycoside hydrolases). In accordance, laccase, manganese peroxidase (MnP) as well as versatile peroxidase (VP) activities were detected in the fungal culture supernatants. Furthermore, relevant enzymes were visualized via zymography. Consistent with these results, five putative peroxidases (AA2) and three putative laccases (AA1_1) were identified in all -omics dimensions. Further structure and sequence analysis of AA2 proteins supports that two proteins were classified as VPs and three as MnPs, based on their active and Mn[2 +] binding sites. In summary, C. zonata possesses a broad enzyme spectrum expressed under varied conditions, highlighting its potential for identifying efficient lignin-degrading enzymes for enzymatic pretreatment of food industry side streams and other LCBs.}, }
@article {pmid40378285, year = {2025}, author = {Campbell, KR and Goeva, A}, title = {Cells Keep Diverse Company in Diseased Tissues.}, journal = {Cancer research}, volume = {85}, number = {13}, pages = {2351-2352}, doi = {10.1158/0008-5472.CAN-25-2070}, pmid = {40378285}, issn = {1538-7445}, mesh = {Disease Progression ; *Multiomics/methods ; *Spatial Analysis ; Palatine Tonsil/cytology/pathology ; Germinal Center/cytology/pathology ; Spleen/cytology/pathology ; Lupus Erythematosus, Systemic/pathology ; Disease Models, Animal ; *Neoplasms/mortality/pathology ; Humans ; Animals ; Mice ; }, abstract = {Emerging spatial profiling technologies have revolutionized our understanding of how tissue architecture shapes disease progression, yet the contribution of cellular diversity remains underexplored. In this issue, Ding and colleagues introduce multiomics and ecological spatial analysis (MESA), an ecology-inspired framework that integrates spatial and single-cell expression data to quantify tissue diversity across multiple scales. MESA both identifies distinct cellular neighborhoods and computes a variety of diversity metrics alongside the identification of diversity "hotspots." Applied to human tonsil tissue, MESA revealed previously undetected germinal center organization, whereas in spleen tissue of a murine lupus model, MESA highlights increasing cellular diversity with disease progression. Importantly, diversity hotspots do not correspond to conventional compartments identified by existing methods, presenting an orthogonal metric of spatial organization. In colorectal cancer, MESA's diversity metrics outperformed established subtypes at predicting patient survival, whereas in hepatocellular carcinoma, multiomic integration identified significantly more ligand-receptor interactions between immune cells compared with single-modality analysis. This work establishes cellular diversity within tissues as a critical correlate of disease progression and underscores the value of multiomic integration in spatial biology. This article is part of a special series: Driving Cancer Discoveries with Computational Research, Data Science, and Machine Learning/AI.}, }
@article {pmid40378227, year = {2025}, author = {Ha, MK and Postovskaya, A and Kuznetsova, M and Meysman, P and Van Deuren, V and Van Ierssel, S and De Reu, H and Schippers, J and Peeters, K and Besbassi, H and Heyndrickx, L and Willems, B and Mariën, J and Bartholomeus, E and Vercauteren, K and Beutels, P and Van Damme, P and Lion, E and Vlieghe, E and Laukens, K and Coenen, S and Naesens, R and Ariën, KK and Ogunjimi, B}, title = {Celluloepidemiology-A paradigm for quantifying infectious disease dynamics on a population level.}, journal = {Science advances}, volume = {11}, number = {20}, pages = {eadt2926}, pmid = {40378227}, issn = {2375-2548}, mesh = {Humans ; *COVID-19/epidemiology/immunology/virology ; *SARS-CoV-2/immunology ; T-Lymphocytes/immunology ; Machine Learning ; Receptors, Antigen, T-Cell/immunology/metabolism ; Flow Cytometry ; *Communicable Diseases/epidemiology/immunology ; }, abstract = {To complement serology as a tool in public health interventions, we introduced the "celluloepidemiology" paradigm where we leveraged pathogen-specific T cell responses at a population level to advance our epidemiological understanding of infectious diseases, using SARS-CoV-2 as a model. Applying flow cytometry and machine learning on data from more than 500 individuals, we showed that the number of T cells with positive expression of functional markers not only could distinguish patients who recovered from COVID-19 from controls and pre-COVID donors but also identify previously unrecognized asymptomatic patients from mild, moderate, and severe recovered patients. The celluloepidemiology approach was uniquely capable to differentiate health care worker groups with different SARS-CoV-2 exposures from each other. T cell receptor (TCR) profiling strengthened our analysis by revealing that SARS-CoV-2-specific TCRs were more abundant in patients than in controls. We believe that adding data on T cell reactivity will complement serology and augment the value of infection morbidity modeling for populations.}, }
@article {pmid40376739, year = {2025}, author = {Arnold, LE and Hendrix, K and Pan, X and Vollebregt, MA and Yu, M and Kerson, C and Arns, M and Hatsu, IE and DeBeus, R and Hollway, J and Roley-Roberts, ME}, title = {Lifestyle Effects in a Randomized Controlled Trial of Neurofeedback for Attention-Deficit/Hyperactivity Disorder.}, journal = {Journal of child and adolescent psychopharmacology}, volume = {35}, number = {9}, pages = {491-499}, doi = {10.1089/cap.2025.0019}, pmid = {40376739}, issn = {1557-8992}, mesh = {Humans ; *Attention Deficit Disorder with Hyperactivity/therapy ; Male ; Child ; *Neurofeedback/methods ; Female ; *Life Style ; Exercise ; Surveys and Questionnaires ; Sleep Hygiene ; Treatment Outcome ; }, abstract = {Objectives/Background: Multiple factors influence symptom severity in Attention Deficit/Hyperactivity Disorder (ADHD). We examined four of these: diet, sleep hygiene, exercise, and lighting, in the International Collaborative ADHD Neurofeedback (ICAN) randomized clinical trial, which found large significant improvement with both active neurofeedback and control condition without treatment difference. Methods: A total of 142 participants aged 7-10 had breakfast and lunch intake and exercise recorded at each neurofeedback session. Parents completed the Children's Sleep Habits Questionnaire (CSHQ). Parents and teachers rated inattention on Conners3. Lifestyle changes were correlated with inattention changes. Results: At baseline, CSHQ correlated with parent-rated inattention (r = 0.17, p = 0.04), and length of sleep correlated with teacher-rated inattention (r = 0.20, p = 0.03). From baseline to treatment end food group variety (p = 0.029, d = 0.22) and sleep problems (p < 0.0001, d = -0.49) improved significantly, exercise time and protein intake marginally (p = 0.06 - 0.08). Parent-rated inattention improvement correlated with CSHQ improvement (Rho = 0.26, p = 0.002) and marginally with protein intake increase (Rho = 0.18, p = 0.06). The three components of the light-emitting-diode (LED)-induced circadian pathway hypothesis were significant. Conclusions: Most measures improved, but few significantly. How much they impact classroom attention remains unclear. Although parent ratings of inattention improvement correlated with sleep problems improvement, composited parent/teacher ratings (primary outcome) did not. The circadian pathway hypothesis associated with LED lighting was supported. These findings warrant further studies examining the role sleep hygiene can play in improving ADHD symptoms. Meanwhile, attention to sleep hygiene seems appropriate in any treatment plan for ADHD.}, }
@article {pmid40371923, year = {2025}, author = {Cirino, T and Pinto, L and Iwan, M and Dougha, A and Lučić, B and Kraljević, A and Navoyan, Z and Tevosyan, A and Yeghiazaryan, H and Khondkaryan, L and Abelyan, N and Atoyan, V and Babayan, N and Iwashita, Y and Kimura, K and Komasaka, T and Shishido, K and Nakamura, T and Asada, M and Jain, S and Zakharov, AV and Wang, H and Liu, W and Chupakhin, V and Uesawa, Y}, title = {Consensus Modeling Strategies for Predicting Transthyretin Binding Affinity from Tox24 Challenge Data.}, journal = {Chemical research in toxicology}, volume = {38}, number = {6}, pages = {1061-1071}, pmid = {40371923}, issn = {1520-5010}, mesh = {*Prealbumin/metabolism/chemistry ; Humans ; Protein Binding ; Binding Sites ; }, abstract = {Transthyretin (TTR) is a key transporter of the thyroid hormone thyroxine, and chemicals that bind to TTR, displacing the hormone, can disrupt the endocrine system, even at low concentrations. This study evaluates computational modeling strategies developed during the Tox24 Challenge, using a data set of 1512 compounds tested for TTR binding affinity. Individual models from nine top-performing teams were analyzed for performance and uncertainty using regression metrics and applicability domains (AD). Consensus models were developed by averaging predictions across these models, with and without consideration of their ADs. While applying AD constraints in individual models generally improved external prediction accuracy (at the expense of reduced chemical space coverage), it had limited additional benefit for consensus models. Results showed that consensus models outperformed individual models, achieving a root-mean-square error (RMSE) of 19.8% on the test set, compared to an average RMSE of 20.9% for the nine individual models. Outliers consistently identified in several of these models indicate potential experimental artifacts and/or activity cliffs, requiring further investigation. Substructure importance analysis revealed that models prioritized different chemical features, and consensus averaging harmonized these divergent perspectives. These findings highlight the value of consensus modeling in improving predictive performance and addressing model limitations. Future work should focus on expanding chemical space coverage and refining experimental data sets to support public health protection.}, }
@article {pmid40371524, year = {2025}, author = {Li, YH and Zhang, Y}, title = {[Wilderness network construction in Lincang City of Yunnan Province, Southwest China based on landscape connectivity].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {36}, number = {4}, pages = {1233-1243}, doi = {10.13287/j.1001-9332.202504.026}, pmid = {40371524}, issn = {1001-9332}, mesh = {China ; *Conservation of Natural Resources/methods ; *Ecosystem ; Geographic Information Systems ; *Wilderness ; Cities ; *Environment Design ; Models, Theoretical ; *City Planning ; }, abstract = {Constructing wilderness networks based on landscape connectivity is crucial for wilderness conservation. We calculated the continuous spectrum of the wilderness with GIS, identified wilderness sources with morphological spatial pattern analysis (MSPA), constructed wilderness corridors and networks and extracted wilderness strategic points with minimum cumulative resistance model (MCR) and circuit theory. We further analyzed the characte-ristics of the wilderness network, and proposed wilderness protection strategies and ecological planning suggestions for Lincang City. Results showed that wilderness was mainly distributed at 1000-2500 m elevation, with a spatial pattern of more in the south and east, less in the north and west in Lincang City. Grade 3 wilderness covered 55% of the total area, indicating high quality of the study area. Based on the MSPA analysis, we found 27 wilderness sources, most of which were distributed in the eastern and southern areas such as Linxiang and Cangyuan. The western and northern such as Fengqing and Yongde had fewer wilderness sources. There were 63 wilderness corridors in the wilderness network, including 16 important corridors and 47 general corridors. There were 186 strategic points in the wilderness network, including 53 wilderness nodes and 133 barrier points. We constructed the wilderness network of Lincang based in the identified wilderness source areas and extracted wilderness corridors, which had the advantages of high stability, strong resistance to interference, efficient connectivity. Finally, we proposed the "three-zone as a whole" protection strategy and ecological planning suggestions, which had referential value for establishing an ecological security pattern in Lincang City and the practicalization of wilderness protection in China.}, }
@article {pmid40371522, year = {2025}, author = {Dong, WZ and Su, WC and Gou, R and Zhou, HY and Liu, DY}, title = {[Spatial and temporal evolution of ecological risk in Guizhou Province, China from the perspective of ecosystem services and ecosystem health].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {36}, number = {4}, pages = {1211-1221}, doi = {10.13287/j.1001-9332.202504.021}, pmid = {40371522}, issn = {1001-9332}, mesh = {China ; *Ecosystem ; *Conservation of Natural Resources ; Risk Assessment ; Rivers ; Spatio-Temporal Analysis ; Geographic Information Systems ; *Environmental Monitoring/methods ; Ecology ; Models, Theoretical ; }, abstract = {Guizhou Province is an important ecological barrier in the upper reaches of the Yangtze River and the Pearl River. Karst landform in Guizhou is developed, with fragile ecological background. The ecological risk assessment and control of Karst landform are of great significance to ecological security and sustainable development of southwest China and the upper reaches of those two rivers. Based on the InVEST model and vigor-organization-resi-lience model, we quantitatively evaluated the ecosystem services and ecosystem health and constructed the ecological risk assessment model of Guizhou Province. With the help of GIS technology, spatial autocorrelation analysis method and gravity center migration model, we analyzed the spatial and temporal variations of ecological risk in Guizhou Province from 2000 to 2020. The results showed that ecosystem services in Guizhou Province increased from 2000 to 2020, with an annual average growth rate of 0.3%. The ecosystem health status was generally well and showed a good trend, and the annual average growth rate of ecosystem health was 12.6%. The ecological risk was dominated by medium ecological risk. The proportion of extremely low ecological risk area and low ecological risk area increased, the proportion of medium and above ecological risk area decreased, and the overall ecological risk showed a downward trend. The low ecological risk areas were mainly located in the south and southeast of Guizhou Province, while the high ecological risk areas were distributed in the central, western and northern parts of Guizhou Province. The global Moran's I of ecological risk in 2000, 2005, 2010, 2015, and 2020 were 0.856, 0.836, 0.844, 0.804, and 0.768, respectively, indicating that the positive correlation of ecological risk in spatial distribution, but the spatial correlation and spatial agglomeration characteristics were weakened. During the study period, the centroid and trajectory of ecological risk in Guizhou Province were consistent with the distribution area of its corresponding ecological risk. From 2000 to 2020, the spatial distribution pattern of ecological risk in Guizhou Pro-vince was relatively stable. With the evolution of time, the dispersion of spatial distribution of extremely high ecological risk and low ecological risk increased. Ecological risk assessment based on ecosystem services and ecosystem health would provide scientific basis for regional ecological risk management and control.}, }
@article {pmid40369670, year = {2025}, author = {Wu, B and Luo, D and Yue, Y and Yan, H and He, M and Ma, X and Zhao, B and Xu, B and Zhu, J and Wang, J and Jia, J and Sun, M and Xie, Z and Wang, X and Huang, L}, title = {New insights into the cold tolerance of upland switchgrass by integrating a haplotype-resolved genome and multi-omics analysis.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {128}, pmid = {40369670}, issn = {1474-760X}, support = {2021YFYZ0013//Sichuan Province Research Grant/ ; SCCXTD-2020-16//Modern Agricultural Industry System Sichuan Forage Innovation Team/ ; 32071867//National Natural Science Foundation of China/ ; }, mesh = {*Panicum/genetics/physiology ; *Haplotypes ; *Genome, Plant ; *Cold-Shock Response/genetics ; Ecotype ; Gene Expression Regulation, Plant ; Genome-Wide Association Study ; Cold Temperature ; Gene Expression Profiling ; Plant Proteins/genetics/metabolism ; Transcriptome ; Multiomics ; }, abstract = {BACKGROUND: Switchgrass (Panicum virgatum L.) is a bioenergy and forage crop. Upland switchgrass exhibits superior cold tolerance compared to the lowland ecotype, but the underlying molecular mechanisms remain unclear.<br><br>RESULTS: Here, we present a high-quality haplotype-resolved genome of the upland ecotype "Jingji31." We then conduct multi-omics analysis to explore the mechanism underlying its cold tolerance. By comparative transcriptome analysis of the upland and lowland ecotypes, we identify many genes with ecotype-specific differential expression, particularly members of the cold-responsive (COR) gene family, under cold stress. Notably, AFB1, ATL80, HOS10, and STRS2 gene families show opposite expression changes between the two ecotypes. Based on the haplotype-resolved genome of "Jingji31," we detect more cold-induced allele-specific expression genes in the upland ecotype than in the lowland ecotype, and these genes are significantly enriched in the COR gene family. By genome-wide association study, we detect an association signal related to the overwintering rate, which overlaps with a selective sweep region containing a cytochrome P450 gene highly expressed under cold stress. Heterologous overexpression of this gene in rice alleviates leaf chlorosis and wilting under cold stress. We also verify that expression of this gene is suppressed by a structural variation in the promoter region.<br><br>CONCLUSIONS: Based on the high-quality haplotype-resolved genome and multi-omics analysis of upland switchgrass, we characterize candidate genes responsible for cold tolerance. This study advances our understanding of plant cold tolerance, which provides crop breeding for improved cold tolerance.}, }
@article {pmid40369175, year = {2025}, author = {Barroux, M and Househam, J and Lakatos, E and Ronel, T and Baker, AM and Salié, H and Mossner, M and Smith, K and Kimberley, C and Nowinski, S and Berner, A and Gunasri, V and Borgmann, M and Liffers, S and Jansen, M and Caravagna, G and Steiger, K and Slotta-Huspenina, J and Weichert, W and Zapata, L and Giota, E and Lorenzen, S and Alberstmeier, M and Chain, B and Friess, H and Bengsch, B and Schmid, RM and Siveke, JT and Quante, M and Graham, TA}, title = {Evolutionary and immune microenvironment dynamics during neoadjuvant treatment of esophageal adenocarcinoma.}, journal = {Nature cancer}, volume = {6}, number = {5}, pages = {820-837}, pmid = {40369175}, issn = {2662-1347}, support = {U54 CA217376/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Esophageal Neoplasms/immunology/genetics/therapy/pathology/drug therapy ; *Tumor Microenvironment/immunology/genetics/drug effects ; *Adenocarcinoma/immunology/genetics/therapy/pathology/drug therapy ; Neoadjuvant Therapy ; Male ; Female ; Middle Aged ; Aged ; Transcriptome ; }, abstract = {Locally advanced esophageal adenocarcinoma remains difficult to treat and the ecological and evolutionary dynamics responsible for resistance and recurrence are incompletely understood. Here, we performed longitudinal multiomic analysis of patients with esophageal adenocarcinoma in the MEMORI trial. Multi-region multi-timepoint whole-exome and paired transcriptome sequencing was performed on 27 patients before, during and after neoadjuvant treatment. We found major transcriptomic changes during treatment with upregulation of immune, stromal and oncogenic pathways. Genetic data revealed that clonal sweeps through treatment were rare. Imaging mass cytometry and T cell receptor sequencing revealed remodeling of the tumor microenvironment during treatment. The presence of genetic immune escape, a less-cytotoxic T cell phenotype and a lack of clonal T cell expansions were linked to poor treatment response. In summary, there were widespread transcriptional and environmental changes through treatment, with limited clonal replacement, suggestive of phenotypic plasticity.}, }
@article {pmid40368894, year = {2025}, author = {Yi, S and Li, X and Liu, Y and Dong, X and Tu, W}, title = {A sub-meter resolution urban surface albedo dataset for 34 U.S. cities based on deep learning.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {789}, pmid = {40368894}, issn = {2052-4463}, support = {2314709//National Science Foundation (NSF)/ ; }, abstract = {Surface albedo is a key determinant of urban heat islands, which modulates the amount of solar energy absorbed or reflected by urban surfaces, influencing microclimate and thermal comfort. However, high-resolution albedo is usually not available, which makes the understanding of the urban thermal environment at hyperlocal difficult. This study presents the first high-resolution urban albedo maps for 34 major U.S. cities using advanced deep learning models and multisource remote sensing data. By differentiating between impervious and pervious surfaces using a combination of NAIP imagery, roof albedo data, building footprints, land cover classifications, and Sentinel-2 imagery, this work achieves sub-meter resolution in albedo mapping. Employing U-Net for impervious surface classification along with impervious (ISA) and pervious surface albedo (PSA) prediction, these models were validated in selected cities, with ISA showing an R[2] of 0.9028 and MAE of 0.0057, and PSA demonstrating an R[2] of 0.9538 and MAE of 0.0027, highlighting the precision and reliability. The datasets, made publicly available, offer essential insights for urban planning and environmental monitoring.}, }
@article {pmid40367572, year = {2025}, author = {Wang, H and Li, L and Wu, J and Yuan, X and Hong, L and Pu, L and Qin, S and Li, L and Yang, H and Zhang, J}, title = {Multi-omics analyses reveal differences in intestinal flora composition and serum metabolites in Cherry Valley broiler ducks of different body weights.}, journal = {Poultry science}, volume = {104}, number = {8}, pages = {105275}, pmid = {40367572}, issn = {1525-3171}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Ducks/microbiology/blood/physiology/growth &amp; development ; *Body Weight ; RNA, Ribosomal, 16S/analysis ; Metabolomics ; *Metabolome ; Male ; Bacteria/classification/isolation &amp; purification ; Multiomics ; }, abstract = {Fledgling broiler ducks vary in body weight and growth rate. The aim of this study was to investigate the relationship between serum metabolites and the intestinal microbiota in Cherry Valley broiler ducks with different finishing weights and to reveal differences in their metabolic regulation and microbial composition. Serum and cecum content samples were collected from Cherry Valley broiler ducks of different finishing weights. Metabolites were identified and compared using untargeted metabolomics, 16S rRNA gene sequencing, multivariate statistics and bioinformatics. Six key findings emerged. First, serum biochemical parameters showed that AST and ALT levels were significantly lower in the high weight group (Group H) than in the low weight group (Group L), and serum immunoglobulin IgG levels were significantly higher in group H. Second, the chorionic height to crypt depth ratio of the duodenum was significantly higher in group H than in group L. Third, the gut microbial community diversity or abundance was lower in broiler ducks in group L. Fourth, LEfSe analysis showed that the biomarker for group L was Streptococcus, whereas for group H it was Faecalibacterium. Fifth, a total of 127 differential metabolites were identified (49 up-regulated and 78 down-regulated). Finally, Spearman's correlation analysis showed that Spearman's correlation analyses showed that the Lipid-related serum metabolites were higher in low-body recombinant broiler ducks, mainly Lathosterol, Cholesterol, Cynaratriol and Leukotriene B4. In addition to lipid-associated serum metabolites in high-body recombination, The water-soluble vitamin-like metabolite Pantothenate and the antibiotic-like metabolite Tylosin were high. The cecum microbiota is strongly associated with metabolites, especially Faecalibacterium, unclassified Tannerellaceae, Subdoligranulum, Alistipes, and [Ruminococcus] torques_group, with which it exhibits strong Correlation. Broiler ducks with higher body weights have a better intestinal villous structure, enhanced digestion and absorption, higher levels of immunoglobulin secretion and superior growth performance. Broiler ducks with different body weights differed in plasma metabolites and cecum flora. Spearman's correlation analyses showed that the Correlation between differential metabolites and differential gut microbial genera.}, }
@article {pmid40365044, year = {2025}, author = {Ogba, P and Baumann, A and Alabi, T and Archer, N and Eniojukan, J and Ibhawoh, B and DiLiberto, DD}, title = {Enhancing IPTp-SP uptake: Community and stakeholder recommendations for improving access and utilisation - insights from a study in Bayelsa-Nigeria.}, journal = {MalariaWorld journal}, volume = {16}, number = {}, pages = {9}, pmid = {40365044}, issn = {2214-4374}, abstract = {BACKGROUND: Malaria remains a major global health challenge, disproportionately affecting pregnant women and children. In Nigeria, malaria in pregnancy contributes to 70.5% of maternal morbidity and 41.1% of maternal mortality. Recognising these risks, the World Health Organization recommends intermittent preventive treatment with sulfadoxine-pyrimethamine (IPTp-SP) as a key strategy for malaria in pregnancy prevention. However, despite its proven effectiveness, pregnant women's uptake of IPTp-SP remains unacceptably low. This study presents participant-driven recommendations to enhance IPTp-SP uptake, structured within the socio-ecological framework.<br><br>MATERIALS AND METHODS: This study employed an exploratory descriptive qualitative approach to examine the community-level contextual factors influencing IPTp-SP uptake. Data were collected from 53 participants in two communities in Bayelsa, Nigeria. Individual interviews were conducted with 17 key stakeholders (spouses, mothers-in-law, religious leaders, community leaders, and traditional birth attendants) and 6 focus group discussions with 36 pregnant women. Data management and coding were conducted using NVivo 14 QSR International software, following an inductive-deductive thematic analysis approach.<br><br>RESULTS: Participants proposed multi-level interventions to address barriers to IPTp-SP uptake at the individual, interpersonal, community, and healthcare system levels. Key recommendations include: Community-wide education campaigns to raise awareness of IPTp-SP's benefits; comprehensive training for healthcare providers to enhance their knowledge and prescription of IPTp-SP; integration of traditional birth attendants into the formal healthcare system; community-level distribution of IPTp-SP to improve access for pregnant women who do not attend antenatal care; government intervention to ensure the functionality of health centers; addressing workforce shortages, and guaranteeing a consistent supply of IPTp-SP.<br><br>CONCLUSION: These evidence-based, participant-driven recommendations offer a holistic and scalable strategy to improve pregnant women's uptake of IPTp-SP in Nigeria and other malaria-endemic regions. Implementing these recommendations can strengthen malaria prevention efforts, improve maternal and child health outcomes, and support broader public health initiatives.}, }
@article {pmid40361718, year = {2025}, author = {Nițescu, M and Nedelescu, MM and Moroşan, E and Simionescu, AA and Furtunescu, FL and Ştefănescu, BE and Tusaliu, M and Panaitescu, E and Stanciu, AM and Stoian, IM}, title = {Assessment of Food Safety Knowledge and Practices Among Medical Students.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {9}, pages = {}, pmid = {40361718}, issn = {2304-8158}, abstract = {Food safety is an important requirement for protecting human health worldwide. In particular, medical students' education on food safety is essential for them as future physicians, and university education is the first step in acquiring this knowledge. We performed an online survey with 1277 respondents among medical students to assess knowledge, attitudes, and practices (KAPs) related to food safety regarding microbiological contamination. Our findings showed that more than half of the respondents presented a low level of food safety knowledge, with a score between 11-60 points, and only 6% managed to score between 81 and 100 points, which was considered a high level of knowledge. On the contrary, we found that most participants had a high level of good practice: 58% scored more than 25 points, 39% had an average level of good practice (scoring between 21 and 25 points), and 3% of respondents had a low level of good practice (scoring below 21 points). We also noticed a statistically significant difference between total scores of preclinical and clinical years of study among medical students (p = 0.005) regarding food safety knowledge. The frequency of cooking was positively correlated with the level of food safety knowledge, but not with food safety practices. Our study shows that better knowledge on food safety is needed among medical students. Improving knowledge and awareness of food safety in relation to microbiological contamination is a good way to protect themselves and to promote the correct food safety knowledge and measures among their patients.}, }
@article {pmid40361012, year = {2025}, author = {Barkan, R and Cooke, I and Watson, SA and Strugnell, JM}, title = {Synthesis of transcriptomic studies reveals a core response to heat stress in abalone (genus Haliotis).}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {474}, pmid = {40361012}, issn = {1471-2164}, mesh = {Animals ; *Gastropoda/genetics/physiology ; *Heat-Shock Response/genetics ; *Gene Expression Profiling ; *Transcriptome ; Computational Biology/methods ; }, abstract = {BACKGROUND: As climate change causes marine heat waves to become more intense and frequent, marine species increasingly suffer from heat stress. This stress can result in reduced growth, disrupted breeding cycles, vulnerability to diseases and pathogens, and increased mortality rates. Abalone (genus Haliotis) are an ecologically significant group of marine gastropods and are among the most highly valued seafood products. However, heat stress events have had devastating impacts on both farmed and wild populations. Members of this genus are among the most susceptible marine species to climate change impacts, with over 40% of all abalone species listed as threatened with extinction. This has motivated researchers to explore the genetics linked to heat stress in abalone. A substantial portion of publicly available studies has employed transcriptomic approaches to investigate abalone genetic response to heat stress. However, to date, no meta-analysis has been conducted to determine the common response to heat stress (i.e. the core response) across the genus. This study uses a standardized bioinformatic pipeline to reanalyze and compare publicly available RNA-seq datasets from different heat stress studies on abalone.<br><br>RESULTS: Nine publicly available RNA-seq datasets from nine different heat-stress studies on abalone from seven different abalone species and three hybrids were included in the meta-analysis. We identified a core set of 74 differentially expressed genes (DEGs) in response to heat stress in at least seven out of nine studies. This core set of DEGs mainly included genes associated with alternative splicing, heat shock proteins (HSPs), Ubiquitin-Proteasome System (UPS), and other protein folding and protein processing pathways.<br><br>CONCLUSIONS: The detection of a consistent set of genes that respond to heat stress across various studies, despite differences in experimental design (e.g. stress intensity, species studied-geographical distribution, preferred temperature range, etc.), strengthens our proposal that these genes are key elements of the heat stress response in abalone. The identification of the core response to heat stress in abalone lays an important foundation for future research. Ultimately, this study will aid conservation efforts and aquaculture through the identification of resilient populations, genetic-based breeding programs, possible manipulations such as early exposure to stress, gene editing and the use of immunostimulants to enhance thermal tolerance.}, }
@article {pmid40359589, year = {2025}, author = {Silva, MKP and Nicoleti, VYU and Rodrigues, BDPP and Araujo, ASF and Ellwanger, JH and de Almeida, JM and Lemos, LN}, title = {Exploring deep learning in phage discovery and characterization.}, journal = {Virology}, volume = {609}, number = {}, pages = {110559}, doi = {10.1016/j.virol.2025.110559}, pmid = {40359589}, issn = {1096-0341}, mesh = {*Deep Learning ; *Bacteriophages/genetics/isolation &amp; purification/classification ; Metagenomics/methods ; Computational Biology/methods ; Genome, Viral ; Neural Networks, Computer ; Metagenome ; Algorithms ; }, abstract = {Bacteriophages, or bacterial viruses, play diverse ecological roles by shaping bacterial populations and also hold significant biotechnological and medical potential, including the treatment of infections caused by multidrug-resistant bacteria. The discovery of novel bacteriophages using large-scale metagenomic data has been accelerated by the accessibility of deep learning (Artificial Intelligence), the increased computing power of graphical processing units (GPUs), and new bioinformatics tools. This review addresses the recent revolution in bacteriophage research, ranging from the adoption of neural network algorithms applied to metagenomic data to the use of pre-trained language models, such as BERT, which have improved the reconstruction of viral metagenome-assembled genomes (vMAGs). This article also discusses the main aspects of bacteriophage biology using deep learning, highlighting the advances and limitations of this approach. Finally, prospects of deep-learning-based metagenomic algorithms and recommendations for future investigations are described.}, }
@article {pmid40357641, year = {2025}, author = {Pourmohsenin, B and Wiese, A and Ziemert, N}, title = {AutoMLST2: a web server for phylogeny and microbial taxonomy.}, journal = {Nucleic acids research}, volume = {53}, number = {W1}, pages = {W45-W50}, pmid = {40357641}, issn = {1362-4962}, support = {101000794//H2020-FNR-11-2020: SECRETED/ ; TTU09.717//German Center for Infection Research/ ; 390838134//Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection/ ; }, mesh = {*Phylogeny ; *Software ; Internet ; *Archaea/genetics/classification ; *Bacteria/genetics/classification ; Genome, Bacterial ; Genome, Archaeal ; Databases, Genetic ; }, abstract = {Accurate and accessible phylogenetic analysis is essential for understanding microbial taxonomy and evolution, which are integral to microbiology, ecology, and drug discovery, yet it remains a challenging task. AutoMLST2 (https://automlst2.ziemertlab.com) is a web server designed to facilitate automated phylogenetic reconstruction and microbial taxonomy analysis for bacterial and archaeal genomes. It builds on the foundation of AutoMLST, which remains widely used due to its user-friendly interface compared to similar tools. Given its continued popularity and utility, we have enhanced AutoMLST to leverage newer reference databases and computational tools. AutoMLST2 integrates the Genome Taxonomy Database, extends support to archaeal genomes, and improves analytical flexibility. Key improvements include more customizable processing modes, containerization to prevent queue accumulations, and parallel computing for large-scale studies. By incorporating up-to-date databases and workflows, AutoMLST2 continues to provide an accessible and efficient platform for researchers in microbiology, evolutionary ecology, and natural product discovery.}, }
@article {pmid40352255, year = {2025}, author = {Seminar, KB and Damayanthi, E and Priandana, K and Imantho, H and Ligar, BW and Seminar, AU and Krishnajaya, AD and Aditya, MR and Suherman, MIH and Fillah, IF}, title = {AI-based system for food and beverage selection towards precision nutrition in Indonesian restaurants.}, journal = {Frontiers in nutrition}, volume = {12}, number = {}, pages = {1590523}, pmid = {40352255}, issn = {2296-861X}, abstract = {The complexity surrounding food selection is attributable to the variability in foods, restaurants, and diners. The diversity of foods, where each dish may have a unique recipe across different restaurants, needs to be accounted for in personalized nutrition. However, personalized food selection poses a combinatorial challenge in selecting the most suitable food at a specific restaurant. The key question is how a diner visiting a particular restaurant can be assisted in selecting optimal foods and beverages based on factors such as sex, age, height, weight, and history of non-communicable diseases (NCDs). In this study, a genetic algorithm (GA) is used to develop a system that can address this issue in the context of Indonesian restaurants. In this system, a database with data on registered diners and foods is maintained. Foods comprise staple foods, side dishes, vegetables, and beverages, each containing its energy and nutrient content for a given restaurant. The nutritional adequacy of a single meal is determined by comparing the energy and nutrient content of the menu with the diner's nutritional needs. The novelty of the proposed system lies in combining scientific nutritional data with individual diner profiles for the selection of the best meal for a diner. This system differs from the existing food recommender applications in Indonesia, which typically do not consider specific diners, personalized nutrition, and NCD history. The proposed system is the first developed application prototype for Indonesian restaurants to overcome the inefficiency of the existing applications. In this study, the structure and chromosome content of the food, its corresponding energy and nutrient contents, and GA operators such as crossover, mutation, and tournament selection for determining the best meal using the defined fitness functions are discussed. The proposed system has been tested at Karimata Restaurant and proved to be highly suitable for the ultimate goal of meal selection for individual diners with different needs, and it can be replicated at other restaurants. Furthermore, user-centered evaluation has revealed that the system (a) increases nutritional understanding and health awareness; (b) is easy to use with comprehensive functions; and (c) promotes user satisfaction with personalized recommendations.}, }
@article {pmid40351335, year = {2024}, author = {Li, S and Fan, C and Kargarandehkordi, A and Sun, Y and Slade, C and Jaiswal, A and Benzo, RM and Phillips, KT and Washington, P}, title = {Monitoring Substance Use with Fitbit Biosignals: A Case Study on Training Deep Learning Models Using Ecological Momentary Assessments and Passive Sensing.}, journal = {AI (Basel, Switzerland)}, volume = {5}, number = {4}, pages = {2725-2738}, pmid = {40351335}, issn = {2673-2688}, support = {U54 GM138062/GM/NIGMS NIH HHS/United States ; }, abstract = {Substance use disorders affect 17.3% of Americans. Digital health solutions that use machine learning to detect substance use from wearable biosignal data can eventually pave the way for real-time digital interventions. However, difficulties in addressing severe between-subject data heterogeneity have hampered the adaptation of machine learning approaches for substance use detection, necessitating more robust technological solutions. We tested the utility of personalized machine learning using participant-specific convolutional neural networks (CNNs) enhanced with self-supervised learning (SSL) to detect drug use. In a pilot feasibility study, we collected data from 9 participants using Fitbit Charge 5 devices, supplemented by ecological momentary assessments to collect real-time labels of substance use. We implemented a baseline 1D-CNN model with traditional supervised learning and an experimental SSL-enhanced model to improve individualized feature extraction under limited label conditions. Results: Among the 9 participants, we achieved an average area under the receiver operating characteristic curve score across participants of 0.695 for the supervised CNNs and 0.729 for the SSL models. Strategic selection of an optimal threshold enabled us to optimize either sensitivity or specificity while maintaining reasonable performance for the other metric. Conclusion: These findings suggest that Fitbit data have the potential to enhance substance use monitoring systems. However, the small sample size in this study limits its generalizability to diverse populations, so we call for future research that explores SSL-powered personalization at a larger scale.}, }
@article {pmid40348945, year = {2025}, author = {Chen, J and Liu, J and Liu, S and Li, Z and Gao, C and Wang, Z and Huang, S and Jiang, Z and Yang, H}, title = {Multiomics reveals the synergistic response of gut microbiota and spider A. ventricosus to lead and cadmium toxicity.}, journal = {Bulletin of environmental contamination and toxicology}, volume = {114}, number = {5}, pages = {77}, pmid = {40348945}, issn = {1432-0800}, support = {32001205//National Natural Science Foundation of China/ ; 2023JJ30299//Natural Science Foundation of Hunan Province/ ; 2019JJ50236//Natural Science Foundation of Hunan Province/ ; }, mesh = {Animals ; *Cadmium/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Lead/toxicity ; *Spiders/physiology/drug effects ; Metagenomics ; Multiomics ; }, abstract = {The potential crosstalk between the host and gut microbiota (GM) under heavy metal compound pollution remains unexplored. Herein, using comprehensive analysis of metagenomics, metabolomics, behavioral analysis, and cell morphology to investigate the causal relationship between GM and host responses to cadmium (Cd) and lead (Pb) toxicities. Results indicate that Pb and Cd pollution, alone or together, hinder spider predatory behavior and change the composition and function of GM. Combined exposure reduces protein and exogenous compound metabolism, while single exposure affects energy and lipid metabolism. Gut microbiota helps spider antioxidant activity by increasing glutathione, lipoic acid, and L-cysteine. Oxidative damage, increased Enterobacteriaceae (Salmonella), and lipopolysaccharide (LPS) may harm the midgut barrier. Upregulation of choline and acetylcholine, and downregulation of spermidine, may initiate neurotoxicity. Inhibiting actinomycetes might boost sodium gallate for detoxifying single contaminants. Combined pollution detoxification may involve downregulation of indole synthesis metabolic bacteria, tryptophan, indole metabolites, cytochrome P450 (CYP450), and an increase in Desulfobulbia could remove heavy metals and reduce oxidative stress. Combined pollution has a synergistic effect, making the toxicity of multiple pollutants greater than their individual effects, impacting metal resistance genes (MRGs), and antibiotic resistance ontology (AROs) which used for classifying and describing antibiotic resistance, midgut barrier integrity, oxidative stress, and detoxification. The results help to elucidate the interplay of GM and host's reactions, and aid in monitoring and bioremediation of heavy metal pollution.}, }
@article {pmid40346497, year = {2025}, author = {Sigwart, JD and Wong, NLWS and González, VL and Machado, FM and Greve, C and Schell, T and Chen, Z}, title = {Genome of the enigmatic watering-pot shell and morphological adaptations for anchoring in sediment.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {460}, pmid = {40346497}, issn = {1471-2164}, mesh = {Animals ; *Bivalvia/genetics/anatomy &amp; histology/classification ; Phylogeny ; *Genome ; *Animal Shells/anatomy &amp; histology ; *Geologic Sediments ; *Adaptation, Physiological/genetics ; *Genomics/methods ; }, abstract = {BACKGROUND: In this study, we present the first chromosome-scale genome of Verpa penis (Linnaeus, 1758), and the first for the bivalve clade Anomalodesmata. The present study has two separate foci. Primarily, we provide the genetic resource to bridge further studies from genome to phenome and propose hypotheses to guide future empirical investigations. Secondarily, based on morphology, we outline a conceptual exploration to address their adaptation. Watering-pot shells have been called "the weirdest bivalves" for their fused tubular shell resembling the spout of a watering can. This adventitious tube arose twice convergently in clavagelloidean bivalves. However, previous literature has never provided a convincing adaptive pathway.<br><br>RESULTS: The genome assembly of V. penis was about 507&#xa0;Mb, with contig N50 of 5.33&#xa0;Mb, and has 96.5% of sequences anchored onto 19 pseudochromosomes. Phylogenomic analyses of this new genome in context of other bivalves confirms the placement for Anomalodesmata as sister to the clade Imparidentia. Contrary to expectations from its highly modified body plan, there is no evidence of chromosome reduction compared to the ancestral karyotype of heterodont bivalves (1&#xa0;N&#x2009;=&#x2009;19). Drawing on established principles from engineering as well as morphology, the thought experiment about the adventitious tube seeks to extend current understanding by exploring parallels with other built structures. A new hypothesis explains one possible interpretation of the adaptive significance of this body form: it is potentially structurally optimised for vertical stability in relatively soft sediments, with parallels to the engineering principles of a suction anchor.<br><br>CONCLUSIONS: While the conclusions presented here on morphological interpretations are theoretical, this serves as a foundation for further empirical validation and refinement. Our study offers new insights to a long-standing mystery in molluscan body forms and provides genomic resources that are relevant to understanding molluscan evolution, biomineralisation, and biomimetic design.}, }
@article {pmid40346072, year = {2025}, author = {Bosso, L and Saviano, S and Abagnale, M and Bellardini, D and Bolinesi, F and Botte, V and Buondonno, A and Carotenuto, Y and Casotti, R and Chiusano, ML and Cipolletta, F and Conversano, F and De Domenico, F and Del Gaizo, G and Donnarumma, V and Furia, M and Iudicone, D and Kokoszka, F and Laface, F and Licandro, P and Mangoni, O and Margiotta, F and Mazzocchi, MG and Miralto, M and Montresor, M and Pansera, M and Pedà, C and Percopo, I and Raffini, F and Russo, L and Romeo, T and Saggiomo, M and Sarno, D and Trano, AC and Vannini, J and Vargiu, M and Zampicinini, G and Zingone, A and Cianelli, D and D'Alelio, D}, title = {GIS-based integration of marine data for assessment and management of a highly anthropized coastal area.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {16200}, pmid = {40346072}, issn = {2045-2322}, mesh = {Italy ; *Geographic Information Systems ; *Environmental Monitoring/methods ; Ecosystem ; Humans ; *Conservation of Natural Resources ; Oceans and Seas ; Animals ; Food Chain ; }, abstract = {Monitoring coastal marine environments by evaluating and comparing their chemical, physical, biological, and anthropogenic components is essential for ecological assessment and socio-economic development. In this study, we conducted an integrated multivariate analysis to assess the descriptors of the Marine Strategy Framework Directive at a regional scale in the Tyrrhenian Sea (Italy), with a specific focus on the densely populated coastal zone of the Campania region. Physical, chemical, and biological data were collected and analyzed in 22 sampling sites during three oceanographic surveys in the Gulf of Gaeta (GoG), Naples (GoN), and Salerno (GoS) in autumn 2020. Our results indicated that these three gulfs were distinct overall, with GoN being more divergent and heterogeneous than GoG and GoS. The marine area studied in the GoN had more favorable hydrographic and trophic conditions and food web characteristics, except for the mesozooplankton biomass, and was closer to socio-economic factors compared to the GoS and GoG. Our analysis helped us find the key ecological features that define different sub-regions and connect them to social and economic factors, including human activities. We highlighted the relevance of primary and secondary variables in terms of the comprehensive ecological assessment of a marine area and its impact on specific socio-economic activities. These findings support the need to describe and integrate multiple descriptors at the spatial scale.}, }
@article {pmid40345178, year = {2025}, author = {O'Callaghan, ME and Casey, M and Pearl, D and Hickey, O and Fosse, A and Sigurðsson, SE and Savage, DW and Vehviläinen-Julkunen, K and Bykachev, K and Parviainen, A and Parker, H and Condell, J and Leavey, G and Hart, N and Weihe, P and Petersen, MS and Glynn, L}, title = {COVID-19 open data: An ecological study and international collaboration examining pandemic trends in Northern Periphery arctic countries.}, journal = {Health informatics journal}, volume = {31}, number = {2}, pages = {14604582251315588}, doi = {10.1177/14604582251315588}, pmid = {40345178}, issn = {1741-2811}, mesh = {*International Cooperation ; Humans ; *COVID-19/epidemiology ; Arctic Regions/epidemiology ; *Pandemics/statistics &amp; numerical data ; SARS-CoV-2 ; *Public Health/trends ; }, abstract = {Objectives: In the early stages of the COVID-19 pandemic, evidence generation lagged behind public health responses. This study describes an international collaboration of frontline clinicians who used open data describing COVID-19 trends to generate "practice-based evidence". Methods: Open data resources from nine Northern Periphery and Arctic (NPA) countries were harnessed using the open-source programming language 'R' and our collaborations analyses and insights were published on a public-facing website. The website's visualisations guided teleconference discussions from September 2020 to March 2021, focusing on contextualizing national responses, especially in rural regions. Results: This project facilitated shared learning from COVID-19 trends and highlighted key aspects of national responses. Notably, rural NPA regions experienced less COVID-19 cases and mortality in the first year of the pandemic. Conclusion: This international collaborative effort, driven by open data analysis, provided a platform to share real-world insights. The study offers a potential template for future pandemics and emphasises the importance of sustaining open data resources, including granular data like excess mortality, for effective pandemic learning.}, }
@article {pmid40344895, year = {2025}, author = {Kičić, M and Scheuer, S and Korpilo, S and Vuletić, D and Seletković, A and Haase, D and Krajter Ostoić, S}, title = {Relationships between urban green space types, cultural ecosystem services and disservices - a Public Participation Geographic Information System study in Zagreb, Croatia.}, journal = {The Science of the total environment}, volume = {981}, number = {}, pages = {179549}, doi = {10.1016/j.scitotenv.2025.179549}, pmid = {40344895}, issn = {1879-1026}, mesh = {Croatia ; *Geographic Information Systems ; Cities ; *Ecosystem ; *Conservation of Natural Resources/methods ; *Community Participation ; Humans ; *Parks, Recreational ; }, abstract = {Urban green spaces are important providers of ecosystem services in cities, however cultural ecosystem services remain difficult to quantify. Different types of urban green spaces provide various cultural ecosystem services and differ in how they are perceived and utilized by citizens. In this study, we used a Public Participation GIS (PPGIS) survey to collect data on citizens' perceptions and use of cultural ecosystem services and disservices provided by different types of urban green spaces in Zagreb, Croatia. We collected spatial data from 384 respondents on the perceived provision of 19 different attributes of cultural ecosystem services and disservices in 20 defined types of urban green spaces. We used descriptive statistics, spatial metrics, multivariate analysis and visualization techniques to explore and explain 5757 spatial points collected with the PPGIS questionnaire. Results confirm the importance of parks and forests but also that the water elements and greenery around residential buildings serve as important urban green space for providing benefits for citizens of Zagreb. Based on results presented, cultural ecosystem services are perceived as more important than disservices but in some places both co-exist. Our study builds on current literature by providing a systematic, city-wide assessment of cultural ecosystem services related to different types of urban green spaces, while advancing the availability of methods for their quantification.}, }
@article {pmid40344217, year = {2025}, author = {Schindler, Z and Larysch, E and Fornoff, F and Kröner, K and Obladen, N and Klein, AM and Seifert, T and Vonderach, C and Morhart, C}, title = {Flower power: Modeling floral resources of wild cherry (Prunus avium L.) for bee pollinators based on 3D data.}, journal = {Ecology}, volume = {106}, number = {5}, pages = {e70103}, pmid = {40344217}, issn = {1939-9170}, support = {2819NA071//Bundesministerium f&#xfc;r Ern&#xe4;hrung und Landwirtschaft/ ; }, mesh = {*Pollination/physiology ; *Flowers/physiology ; Animals ; Bees/physiology ; *Models, Biological ; *Prunus avium/physiology ; }, abstract = {Pollinator declines pose a threat to ecosystems and food production. Agriculture contributes to, but also suffers from, the erosion of pollination services. Our study explores the potential of trees in agricultural landscapes to support pollinators by providing floral resources. Our overarching objective is the quantification of floral resources produced by wild cherry (Prunus avium L.) that can be used by flower-visiting and pollinating insects such as bees. Using an innovative approach, we combine pollen measurements with manual counts of flowers on branches and 3D data derived from terrestrial laser scanning. This approach allows us to scale up flower numbers from branches to entire trees. The derived models for estimating the probability of flower occurrence (R[2] c = 0.52, R[2] m = 0.50) and the number of flowers per branch (R[2] c = 0.88, R[2] m = 0.84), as well as the number of flowers per tree (R[2] = 0.83), show good model fits with only a small set of predictors. The model fits indicate that, at the branch level, predicting flowering probability is more challenging than predicting flower abundance. We found differences in the number of flowers per branch in different crown sections, suggesting that floral resources are heterogeneously distributed. Furthermore, we demonstrate that the number of flowers per tree increases exponentially with tree dimension (stem diameter, crown volume). Therefore, large trees provide disproportionately more floral resources than small trees and are particularly worthy of conservation efforts. For example, our models estimate that a single tree with a stem diameter of 25 cm carries 195,535 flowers (95% CI: 159,991-237,318), thus providing about 57 cm[3] (95% CI: 32-88 cm[3]) of pollen and producing 170 g (95% CI: 48-345 g) nectar sugar per 24 h. This amount of pollen is sufficient to rear, for example, 5202 larvae (95% CI: 2886-8022) of Lasioglossum laticeps, a common and generalist sweat bee of cherry trees. In contrast, a smaller tree with a stem diameter of 10 cm provides only 8% of these resources. In conclusion, we demonstrate how our results contribute to the broader single-large-or-several-small debate in nature conservation by highlighting the value of large trees. Additionally, we show how information gathered at the branch level may be nondestructively upscaled to entire trees.}, }
@article {pmid40344154, year = {2025}, author = {Babič, J and Kunavar, T and Oztop, E and Kawato, M}, title = {Success-efficient/failure-safe strategy for hierarchical reinforcement motor learning.}, journal = {PLoS computational biology}, volume = {21}, number = {5}, pages = {e1013089}, pmid = {40344154}, issn = {1553-7358}, mesh = {Humans ; *Reinforcement, Psychology ; *Learning/physiology ; Male ; Female ; Computational Biology ; Movement/physiology ; Adult ; Young Adult ; Psychomotor Performance/physiology ; Motor Skills/physiology ; }, abstract = {Our study explores how ecological aspects of motor learning enhance survival by improving movement efficiency and mitigating injury risks during task failures. Traditional motor control theories mainly address isolated body movements and often overlook these ecological factors. We introduce a novel computational motor control approach, incorporating ecological fitness and a strategy that alternates between success-driven movement efficiency and failure-driven safety, akin to win-stay/lose-shift tactics. In our experiments, participants performed squat-to-stand movements under novel force perturbations. They adapted effectively through various adaptive motor control mechanisms to avoid falls, reducing failure rates rapidly. The results indicate a high-level ecological controller in human motor learning that switches objectives between safety and movement efficiency, depending on failure or success. This approach is supported by policy learning, internal model adaptation, and adaptive feedback control. Our findings offer a comprehensive perspective on human motor control, integrating risk management in a hierarchical reinforcement learning framework for real-world environments.}, }
@article {pmid40344046, year = {2025}, author = {Ramihangihajason, TA and Weber, JL and Rakotondraompiana, S and Roger, E and Faramalala, MH and Rakotoniaina, S}, title = {Natural capital accounting as a decision support tool for environmental management of a protected area in Madagascar.}, journal = {PloS one}, volume = {20}, number = {5}, pages = {e0321948}, pmid = {40344046}, issn = {1932-6203}, mesh = {Madagascar ; *Conservation of Natural Resources/methods ; Ecosystem ; Biodiversity ; Forests ; Animals ; *Decision Support Techniques ; Humans ; Birds ; }, abstract = {Ecosystem change affects the availability of resources and services provided by nature. Ecosystem Natural capital accounting helps track these changes and supports better decision-making for managing the environment. This approach aims to assess changes in the stocks and flows of natural resources and the possibility to integrate them into economic and political decisions. The protected area of Mahavavy-Kinkony Complex, in North-Western of Madagascar, was chosen to implement this approach due to its many types of ecosystems as well as important reserves of threatened birds. In five years (2013-2018), we have observed a reduction in woodland cover (forest and mangrove) due to both regulated and illegal logging, linked to urban expansion and increasing of human pressure. This loss of woodland compromises not only biodiversity but also the capacity of ecosystems to provide ecosystem services. At the same time, the silting up of surface waters is compromising water quality and the health of aquatic ecosystems. In addition, the increase in agricultural land at the expense of forested areas raises concerns about the continuing degradation of natural ecosystems. All of these changes can be observed inside local socio-ecological landscape type. Each socio-ecological landscape type shows the potential variation in the production of ecosystem services.}, }
@article {pmid40343940, year = {2025}, author = {Longo, L and Veronese, M and Cagnato, C and Sorrentino, G and Tetruashvili, A and Belfer-Cohen, A and Jakeli, N and Meshveliani, T and Meneghetti, M and Zoleo, A and Marcomini, A and Artioli, G and Badetti, E and Hardy, K}, title = {Direct evidence for processing Isatis tinctoria L., a non-nutritional plant, 32-34,000 years ago.}, journal = {PloS one}, volume = {20}, number = {5}, pages = {e0321262}, pmid = {40343940}, issn = {1932-6203}, mesh = {*Plant Leaves/chemistry/ultrastructure ; Humans ; *Isatis/chemistry/anatomy &amp; histology ; Spectrum Analysis, Raman ; Spectroscopy, Fourier Transform Infrared ; Archaeology ; History, Ancient ; }, abstract = {Recovering evidence for the intentional use of plants in the Palaeolithic is challenging due to their perishable nature as, unlike chipped stone or bone artefacts, plant remains are rarely preserved. This has created a paradigm for the Palaeolithic in which plants seldom feature, resulting in a partial and skewed perspective; in fact, plants were as essential to human life then as they are today. Here, we combine morphological and spectroscopic analyses (µ-Raman, µ-FTIR) to provide robust multiscale physical and biomolecular evidence for the deliberate pounding and grinding of Isatis tinctoria L. leaves 34-32,000 years ago. The leaf epidermis fragments were found entrapped in the topography of the used surface of unmodified pebbles, in association with use-wear traces. Although their bitter taste renders them essentially inedible, the leaves have well-recognised medicinal properties and contain indigotin precursors, the chromophore responsible for the blue colour of woad, a plant-based dye that is insoluble in water. We used a stringent approach to contamination control and biomolecular analysis to provide evidence for a new perspective on human behaviour, and the applied technical and ecological knowledge that is likely to have prevailed in the Upper Palaeolithic. Whether this plant was used as a colourant, as medicine, or indeed for both remains unknown, but offers a new perspective on the fascinating possibilities of non-edible plant use.}, }
@article {pmid40343039, year = {2025}, author = {Cuenca, PR and Souza, FN and do Nascimento, RC and da Silva, AG and Eyre, MT and Santana, JO and de Oliveira, DS and de Souza, EVR and Palma, FAG and de Carvalho Santiago, DC and Dos Santos Ribeiro, P and Dos Santos, PEF and Khalil, H and Read, JM and Cremonese, C and Costa, F and Giorgi, E}, title = {Using step selection functions to analyse human mobility using telemetry data in infectious disease epidemiology: a case study of leptospirosis.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {40343039}, support = {/WT_/Wellcome Trust/United Kingdom ; R01 AI160780/AI/NIAID NIH HHS/United States ; }, abstract = {Human movement plays a critical role in the transmission of infectious diseases, especially those with environmental drivers like leptospirosis-a zoonotic bacterial infection linked to mud and water contact. Using GPS loggers, we collected detailed telemetry data to understand how fine-scale movements can be analysed in the context of an infectious disease. We recruited individuals living in urban slums in Salvador, Brazil to analyse how they interact with environmental risk factors such as domestic rubbish piles, open sewers, and a local stream. We aimed to identify differences in movement patterns inside the study areas by gender, age, and leptospirosis serological status. Step-selection functions, a spatio-temporal model used in animal movement ecology, estimated selection coefficients to represent the likelihood of movement toward specific environmental factors. With 128 participants wearing GPS devices for 24 to 48 hours, recording locations every 35 seconds during active daytime hours, we segmented movements into morning, midday, afternoon, and evening. Our results suggested women moved closer to the central stream and farther from open sewers compared to men, while serologically positive individuals avoided open sewers. This study introduces a novel method for analysing human telemetry data in infectious disease research.}, }
@article {pmid40341906, year = {2025}, author = {Shoemaker, WR and Sánchez, &#xc1; and Grilli, J}, title = {Macroecological patterns in experimental microbial communities.}, journal = {PLoS computational biology}, volume = {21}, number = {5}, pages = {e1013044}, pmid = {40341906}, issn = {1553-7358}, mesh = {*Models, Biological ; *Ecology/methods ; Biodiversity ; Ecosystem ; *Microbiota/physiology ; Computational Biology ; }, abstract = {Ecology has historically benefited from the characterization of statistical patterns of biodiversity within and across communities, an approach known as macroecology. Within microbial ecology, macroecological approaches have identified universal patterns of diversity and abundance that can be captured by effective models. Experimentation has simultaneously played a crucial role, as the advent of high-replication community time-series has allowed researchers to investigate underlying ecological forces. However, there remains a gap between experiments performed in the laboratory and macroecological patterns documented in natural systems, as we do not know whether these patterns can be recapitulated in the lab and whether experimental manipulations produce macroecological effects. This work aims at bridging the gap between experimental ecology and macroecology. Using high-replication time-series, we demonstrate that microbial macroecological patterns observed in nature exist in a laboratory setting, despite controlled conditions, and can be unified under the Stochastic Logistic Model of growth (SLM). We found that demographic manipulations (e.g., migration) impact observed macroecological patterns. By modifying the SLM to incorporate said manipulations alongside experimental details (e.g., sampling), we obtain predictions that are consistent with macroecological outcomes. By combining high-replication experiments with ecological models, microbial macroecology can be viewed as a predictive discipline.}, }
@article {pmid40339581, year = {2025}, author = {Pekar, JE and Lytras, S and Ghafari, M and Magee, AF and Parker, E and Wang, Y and Ji, X and Havens, JL and Katzourakis, A and Vasylyeva, TI and Suchard, MA and Hughes, AC and Hughes, J and Rambaut, A and Robertson, DL and Dellicour, S and Worobey, M and Wertheim, JO and Lemey, P}, title = {The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2.}, journal = {Cell}, volume = {188}, number = {12}, pages = {3167-3183.e18}, pmid = {40339581}, issn = {1097-4172}, support = {U19 AI135995/AI/NIAID NIH HHS/United States ; R01 AI153044/AI/NIAID NIH HHS/United States ; T15 LM011271/LM/NLM NIH HHS/United States ; R01 AI162611/AI/NIAID NIH HHS/United States ; 75N93021C00015/AI/NIAID NIH HHS/United States ; R01 AI135992/AI/NIAID NIH HHS/United States ; }, mesh = {*Chiroptera/virology ; Animals ; SARS-CoV-2/genetics ; Phylogeny ; Phylogeography ; *Severe acute respiratory syndrome-related coronavirus/genetics/classification ; Humans ; COVID-19/virology ; Genome, Viral ; Disease Reservoirs/virology ; *Betacoronavirus/genetics/classification ; Evolution, Molecular ; }, abstract = {The emergence of SARS-CoV in 2002 and SARS-CoV-2 in 2019 led to increased sampling of sarbecoviruses circulating in horseshoe bats. Employing phylogenetic inference while accounting for recombination of bat sarbecoviruses, we find that the closest-inferred bat virus ancestors of SARS-CoV and SARS-CoV-2 existed less than a decade prior to their emergence in humans. Phylogeographic analyses show bat sarbecoviruses traveled at rates approximating their horseshoe bat hosts and circulated in Asia for millennia. We find that the direct ancestors of SARS-CoV and SARS-CoV-2 are unlikely to have reached their respective sites of emergence via dispersal in the bat reservoir alone, supporting interactions with intermediate hosts through wildlife trade playing a role in zoonotic spillover. These results can guide future sampling efforts and demonstrate that viral genomic regions extremely closely related to SARS-CoV and SARS-CoV-2 were circulating in horseshoe bats, confirming their importance as the reservoir species for SARS viruses.}, }
@article {pmid40338955, year = {2025}, author = {Benjamin, JR and Neibauer, J and Anthony, H and Vazquez, J and Rawhouser, A and Dunham, JB}, title = {A partner-driven decision support model to inform the reintroduction of bull trout.}, journal = {PloS one}, volume = {20}, number = {5}, pages = {e0323427}, pmid = {40338955}, issn = {1932-6203}, mesh = {Animals ; *Trout/physiology ; *Conservation of Natural Resources/methods ; Ecosystem ; *Decision Support Techniques ; Decision Making ; }, abstract = {Assessments of species reintroductions involve a series of complex decisions that include human perspectives and ecological contexts. Here, we present a reintroduction assessment involving bull trout (Salvelinus confluentus) using a structured decision-making process. We approached this assessment by engaging partners representing public utilities, government agencies, and Tribes with shared interests in a potential reintroduction. These individuals identified objectives, decision alternatives, and ecological scenarios that were incorporated into a co-produced simulation-based model of potential reintroduction outcomes. The model included mathematical representations of habitat availability, life history expression, and assumptions regarding constraints on potential bull trout populations. Within each recipient stream, partners chose to explore a wide range of decision alternatives and simulated scenarios affecting reintroduction success. Results suggested that 1) reintroductions using eggs or adults were most optimal, 2) adding more individuals resulted in diminishing returns, 3) access to migratory habitat could improve success, and 4) the diversity of opportunities for life history expression led to improved reintroduction opportunities. In addition, modeled scenarios indicated some recipient streams consistently produced lower abundance of reintroduced bull trout. This work contributes a novel example to a growing portfolio of reintroduction assessments that may inform future conservation for bull trout and many other species facing similar challenges.}, }
@article {pmid40335533, year = {2025}, author = {Pakulnicka, J and Kruk, M}, title = {Water beetle networks differences and migration between natural lakes and post-exploitation water bodies.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {15898}, pmid = {40335533}, issn = {2045-2322}, mesh = {Animals ; *Coleoptera/physiology ; *Lakes ; Ecosystem ; *Animal Migration ; Biodiversity ; }, abstract = {Water deficits are a serious problem around the world, which also affects young landscapes, where lakes are most abundant. This poses a threat to many habitats and biological diversity found here. The relationships between species in the ecological networks of lakes at different stages of development and in nearby post-exploitation water bodies remain poorly understood. To better understand the functioning of beetle communities in different ecosystems, we created five network models that we subjected to graph analysis. By analysing the general attributes of the network (number of neighbours, shortest path, characteristic path length, clustering coefficient, network centralisation, network density and network heterogeneity) and those related to the nodes (NCC-Node Closeness Centrality, NBC-Node Betweenness Centrality, NDC-Node Degree Centrality) and to the edges (EBC-Edge Betweenness Centrality and correlations between the biomass of species as nodes), we were able to determine the role of each species in the networks and the relationships between the species. We then used the machine learning ensemble modelling XGBoost-SHAP to identify species that are particularly important in migrations between water bodies and to assess the direction and strength of migrations using Shapley values. Our analyses are based on faunal material from 25 lakes (mesotrophic, eutrophic, dystrophic) and 31-post-exploitation water bodies (clay pits and gravel pits) in northern Poland, in the Masurian Lake District. We found a total of 169 species representing different ecological and functional components. We have shown that the structures of the network between the biomass of species in the analysed five water types differ significantly. The highest value for network density was recorded in eutrophic lakes and clay ponds, the lowest in dystrophic lakes. In eutrophic lakes these are mainly eurybionts, in clay pits-rheophiles and in gravel pits-argilophiles and tyrphophiles. The relationship between the species with the highest NBC and EBC values is particularly important in order to maintain the stability of the network. The periphery of the network usually consists of larger predators that do not compete with each other. By analysing the migration directions of beetles between different ecosystems, we were able to demonstrate a greater affinity of the beetle fauna, especially the argilophiles (e.g. Scarodytes halensis and Laccobius minutus) inhabiting gravel pits, to dystrophic lakes. The beetles in clay pits originate mainly from mesotrophic lakes. These are mainly rheophiles, mostly weakly flying species, such as: Haliplus fluviatilis, Haliplus fulvus, Ilybius fenestratus, Hygrotus vericolor and Haliplus flavicollis. These species are important for the stability of ecological networks in the studied lake types. Their movements between the ecosystems studied in turn contribute to the functional connectivity between the individual lakes, which ensures the stabilisation of biotic relationships at the landscape level. At the same time, they generally also indicate the optimisation of environmental conditions in post-exploitation water bodies, which makes them potential substitute habitats for natural lakes.}, }
@article {pmid40334559, year = {2025}, author = {Semcesen, PO and Wells, MG and Sherlock, C and Gutierrez, RF and Rochman, CM}, title = {Wind driven transport of macroplastic debris in a large urban harbour measured by GPS-tracked drifters.}, journal = {Marine pollution bulletin}, volume = {217}, number = {}, pages = {118034}, doi = {10.1016/j.marpolbul.2025.118034}, pmid = {40334559}, issn = {1879-3363}, mesh = {*Wind ; *Plastics/analysis ; *Environmental Monitoring/methods ; Ontario ; Geographic Information Systems ; }, abstract = {The transport pathways of floating plastic debris in Toronto Harbour, Ontario, Canada, were assessed using a series of GPS-tracked drifter bottles. The drifter trajectories were largely controlled by winds, and they could traverse the 2 km wide harbour within a day. The average ratio of drifter speed to wind speed (the wind factor) is consistent with values of 2-5 % used in modelling dispersion of marine debris. However, significant variability in wind factors meant some drifters travelled 2-5 times faster than expected in small waterbodies (Toronto Harbour), and as much as 7 times faster in large waterbodies (Lake Ontario). Importantly, based on our calculated wind factor equations and the coincident accumulation of our drifters with real plastic debris, we can justify the use of wind factors when studying plastic debris transport. Most (75 %) of the drifters that were released in the harbour, stayed within the harbour, accumulating downwind. However, 14 of all 66 drifters escaped Toronto Harbour, where ∼70 % escaped through the West Gap while ∼30 % escaped via the Outer Harbour. One drifter made a 290 km journey across Lake Ontario in a period of 14 days, demonstrating that Toronto is a potential source of plastic debris throughout Lake Ontario.}, }
@article {pmid40333133, year = {2025}, author = {Niculescu, AG and Mitache, MM and Grumezescu, AM and Chifiriuc, MC and Mihai, MM and Tantu, MM and Tantu, AC and Popa, LG and Grigore, GA and Cristian, RE and Popa, MI and Vrancianu, CO}, title = {From Microbial Ecology to Clinical Challenges: The Respiratory Microbiome's Role in Antibiotic Resistance.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {4}, pages = {}, pmid = {40333133}, issn = {2076-0817}, support = {CNFIS-FDI-2024-F-0484 INOVEX//University of Bucharest/ ; Pillar III, Component C9/Investment no. 8 (I8) - contract CF 68//; Ministry of Research, Innovation and Digitalization through the National Recovery and Resilience Plan (PNRR) of Romania/ ; project no. 23020101, Contract no. 7N from 3 January 2023//The core program within the National Research Development and Innovation Plan, 2022-2027', carried out with the support of the Ministry of Research, Innovation and Digitalization (MCID)/ ; }, mesh = {Humans ; *Microbiota/drug effects ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Respiratory Tract Infections/microbiology/drug therapy ; *Drug Resistance, Microbial ; Probiotics ; *Drug Resistance, Bacterial ; *Respiratory System/microbiology ; }, abstract = {Antibiotic resistance represents a growing public health threat, with airborne drug-resistant strains being especially alarming due to their ease of transmission and association with severe respiratory infections. The respiratory microbiome plays a pivotal role in maintaining respiratory health, influencing the dynamics of antibiotic resistance among airborne pathogenic microorganisms. In this context, this review proposes the exploration of the complex interplay between the respiratory microbiota and antimicrobial resistance, highlighting the implications of microbiome diversity in health and disease. Moreover, strategies to mitigate antibiotic resistance, including stewardship programs, alternatives to traditional antibiotics, probiotics, microbiota restoration techniques, and nanotechnology-based therapeutic interventions, are critically presented, setting an updated framework of current management options. Therefore, through a better understanding of respiratory microbiome roles in antibiotic resistance, alongside emerging therapeutic strategies, this paper aims to shed light on how the global health challenges posed by multi-drug-resistant pathogens can be addressed.}, }
@article {pmid40332368, year = {2025}, author = {Zheng, K and Feng, Y and Liu, R and Zhang, Y and Fan, D and Zhong, K and Tang, X and Zhang, Q and Cao, S}, title = {Bioinformatics Analysis Reveals the Evolutionary Characteristics of the Phoebe bournei ARF Gene Family and Its Expression Patterns in Stress Adaptation.}, journal = {International journal of molecular sciences}, volume = {26}, number = {8}, pages = {}, pmid = {40332368}, issn = {1422-0067}, mesh = {*Gene Expression Regulation, Plant ; *Stress, Physiological/genetics ; Phylogeny ; *Evolution, Molecular ; *Computational Biology/methods ; *Plant Proteins/genetics/metabolism ; *Transcription Factors/genetics/metabolism ; *Multigene Family ; *Adaptation, Physiological/genetics ; *Poaceae/genetics ; Indoleacetic Acids/metabolism ; Promoter Regions, Genetic ; }, abstract = {Auxin response factors (ARFs) are pivotal transcription factors that regulate plant growth, development, and stress responses. Yet, the genomic characteristics and functions of ARFs in Phoebe bournei remain undefined. In this study, 25 PbARF genes were identified for the first time across the entire genome of P. bournei. Phylogenetic analysis categorized these genes into five subfamilies, with members of each subfamily displaying similar conserved motifs and gene structures. Notably, Classes III and V contained the largest number of members. Collinearity analysis suggested that segmental duplication events were the primary drivers of PbARF gene family expansion. Structural analysis revealed that all PbARF genes possess a conserved B3 binding domain and an auxin response element, while additional motifs varied among different classes. Promoter cis-acting element analysis revealed that PbARF genes are extensively involved in hormonal responses-particularly to abscisic acid and jasmonic acid and abiotic stresses-as well as abiotic stresses, including heat, drought, light, and dark. Tissue-specific expression analysis showed that PbARF25, PbARF23, PbARF19, PbARF22, and PbARF20 genes (class III), and PbARF18 and PbARF11 genes (class V) consistently exhibited high expression levels in the five tissues. In addition, five representative PbARF genes were analyzed using qRT-PCR. The results demonstrated significant differences in the expression of PbARF genes under various abiotic stress conditions (drought, salt stress, light, and dark), indicating their important roles in stress response. This study laid a foundation for elucidating the molecular evolution mechanism of ARF genes in P. bournei and for determining the candidate genes for stress-resistance breeding.}, }
@article {pmid40331936, year = {2025}, author = {Li, H and Wang, R and Pan, J and Chen, J and Hao, X}, title = {Bioinformatics Analysis of the Glutamate-Gated Chloride Channel Family in Bursaphelenchus xylophilus.}, journal = {International journal of molecular sciences}, volume = {26}, number = {8}, pages = {}, pmid = {40331936}, issn = {1422-0067}, support = {202403//Key Laboratory of National Forestry and Grassland Administration on Prevention and Control Technology of Pine Wilt Disease/ ; 202401BD070001-115//Yunnan Fundamental Research Projects/ ; LXXK-2023M06, LXXK-2024Z04//Southwest Forestry University Forestry major in Yunnan Province First-Class Construction Discipline/ ; }, mesh = {*Chloride Channels/genetics/metabolism/chemistry ; Animals ; *Computational Biology/methods ; Phylogeny ; *Tylenchida/genetics/metabolism ; Multigene Family ; Amino Acid Sequence ; }, abstract = {Glutamate-gated chloride channels (GluCls), a class of ion channels found in the nerve and muscle cells of invertebrates, are involved in vital life processes. Bursaphelenchus xylophilus, the pathogen of pine wilt disease, has induced major economic and ecological losses in invaded areas of Asia and Europe. We identified 33 GluCls family members by sequence alignment analysis. A subsequent bioinformatic analysis revealed the physicochemical properties, protein structure, and gene expression patterns in different developmental stages. The results showed that GluCls genes are distributed across all six chromosomes of B. xylophilus. These proteins indicated a relatively conserved structure by NCBI-conserved domains and InterPro analysis. A gene structure analysis revealed that GluCls genes consist of 5 to 14 exons. Expression pattern analysis revealed BxGluCls were extensively involved in the development of second instar larvae of B. xylophilus. Furthermore, BxGluCls15, BxGluCls25, and BxGluCls28 were mainly associated with the development of eggs of B. xylophilus. BxGluCls12, BxGluCls18, and BxGluCls32 were predominantly linked to nematode resistance and adaptation. Investigation the structure and expression patterns of BxGluCls is crucial to understand the developmental trends of B. xylophilus. It also helps identify molecular targets for the development of biopesticides or drugs designed to control this nematode.}, }
@article {pmid40329811, year = {2025}, author = {Yang, Y and Liu, X and Wu, J and Svenning, JC and Liu, J and Shrestha, N}, title = {A comprehensive county-level distribution database of alien and invasive plants in China.}, journal = {Ecology}, volume = {106}, number = {5}, pages = {e70084}, pmid = {40329811}, issn = {1939-9170}, support = {2022YFC2601100//National Key Research and Development Program of China/ ; DNRF173//Danmarks Grundforskningsfond/ ; }, mesh = {*Introduced Species ; China ; *Plants/classification ; *Databases, Factual ; Biodiversity ; }, abstract = {Over the past half century, international trade and exchange have continued to increase in China, resulting in the widespread introduction of alien plant species. The accumulation of these alien species has accelerated invasion events, posing serious threats to local ecological security and economic development. Comprehensive and accurate species distribution records are extremely important for early detection, understanding dispersal dynamics, and supporting various management strategies and research initiatives. However, biodiversity databases, both global and local, often lack comprehensive and high-resolution distribution data for alien invasive plant species (AIPs). This limitation is particularly evident in China, where local databases typically provide coarse spatial data, often restricted to the provincial level, leading to a substantial underestimation of the actual distribution of AIPs. Here, we fill this gap by creating the most comprehensive distribution database for AIPs in China at a much finer spatial resolution. By integrating 73,469 distribution records from China's online herbarium, biodiversity databases, flora, published literature, and 173,396 georeferenced records from GBIF, we built the county-level distribution database for 400 AIPs and report for the first time their presence in 2684 administrative counties in China (92.5% of the total counties). Notably, our database provides 2.58 times more distribution records than global biodiversity data repositories such as GBIF and also includes the earliest introduction dates for each AIP. The temporal range of the records spans from 1607 to 2023, capturing over 400 years of AIP presence in China. These rigorously quality-controlled georeferenced data can be used to examine the dynamics and influencing factors of plant invasions in China. They can also serve as the most updated data reference for policy makers in designing effective AIP management policies in China. We encourage users to cite this data paper when utilizing the data, and there are no restrictions on its use for non-commercial purposes.}, }
@article {pmid40329386, year = {2025}, author = {Hou, L and Zhao, Z and Steger-Mähnert, B and Jiao, N and Herndl, GJ and Zhang, Y}, title = {Microbial metabolism in laboratory reared marine snow as revealed by a multi-omics approach.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {114}, pmid = {40329386}, issn = {2049-2618}, support = {42206098//National Natural Science Foundation of China-China Academy of General Technology Joint Fund for Basic Research/ ; 42125603//National Natural Science Foundation of China-China Academy of General Technology Joint Fund for Basic Research/ ; MELRS2327//State Key Laboratory of Marine Environmental Science/ ; I4978-B//Austrian Science Fund/ ; }, mesh = {*Snow/microbiology ; Gammaproteobacteria/metabolism/genetics/classification ; Metagenomics/methods ; Metagenome ; *Seawater/microbiology ; *Microbiota ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Phytoplankton/microbiology/metabolism ; Multiomics ; }, abstract = {BACKGROUND: Marine snow represents an organic matter-rich habitat and provides substrates for diverse microbial populations in the marine ecosystem. However, the functional diversity and metabolic interactions within the microbial community inhabiting marine snow remain largely underexplored, particularly for specific metabolic pathways involved in marine snow degradation. Here, we used a multi-omics approach to explore the microbial response to laboratory-reared phytoplankton-derived marine snow.<br><br>RESULTS: Our results demonstrated a dramatic shift in both taxonomic and functional profiles of the microbial community after the formation of phytoplankton-derived marine snow using a rolling tank system. The changes in microbial metabolic processes were more pronounced in the metaproteome than in the metagenome in response to marine snow. Fast-growing taxa within the Gammaproteobacteria were the most dominant group at both the metagenomic and metaproteomic level. These Gammaproteobacteria possessed a variety of carbohydrate-active enzymes (CAZymes) and transporters facilitating substrate cleavage and uptake, respectively. Analysis of metagenome-assembled genomes (MAGs) revealed that the response to marine snow amendment was primarily mediated by Alteromonas, Vibrio, and Thalassotalea. Among these, Alteromonas exclusively expressing auxiliary activities 2 (AA2) of the CAZyme subfamily were abundant in both the free-living (FL) and marine snow-attached (MA) microbial communities. Thus, Alteromonas likely played a pivotal role in the degradation of marine snow. The enzymes of AA2 produced by these Alteromonas MAGs are capable of detoxifying peroxide intermediates generated during the breakdown of marine snow into smaller poly- and oligomers, providing available substrates for other microorganisms within the system. In addition, Vibrio and Thalassotalea MAGs exhibited distinct responses to these hydrolysis products of marine snow in different size fractions, suggesting a distinct niche separation. Although chemotaxis proteins were found to be enriched in the proteome of all three MAGs, differences in transporter proteins were identified as the primary factor contributing to the niche separation between these two groups. Vibrio in the FL fraction predominantly utilized ATP-binding cassette transporters (ABCTs), while Thalassotalea MAGs in the MA fraction primarily employed TonB-dependent outer membrane transporters (TBDTs).<br><br>CONCLUSIONS: Our findings shed light on the essential metabolic interactions within marine snow-degrading microbial consortia, which employ complementary physiological mechanisms and survival strategies to effectively scavenge marine snow. This work advances our understanding of the fate of marine snow and the role of microbes in carbon sequestration in the ocean. Video Abstract.}, }
@article {pmid40328721, year = {2025}, author = {Zhang, H and Wen, T and Wang, Z and Zhao, X and Wu, H and Xiang, P and Ma, Y}, title = {[Multi-omics analysis of hormesis effect of lanthanum chloride on carotenoid synthesis in Rhodotorula mucilaginosa].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {41}, number = {4}, pages = {1631-1648}, doi = {10.13345/j.cjb.240537}, pmid = {40328721}, issn = {1872-2075}, mesh = {*Lanthanum/pharmacology ; *Rhodotorula/metabolism/drug effects/genetics ; *Carotenoids/metabolism ; *Hormesis/drug effects ; Fermentation ; Multiomics ; }, abstract = {Hormesis effect has been observed in the secondary metabolite synthesis of microorganisms induced by rare earth elements. However, the underlying molecular mechanism remains unclear. To analyze the molecular mechanism of the regulatory effect of Rhodotorula mucilaginosa in the presence of lanthanum chloride, different concentrations of lanthanum chloride were added to the fermentation medium of Rhodotorula mucilaginosa, and the carotenoid content was subsequently measured. It was found that the concentrations of La[3+] exerting the promotional and inhibitory effects were 0-100 mg/L and 100-400 mg/L, respectively. Furthermore, the expression of 33 genes and the synthesis of 55 metabolites were observed to be up-regulated, while the expression of 85 genes and the synthesis of 123 metabolites were found to be down-regulated at the concentration range of the promotional effect. Notably, the expression of carotenoid synthesis-related genes except AL1 was up-regulated. Additionally, the content of β-carotene, lycopene, and astaxanthin demonstrated increases of 10.74%, 5.02%, and 3.22%, respectively. The expression of 5 genes and the synthesis of 91 metabolites were up-regulated, while the expression of 35 genes and the synthesis of 138 metabolites were down-regulated at the concentration range of the inhibitory effect. Meanwhile, the content of β-carotene, lycopene, and astaxanthin decreased by 21.73%, 34.81%, and 35.51%, respectively. In summary, appropriate concentrations of rare earth ions can regulate the synthesis of secondary metabolites by modulating the activities of various enzymes involved in metabolic pathways, thereby exerting the hormesis effect. The findings of this study not only contribute to our comprehension for the mechanism of rare earth elements in organisms but also offer a promising avenue for the utilization of rare earth elements in diverse fields, including agriculture, pharmaceuticals, and healthcare.}, }
@article {pmid40327938, year = {2025}, author = {Wang, H and Xie, G and Zhang, Z and Han, J and Zhang, Y and Xu, T and Yin, D}, title = {PFHxA and PFHxS promote breast cancer progression in 3D culture: MEX3C-associated immune infiltration revealed by bioinformatics and machine learning.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138458}, doi = {10.1016/j.jhazmat.2025.138458}, pmid = {40327938}, issn = {1873-3336}, mesh = {Humans ; Machine Learning ; Cell Line, Tumor ; Female ; *Fluorocarbons/toxicity ; Computational Biology ; Cell Movement/drug effects ; Cell Proliferation/drug effects ; *RNA-Binding Proteins/genetics/metabolism ; Tumor Microenvironment/drug effects ; *Triple Negative Breast Neoplasms/immunology/pathology/genetics ; *Sulfonic Acids/toxicity ; Disease Progression ; }, abstract = {Per- and polyfluoroalkyl substances (PFAS) are persistent environmental contaminants with widespread use and bioaccumulative potential. Short-chain PFAS such as perfluorohexanoic acid (PFHxA) and perfluorohexane sulfonate (PFHxS) have been introduced as safer alternatives to long-chain PFAS, yet their toxicological impacts remain poorly defined. In this study, we employed a 3D Gelatin methacryloyl (GelMA) hydrogel model to mimic the tumor microenvironment and investigated the effects of PFHxA and PFHxS on triple-negative breast cancer (TNBC) progression. At environmentally relevant concentrations (0.1-10 μM), both compounds significantly enhanced proliferation, migration, and invasion of MDA-MB-231 cells. Transcriptomic and machine learning analyses identified MEX3C as a key gene upregulated by PFAS exposure. Gene set enrichment analysis (GSEA) revealed activation of the PI3K-AKT-mTOR signaling pathway, which was further supported by siRNA-mediated knockdown of MEX3C, leading to a marked reduction in the expression levels of phosphorylated PI3K, AKT, and mTOR proteins. Furthermore, immune cell co-culture experiments showed that MDA-MB-231 cells with high MEX3C expression promoted M2 macrophage polarization, suppressed M1 polarization, and enhanced macrophage chemotactic activity, the immunomodulatory effects were significantly attenuated upon MEX3C knockdown. These findings establish MEX3C as a central mediator of PFAS-induced tumor progression and immune remodeling. This study provides mechanistic insight into the carcinogenic potential of emerging short-chain PFAS and underscores the need for stricter regulation to safeguard public health.}, }
@article {pmid40326463, year = {2025}, author = {Vogelsmeier, LVDE and Jongerling, J and Ulitzsch, E}, title = {Accounting for Measurement Invariance Violations in Careless Responding Detection in Intensive Longitudinal Data: Exploratory vs. Partially Constrained Latent Markov Factor Analysis.}, journal = {Multivariate behavioral research}, volume = {60}, number = {5}, pages = {878-897}, doi = {10.1080/00273171.2025.2492016}, pmid = {40326463}, issn = {1532-7906}, mesh = {Humans ; Longitudinal Studies ; Factor Analysis, Statistical ; *Markov Chains ; *Models, Statistical ; Computer Simulation ; Data Interpretation, Statistical ; }, abstract = {Intensive longitudinal data (ILD) collection methods like experience sampling methodology can place significant burdens on participants, potentially resulting in careless responding, such as random responding. Such behavior can undermine the validity of any inferences drawn from the data if not properly identified and addressed. Recently, a confirmatory mixture model (here referred to as fully constrained latent Markov factor analysis, LMFA) has been introduced as a promising solution to detect careless responding in ILD. However, this method relies on the key assumption of measurement invariance of the attentive responses, which is easily violated due to shifts in how participants interpret items. If the assumption is violated, the ability of the fully constrained LMFA to accurately identify careless responding is compromised. In this study, we evaluated two more flexible variants of LMFA-fully exploratory LMFA and partially constrained LMFA-to distinguish between careless and attentive responding in the presence of non-invariant attentive responses. Simulation results indicated that the fully exploratory LMFA model is an effective tool for reliably detecting and interpreting different types of careless responding while accounting for violations of measurement invariance. Conversely, the partially constrained model struggled to accurately detect careless responses. We end by discussing potential reasons for this.}, }
@article {pmid40325107, year = {2025}, author = {Pitogo, KME and Meneses, CG and Flores, ABA and Saavedra, AJL and Amarga, AKS and Angeles, MD and Lucañas, CC and Decena, SCP and Venturina, REL and Fidelino, JS and Pantinople, D and Cabañas, AJC and Herr, MW and Bernstein, JM and Chan, KO and Sanguila, MB and Mallari, NA and Brown, RM and Supsup, CE}, title = {Caught in statistical noise: pitfalls of a unidimensional approach to understanding biodiversity-conflict relationships.}, journal = {npj biodiversity}, volume = {4}, number = {1}, pages = {17}, pmid = {40325107}, issn = {2731-4243}, }
@article {pmid40324147, year = {2025}, author = {Gilpin, W}, title = {Optimization hardness constrains ecological transients.}, journal = {PLoS computational biology}, volume = {21}, number = {5}, pages = {e1013051}, pmid = {40324147}, issn = {1553-7358}, mesh = {*Ecosystem ; *Models, Biological ; Computer Simulation ; Computational Biology ; Biological Evolution ; }, abstract = {Living systems operate far from equilibrium, yet few general frameworks provide global bounds on biological transients. In high-dimensional biological networks like ecosystems, long transients arise from the separate timescales of interactions within versus among subcommunities. Here, we use tools from computational complexity theory to frame equilibration in complex ecosystems as the process of solving an analogue optimization problem. We show that functional redundancies among species in an ecosystem produce difficult, ill-conditioned problems, which physically manifest as transient chaos. We find that the recent success of dimensionality reduction methods in describing ecological dynamics arises due to preconditioning, in which fast relaxation decouples from slow solving timescales. In evolutionary simulations, we show that selection for steady-state species diversity produces ill-conditioning, an effect quantifiable using scaling relations originally derived for numerical analysis of complex optimization problems. Our results demonstrate the physical toll of computational constraints on biological dynamics.}, }
@article {pmid40324092, year = {2025}, author = {Compton, ZT and Vincze, O and Mellon, W and Tollis, M and Abegglen, L and Schiffman, JD and Giraudeau, M and Boddy, AM and Maley, CC}, title = {Paradoxical indeed.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {19}, pages = {e2504512122}, pmid = {40324092}, issn = {1091-6490}, support = {T32 CA272303/CA/NCI NIH HHS/United States ; U54 CA217376/CA/NCI NIH HHS/United States ; }, }
@article {pmid40323496, year = {2025}, author = {Oyelayo, EA and Taiwo, TJ and Oyelude, SO and Alao, JO}, title = {The global impact of industrialisation and climate change on antimicrobial resistance: assessing the role of Eco-AMR Zones.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {6}, pages = {625}, pmid = {40323496}, issn = {1573-2959}, mesh = {*Industrial Development ; *Drug Resistance, Microbial/genetics ; *Climate Change ; Temperature ; Environmental Monitoring ; Genes, Microbial ; Computational Biology ; Anti-Bacterial Agents ; }, abstract = {This study examines the relationship between industrialisation, climate change, and antimicrobial resistance (AMR) gene prevalence. Data analysis from the top 20 highly industrialised and the top 20 least industrialised nations revealed that industrial activities significantly contribute to global warming, with temperature increases of up to 2 °C observed in highly industrialised regions. These environmental changes influence the distribution and evolution of AMR genes, as rising temperatures can affect bacterial resistance in a manner similar to antibiotics. Through a bioinformatics approach, a marked disparity in AMR gene frequencies was observed between highly industrialised and less industrialised nations, with developed countries reporting higher frequencies due to extensive antibiotic use and advanced monitoring systems. 'Eco-AMR Zones' is proposed as a solution to specialised areas by promoting sustainable industrial practices, enforcing pollution controls, and regulating antibiotic use to mitigate AMR's environmental and public health impacts. These zones, supported by collaboration across various sectors, offer a promising approach to preserving antibiotic effectiveness and reducing environmental degradation. The study emphasises the importance of integrated global strategies that address both the ecological and public health challenges posed by AMR, advocating for sustainable practices, international collaboration, and ongoing research to combat the evolving threats of climate change and antimicrobial resistance.}, }
@article {pmid40321106, year = {2025}, author = {Brazier, T and Stetsenko, R and Roze, D and Glémin, S}, title = {Mating system and the evolution of recombination rates in seed plants.}, journal = {Journal of evolutionary biology}, volume = {38}, number = {7}, pages = {920-929}, doi = {10.1093/jeb/voaf008}, pmid = {40321106}, issn = {1420-9101}, support = {ANR-19-CE12472//Agence Nationale de la Recherche/ ; }, mesh = {*Magnoliopsida/genetics ; Genome, Plant ; Chromosomes, Plant ; Genome Size ; *Recombination, Genetic ; *Biological Evolution ; *Self-Fertilization/genetics ; Pollination ; Life History Traits ; Datasets as Topic ; Longevity ; Selection, Genetic ; }, abstract = {Meiotic recombination is a central mechanism underlying sexual reproduction among eukaryotes. In many species, the recombination rate is strongly constrained by chromosome size, as the number of crossovers per chromosome generally ranges between one and no more than a few (around three to five). Yet, recombination rates are variable and can evolve between species, in particular when they differ in their reproductive system. According to theory, indirect selection towards higher recombination rates is expected to be stronger in inbred populations, such as selfing species compared with randomly mating species. To test for the impact of the mating system on the evolution of recombination rates, we leveraged a dataset with genetic maps, genome sizes, chromosome numbers, and life history traits in 200 seed plant species. After controlling for the chromosome size effect, the phylogeny, and map quality, we found a joint positive effect of the mating system and longevity on recombination rates, with higher recombination rates in mixed-mating and selfing species. We also found that mixed-mating and selfing species had a significantly higher number of crossovers in larger chromosomes than outcrossing species, suggesting selection for relaxed crossover interference in these former species. Our results point to the mating system as an important factor potentially shaping the evolution of recombination despite mechanical constraints acting on the number of crossovers per chromosome.}, }
@article {pmid40319682, year = {2025}, author = {Hwang, H and Kim, D and Kim, S and Kim, JY and Kim, ES and Yang, T and Lee, N and Piao, Y and Park, BJ and Lee, DK}, title = {Optimizing urban green spaces using a decision-support model for carbon sequestration and ecological connectivity.}, journal = {Journal of environmental management}, volume = {384}, number = {}, pages = {125058}, doi = {10.1016/j.jenvman.2025.125058}, pmid = {40319682}, issn = {1095-8630}, mesh = {*Carbon Sequestration ; *Decision Support Techniques ; Cities ; *Conservation of Natural Resources/methods ; Ecosystem ; }, abstract = {Urban green spaces (UGSs) are vital for enhancing urban ecological health and resident well-being. However, their diverse functions need to be balanced based on spatial limitations and varying stakeholder preferences. Integrated planning approaches are needed to exploit the multiple benefits of UGSs. This study introduces a multi-objective decision-support model designed to optimize UGS planning by simultaneously addressing carbon sequestration, ecological connectivity, and cost constraints. The model incorporates the non-dominated sorting genetic algorithm II to identify Pareto-optimal solutions for tailored decision-making strategies that balance different priorities. The model indicated that ecological connectivity can be improved by 7.57 % while meeting carbon-reduction and budgetary targets. The model effectively balanced trade-offs, underscoring the importance of both the quantity and strategic placement of green space. This decision-support framework empowers decision-makers to rapidly simulate and validate optimal scenarios, effectively balance competing objectives, and provide a scientific basis through verifiable feedback, ultimately promoting the development of sustainable urban environments.}, }
@article {pmid40319413, year = {2025}, author = {Wang, Y and Mao, Z and Yu, J and Feng, B and Zhang, Z and Zhong, L and Tang, Y}, title = {Construction of risk management system for polluted sites in coal industry clusters.}, journal = {Environmental geochemistry and health}, volume = {47}, number = {6}, pages = {195}, pmid = {40319413}, issn = {1573-2983}, mesh = {*Coal Industry ; *Risk Management/methods ; China ; *Coal ; *Environmental Pollution/prevention &amp; control/statistics &amp; numerical data ; Soil/chemistry ; Groundwater/chemistry ; Environmental Restoration and Remediation ; Environmental Monitoring ; Risk Assessment ; Decision Making, Organizational ; *Coal Mining ; Decision Making, Computer-Assisted ; Algorithms ; *Environmental Pollutants/analysis ; }, abstract = {Coal has always been the main source of energy in China, accounting for more than 60% of primary energy production and consumption. As a result of coal mining, coal industry agglomerations such as mining, coal chemical industry, and so on have been gradually formed, and there are many types of industries in the agglomerations, complex sources of pollutants, and sensitive soil and water environments, and all kinds of industrial sites and solid waste dumps of coal-related industries may pollute the soil and groundwater, and have a certain impact on the ecological environment. However, at present, there is a lack of a targeted region-wide pollution risk management technology system for the polluted sites in the agglomeration area, therefore, it is particularly important to construct a scientific and complete soil-groundwater risk management system and propose more targeted and effective control strategies for the polluted sites in the coal industry agglomeration area. Based on the domestic and international experience and historical data, this paper takes the coal industry cluster area as the research object classifies the land in the area according to the land use type into construction land, agricultural land, and another ecological land, and carries out the risk zoning and grading based on the dosage-effect model and the potential ecological hazard index method respectively, assesses the appropriateness, feasibility, and necessity of the implementation of risk control for the polluted plots, and then designs and develops a risk control decision-making framework by using the hierarchical analysis method. Hierarchical analysis was used to design and develop a decision-making framework for risk management, and finally, the optimal risk management and remediation strategy was proposed based on the AHP + TOPSIS algorithm, which combined with the contaminated land conditions to propose a suitable solution.}, }
@article {pmid40318965, year = {2025}, author = {Lucca, E and Kofinas, D and Avellán, T and Kleemann, J and Mooren, CE and Blicharska, M and Teutschbein, C and Sperotto, A and Sušnik, J and Milliken, S and Fader, M and Đorđević, D and Dašić, T and Vasilić, V and Taiwo, B and Baubekova, A and Pineda-Martos, R and Spyropoulou, A and Baganz, GFM and El Jeitany, J and Oral, HV and Merheb, M and Castelli, G and Pagano, A and Sambo, B and Suškevičs, M and Arnold, M and Rađenović, T and Psomas, A and Masia, S and La Jeunesse, I and Amorocho-Daza, H and Das, SS and Bresci, E and Munaretto, S and Brouwer, F and Laspidou, C}, title = {Corrigendum to "Integrating 'nature' in the water-energy-food nexus: Current perspectives and future directions" [Science of The Total Environment, Volume 966, 2025, 178600].}, journal = {The Science of the total environment}, volume = {980}, number = {}, pages = {179482}, doi = {10.1016/j.scitotenv.2025.179482}, pmid = {40318965}, issn = {1879-1026}, }
@article {pmid40318638, year = {2025}, author = {Aguilar-Gómez, D and Bejder, J and Graae, J and Ko, Y and Vaughn, A and Clement, K and Tristani-Firouzi, M and Lee, JY and Nordsborg, NB and Nielsen, R and Ilardo, M}, title = {Genetic and training adaptations in the Haenyeo divers of Jeju, Korea.}, journal = {Cell reports}, volume = {44}, number = {5}, pages = {115577}, pmid = {40318638}, issn = {2211-1247}, support = {R00 HG011658/HG/NHGRI NIH HHS/United States ; R01 GM138634/GM/NIGMS NIH HHS/United States ; R35 GM153400/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Diving/physiology ; Female ; *Adaptation, Physiological/genetics ; Republic of Korea ; Adult ; Selection, Genetic ; Pregnancy ; Blood Pressure/genetics ; }, abstract = {Natural selection and relative isolation have shaped the genetics and physiology of unique human populations from Greenland to Tibet. Another such population is the Haenyeo, the all-female Korean divers renowned for their remarkable diving abilities in frigid waters. Apnea diving induces considerable physiological strain, particularly in females diving throughout pregnancy. In this study, we explore the hypothesis that breath-hold diving has shaped physiological and genetic traits in the Haenyeo. We identified pronounced bradycardia during diving, a likely training effect. We paired natural selection and genetic association analyses to investigate adaptive genetic variation that may mitigate the effects of diving on pregnancy through an associated reduction of diastolic blood pressure. Finally, we identified positively selected variation in a gene previously associated with cold water tolerance, which may contribute to reduced hypothermia susceptibility. These findings highlight the importance of traditional diving populations for understanding genetic and physiological adaptation.}, }
@article {pmid40318544, year = {2025}, author = {Gomes, MLS and Cestari, VRF and Florêncio, RS and Yamamura, M and Santos, JO and Sales, LBF and Silva, RR and Oriá, MOB}, title = {Spatial-temporal analysis of cervical cancer screening and social and health indicators in Brazil.}, journal = {Public health}, volume = {243}, number = {}, pages = {105747}, doi = {10.1016/j.puhe.2025.105747}, pmid = {40318544}, issn = {1476-5616}, mesh = {Humans ; Female ; Brazil/epidemiology ; *Uterine Cervical Neoplasms/diagnosis/epidemiology ; Adult ; Middle Aged ; *Early Detection of Cancer/statistics &amp; numerical data ; Spatio-Temporal Analysis ; Socioeconomic Factors ; *Health Status Indicators ; }, abstract = {OBJECTIVE: To identify the spatial-temporal patterns of cervical cancer (CC) screening in Brazil from 2013 to 2022 and its relationship with social and health indicators.<br><br>STUDY DESIGN: This ecological study uses data from the Cancer Information System (SISCAN) of the Brazilian Unified Health System's Department of Informatics.<br><br>METHODS: The study analyzed women aged 25 to 64 who underwent CC screening in 5570 municipalities across Brazil. Global Moran's I and the Local Index of Spatial Autocorrelation (LISA) were employed to investigate clustering. The purely spatial scan statistic technique was used for spatial cluster detection. Temporal trends were assessed using joinpoint regression. GeoDa, SaTScan, GWR, and QGIS software were used for the analysis.<br><br>RESULTS: The global clustering analysis of CC screening proportions revealed significant spatial autocorrelation (Moran's I&#xa0;=&#xa0;0.530). Clusters of municipalities with low screening rates were significantly observed in the Northern (Amap&#xe1;, Amazonas, Rond&#xf4;nia, Roraima) and Northeastern (Piau&#xed;, Pernambuco) regions. The Gini Index (&#x3b2;&#xa0;=&#xa0;-2.60), the Municipal Human Development Index (MHDI) (&#x3b2;&#xa0;=&#xa0;-10.5), and the Social Vulnerability Index (SVI) (&#x3b2;&#xa0;=&#xa0;-9.14) showed negative associations. Conversely, Family Health Strategy (FHS) coverage (&#x3b2;&#xa0;=&#xa0;2.18) demonstrated a positive impact on screening rates. In terms of temporal trends, the screening proportion gradually increased from 5.4&#xa0;% in 2014 to 10.5&#xa0;% in 2022.<br><br>CONCLUSION: Areas with a high risk of low CC screening rates were identified in the Northern and Northeastern regions of Brazil, which are characterized by socioeconomic and demographic disparities, vulnerabilities, and inequalities.}, }
@article {pmid40317095, year = {2025}, author = {Seizer, L and Pascher, A and Branz, S and Schmitt, N and Löchner, J and Schuller, BW and Rohleder, N and Renner, TJ}, title = {Bridging acute and chronic stress effects on inflammation: protocol for a mixed-methods intensive longitudinal study.}, journal = {BMC psychology}, volume = {13}, number = {1}, pages = {464}, pmid = {40317095}, issn = {2050-7283}, mesh = {Humans ; Longitudinal Studies ; *Stress, Psychological/metabolism/immunology/complications ; *Inflammation/metabolism/psychology/immunology ; Saliva/chemistry ; Male ; Female ; Young Adult ; Chronic Disease ; Adult ; Ecological Momentary Assessment ; Biomarkers/metabolism ; Cytokines/metabolism ; Research Design ; }, abstract = {Acute stress triggers adaptive physiological responses-including transient increases in inflammatory cytokines-while chronic stress is associated with sustained inflammatory activity that may underlie the development of various disorders. Despite extensive research on each stress type individually, the transition and interaction between them remain underexplored. This study aims to address this gap by employing an intensive longitudinal measurement burst design. Healthy university students will be recruited and monitored over three one-week assessment bursts, spaced by three-month breaks. Participants will complete ecological momentary assessments four times daily, recording their emotional states, stress experiences, and daily incidents. Simultaneously, saliva samples will be collected at matching time points to measure biomarkers of immune and stress system activity. In addition, daily audio diaries will provide qualitative context through advanced speech analysis techniques. Data will be analyzed using a multi-level modeling approach to differentiate within-person dynamics from between-person variability, accounting for potential moderators. The findings are expected to shed light on how repeated acute stressors transition into chronic stress and how chronic stress burden may influence acute stress responses.}, }
@article {pmid40316929, year = {2025}, author = {Demsash, AW and Abebe, R and Gezimu, W and Kitil, GW and Tizazu, MA and Lambebo, A and Bekele, F and Alemu, SS and Jarso, MH and Dube, GN and Wedajo, LF and Purohit, S and Kalayou, MH}, title = {Data-driven machine learning algorithm model for pneumonia prediction and determinant factor stratification among children aged 6-23 months in Ethiopia.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {647}, pmid = {40316929}, issn = {1471-2334}, mesh = {Humans ; Ethiopia/epidemiology ; Infant ; *Pneumonia/epidemiology/diagnosis ; *Machine Learning ; Female ; Male ; Algorithms ; Risk Factors ; }, abstract = {INTRODUCTION: Pneumonia is the leading cause of child morbidity and mortality and accounts for 5.6 million under-five child deaths. Pneumonia has a significant impact on the quality of life, the country's economy, and the survival of children. Therefore, this study aimed to develop data-driven predictive model using machine learning algorithms to predict pneumonia and stratify the determinant factors among children aged 6-23 months in Ethiopia.<br><br>METHODS: A total of 2035 samples of children were used from the 2016 Ethiopian Demographic and Health Survey dataset. Jupyter Notebook from Anaconda Navigators was used for data management and analysis. Important libraries such as Pandas, Seaborn, and Numpy were imported from Python. The data was pre-processed into a training and testing dataset with a 4:1 ratio, and tenfold cross-validation was used to reduce bias and enhance the models' performance. Six machine learning algorithms were used for model building and comparison, and confusion matrix elements were used to evaluate the performance of each algorithm. Principal component analysis and heatmap function were used for correlation detection between features. Feature importance score was used to identify and stratify the most important predictors of pneumonia.<br><br>RESULTS: From 2035 total samples, 16.6%, 20.1%, and 24.2% of children had short rapid breath, fever, and cough respectively. The overall magnitude of pneumonia among children aged 6-23&#xa0;months was 31.3% based on the 2016 EDHS report. A random forest algorithm is the relatively best performance model to predict pneumonia and stratify its determinates with 91.3% accuracy. The health facility visits, child sex, initiation of breastfeeding, birth interval, birth weight, husbands' education, women's age, and region, are the top eight important predictors of pneumonia among children with important scores of more than 5% to 20% respectively.<br><br>CONCLUSIONS: Random forest is the best model to predict pneumonia and stratify its determinant factors. The implications of this study are profound for advanced research methodology, tailored to promote effective health interventions such as lifestyle modification and behavioral intervention, based on individuals' unique features, specifically for stakeholders to take proactive childcare interventions. The study would serve as pioneering evidence for future research, and researchers are recommended to use deep learning algorithms to enhance prediction accuracy.}, }
@article {pmid40314555, year = {2025}, author = {Yu, Z and Li, S and Yang, W and Chen, J and Rahman, MA and Wang, C and Ma, W and Yao, X and Xiong, J and Xu, C and Zhou, Y and Chen, J and Huang, K and Gao, X and Fensholt, R and Weng, Q and Zhou, W}, title = {Enhancing Climate-Driven Urban Tree Cooling with Targeted Nonclimatic Interventions.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {18}, pages = {9082-9092}, doi = {10.1021/acs.est.4c14275}, pmid = {40314555}, issn = {1520-5851}, mesh = {*Trees ; Cities ; *Climate ; }, abstract = {Urban trees play a pivotal role in mitigating heat, yet the global determinants and patterns of their cooling efficiency (CE) remain elusive. Here, we quantify the diel CE of 229 cities across four climatic zones and employ a machine-learning model to assess the influence of variables on CE. We found that for every 10% increase in tree cover, surface temperatures are reduced by 0.25 °C during the day and 0.04 °C at night. Trees in humid regions exhibit the highest daytime CE, while those in arid zones demonstrate the greatest cooling effect at night. This can be explained by the difference in canopy density between the humid and arid zones. During the day, the high canopy density in the humid zone converts more solar radiation into latent heat flux. At night, the low canopy density in the arid zone intercepts less longwave radiation, which favors surface cooling. While climatic factors contribute nearly twice as much to CE as nonclimatic ones, our findings suggest that optimizing CE is possible by managing variables within specific thresholds due to their nonlinear effects. For instance, we revealed that in arid regions, an impervious surface coverage of approximately 60% is optimal, whereas in humid areas, reducing it to around 40% maximizes cooling benefits. These insights underscore the need for targeted management of nonclimatic factors to sustain tree cooling benefits and offer practical guidance for designing climate-resilient, nature-based urban strategies.}, }
@article {pmid40312707, year = {2025}, author = {Ketchaji, A and Fokam, J and Assah, F and Ateba, F and Wandji, ML and Pamen, JNB and Djoko, GRP and Seugnou, CDN and Kah, E and Atangana, AF and Ateudjieu, J}, title = {The impact of short message service reminders or peer home visits on adherence to antiretroviral therapy and viral load suppression among HIV-Infected adolescents in Cameroon: a randomized controlled trial.}, journal = {AIDS research and therapy}, volume = {22}, number = {1}, pages = {49}, pmid = {40312707}, issn = {1742-6405}, mesh = {Humans ; *HIV Infections/drug therapy/virology ; Adolescent ; Female ; Cameroon/epidemiology ; Male ; *Viral Load/drug effects ; *Text Messaging ; *House Calls ; Young Adult ; *Medication Adherence ; *Anti-HIV Agents/therapeutic use ; *Reminder Systems ; Peer Group ; }, abstract = {BACKGROUND: Adherence to antiretroviral therapy (ART) and viral load suppression (VLS) constitute one of the key challenges to control human immunodeficiency virus (HIV), especially during adolescence. This trial aimed at assessing the impact of short message services (SMS) or peer home visits (PHV) on adherence to ART and VL suppression among adolescents living with HIV (ALWHIV) in Cameroon.<br><br>METHODS: A randomized controlled trial (RCT) was conducted from July 2018 to February 2019 at the Mother and Child Center of the Chantal Biya Foundation in Yaounde. Eligible ALWHIV (15-19 years), with a fully disclosed HIV status, with availability of phone and guardian's consent, were randomly assigned to receive either daily SMS or bi-weekly PHV for a six-months period. The control-group received standard of care according to the national guidelines. Study investigators and participants were not blinded to the interventions group allocation, and no adverse events or side effects were observed. Adjusted logistic regression was used to assess the impact of interventions on outcomes. The study was approved by The Pan-African Clinical Trials Registry with PACTR201904582515723 at (www.pactr.org).<br><br>RESULTS: Adherence to ART increased in the PHV (aRR: 4.3; 95% CI: 2.2-8.3; p&#x2009;<&#x2009;0.001) and SMS (aRR: 3.1, 95% CI: 2.1-5.3; p&#x2009;<&#x2009;0.001) groups compared to the control-group. Likewise, VL suppression was higher in PHV (aRR: 2.1; 95% CI: 1.9-7.5 p&#x2009;<&#x2009;0.001) and SMS (aRR: 3.2; 95% CI: 1.8-5.4; p&#x2009;<&#x2009;0.001) groups compared to the control-group. Based on CI, both interventions showed similar benefits on improving adherence and VLS.<br><br>CONCLUSIONS: Among ALHIV, SMS or PHV contribute substantially to improving adherence and VL suppression among ALWHIV. Implementing such strategies would support efforts in eliminating pediatric AIDS in low- and middle-income countries.}, }
@article {pmid40307720, year = {2025}, author = {Moreau, SJM and Marchal, L and Boulain, H and Musset, K and Labas, V and Tomas, D and Gauthier, J and Drezen, JM}, title = {Multi-omic approach to characterize the venom of the parasitic wasp Cotesia congregata (Hymenoptera: Braconidae).}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {431}, pmid = {40307720}, issn = {1471-2164}, support = {ANR-12-ADAP-0001//Agence Nationale de la Recherche/ ; ANR-12-ADAP-0001//Agence Nationale de la Recherche/ ; ANR-12-ADAP-0001//Agence Nationale de la Recherche/ ; ANR-12-ADAP-0001//Agence Nationale de la Recherche/ ; ANR-12-ADAP-0001//Agence Nationale de la Recherche/ ; ANR-12-ADAP-0001//Agence Nationale de la Recherche/ ; SMHART project 35069//European Regional Development Fund/ ; SMHART project 35069//European Regional Development Fund/ ; }, mesh = {Animals ; *Wasps/genetics/virology/metabolism ; *Wasp Venoms/genetics/metabolism/chemistry ; Female ; *Proteomics/methods ; Insect Proteins/genetics/metabolism/chemistry ; Multiomics ; }, abstract = {BACKGROUND: Cotesia congregata is a parasitoid Hymenoptera belonging to the Braconidae family and carrying CCBV (Cotesia congregata Bracovirus), an endosymbiotic polydnavirus. CCBV virus is considered as the main virulence factor of this species, which has raised questions, over the past thirty years, about the potential roles of venom in the parasitic interaction between C. congregata and its host, Manduca sexta (Lepidoptera: Sphingidae). To investigate C. congregata venom composition, we identified genes overexpressed in the venom glands (VGs) compared to ovaries, analyzed the protein composition of this fluid and performed a detailed analysis of conserved domains of these proteins.<br><br>RESULTS: Of the 14 140 known genes of the C. congregata genome, 659 genes were significantly over-expressed (with 10-fold or higher changes in expression) in the VGs of female C. congregata, compared with the ovaries. We identified 30 proteins whose presence was confirmed in venom extracts by proteomic analyses. Twenty-four of these were produced as precursor molecules containing a predicted signal peptide. Six of the proteins lacked a predicted signal peptide, suggesting that venom production in C. congregata also involves non-canonical secretion mechanisms. We have also analysed 18 additional proteins and peptides of interest whose presence in venom remains uncertain, but which could play a role in VG function.<br><br>CONCLUSIONS: Our results show that the venom of C. congregata not only contains proteins (including several enzymes) homologous to well-known venomous compounds, but also original proteins that appear to be specific to this species. This exhaustive study sheds a new light on this venom composition, the molecular diversity of which was unexpected. These data pave the way for targeted functional analyses and to better understand the evolutionary mechanisms that have led to the formation of the venomous arsenals we observe today in parasitoid insects.}, }
@article {pmid40307287, year = {2025}, author = {Wu, J and He, D and Wang, Y and Liu, S and Du, Y and Wang, H and Tan, S and Zhang, D and Xie, J}, title = {An integrated transcriptome, metabolome, and microbiome dataset of Populus under nutrient-poor conditions.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {717}, pmid = {40307287}, issn = {2052-4463}, mesh = {*Metabolome ; *Microbiota ; Nutrients ; Plant Roots/microbiology/metabolism ; *Populus/microbiology/genetics/metabolism ; Rhizosphere ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; *Transcriptome ; Datasets as Topic ; }, abstract = {The rhizosphere microbiota recruited by plants contributes significantly to maintaining host productivity and resisting stress. However, the genetic mechanisms by which plants regulate this recruitment process remain largely unclear. Here, we generated a comprehensive dataset, including 27 root transcriptomes, 27 root metabolomes, and 54 bulk or rhizosphere soil 16S rRNA amplicons across nine poplar species from four sections grown in nutrient-poor natural soil, along with eleven growth phenotype data. We provided a thorough description of this dataset, followed by a comprehensive co-expression network analysis example that broke down the wall of the four-way relationship between plant gene-metabolite-microbe-phenotype, thus identifying the links between plant gene expression, metabolite accumulation, growth behavior, and rhizosphere microbiome variation under nutrient-poor conditions. Overall, this dataset enhances our understanding of plant and microbe interactions, offering valuable strategies and novel insights for resolving how plants regulate rhizosphere microbial compositions and functions, thereby improving host fitness, which will benefit future research.}, }
@article {pmid40306212, year = {2025}, author = {Nica, I and Georgescu, I}, title = {The ecological impact of agricultural production on CO2 emissions in India: Pathways to sustainable agriculture.}, journal = {Journal of environmental management}, volume = {384}, number = {}, pages = {125548}, doi = {10.1016/j.jenvman.2025.125548}, pmid = {40306212}, issn = {1095-8630}, mesh = {India ; *Agriculture ; *Carbon Dioxide/analysis ; Animals ; }, abstract = {This study examines the relationship between CO2 emissions and agricultural production in India from 1990 to 2023, using an Autoregressive Distributed Lag (ARDL) model. Key agricultural indicators analyzed include the Food Production Index (FPI), Cereal Production (CP), Livestock Production Index (LPI), and the value added by Agriculture, Forestry, and Fishing (AFF). The results show that on the long run, a 1 % increase in FPI leads to a 7.86 unit increase in CO2 emissions per capita, while a 1 % increase in livestock production results in a 3.28 unit decrease in CO2 emissions per capita. In the short run, a similar increase in food production and livestock production also influences CO2 emissions, with notable but varying impacts over time. These findings underline the environmental trade-offs between food security and CO2 emissions, emphasizing the need for sustainable agricultural practices. This research contributes to existing literature by utilizing a broad set of agricultural indicators and robust ARDL analysis to examine both short- and long-term effects, providing a more comprehensive understanding of agricultural sustainability. The study was prompted by India's rapid agricultural growth, driven by its growing population and economic expansion, which has raised significant environmental concerns. Unlike prior research that often takes a generalized or global approach, this study offers an India-specific analysis that captures the country's distinct socio-economic and ecological conditions. By focusing on nationally relevant agricultural indicators and sustainability challenges, the research provides context-sensitive insights that can support effective and targeted policy design. The findings highlight the importance of policies that align agricultural productivity with sustainability, supporting the UN Sustainable Development Goals on climate action and food security.}, }
@article {pmid40305182, year = {2025}, author = {Uemura, NA and Nakane, D}, title = {Type IV Pili in Thermophilic Bacteria: Mechanisms and Ecological Implications.}, journal = {Biomolecules}, volume = {15}, number = {4}, pages = {}, pmid = {40305182}, issn = {2218-273X}, support = {24KJ1131//Japan Society for the Promotion of Science/ ; 21K07020//Japan Society for the Promotion of Science/ ; 22H05066//Japan Society for the Promotion of Science/ ; }, mesh = {*Fimbriae, Bacterial/metabolism/physiology ; *Thermus thermophilus/metabolism/physiology/genetics ; }, abstract = {Type IV pili (T4P) machinery is critical for bacterial surface motility, protein secretion, and DNA uptake. This review highlights the ecological significance of T4P-dependent motility in Thermus thermophilus, a thermophilic bacterium isolated from hot springs. Unlike swimming motility, the T4P machinery enables bacteria to move over two-dimensional surfaces through repeated cycles of extension and retraction of pilus filaments. Notably, T. thermophilus exhibits upstream-directed migration under shear stress, known as rheotaxis, which appears to represent an adaptive strategy unique to thermophilic bacteria thriving in rapid water flows. Furthermore, T4P contributes to the capture of DNA and phages, indicating their multifunctionality in natural environments. Understanding the T4P dynamics provides insights into bacterial survival and evolution in extreme habitats.}, }
@article {pmid40304278, year = {2025}, author = {Lentendu, G and Singer, D and Agatha, S and Bahram, M and Hannula, SE and Helder, J and Tedersoo, L and Traunspurger, W and Geisen, S and Lara, E}, title = {EukFunc: A Holistic Eukaryotic Functional Reference for Automated Profiling of Soil Eukaryotes.}, journal = {Molecular ecology resources}, volume = {25}, number = {7}, pages = {e14118}, doi = {10.1111/1755-0998.14118}, pmid = {40304278}, issn = {1755-0998}, support = {PID2021-128499NB-I00 10.13039/501100011033//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; 182531//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; }, mesh = {*Soil/parasitology ; *Eukaryota/classification/genetics/physiology ; Animals ; Nematoda/classification/genetics ; *Computational Biology/methods ; Fungi/classification/genetics ; *Soil Microbiology ; }, abstract = {The soil eukaryome constitutes a significant portion of Earth's biodiversity that drives major ecosystem functions, such as controlling carbon fluxes and plant performance. Currently, however, we miss a standardised approach to functionally classify the soil eukaryome in a holistic way. Here we compiled EukFunc, the first functional reference database that characterises the most abundant and functionally important soil eukaryotic groups: fungi, nematodes and protists. We classified the 14,060 species in the database based on their mode of nutrient acquisition into the main functional classes of symbiotroph (40%), saprotroph (26%), phototroph (17%), predator (16%) and unknown (2%). EukFunc provides further detailed information about nutrition mode, including a secondary functional class (i.e., for organisms with multiple nutrition modes), and preyed or associated organisms for predatory or symbiotic taxa, respectively. EukFunc is available in multiple formats for user-friendly functional analyses of specific taxa or annotations of metabarcoding datasets, both embedded in the R package EukFunc. Using a soil dataset from alpine and subalpine meadows, we highlighted the extended ecological insights obtained from combining functional information across the entire soil eukaryome as compared to focusing on fungi, protists or nematodes individually. EukFunc streamlines the annotation process, enhances efficiency and accuracy, and facilitates the investigation of the functional roles of soil eukaryotes-a prerequisite to better understanding soil systems.}, }
@article {pmid40303041, year = {2024}, author = {McDuie, F and T Overton, C and A Lorenz, A and L Matchett, E and L Mott, A and A Mackell, D and T Ackerman, J and De La Cruz, SEW and Patil, VP and Prosser, DJ and Takekawa, JY and Orthmeyer, DL and Pitesky, ME and Díaz-Muñoz, SL and Riggs, BM and Gendreau, J and Reed, ET and Petrie, MJ and Williams, CK and Buler, JJ and Hardy, MJ and Ladman, BS and Legagneux, P and Bêty, J and Thomas, PJ and Rodrigue, J and Lefebvre, J and Casazza, ML}, title = {Mitigating Risk: Predicting H5N1 Avian Influenza Spread with an Empirical Model of Bird Movement.}, journal = {Transboundary and emerging diseases}, volume = {2024}, number = {}, pages = {5525298}, pmid = {40303041}, issn = {1865-1682}, mesh = {Animals ; *Influenza in Birds/epidemiology/virology/transmission/prevention &amp; control ; *Influenza A Virus, H5N1 Subtype/physiology ; *Animal Migration ; Birds ; Geographic Information Systems ; Disease Outbreaks/veterinary ; Animals, Wild ; }, abstract = {Understanding timing and distribution of virus spread is critical to global commercial and wildlife biosecurity management. A highly pathogenic avian influenza virus (HPAIv) global panzootic, affecting ~600 bird and mammal species globally and over 83 million birds across North America (December 2023), poses a serious global threat to animals and public health. We combined a large, long-term waterfowl GPS tracking dataset (16 species) with on-ground disease surveillance data (county-level HPAIv detections) to create a novel empirical model that evaluated spatiotemporal exposure and predicted future spread and potential arrival of HPAIv via GPS tracked migratory waterfowl through 2022. Our model was effective for wild waterfowl, but predictions lagged HPAIv detections in poultry facilities and among some highly impacted nonmigratory species. Our results offer critical advance warning for applied biosecurity management and planning and demonstrate the importance and utility of extensive multispecies tracking to highlight potential high-risk disease spread locations and more effectively manage outbreaks.}, }
@article {pmid40299786, year = {2025}, author = {Xiao, Y and Elmasry, M and Bai, JDK and Chen, A and Chen, Y and Jackson, B and Johnson, JO and Prasanna, P and Chen, C and Damaghi, M}, title = {Eco-Evolutionary Guided Pathomic Analysis Detects Biomarkers to Predict Ductal Carcinoma In Situ Upstaging.}, journal = {Cancer research}, volume = {85}, number = {13}, pages = {2537-2547}, doi = {10.1158/0008-5472.CAN-24-2070}, pmid = {40299786}, issn = {1538-7445}, support = {R21CA258493-02S1//National Institutes of Health (NIH)/ ; R01GM148970//National Institute of General Medical Sciences (NIGMS)/ ; U01 CA261841/CA/NCI NIH HHS/United States ; R01 CA297843/CA/NCI NIH HHS/United States ; R01CA272601//National Institutes of Health (NIH)/ ; R01 CA272601/CA/NCI NIH HHS/United States ; U01CA261841//National Institutes of Health (NIH)/ ; R01CA249016//National Institutes of Health (NIH)/ ; R01CA297843//National Institutes of Health (NIH)/ ; }, mesh = {Humans ; Female ; *Breast Neoplasms/pathology/metabolism/diagnosis/genetics ; *Biomarkers, Tumor/metabolism/analysis ; *Carcinoma, Intraductal, Noninfiltrating/pathology/metabolism/diagnosis/genetics ; Tumor Microenvironment ; Retrospective Studies ; Neoplasm Staging ; Disease Progression ; Middle Aged ; Prognosis ; }, abstract = {UNLABELLED: Cancers evolve in a dynamic ecosystem. Thus, characterizing the ecological dynamics of cancer is crucial to understanding cancer evolution, which can lead to the discovery of biomarkers to predict disease progression. Ductal carcinoma in situ (DCIS) is an early-stage breast cancer characterized by abnormal epithelial cell growth confined within the milk ducts, and biomarkers are needed to predict which cases will progress to aggressive disease. In this study, we showed that ecological analysis of hypoxia and acidosis biomarkers can significantly improve prediction of DCIS upstaging. Quantitative analyses were performed on immunohistologic images from a retrospective cohort of DCIS specimens collected from biopsy samples. First, an eco-evolutionary designed approach was developed to define habitats in the tumor intraductal microenvironment based on oxygen diffusion distance. Then, cancer cells with metabolic phenotypes attributed to their habitats were identified, including a hypoxia-responding CA9+ phenotype and an acid-adapted LAMP2b+ phenotype. Whereas these markers have traditionally shown limited, if any, predictive capabilities for DCIS progression when analyzed from an ecological perspective, their power to differentiate between non-upstaged and upstaged DCIS increased significantly. Additionally, the distribution of distinct niches with specific spatial patterns of these biomarkers predicted patient upstaging. The niches were characterized by pattern analysis of both cellular and spatial features. A random forest classifier that was trained and underwent a five-fold validation on the biopsy cohort achieved an AUC of 0.74 for predicting clinical outcome. These results affirm the importance of tumor ecological features in eco-evolutionary-designed approaches for biomarker discovery.<br><br>SIGNIFICANCE: Evolutionary dynamics of the various niches composing the tumor ecosystem can be harnessed for predicting cancer progression, demonstrating how eco-evolutionary-designed approaches can guide biomarkers discovery studies in the era of digital pathology. This article is part of a special series: Driving Cancer Discoveries with Computational Research, Data Science, and Machine Learning/AI.}, }
@article {pmid40298711, year = {2025}, author = {Prado, SI and Novais, MAP}, title = {Acute viral bronchiolitis in Brazil: characteristics of length of stay and hospital costs.}, journal = {Ciencia &amp; saude coletiva}, volume = {30}, number = {4}, pages = {e07402023}, doi = {10.1590/1413-81232025304.07402023}, pmid = {40298711}, issn = {1678-4561}, mesh = {Humans ; Brazil ; Infant ; Retrospective Studies ; *Length of Stay/statistics &amp; numerical data/economics ; Acute Disease ; Child, Preschool ; *Hospitalization/economics/statistics &amp; numerical data ; *Bronchiolitis, Viral/economics/therapy/epidemiology ; *Hospital Costs/statistics &amp; numerical data ; Longitudinal Studies ; Male ; Female ; National Health Programs/economics ; }, abstract = {The objective of the study was to evaluate the length of stay in pediatric hospitalizations for acute viral bronchiolitis in the Brazilian Health System (SUS) and the costs of hospitalizations. This was a quantitative, observational, and ecological study, based on a retrospective and longitudinal analysis of data from the Department of Informatics of the Unified Health System (DATASUS; 2012-2021) using descriptive statistics and Tukey's paired test. Regarding the mean value of AIH/HAA Hospital Admission Authorization, among the regions, the high costs of hospitalizations are located more frequent in the Southeast region and the lowest proportion is directed to the corresponds to the North region. In the length of hospital stay among the regions, the shortest mean stay was identified in the Central West region (2.5 days) and the greatest stay in the Northeast region (3.1 days). Considering the age group of one year of life, its representativeness was 57% when compared to the age group of 1-4 years (43%). The fragility of the implementation of primary public policies in the prevention of bronchiolitis contributes to high hospital costs and significant economic impacts on the national healthcare system.}, }
@article {pmid40297776, year = {2025}, author = {Schwarzerova, J and Olesova, D and Jureckova, K and Kvasnicka, A and Kostoval, A and Friedecky, D and Sekora, J and Pomenkova, J and Provaznik, V and Popelinsky, L and Weckwerth, W}, title = {Enhanced metabolomic predictions using concept drift analysis: identification and correction of confounding factors.}, journal = {Bioinformatics advances}, volume = {5}, number = {1}, pages = {vbaf073}, pmid = {40297776}, issn = {2635-0041}, abstract = {MOTIVATION: The increasing use of big data and optimized prediction methods in metabolomics requires techniques aligned with biological assumptions to improve early symptom diagnosis. One major challenge in predictive data analysis is handling confounding factors-variables influencing predictions but not directly included in the analysis.<br><br>RESULTS: Detecting and correcting confounding factors enhances prediction accuracy, reducing false negatives that contribute to diagnostic errors. This study reviews concept drift detection methods in metabolomic predictions and selects the most appropriate ones. We introduce a new implementation of concept drift analysis in predictive classifiers using metabolomics data. Known confounding factors were confirmed, validating our approach and aligning it with conventional methods. Additionally, we identified potential confounding factors that may influence biomarker analysis, which could introduce bias and impact model performance.<br><br>Based on biological assumptions supported by detected concept drift, these confounding factors were incorporated into correction of prediction algorithms to enhance their accuracy. The proposed methodology has been implemented in Semi-Automated Pipeline using Concept Drift Analysis for improving Metabolomic Predictions (SAPCDAMP), an open-source workflow available at https://github.com/JanaSchwarzerova/SAPCDAMP.}, }
@article {pmid40296452, year = {2025}, author = {Wang, S and Kaur, S and Kunath, BJ and May, P and Richardson, L and Rogers, AB and Wilmes, P and Finn, RD and Vizcaíno, JA}, title = {An Approach to Integrate Metagenomics, Metatranscriptomics and Metaproteomics Data in Public Data Resources.}, journal = {Proteomics}, volume = {25}, number = {17-18}, pages = {33-42}, pmid = {40296452}, issn = {1615-9861}, support = {/WT_/Wellcome Trust/United Kingdom ; 223745/Z/21/Z//Wellcome/ ; //EMBL Core Funding/ ; C19/BM/13684739//National Research Fund Luxembourg (FNR)/ ; }, mesh = {*Metagenomics/methods ; *Proteomics/methods ; Humans ; Databases, Protein ; Metagenome ; *Transcriptome ; Animals ; Pilot Projects ; }, abstract = {The availability of public metaproteomics, metagenomics and metatranscriptomics data in public resources such as MGnify (for metagenomics/metatranscriptomics) and the PRIDE database (for metaproteomics), continues to increase. When these omics techniques are applied to the same samples, their integration offers new opportunities to understand the structure (metagenome) and functional expression (metatranscriptome and metaproteome) of the microbiome. Here, we describe a pilot study aimed at integrating public multi-meta-omics datasets from studies based on human gut and marine hatchery samples. Reference search databases (search DBs) were built using assembled metagenomic (and metatranscriptomic, where available) sequence data followed by de novo gene calling, using both data from the same sampling event and from independent samples. The resulting protein sets were evaluated for their utility in metaproteomics analysis. In agreement with previous studies, the highest number of peptide identifications was generally obtained when using search DBs created from the same samples. Data integration of the multi-omics results was performed in MGnify. For that purpose, the MGnify website was extended to enable the visualisation of the resulting peptide/protein information from three reanalysed metaproteomics datasets. A workflow (https://github.com/PRIDE-reanalysis/MetaPUF) has been developed allowing researchers to perform equivalent data integration, using paired multi-omics datasets. This is the first time that a data integration approach for multi-omics datasets has been implemented from public data available in the world-leading MGnify and PRIDE resources.}, }
@article {pmid40295976, year = {2025}, author = {Liberati, F and Pose Marino, TM and Bottoni, P and Canestrelli, D and Castrignanò, T}, title = {HPC-T-Assembly: a pipeline for de novo transcriptome assembly of large multi-specie datasets.}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {113}, pmid = {40295976}, issn = {1471-2105}, mesh = {*Software ; *Transcriptome ; *Gene Expression Profiling/methods ; Sequence Analysis, RNA/methods ; Computational Biology/methods ; Databases, Genetic ; RNA-Seq/methods ; }, abstract = {BACKGROUND: Recent years have seen a substantial increase in RNA-seq data production, with this technique becoming the primary approach for gene expression studies across a wide range of non-model organisms. The majority of these organisms lack a well-annotated reference genome to serve as a basis for studying differentially expressed genes (DEGs). As an alternative cost-effective protocol to using a reference genome, the assembly of RNA-seq raw reads is performed to produce what is referred to as a 'de novo transcriptome,' serving as a reference for subsequent DEGs' analysis. This assembly step for conventional DEGs analysis pipelines for non-model organisms is a computationally expensive task. Furthermore, the complexity of the de novo transcriptome assembly workflows poses a challenge for researchers in implementing best-practice techniques and the most recent software versions, particularly when applied to various organisms of interest.<br><br>RESULTS: To address computational challenges in transcriptomic analyses of non-model organisms, we present HPC-T-Assembly, a tool for de novo transcriptome assembly from RNA-seq data on high-performance computing (HPC) infrastructures. It is designed for straightforward setup via a Web-oriented interface, allowing analysis configuration for several species. Once configuration data is provided, the entire parallel computing software for assembly is automatically generated and can be launched on a supercomputer with a simple command line. Intermediate and final outputs of the assembly pipeline include additional post-processing steps, such as assembly quality control, ORF prediction, and transcript count matrix construction.<br><br>CONCLUSION: HPC-T-Assembly allows users, through a user-friendly Web-oriented interface, to configure a run for simultaneous assemblies of RNA-seq data from multiple species. The parallel pipeline, launched on HPC infrastructures, significantly reduces computational load and execution times, enabling large-scale transcriptomic and meta-transcriptomics analysis projects.}, }
@article {pmid40295704, year = {2024}, author = {Grunnill, M and Eshaghi, A and Damodaran, L and Nagra, S and Gharouni, A and Braukmann, T and Clark, S and Peci, A and Isabel, S and Banh, P and Plessis, LD and Murall, CL and Colijn, C and Mubareka, S and Hasso, M and Bahl, J and Mostafa, HH and Gubbay, JB and Patel, SN and Wu, J and Duvvuri, VR}, title = {Inferring enterovirus D68 transmission dynamics from the genomic data of two 2022 North American outbreaks.}, journal = {Npj viruses}, volume = {2}, number = {1}, pages = {34}, pmid = {40295704}, issn = {2948-1767}, abstract = {Enterovirus D68 (EV-D68) has emerged as a significant cause of acute respiratory illness in children globally, notably following its extensive outbreak in North America in 2014. A recent outbreak of EV-D68 was observed in Ontario, Canada, from August to October 2022. Our phylogenetic analysis revealed a notable genetic similarity between the Ontario outbreak and a concurrent outbreak in Maryland, USA. Utilizing Bayesian phylodynamic modeling on whole genome sequences (WGS) from both outbreaks, we determined the median peak time-varying reproduction number (Rt) to be 2.70, 95% HPD (1.76, 4.08) in Ontario and 2.10, 95% HPD (1.41, 3.17) in Maryland. The Rt trends in Ontario closely matched those derived via EpiEstim using reported case numbers. Our study also provides new insights into the median infection duration of EV-D68, estimated at 7.94 days, 95% HPD (4.55, 12.8) in Ontario and 10.8 days, 95% HPD (5.85, 18.6) in Maryland, addressing the gap in the existing literature surrounding EV-D68's infection period. We observed that the estimated Time since the Most Recent Common Ancestor (TMRCA) and the epidemic's origin coincided with the easing of COVID-19 related social contact restrictions in both areas. This suggests that the relaxation of non-pharmaceutical interventions, initially implemented to control COVID-19, may have inadvertently facilitated the spread of EV-D68. These findings underscore the effectiveness of phylodynamic methods in public health, demonstrating their broad application from local to global scales and underscoring the critical role of pathogen genomic data in enhancing public health surveillance and outbreak characterization.}, }
@article {pmid40294093, year = {2025}, author = {Williams, B and Balvanera, SM and Sethi, SS and Lamont, TAC and Jompa, J and Prasetya, M and Richardson, L and Chapuis, L and Weschke, E and Hoey, A and Beldade, R and Mills, SC and Haguenauer, A and Zuberer, F and Simpson, SD and Curnick, D and Jones, KE}, title = {Unlocking the soundscape of coral reefs with artificial intelligence: pretrained networks and unsupervised learning win out.}, journal = {PLoS computational biology}, volume = {21}, number = {4}, pages = {e1013029}, pmid = {40294093}, issn = {1553-7358}, mesh = {*Coral Reefs ; Animals ; Acoustics ; *Unsupervised Machine Learning ; *Artificial Intelligence ; Ecosystem ; Algorithms ; Neural Networks, Computer ; Computational Biology ; Fishes/physiology ; Machine Learning ; Environmental Monitoring/methods ; }, abstract = {Passive acoustic monitoring can offer insights into the state of coral reef ecosystems at low-costs and over extended temporal periods. Comparison of whole soundscape properties can rapidly deliver broad insights from acoustic data, in contrast to detailed but time-consuming analysis of individual bioacoustic events. However, a lack of effective automated analysis for whole soundscape data has impeded progress in this field. Here, we show that machine learning (ML) can be used to unlock greater insights from reef soundscapes. We showcase this on a diverse set of tasks using three biogeographically independent datasets, each containing fish community (high or low), coral cover (high or low) or depth zone (shallow or mesophotic) classes. We show supervised learning can be used to train models that can identify ecological classes and individual sites from whole soundscapes. However, we report unsupervised clustering achieves this whilst providing a more detailed understanding of ecological and site groupings within soundscape data. We also compare three different approaches for extracting feature embeddings from soundscape recordings for input into ML algorithms: acoustic indices commonly used by soundscape ecologists, a pretrained convolutional neural network (P-CNN) trained on 5.2 million hrs of YouTube audio, and CNN's which were trained on each individual task (T-CNN). Although the T-CNN performs marginally better across tasks, we reveal that the P-CNN offers a powerful tool for generating insights from marine soundscape data as it requires orders of magnitude less computational resources whilst achieving near comparable performance to the T-CNN, with significant performance improvements over the acoustic indices. Our findings have implications for soundscape ecology in any habitat.}, }
@article {pmid40293859, year = {2025}, author = {Wastler, HM and Cowan, HR and Breitborde, NJK and Tabares, JV and Yu, M and Pan, X and Boettner, B and Browning, C and Bryan, CJ}, title = {Ecological Momentary Assessment of Emotion Regulation and Suicidal Ideation in First-Episode Psychosis.}, journal = {Schizophrenia bulletin}, volume = {51}, number = {6}, pages = {1718-1729}, pmid = {40293859}, issn = {1745-1701}, support = {YIG-0-184-20//American Foundation for Suicide Prevention/ ; }, mesh = {Humans ; *Ecological Momentary Assessment ; *Suicidal Ideation ; *Psychotic Disorders/physiopathology ; Male ; Female ; *Emotional Regulation/physiology ; Adult ; Young Adult ; Adolescent ; *Affect/physiology ; }, abstract = {Individuals with first-episode psychosis (FEP) are at increased risk for suicide, though few studies have examined the extent to which emotion regulation abnormalities contribute to this risk. The current study sought to address this gap by examining which stages of emotion regulation (ie, identification, selection, implementation) are related to suicidal ideation among individuals with FEP. Forty-one participants completed 28 days of ecological momentary assessment to assess suicidal ideation, negative affect, and emotion regulation in real-time. Results indicated that all 3 stages of emotion regulation were related to suicidal ideation in FEP. Specifically, within-person emotion regulation interacted with between-person negative affect to predict concurrent suicidal ideation (identification stage). Additionally, decreased use of adaptive strategies and increased use of maladaptive strategies were associated with more severe suicidal ideation (selection stage). Finally, decreased emotion regulation effectiveness was associated with more severe suicidal ideation (implementation stage). These findings suggest that emotion regulation difficulties might contribute to the high rates of suicide risk among individuals with FEP. Additional research is needed to determine whether these emotion regulation difficulties are unique to FEP or if they also appear in other high-risk groups.}, }
@article {pmid40292360, year = {2025}, author = {Andersen, ZJ and Badyda, A and Tzivian, L and Dzhambov, AM and Paunovic, K and Savic, S and Jacquemin, B and Dragic, N}, title = {Air pollution inequalities in Europe: A deeper understating of challenges in Eastern Europe and pathways forward towards closing the gap between East and West.}, journal = {Environmental epidemiology (Philadelphia, Pa.)}, volume = {9}, number = {3}, pages = {e383}, pmid = {40292360}, issn = {2474-7882}, }
@article {pmid40292044, year = {2025}, author = {Edelson, JB and Huang, J and Wang, Z and Tam, V and Lefktowitz, D and O'Connor, MJ and White, R and Ha, L and Wittlieb-Weber, CA and Rossano, JW and Lin, K and Cousino, MK and Lane-Fall, M and O'Byrne, ML}, title = {Identifying the determinants of health-related quality of life in children after heart transplant.}, journal = {JHLT open}, volume = {8}, number = {}, pages = {100250}, pmid = {40292044}, issn = {2950-1334}, abstract = {BACKGROUND: Pediatric heart transplant (PHT) recipients have impaired health-related quality of life (HRQOL) that is not fully explained by cardiac limitations. Environment is known to influence HRQOL in other chronic disease populations but is less understood in PHT. Understanding the determinants of HRQOL is a necessary step in identifying high-risk groups and designing actionable interventions.<br><br>METHODS: This cross-sectional study includes 8- to 18-year heart transplant (HT) recipients and their families. Generalized estimating equations were used to evaluate the associations of individual characteristics (diagnosis, pulmonary capillary wedge pressure [PCWP], cardiac index [CI]), microenvironment (parent education level, financial security, parental stress [PSI], assessment of child anxiety) and macroenvironment [Child Opportunity Index (COI)] with HRQOL.<br><br>RESULTS: Of 31 participants, 32% self-identified as Black, and 40% had congenital heart disease. On cardiac catheterization, 61% had a CI &#x2265;3&#xa0;liter/min/m[2] and PCWP &#x2264;10&#xa0;mm&#xa0;Hg. Most households had &#x2265;1 parent who had completed college (58%); 28% of households expressed difficulty paying bills. The PSI showed elevated parental stress [64.5 (interquartile range [IQR] 52.0, 77.8)], while the COI was low [73.0 (IQR 44.5, 89.0)] as was HRQOL [Pediatric Quality of Life 4.0 Core Scales 71.7 (IQR 64.2-82.5), Pediatric Cardiac Quality of Life Index 61.8 (IQR 55.7-74.8)]. Higher parental stress (p = 0.036), higher parental perception of child anxiety (p = 0.058), lower Max VO2 (p = 0.059), and higher PCWP (p = 0.006) were independently associated with worse quality of life.<br><br>CONCLUSIONS: HRQOL in children after heart transplant is reduced and determined not only by traditional measures of cardiovascular function, but also by patient psychology and their household environment, highlighting the utility of using an adapted ecological systems framework to understand HRQOL.}, }
@article {pmid40288322, year = {2025}, author = {Zhou, H and Wu, Z and Wang, X and Jiang, L and Sun, H and Li, H and Yan, Z and Wang, Y and Yao, X and Zhang, C and Tang, J}, title = {6PPD-quinone exposure induces oxidative damage and physiological disruption in Eisenia fetida: An integrated analysis of phenotypes, multi-omics, and intestinal microbiota.}, journal = {Journal of hazardous materials}, volume = {493}, number = {}, pages = {138334}, doi = {10.1016/j.jhazmat.2025.138334}, pmid = {40288322}, issn = {1873-3336}, mesh = {*Oligochaeta/drug effects/physiology/metabolism ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Soil Pollutants/toxicity ; *Oxidative Stress/drug effects ; *Phenylenediamines/toxicity ; Phenotype ; Reactive Oxygen Species/metabolism ; Metabolomics ; Transcriptome/drug effects ; Multiomics ; Benzoquinones ; }, abstract = {The environmental prevalence of the tire wear-derived emerging pollutant N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine-quinone (6PPD-Q) has increasingly raised public concern. However, knowledge of the adverse effects of 6PPD-Q on soil fauna is scarce. In this study, we elucidated its impact on soil fauna, specifically on the earthworm Eisenia fetida. Our investigation encompassed phenotypic, multi-omics, and microbiota analyses to assess earthworm responses to a gradient of 6PPD-Q contamination (10, 100, 1000, and 5000 μg/kg dw soil). Post-28-day exposure, 6PPD-Q was found to bioaccumulate in earthworms, triggering reactive oxygen species production and consequent oxidative damage to coelomic and intestinal tissues. Transcriptomic and metabolomic profiling revealed several physiological perturbations, including inflammation, immune dysfunction, metabolic imbalances, and genetic toxicity. Moreover, 6PPD-Q perturbed the intestinal microbiota, with high dosages significantly suppressing microbial functions linked to metabolism and information processing (P < 0.05). These alterations were accompanied by increased mortality and weight loss in the earthworms. Specifically, at an environmental concentration of 6PPD-Q (1000 μg/kg), we observed a substantial reduction in survival rate and physiological disruptions. This study provides important insights into the environmental hazards of 6PPD-Q to soil biota and reveals the underlying toxicological mechanisms, underscoring the need for further research to mitigate its ecological footprint.}, }
@article {pmid40287834, year = {2025}, author = {Mohanty, A and Srinivasan, A and Udupaa, P and Catchpoole, D}, title = {Multiomics and tumor banking: comprehensive plaforms- integrating cancer diversity, biomarker discovery and personalised cancer care in India.}, journal = {Human molecular genetics}, volume = {}, number = {}, pages = {}, doi = {10.1093/hmg/ddaf033}, pmid = {40287834}, issn = {1460-2083}, abstract = {Biobanks are innovative biomedical research infrastructures that play a crucial role in advancing cancer research by supporting investigations into the etiology, progression, and therapeutic interventions of the disease. Biobanks have significantly contributed to personalized medicine by providing high-quality bio specimen resources and expertise in tissue handling, essential for understanding the interplay of genetic, ecological, and lifestyle factors on cancer biology, human health, and mortality. By linking bio specimens with clinical, pathological, and epidemiological data, biobanks are central in the discovery and development of cancer therapeutics through biomarkers. In this review, the importance of managing biobanks as integral parts of data generation and analytics continuum driving precision medicine is pointed out. The advent of multi-OMICS analytics, combined with artificial intelligence, systems biology, and deep machine learning, has elevated the importance of bio banking human bio specimens as not only a biological resource but also an informatics asset. Here, we examine the impact of bio banking in facilitating translational, bench-to-bedside cancer research, with a focus on multi-OMICS data-driven biomarker discovery and precision oncology. In addition, we discuss one of the major innovations in biobank management: the hub-and-spoke model. This centralized system leverages core expertise and resources while collecting bio specimens from diverse geographic regions, thereby capturing the heterogeneity of cancer biology. The hub-and-spoke approach is particularly advantageous for countries like India, characterized by vast geographic and demographic diversity. It ensures complete coverage of the different types of cancers, disease stages, and population groups in addressing the complexity and diversity of cancer biology.}, }
@article {pmid40287826, year = {2025}, author = {Gerhardt, K and Ruiz-Perez, CA and Rodriguez-R, LM and Jain, C and Tiedje, JM and Cole, JR and Konstantinidis, KT}, title = {FastAAI: efficient estimation of genome average amino acid identity and phylum-level relationships using tetramers of universal proteins.}, journal = {Nucleic acids research}, volume = {53}, number = {8}, pages = {}, pmid = {40287826}, issn = {1362-4962}, support = {DBI1356288NSF//NSF/ ; }, mesh = {Phylogeny ; *Genome, Bacterial ; *Software ; *Bacteria/genetics/classification ; *Amino Acids/genetics ; *Computational Biology/methods ; }, abstract = {Estimation of whole-genome relatedness and taxonomic identification are two important bioinformatics tasks in describing environmental or clinical microbiomes. The genome-aggregate Average Nucleotide Identity is routinely used to derive the relatedness of closely related (species level) microbial and viral genomes, but it is not appropriate for more divergent genomes. Average Amino-acid Identity (AAI) can be used in the latter cases, but no current AAI implementation can efficiently compare thousands of genomes. Here we present FastAAI, a tool that estimates whole-genome pairwise relatedness using shared tetramers of universal proteins in a matter of microseconds, providing a speedup of up to 5 orders of magnitude when compared with current methods for calculating AAI or alternative whole-genome metrics. Further, FastAAI resolves distantly related genomes related at the phylum level with comparable accuracy to the phylogeny of ribosomal RNA genes, substantially improving on a known limitation of current AAI implementations. Our analysis of the resulting AAI matrices also indicated that bacterial lineages predominantly evolve gradually, rather than showing bursts of diversification, and that AAI thresholds to define classes, orders, and families are generally elusive. Therefore, FastAAI uniquely expands the toolbox for microbiome analysis and allows it to scale to millions of genomes.}, }
@article {pmid40287646, year = {2025}, author = {He, L and Zou, Q and Wang, Y}, title = {metaTP: a meta-transcriptome data analysis pipeline with integrated automated workflows.}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {111}, pmid = {40287646}, issn = {1471-2105}, support = {62102269//National Natural Science Foundation of China/ ; }, mesh = {*Metagenomics/methods ; Computational Biology/methods ; *Software ; *Gene Expression Profiling/methods ; *Microbiota ; Data Collection ; Quality Control ; Workflow ; RNA, Untranslated ; Molecular Sequence Annotation ; Rhizosphere ; Automation ; }, abstract = {BACKGROUND: The accessibility of sequencing technologies has enabled meta-transcriptomic studies to provide a deeper understanding of microbial ecology at the transcriptional level. Analyzing omics data involves multiple steps that require the use of various bioinformatics tools. With the increasing availability of public microbiome datasets, conducting meta-analyses can reveal new insights into microbiome activity. However, the reproducibility of data is often compromised due to variations in processing methods for sample omics data. Therefore, it is essential to develop efficient analytical workflows that ensure repeatability, reproducibility, and the traceability of results in microbiome research.<br><br>RESULTS: We developed metaTP, a pipeline that integrates bioinformatics tools for analyzing meta-transcriptomic data comprehensively. The pipeline includes quality control, non-coding RNA removal, transcript expression quantification, differential gene expression analysis, functional annotation, and co-expression network analysis. To quantify mRNA expression, we rely on reference indexes built using protein-coding sequences, which help overcome the limitations of database analysis. Additionally, metaTP provides a function for calculating the topological properties of gene co-expression networks, offering an intuitive explanation for correlated gene sets in high-dimensional datasets. The use of metaTP is anticipated to support researchers in addressing microbiota-related biological inquiries and improving the accessibility and interpretation of microbiota RNA-Seq data.<br><br>CONCLUSIONS: We have created a conda package to integrate the tools into our pipeline, making it a flexible and versatile tool for handling meta-transcriptomic sequencing data. The metaTP pipeline is freely available at: https://github.com/nanbei45/metaTP .}, }
@article {pmid40286849, year = {2025}, author = {Bartas, M and Petrovič, M and Brázda, V and Trenz, O and Ďurčanský, A and Šťastný, J}, title = {CpX Hunter web tool allows high-throughput identification of CpG, CpA, CpT, and CpC islands: A case study in Drosophila genome.}, journal = {The Journal of biological chemistry}, volume = {301}, number = {6}, pages = {108537}, pmid = {40286849}, issn = {1083-351X}, mesh = {Animals ; *CpG Islands ; *Drosophila melanogaster/genetics ; DNA Methylation ; Internet ; *Software ; *Genome, Insect ; }, abstract = {With continuous advances in DNA sequencing methods, accessibility to high-quality genomic information for all living organisms is ever-increasing. However, to interpret this information effectively and formulate hypotheses, users often require higher level programming skills. Therefore, the generation of web-based tools is becoming increasingly popular. CpG island regions in genomes are often found in gene promoters and are prone to DNA methylation, with their methylation status determining if a gene is expressed. Notably, understanding the biological impact of CpX modifications on genomic regulation is becoming increasingly important as these modifications have been associated with diseases such as cancer and neurodegeneration. However, there is currently no easy-to-use, scalable tool to detect and quantify CpX islands in full genomes. We have developed a Java-based web server for CpX island analyses that benefits from the DNA Analyzer Web server environment and overcomes several limitations. For a pilot demonstration study, we selected a well-described model organism Drosophila melanogaster. Subsequent analysis of the obtained CpX islands revealed several interesting and previously undescribed phenomena. One of them is the fact, that nearly half of long CpG islands were located on chromosome X, and that long CpA and CpT islands were significantly overrepresented at the subcentromeric regions of autosomes (chr2 and chr3) and also on chromosome Y. Wide genome overlays of predicted CpX islands revealed their co-occurrence with various (epi)genomics features comprising cytosine methylations, accessible chromatin, transposable elements, or binding of transcription factors and other proteins. CpX Hunter is freely available as a web tool at: https://bioinformatics.ibp.cz/#/analyse/cpg.}, }
@article {pmid40286830, year = {2025}, author = {Yu, X and Yao, R and Yao, R and Jin, X and Huang, J and Liang, Q and Jin, LN and Sun, J}, title = {Mechanistic understanding of the toxic effects of tri-n-butyl phosphate (TnBP) and tricresyl phosphate (TCP) to Escherichia coli: Evidence from alterations in biomarker expression and perturbations of the metabolic network.}, journal = {Comparative biochemistry and physiology. Toxicology &amp; pharmacology : CBP}, volume = {295}, number = {}, pages = {110211}, doi = {10.1016/j.cbpc.2025.110211}, pmid = {40286830}, issn = {1532-0456}, mesh = {*Escherichia coli/drug effects/metabolism ; Oxidative Stress/drug effects ; Biomarkers/metabolism ; *Organophosphates/toxicity ; *Metabolic Networks and Pathways/drug effects ; *Flame Retardants/toxicity ; Reactive Oxygen Species/metabolism ; Metabolomics ; Escherichia coli Proteins/metabolism ; *Plasticizers/toxicity ; }, abstract = {Tri-n-butyl phosphate (TnBP) and tricresyl phosphate (TCP), emerging flame retardants and plasticizers, have garnered increasing attention due to their potential risks to ecosystem. A few researches regarding the toxicological mechanisms of TnBP and TCP had been performed, while molecular-level toxic effects of them and metabolic response using microbial models are the lack of relevant investigation. Thus, we investigated the cytotoxicity, oxidative stress response, and metabolic response in E. coli exposed to TnBP and TCP. Exposure to them significantly increased the activities of antioxidant enzymes, indicating activation of the antioxidant defense system. Excessive accumulation of reactive oxygen species (ROS) triggered various biological events, including a reduction in membrane potential (MP), decrease of adenosine triphosphatase (ATPase) activity, and increased malondialdehyde (MDA) content. These findings suggested that oxidative damage compromised membrane proteins function, membrane stability, and intracellular homeostasis. GC-MS and LC-MS-based metabolomics analyses revealed that TnBP and TCP strongly disrupted multiple metabolic pathways, including carbohydrate metabolism, nucleotide metabolism, lipid metabolism, beta-alanine metabolism, pyruvate metabolism and oxidative phosphorylation. These disruptions highlighted the inhibitory effects on molecular functions and metabolic processes. Notably, lipids biomarkers e.g., PC(11:0/16:0), PA(17:1(9Z)/18:2(9Z,12Z)), PE(17:0/14:1(9Z)), and LysoPE(0:0/18:1(11Z)) were significantly altered, verifying that the regulation of lipid-associated metabolite synthesis plays a protective role in maintaining cellular membrane function. In summary, this study enhances our understanding of TnBP and TCP toxicity in E. coli, providing novel insights into their toxicological mechanisms at molecular and network levels. These findings underscore the ecological risks posed by organophosphate flame retardants in aquatic ecosystem.}, }
@article {pmid40284070, year = {2025}, author = {Lu, F and Yi, B and Qin, K and Bu, ZJ}, title = {Long-Term Nitrogen Addition Eliminates the Cooling Effect on Climate in a Temperate Peatland.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {8}, pages = {}, pmid = {40284070}, issn = {2223-7747}, support = {U23A2003//National Natural Science Foundation of China/ ; 42407354//National Natural Science Foundation of China/ ; 42371050//National Natural Science Foundation of China/ ; 20210402032GH//Jilin Provincial Science and Technology Development Pro-ject/ ; 20230203002SF//Jilin Provincial Science and Technology Development Pro-ject/ ; JP230021//Fundamental Research Funds for the Central Universities/ ; }, abstract = {Peatlands play a crucial role in global carbon (C) sequestration, but their response to long-term nitrogen (N) deposition remains uncertain. This study investigates the effects of 12 years of simulated N addition on CO2 and CH4 fluxes in a temperate peatland through in situ monitoring. The results demonstrate that long-term N addition significantly reduces net ecosystem exchange (NEE), shifting the peatland from a C sink to a C source. This transition is primarily driven by a decline in aboveground plant productivity, as Sphagnum mosses were suppressed and even experienced mortality, while graminoid plants thrived under elevated N conditions. Although graminoid cover increased, it did not compensate for the GPP loss caused by Sphagnum decline. Instead, it further increased CH4 emissions. These findings suggest that sustained N input may diminish the C sequestration function of peatlands, significantly weakening their global cooling effect.}, }
@article {pmid40278529, year = {2025}, author = {Fabio, RA and Semino, M and Perina, M and Martini, M and Riccio, E and Pili, G and Pani, D and Chessa, M}, title = {Virtual Reality as a Tool for Upper Limb Rehabilitation in Rett Syndrome: Reducing Stereotypies and Improving Motor Skills.}, journal = {Pediatric reports}, volume = {17}, number = {2}, pages = {}, pmid = {40278529}, issn = {2036-749X}, abstract = {BACKGROUND/OBJECTIVES: Rett Syndrome (RTT) is a rare neurodevelopmental disorder that causes the loss of motor, communicative, and cognitive skills. While no cure exists, rehabilitation plays a crucial role in improving quality of life. Virtual Reality (VR) has shown promise in enhancing motor function and reducing stereotypic behaviors in RTT. This study aims to assess the impact of VR training on upper limb motor skills in RTT patients, focusing on reaching and hand-opening tasks, as well as examining its role in motivation and engagement during rehabilitation.<br><br>METHODS: Twenty RTT patients (aged 5-33) were randomly assigned to an experimental group (VR training) and a control group (standard rehabilitation). Pre- and post-tests evaluated motor skills and motivation in both VR and real-world contexts. The VR training involved 40 sessions over 8 weeks, focusing on fine motor tasks. Non-parametric statistical methods were used to analyze the data.<br><br>RESULTS: Results indicated significant improvements in the experimental group for motor parameters, including reduced stereotypy intensity and frequency, faster response times, and increased correct performance. These improvements were consistent across VR and ecological conditions. Moreover, attention time increased, while the number of aids required decreased, highlighting enhanced engagement and independence. However, motivation levels remained stable throughout the sessions.<br><br>CONCLUSIONS: This study demonstrates the potential of VR as a tool for RTT rehabilitation, addressing both motor and engagement challenges. Future research should explore the customization of VR environments to maximize the generalization of skills and sustain motivation over extended training periods.}, }
@article {pmid40277515, year = {2025}, author = {Kargarandehkordi, A and Li, S and Lin, K and Phillips, KT and Benzo, RM and Washington, P}, title = {Fusing Wearable Biosensors with Artificial Intelligence for Mental Health Monitoring: A Systematic Review.}, journal = {Biosensors}, volume = {15}, number = {4}, pages = {}, pmid = {40277515}, issn = {2079-6374}, support = {MedRes_2023_00002689//Hawai'i Community Foundation/ ; 2406251//U.S. National Science Foundation/ ; 1U54GM138062-02A1/NH/NIH HHS/United States ; U54 GM138062/GM/NIGMS NIH HHS/United States ; U54GM138062/GM/NIGMS NIH HHS/United States ; }, mesh = {*Wearable Electronic Devices ; *Biosensing Techniques ; Humans ; *Artificial Intelligence ; *Mental Health ; Monitoring, Physiologic ; Heart Rate ; }, abstract = {The development of digital instruments for mental health monitoring using biosensor data from wearable devices can enable remote, longitudinal, and objective quantitative benchmarks. To survey developments and trends in this field, we conducted a systematic review of artificial intelligence (AI) models using data from wearable biosensors to predict mental health conditions and symptoms. Following PRISMA guidelines, we identified 48 studies using a variety of wearable and smartphone biosensors including heart rate, heart rate variability (HRV), electrodermal activity/galvanic skin response (EDA/GSR), and digital proxies for biosignals such as accelerometry, location, audio, and usage metadata. We observed several technical and methodological challenges across studies in this field, including lack of ecological validity, data heterogeneity, small sample sizes, and battery drainage issues. We outline several corresponding opportunities for advancement in the field of AI-driven biosensing for mental health.}, }
@article {pmid40276974, year = {2025}, author = {Blin, K and Shaw, S and Vader, L and Szenei, J and Reitz, ZL and Augustijn, HE and Cediel-Becerra, JDD and de Crécy-Lagard, V and Koetsier, RA and Williams, SE and Cruz-Morales, P and Wongwas, S and Segurado Luchsinger, AE and Biermann, F and Korenskaia, A and Zdouc, MM and Meijer, D and Terlouw, BR and van der Hooft, JJJ and Ziemert, N and Helfrich, EJN and Masschelein, J and Corre, C and Chevrette, MG and van Wezel, GP and Medema, MH and Weber, T}, title = {antiSMASH 8.0: extended gene cluster detection capabilities and analyses of chemistry, enzymology, and regulation.}, journal = {Nucleic acids research}, volume = {53}, number = {W1}, pages = {W32-W38}, pmid = {40276974}, issn = {1362-4962}, support = {//Hessian Ministry for Science and the Arts/ ; MSC 101072485//Horizon Europe Programme/ ; NNF20CC0035580//Novo Nordisk Foundation/ ; 948770//Horizon 2020/ ; DNRF137//Danish National Research Foundation/ ; 101000392//Horizon 2020/ ; //Translational Biodiversity Genomics/ ; //Microbial Secondary Metabolites/ ; RM1GM145426/NH/NIH HHS/United States ; KICH1.LWV04.21.013//NWO/ ; 101055020//ERC/ ; G061821N//FWO/ ; I008520N//FWO/ ; NNF22OC0079021//Novo Nordisk Foundation/ ; 504947087//German Research Foundation/ ; //The Royal Thai Government/ ; RM1 GM145426/GM/NIGMS NIH HHS/United States ; TTU09.716//German Center for Infection Research/ ; OCENW.XL21.XL21.088//ERC/ ; }, mesh = {*Multigene Family ; *Genetic Techniques ; *Software ; *Polyketide Synthases/metabolism ; *Peptide Synthases/metabolism ; Terpenes/chemistry ; }, abstract = {Microorganisms synthesize small bioactive compounds through their secondary or specialized metabolism. Those compounds play an important role in microbial interactions and soil health, but are also crucial for the development of pharmaceuticals or agrochemicals. Over the past decades, advancements in genome sequencing have enabled the identification of large numbers of biosynthetic gene clusters directly from microbial genomes. Since its inception in 2011, antiSMASH (https://antismash.secondarymetabolites.org/), has become the leading tool for detecting and characterizing these gene clusters in bacteria and fungi. This paper introduces version 8 of antiSMASH, which has increased the number of detectable cluster types from 81 to 101, and has improved analysis support for terpenoids and tailoring enzymes, as well as improvements in the analysis of modular enzymes like polyketide synthases and nonribosomal peptide synthetases. These modifications keep antiSMASH up-to-date with developments in the field and extend its overall predictive capabilities for natural product genome mining.}, }
@article {pmid40275196, year = {2025}, author = {Li, Q}, title = {Assessing and adjusting for bias in ecological analysis using multiple sample datasets.}, journal = {BMC medical research methodology}, volume = {25}, number = {1}, pages = {112}, pmid = {40275196}, issn = {1471-2288}, support = {P2C HD042854/HD/NICHD NIH HHS/United States ; }, mesh = {Humans ; Bias ; Kenya ; *Ecology/methods ; *Datasets as Topic ; Health Surveys ; Models, Statistical ; Data Interpretation, Statistical ; Computer Simulation ; }, abstract = {BACKGROUND: Ecological analysis utilizes group-level aggregate measures to investigate the complex relationships between individuals or groups and their environment. Despite its extensive applications across various disciplines, this approach remains susceptible to several biases, including ecological fallacy.<br><br>METHODS: Our study identified another significant source of bias in ecological analysis when using multiple sample datasets, a common practice in fields such as public health and medical research. We show this bias is proportional to the sampling fraction used during data collection. We propose two adjustment methods to address this bias: one that directly accounts for the sampling fraction and another based on measurement error models. The effectiveness of these adjustments is evaluated through formal mathematical derivations, simulations, and empirical analysis using data from the 2014 Kenya Demographic and Health Survey.<br><br>RESULTS: Our findings reveal that the sampling fraction bias can lead to significant underestimation of true relationships when using aggregate measures from multiple sample datasets. Both adjustment methods effectively mitigate this bias, with the measurement-error-adjusted estimator showing particular robustness in real-world applications. The results highlight the importance of accounting for sampling fraction bias in ecological analyses to ensure accurate inference.<br><br>CONCLUSION: Beyond the ecological fallacy uncovered by Robinson's seminar work, our research identified another critical bias in ecological analysis that is likely just as prevalent and consequential. The proposed adjustment methods provide potential tools for researchers to adjust for this bias, thereby improving the validity of ecological inferences. This study underscores the need for caution when pooling aggregate measures from multiple sample datasets and offers potential solutions to enhance the reliability of ecological analyses in various research domains.<br><br>CLINICAL TRIAL NUMBER: Not applicable.}, }
@article {pmid40275133, year = {2025}, author = {Antala, M and Kovar, M and Sporinová, L and Filacek, A and Juszczak, R and Zivcak, M and Shomali, A and Prasad, R and Brestic, M and Rastogi, A}, title = {Correction: High-throughput phenotyping of buckwheat (Fagopyrum esculentum Moench.) genotypes under water stress: exploring drought resistance for sustainable agriculture.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {517}, pmid = {40275133}, issn = {1471-2229}, }
@article {pmid40273607, year = {2025}, author = {Nkoh, JN and Ye, T and Shang, C and Li, C and Tu, J and Li, S and Wu, Z and Chen, P and Hussain, Q and Esemu, SN}, title = {Deciphering the mechanisms for preferential tolerance of Escherichia coli BL21 to Cd(II) over Cu(II) and Ni(II): A combined physiological, biochemical, and multiomics perspective.}, journal = {Ecotoxicology and environmental safety}, volume = {297}, number = {}, pages = {118195}, doi = {10.1016/j.ecoenv.2025.118195}, pmid = {40273607}, issn = {1090-2414}, mesh = {*Escherichia coli/drug effects/physiology/metabolism ; *Cadmium/toxicity ; *Nickel/toxicity ; *Copper/toxicity ; Oxidative Stress/drug effects ; Escherichia coli Proteins/metabolism/genetics ; Hydrogen Peroxide/metabolism ; Multiomics ; }, abstract = {Environmental pollution severely affects ecological functions/health, and nondegradable pollutants such as heavy metals (HMs) cause significant damage to living organisms. Escherichia coli is one of the most studied life forms, and its response to oxidative stress is driven by a complex ensemble of mechanisms driven by transcriptomic-level adjustments. However, the magnitude of the physiological, metabolic, and biochemical alterations and their relationships with transcriptomic changes remain unclear. Studying the growth of E. coli in Cd-, Cu-, and Ni-polluted media at pH 5.0, we observed that (i) downregulation of the alkyl hydroperoxide complex, glutathione reductase, and glutathione S-transferase by Cd inhibited H2O2 degradation, and the accumulated H2O2 was respectively 2.7, 1.7, and 2.4 times greater than that in the control, Cu, and Ni treatments; (ii) Zn-associated resistance protein (ZraP) was the major scavenger of Cd, with a 140.7-fold increase in its expression; (iii) the P-type Cu[+] transporter (CopA), multicopper oxidase (CueO), and heteromultimeric transport system (CusCBAF) controlled the excretion and detoxification of Cu; (iv) the Cd[2+]/Zn[2+]/Pb[2+]-exporting P-type ATPase (ZntA) and transcriptional activator ZntR were the major transporters of Ni; (v) Cd upregulated biofilm formation and synthesis of secondary metabolites more than Cu and Ni, which resulted in increased adsorption and improved tolerance; and (vi) the activity of superoxide dismutase in Cu-spiked cells was 153.2 %, 141.7 %, and 172.7 % higher and corresponded to 85.7 %, 524.5 %, and 491.5 % lower O2[●][-] in the control, Cd-, and Ni-spiked cells, respectively. This study reveals E. coli's preferential tolerance mechanisms to Cd rather than Cu and Ni and demonstrates mechanisms for its survival in highly polluted environments.}, }
@article {pmid40273274, year = {2025}, author = {Chen, N}, title = {The impact of the rural digital economy on China's new-type urbanization.}, journal = {PloS one}, volume = {20}, number = {4}, pages = {e0321663}, pmid = {40273274}, issn = {1932-6203}, mesh = {China ; *Urbanization/trends ; *Rural Population ; Humans ; *Economic Development/trends ; Agriculture ; }, abstract = {The Chinese government is vigorously implementing the rural revitalization strategy and accelerating the process of new-type urbanization. The rapid development of the rural digital economy has emerged as a new driving force for new-type urbanization. This study aims to explore how the rural digital economy impacts China's new-type urbanization from direct, heterogeneous, and indirect perspectives. Using the provincial-level panel data in China from 2014 to 2022, a mixed-methods approach is employed for the empirical research. The CRITIC and Entropy TOPSIS are used to assess the comprehensive development level and temporal characteristics of the rural digital economy and new-type urbanization. Moreover, a global-local auto-correlation analysis is carried out to depict the spatial distribution of the two variables. Subsequently, a two-way fixed effects model is constructed to verify the direct impact of the rural digital economy on new-type urbanization, as well as its structural and spatial heterogeneity characteristics. Finally, an mediating effect model is established to explore the impact paths through which the rural digital economy impacts new-type urbanization. The results show that the rural digital economy has significantly promoted new-type urbanization. Specifically, rural digital infrastructure, digital transformation of agriculture, agricultural production service informatization have a significant positive effect, while the role of rural life digitization is not significant. The rural digital economy has more significant positive impact on population agglomeration and economic growth, followed by social public service, but has no significant impact on ecological environmental protection and urban-rural coordination. Additionally, the qualitative analysis identifies geographical region, poverty, demographic structure and social equality as notable influencing factors in this impact. Further mechanism analysis result indicates that the rural digital economy impacts new-type urbanization through rural human capital improvement, agricultural economic growth and rural industrial structure upgrading. This research contributes to the existing body of knowledge by providing the practical path of rural development to promote new-type urbanization in the context of the digital economy, also clarifies the weak points and key links in this process. It also highlights the need for further research into the institutional factors that influence this relationship to enhances the policy applicability.}, }
@article {pmid40273037, year = {2025}, author = {Wu, KC and Belza, B and L Berry, D and M Lewis, F and L Hartzler, A and Zaslavsky, O}, title = {UTI risk factors in older people living with dementia: A conceptual framework and a scoping review.}, journal = {Dementia (London, England)}, volume = {24}, number = {7}, pages = {1417-1446}, doi = {10.1177/14713012251326129}, pmid = {40273037}, issn = {1741-2684}, mesh = {Humans ; *Dementia/complications ; Risk Factors ; *Urinary Tract Infections/prevention &amp; control/epidemiology ; Aged ; }, abstract = {Background and Aims: UTIs greatly impact hospitalization rates for people living with dementia. This study aims to craft a framework through a scoping review, assessing UTI symptoms, risk factors, and non-pharmacological prevention strategies in older people living with dementia. Research Design and Methods: Our scoping review followed PRISMA-ScR guidelines, exploring databases (PubMed, CINAHL, Embase, Web of Science) for topics like geriatric care, urinary tract issues published from January 1977 to April 2023. Two reviewers assessed data, organizing it using the Social-Ecological Model to construct the UTI Prevention (UTIP) framework. Results: The literature review scrutinized 1394 articles, selecting 14 through rigorous evaluation. It detailed demographic characteristics, synthesized UTI symptoms, 14 risk factors, and seven outcomes for older people living with dementia. Moreover, it outlined ten preventive domains and proposed a comprehensive UTI Prevention (UTIP) framework spanning individual, relational, community, and societal levels. This framework aims to prevent UTIs among older people living with dementia, integrating risk factors and outcomes to bolster effective prevention strategies for this population. Discussion and Implications: The review introduced a UTIP framework, and non-pharmacological preventive measures tailored for elderly people living with dementia. However, some factors in the framework require further validation to strengthen their associations with outcomes. Preventive measures from studies had limitations like small sample sizes, bias risks, and inconsistent findings. Future research should prioritize robust randomized trials with strong statistical power, strict criteria, and consistent individual-level interventions to boost outcome reliability and validity. Such efforts will enhance the credibility of findings and contribute significantly to refining preventive strategies for this vulnerable population.}, }
@article {pmid40270457, year = {2025}, author = {Selim, S and San, BT and Koc-San, D and Selim, C}, title = {A two-level approach to geospatial identification of optimal pitaya cultivation sites using multi-criteria decision analysis.}, journal = {Journal of the science of food and agriculture}, volume = {105}, number = {11}, pages = {5851-5862}, doi = {10.1002/jsfa.14297}, pmid = {40270457}, issn = {1097-0010}, mesh = {*Fruit/growth &amp; development/chemistry ; Geographic Information Systems ; Decision Support Techniques ; *Cactaceae/growth &amp; development/chemistry ; Soil/chemistry ; Temperature ; }, abstract = {BACKGROUND: Pitaya, also known as dragon fruit, is one of the most popular and expensive fruits in the world. It has been commercially produced since the early 20th century. This plant requires a specific growing environment and ecological conditions, so it is typically cultivated under greenhouse conditions in Türkiye. However, there is a clear need for a comprehensive assessment of outdoor adaptation and/or outdoor growing areas for sustainable yield at the regional scale.<br><br>RESULTS: This study presents a multi-criteria decision-making analysis-based geographical information system (GIS) study to identify and evaluate the suitability of outdoor growing areas for pitaya. In this study, eight crucial factors were identified for outdoor pitaya cultivation: temperature, rainfall, soil pH, soil depth, land use capability, altitude, slope and aspect. An analytical hierarchy process was conducted to determine the weights for each parameter, followed by a weighted overlay analysis using GIS tools. The range of weight values was obtained between 0.2748 and 0.0319. The area of the best places for pitaya cultivation was calculated to be 9245.7&#x2009;ha (11.7%). It was determined that 32.63%, 37.57% and 18.1% of the locations were moderately suitable, less appropriate and unsuitable, respectively.<br><br>CONCLUSION: The selection of comparable production sites will be guided by the study. Such suitable site selection studies are extremely significant since the cultivation of the pitaya plant, which has a high commercial value for economically developing countries, will be crucial to the growth of agricultural employment in these nations. Future research will be guided by this study's methodology and analysis strategies. &#xa9; 2025 Society of Chemical Industry.}, }
@article {pmid40266389, year = {2025}, author = {Xinyi, B and Qingbiao, G and Songbo, W and Jin, L and Jiren, X}, title = {Identifying the spatio-temporal evolution and driving mechanisms of ecosystem service value in high groundwater table coal mining areas.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {5}, pages = {581}, pmid = {40266389}, issn = {1573-2959}, support = {No. 2024cx2152//the Graduate Innovation Fund Project of Anhui University of Science and Technology/ ; 2024cxcysj094//the Provincial graduate student innovation and entrepreneurship practice project/ ; NO. KSXTJC202401//Engineering Research Center of Mining Area Environmental And Disaster Cooperative Monitoring (Anhui University of Science and Technology)/ ; No. 52274164//the Natural Science Foundation of China/ ; No. 2308085Y31//the Anhui Provincial Natural Science Foundation/ ; No. 2022QNRC001//the Young Elite Scientists Sponsorship Program by CAST/ ; No. GJNY-21-41-15//the Open Fund of State Key Laboratory of Water Resource Protection and Utilization in Coal Mining/ ; }, mesh = {*Coal Mining ; *Environmental Monitoring ; *Ecosystem ; *Groundwater/chemistry ; *Conservation of Natural Resources/methods ; Spatio-Temporal Analysis ; China ; }, abstract = {In coal mining areas with high groundwater tables, surface subsidence has emerged as a non-negligible phenomenon, stemming from long-term coal mining activities. Employing the Huainan mining area as an exemplar, this research meticulously examines the temporal and spatial attributes of ecosystem service value (ESV) across distinct timeframes of 2005, 2010, 2015, and 2020, utilizing the refined equivalent factor approach in conjunction with spatial analysis methodologies. To delve into the primary forces driving the observed changes, the optimal parameter-based geographical detector (OPGD) model is subsequently utilized as a tool for analysis. Lastly, the study delves into the trade-offs and synergies existing between four exemplary services at the grid level, utilizing Spearman correlation coefficient and bivariate spatial autocorrelation. The findings suggest that: (1) From 2005 to 2020, the total ESV in the Huainan mining area demonstrated a general increasing tendency, primarily attributed to the increase in waters. (2) Throughout the research period, the ecosystem service functions in the coal mining area all exhibited relatively significant hydrological regulation and waste treatment capabilities. (3) Vegetation factors significantly influenced the ESV in the Huainan mining area. (4) The Huainan mining area predominantly exhibited synergistic effects among ecosystem services, with the most pronounced synergy occurring between cultural services (CS) and regulating services (RS). All services were transitioning towards an enhanced trend of synergistic effects. (5) Significant spatial variations are present in the observed trade-offs and synergies among diverse ecosystem services. The aforementioned research findings will provide scientific theoretical guidance for rational mining activities and ecological environmental governance in coal mining areas.}, }
@article {pmid40259303, year = {2025}, author = {Yano, KM and Zucchi, P and Novais, MAP}, title = {Psychiatric hospitalizations in the Unified Health System: an observational study on hospitalization rates from 2012 to 2023.}, journal = {BMC public health}, volume = {25}, number = {1}, pages = {1463}, pmid = {40259303}, issn = {1471-2458}, support = {2022/10716-2//S&#xe3;o Paulo State Research Foundation (FAPESP)/ ; }, mesh = {Humans ; *Hospitalization/trends/statistics &amp; numerical data ; Brazil/epidemiology ; Female ; Male ; Adult ; Middle Aged ; Adolescent ; *Mental Disorders/therapy/epidemiology ; Aged ; Young Adult ; Aged, 80 and over ; Child ; Infant ; Child, Preschool ; *National Health Programs/statistics &amp; numerical data ; Infant, Newborn ; }, abstract = {BACKGROUND: Psychiatric care in Brazil is based on the National Mental Health Policy and is aligned with the guidelines of the Brazilian Unified Health System. It is based on the preeminence of care in the extra-hospital context over the hospital context. Hospital admissions should occur solely when extra-hospital resources prove insufficient for the proper management of the mental health condition.<br><br>METHOD: It refers to a time series investigation of a descriptive, ecological, and observational nature. We used publicly available hospital admissions data from the Brazilian Unified Health System's Department of Informatics. The study looked at information on diseases in ICD-10 group V that affected both men and women aged 0 to 80 or older, from 2012 to 2023. The information was analyzed using the statistical software SPSS 20.0, as well as Jointpoint, through permutation tests, with the aim of evaluating the temporal trend of hospitalization and mortality rates. The joinpoint regression model used a log-linear method to set up a series of connected lines on a logarithmic scale and the Monte Carlo permutation method to figure out the direction or statistical significance. A significance level of 5% was established for the execution of all statistical tests.<br><br>RESULTS: Overall, a trend of reduction in psychiatric hospitalization rates was observed. However, these trends exhibited fluctuations when analyzed in isolation with respect to the type of disorder, gender, and age group. In contrast to the general trend, the number of hospitalizations for affective disorders and disorders linked to stress and somatization went up. This was especially true between 2021 and 2023, when the number of hospitalizations for other disorders went down more significantly. The predominance of hospitalizations in the male gender was significant. However, the trends of decrease were less pronounced in the male group, especially regarding hospitalizations associated with alcohol and other substance use, which draws attention to the hospitalization rates of the female sex. As it relates to dementias, the national picture shows that hospitalizations are going down, and most of the patients are women and older adults or people who are very old. However, an analysis of the state scenario showed that hospitalizations went up for adults, more than for the elderly combined, with more men than women.<br><br>CONCLUSION: the results achieved in this research confirm the findings, both nationally and internationally. Studies have shown that investments made through the National Mental Health Policy and the effects of Covid-19 led to a drop in the number of people admitted to psychiatric hospitals. This was because of the restructuring of the care model, which meant that hospitalizations had to be prioritized to meet the needs of Covid-19, which hurt people with mental disorders.}, }
@article {pmid40258091, year = {2025}, author = {Hashem, I and Wang, J and Van Impe, JFM}, title = {A Discretized Overlap Resolution Algorithm (DORA) for resolving spatial overlaps in individual-based models of microbes.}, journal = {PLoS computational biology}, volume = {21}, number = {4}, pages = {e1012974}, pmid = {40258091}, issn = {1553-7358}, mesh = {*Algorithms ; *Models, Biological ; Computational Biology/methods ; Computer Simulation ; Biofilms/growth &amp; development ; }, abstract = {Individual-based modeling (IbM) is an instrumental tool for simulating spatial microbial growth, with applications in both microbial ecology and biochemical engineering. Unlike Cellular Automata (CA), which use a fixed grid of cells with predefined rules for interactions, IbMs model the individual behaviors of cells, allowing complex population dynamics to emerge. IbMs require more detailed modeling of individual interactions, which introduces significant computational challenges, particularly in resolving spatial overlaps between cells. Traditionally, this is managed using arrays or kd-trees, which require numerous pairwise comparisons and become inefficient as population size increases. To address this bottleneck, we introduce the Discretized Overlap Resolution Algorithm (DORA), which employs a grid-based framework to efficiently manage overlaps. By discretizing the simulation space further and assigning circular cells to specific grid units, DORA transforms the computationally intensive pairwise comparison process into a more efficient grid-based operation. This approach significantly reduces the computational load, particularly in simulations with large cell populations. Our evaluation of DORA, through simulations of microbial colonies and biofilms under varied nutrient conditions, demonstrates its superior computational efficiency and ability to accurately capture microbial growth dynamics compared to conventional methods. DORA's grid-based strategy enables the modeling of densely populated microbial communities within practical computational timeframes, thereby expanding the scope and applicability of individual-based modeling.}, }
@article {pmid40253884, year = {2025}, author = {Wang, X and Zhao, C and Huang, G and Liu, H and Zhu, X and Huang, J}, title = {Quantifying leachate discharge and assessing environmental risks of gully-type coal-based solid waste dumps in small watersheds: A refined hydrological modeling approach for mitigation strategies.}, journal = {Water research}, volume = {282}, number = {}, pages = {123655}, doi = {10.1016/j.watres.2025.123655}, pmid = {40253884}, issn = {1879-2448}, mesh = {*Water Pollutants, Chemical/analysis ; *Coal ; Environmental Monitoring/methods ; Models, Theoretical ; Hydrology ; Risk Assessment ; *Solid Waste/analysis ; *Refuse Disposal ; }, abstract = {Rainfall-induced leaching from extensive coal-based solid waste storage results in a long-term risk to watershed's water quality and safety. The leachate carries heavy metals and other contaminants, which migrate and accumulate through the watershed, leading to a persistent deterioration of downstream water environment. However, the lack of systematic research on the release, accumulation, and spatial-scale migration dynamics of leachate limits effective management of diffused leachate pollutions. This study presents a novel cross-scale coupling framework which integrates multi-source remote sensing data with Soil and Water Assessment Tool (SWAT) model, employing a strategy that transfers parameters from large basins to accurately quantify the hydrological processes in coal waste sub-basins. Additionally, a comprehensive analysis is performed on the hydrological characteristics, leachate generation, and watershed migration dynamics in gangue dump sub-watersheds, providing a new methodological framework for managing mining-related leachate pollution. The large basin model demonstrated strong performance (R[2] = 0.79, NSE = 0.66 for calibration; R[2] = 0.74, NSE = 0.59 for verification), while the sub-basin model exhibited excellent accuracy (R[2] = 0.94, NSE = 0.92 for calibration; R[2] = 0.81, NSE = 0.77 for verification). High-resolution drone data estimated the annual leachate production to be 3366.87 m[3]. Simulations revealed that leachate migration peaks in the summer months (July to September), significantly increasing downstream pollution risks. Risk assessments indicate that vegetation in land restoration areas reduces leachate production and migration via evapotranspiration and other processes. This study provides an adaptable methodological framework for managing mining-related leachate pollution and highlights the critical importance of optimal reclamation strategies for mitigating pollution and restoring degraded landscapes.}, }
@article {pmid40253432, year = {2025}, author = {Kelliher, JM and Aljumaah, M and Bordenstein, SR and Brister, JR and Chain, PSG and Dundore-Arias, JP and Emerson, JB and Fernandes, VMC and Flores, R and Gonzalez, A and Hansen, ZA and Hatcher, EL and Jackson, SA and Kellogg, CA and Madupu, R and Miller, CML and Mirzayi, C and Moustafa, AM and Mungall, C and Oliver, A and Pariente, N and Pett-Ridge, J and Record, S and Reji, L and Reysenbach, AL and Rich, VI and Richardson, L and Schriml, LM and Shabman, RS and Sierra, MA and Sullivan, MB and Sundaramurthy, P and Thibault, KM and Thompson, LR and Tighe, S and Vereen, E and Eloe-Fadrosh, EA}, title = {Microbiome data management in action workshop: Atlanta, GA, USA, June 12-13, 2024.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {40}, pmid = {40253432}, issn = {2524-6372}, support = {2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; }, abstract = {Microbiome research is revolutionizing human and environmental health, but the value and reuse of microbiome data are significantly hampered by the limited development and adoption of data standards. While several ongoing efforts are aimed at improving microbiome data management, significant gaps still remain in terms of defining and promoting adoption of consensus standards for these datasets. The Strengthening the Organization and Reporting of Microbiome Studies (STORMS) guidelines for human microbiome research have been endorsed and successfully utilized by many research organizations, publishers, and funding agencies, and have been recognized as a consensus community standard. No equivalent effort has occurred for environmental, synthetic, and non-human host-associated microbiomes. To address this growing need within the microbiome research community, we convened the Microbiome Data Management in Action Workshop (June 12-13, 2024, in Atlanta, GA, USA), to bring together key decision makers in microbiome science including researchers, publishers, funders, and data repositories. The 50 attendees, representing the diverse and interdisciplinary nature of microbiome research, discussed recent progress and challenges, and brainstormed actionable recommendations and paths forward for coordinated environmental microbiome data management and the modifications necessary for the STORMS guidelines to be applied to environmental, non-human host, and synthetic microbiomes. The outcomes of this workshop will form the basis of a formalized data management roadmap to be implemented across the field. These best practices will drive scientific innovation now and in years to come as these data continue to be used not only in targeted reanalyses but in large-scale models and machine learning efforts.}, }
@article {pmid40249863, year = {2025}, author = {Wu, Q and Cheng, S and Zhang, W and Zhao, J and Zhang, L and Lv, M and Ma, J and Ding, J and Wang, S and Zheng, X and Gao, J and Liu, R and Yin, Y and Shi, J and Qu, G and Jiang, G}, title = {Heterogeneous Single-Cell Distribution of Trace-Level Metal Mixtures in Tetrahymena thermophila Using Mass Cytometry.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {16}, pages = {7855-7866}, doi = {10.1021/acs.est.4c12818}, pmid = {40249863}, issn = {1520-5851}, mesh = {*Tetrahymena thermophila/metabolism ; *Metals, Heavy ; Water Pollutants, Chemical ; }, abstract = {The uptake of heavy metals by unicellular organisms can lead to the bioaccumulation of these metals in higher organisms, detrimentally affecting organismal health and ultimately impacts the ecosystems. By studying the uptake and accumulation of heavy metals in unicellular organisms, we gain insights into potential risks associated with low-dose heavy metal exposure in aquatic environments. Thus, to investigate the accumulation characteristics of Mo, Ag, Cd, Sn, Sb, Hg, Tl, and Pb mixtures in single Tetrahymena thermophila cells, we developed a label-free approach for the simultaneous absolute quantification of multiple metals in a single cell using mass cytometry. Our results demonstrated the dynamic changes in metal concentrations in T. thermophila, and the competition between metals in uptake and excretory pathways resulted in heterogeneous accumulation and bioconcentration of these metals. Additionally, our findings revealed the limited capacity of T. thermophila to excrete Cd and Hg, suggesting a higher risk for T. thermophila cells when exposed to Cd and Hg over an extended period. Therefore, the current study provides valuable data for a more comprehensive understanding of the impact of low-dose heavy metals on aquatic ecosystems.}, }
@article {pmid40249276, year = {2025}, author = {May, SA and Rosenbaum, SW and Pearse, DE and Kardos, M and Primmer, CR and Baetscher, DS and Waples, RS}, title = {The Genomics Revolution in Nonmodel Species: Predictions vs. Reality for Salmonids.}, journal = {Molecular ecology}, volume = {34}, number = {23}, pages = {e17758}, pmid = {40249276}, issn = {1365-294X}, support = {//USDA-ARS/ ; }, mesh = {*Genomics/methods/trends ; Animals ; *Salmonidae/genetics ; Genome ; Computational Biology ; }, abstract = {The increasing feasibility of whole-genome sequencing has been highly anticipated, promising to transform our understanding of the biology of nonmodel species. Notably, dramatic cost reductions beginning around 2007 with the advent of high-throughput sequencing inspired publications heralding the 'genomics revolution', with predictions about its future impacts. Although such predictions served as useful guideposts, value is added when statements are evaluated with the benefit of hindsight. Here, we review 10 key predictions made early in the genomics revolution, highlighting those realised while identifying challenges limiting others. We focus on predictions concerning applied aspects of genomics and examples involving salmonid species which, due to their socioeconomic and ecological significance, have been frontrunners in applications of genomics in nonmodel species. Predicted outcomes included enhanced analytical power, deeper insights into the genetic basis of phenotype and fitness variation, disease management and breeding program advancements. Although many predictions have materialised, several expectations remain unmet due to technological, analytical and knowledge barriers. Additionally, largely unforeseen advancements, including the identification and management applicability of large-effect loci, close-kin mark-recapture, environmental DNA and gene editing have added under-anticipated value. Finally, emerging innovations in artificial intelligence and bioinformatics offer promising new directions. This retrospective evaluation of the impacts of the genomic revolution offers insights into the future of genomics for nonmodel species.}, }
@article {pmid40248649, year = {2025}, author = {Boyes, D and Januszczak, I and ,  and ,  and ,  and ,  and ,  and ,  and ,  and ,  and Mitchell, R}, title = {The genome sequence of the Warted Knot-Horn moth, Acrobasis repandana Fabricius, 1798.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {50}, pmid = {40248649}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female specimen of Acrobasis repandana (Warted Knot-Horn moth; Arthropoda; Insecta; Lepidoptera; Pyralidae). The genome sequence has a total length of 620.40 megabases. Most of the assembly (99.78%) is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.21 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,522 protein-coding genes.}, }
@article {pmid40247661, year = {2025}, author = {Abraham, AJ and Duvall, ES and Doughty, CE and Riond, B and Ortmann, S and Terranova, M and le Roux, E and Clauss, M}, title = {Sodium Retention in Large Herbivores: Physiological Insights and Zoogeochemical Consequences.}, journal = {Journal of experimental zoology. Part A, Ecological and integrative physiology}, volume = {343}, number = {6}, pages = {664-676}, pmid = {40247661}, issn = {2471-5646}, support = {//A.J.A. acknowledges Horizon Europe Marie Sk&#x142;odowska-Curie Actions Grant Agreement No. 101062339./ ; }, mesh = {Animals ; Cattle/physiology ; Feces/chemistry ; *Herbivory/physiology ; *Sodium/urine/metabolism ; Horses/physiology/metabolism ; Female ; }, abstract = {The assimilation, retention, and release of nutrients by animals fundamentally shapes their physiology and contributions to ecological processes (e.g., zoogeochemistry). Yet, information on the transit of nutrients through the bodies of large mammals remains scarce. Here, we examined how sodium (Na), a key element for animal health and ecosystem functioning, travels differently through fecal and urinary systems of cows (Bos taurus) and horses (Equus ferus caballus). We provided a large dose of Na and compared its timing of release in feces and urine to that of nonabsorbable markers. Na excretion by urine occurred approximately twice as fast as excretion by feces, yet both were shorter than indigestible particle markers. These differences correspond to rapid absorption of Na in the upper gastrointestinal tract and transport by blood to the kidneys (urine Na excretion) or resecretion of Na into the lower intestinal tract (fecal Na excretion). Interestingly, for cows, we found a second peak of Na excretion in urine and feces > 96 h after dosage. This result may indicate that surplus Na can be rapidly absorbed and stored in specific body cells (e.g., skin), from which it is later released. Using a propagule dispersal model, we found that the distance of cattle- and horse-driven nutrient dispersal by urine was 31% and 36% less than the fecal pathway and 60% and 41% less than the particle marker pathway, which is commonly used to estimate nutrient dispersal. Future physiological and zoogeochemical studies should resolve different pathways of nutrient retention and release from large mammals.}, }
@article {pmid40247093, year = {2025}, author = {Yang, J and Chen, YN and Fang, CY and Li, Y and Ke, HQ and Guo, RQ and Xiang, P and Xiao, YL and Zhang, LW and Liu, H}, title = {Investigating immune cell infiltration and gene expression features in pterygium pathogenesis.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {13352}, pmid = {40247093}, issn = {2045-2322}, support = {ZKF2024042//National clinical key specialty ophthalmology open foundation/ ; ZKF2024041//National clinical key specialty ophthalmology open foundation/ ; 202208535051//China Scholarship Council/ ; 81860171//National Natural Science Foundation of China/ ; 82460201//National Natural Science Foundation of China/ ; 202205AC160016//Yunnan Young and middle-aged Academic and technical leader Project/ ; L2019029//Yunnan Provincial Health Committee Training program for leading medical talents/ ; YDYXJJ2024-0003//Yunnan University Medical Research Foundation/ ; }, mesh = {Humans ; *Pterygium/genetics/immunology/pathology ; Gene Expression Profiling ; Computational Biology/methods ; Conjunctiva/pathology/metabolism/immunology ; Transcriptome ; *Gene Expression Regulation ; Biomarkers/metabolism ; }, abstract = {Pterygium is a prevalent ocular disease characterized by abnormal conjunctival tissue proliferation, significantly impacting patients' quality of life. However, the underlying molecular mechanisms driving pterygium pathogenesis remain inadequately understood. This study aimed to investigate gene expression changes following pterygium excision and their association with immune cell infiltration. Clinical samples of pterygium and adjacent relaxed conjunctival tissue were collected for transcriptomic analysis using RNA sequencing combined with bioinformatics approaches. Machine learning algorithms, including LASSO, SVM-RFE, and Random Forest, were employed to identify potential diagnostic biomarkers. GO, KEGG, GSEA, and GSVA were utilized for enrichment analysis. Single-sample GSEA was employed to analyze immune infiltration. The GSE2513 and GSE51995 datasets from the GEO database, along with clinical samples, were selected for validation analysis. Differentially expressed genes (DEGs) were identified from the PRJNA1147595 and GSE2513 datasets, revealing 2437 DEGs and 172 differentially regulated genes (DRGs), respectively. There were 52 co-DEGs shared by both datasets, and four candidate biomarkers (FN1, SPRR1B, SERPINB13, EGR2) with potential diagnostic value were identified through machine learning algorithms. Single-sample GSEA demonstrated increased Th2 cell infiltration and decreased CD8 + T cell presence in pterygium tissues, suggesting a crucial role of the immune microenvironment in pterygium pathogenesis. Analysis of the GSE51995 dataset and qPCR results revealed significantly higher expression levels of FN1 and SPRR1B in pterygium tissues compared to conjunctival tissues, but SERPINB13 and EGR2 expression levels were not statistically significant. Furthermore, we identified four candidate drugs targeting the two feature genes FN1 and SPRR1B. This study provides valuable insights into the molecular characteristics and immune microenvironment of pterygium. The identification of potential biomarkers FN1 and SPRR1B highlights their significance in pterygium pathogenesis and lays a foundation for further exploration aimed at integrating these findings into clinical practice.}, }
@article {pmid40246854, year = {2025}, author = {He, B and Zhang, H and Qin, T and Shi, B and Wang, Q and Dong, W}, title = {A simultaneous EEG and eye-tracking dataset for remote sensing object detection.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {651}, pmid = {40246854}, issn = {2052-4463}, support = {42230103//National Science Foundation of China | Key Programme/ ; }, mesh = {*Electroencephalography ; Humans ; *Eye-Tracking Technology ; *Remote Sensing Technology ; Artificial Intelligence ; }, abstract = {We introduce the EEGET-RSOD, a simultaneous electroencephalography (EEG) and eye-tracking dataset for remote sensing object detection. This dataset contains EEG and eye-tracking data when 38 remote sensing experts located specific objects in 1,000 remote sensing images within a limited time frame. This task reflects the typical cognitive processes associated with human visual search and object identification in remote sensing imagery. To our knowledge, EEGET-RSOD is the first publicly available dataset to offer synchronized eye-tracking and EEG data for remote sensing images. This dataset will not only advance the study of human visual cognition in real-world environment, but also bridge the gap between human cognition and artificial intelligence, enhancing the interpretability and reliability of AI models in geospatial applications.}, }
@article {pmid40245396, year = {2025}, author = {Melia, R and Musacchio Schafer, K and Rogers, ML and Wilson-Lemoine, E and Joiner, TE}, title = {The Application of AI to Ecological Momentary Assessment Data in Suicide Research: Systematic Review.}, journal = {Journal of medical Internet research}, volume = {27}, number = {}, pages = {e63192}, pmid = {40245396}, issn = {1438-8871}, mesh = {Humans ; *Ecological Momentary Assessment ; *Artificial Intelligence ; *Suicide ; *Suicidal Ideation ; }, abstract = {BACKGROUND: Ecological momentary assessment (EMA) captures dynamic processes suitable to the study of suicidal ideation and behaviors. Artificial intelligence (AI) has increasingly been applied to EMA data in the study of suicidal processes.<br><br>OBJECTIVE: This review aims to (1) synthesize empirical research applying AI strategies to EMA data in the study of suicidal ideation and behaviors; (2) identify methodologies and data collection procedures used, suicide outcomes studied, AI applied, and results reported; and (3) develop a standardized reporting framework for researchers applying AI to EMA data in the future.<br><br>METHODS: PsycINFO, PubMed, Scopus, and Embase were searched for published articles applying AI to EMA data in the investigation of suicide outcomes. The PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines were used to identify studies while minimizing bias. Quality appraisal was performed using CREMAS (adapted STROBE [Strengthening the Reporting of Observational Studies in Epidemiology] Checklist for Reporting Ecological Momentary Assessment Studies).<br><br>RESULTS: In total, 1201 records were identified across databases. After a full-text review, 12 (1%) articles, comprising 4398 participants, were included. In the application of AI to EMA data to predict suicidal ideation, studies reported mean area under the curve (0.74-0.86), sensitivity (0.64-0.81), specificity (0.73-0.86), and positive predictive values (0.72-0.77). Studies met between 4 and 13 of the 16 recommended CREMAS reporting standards, with an average of 7 items met across studies. Studies performed poorly in reporting EMA training procedures and treatment of missing data.<br><br>CONCLUSIONS: Findings indicate the promise of AI applied to self-report EMA in the prediction of near-term suicidal ideation. The application of AI to EMA data within suicide research is a burgeoning area hampered by variations in data collection and reporting procedures. The development of an adapted reporting framework by the research team aims to address this.<br><br>TRIAL REGISTRATION: Open Science Framework (OSF); https://doi.org/10.17605/OSF.IO/NZWUJ and PROSPERO CRD42023440218; https://www.crd.york.ac.uk/PROSPERO/view/CRD42023440218.}, }
@article {pmid40245036, year = {2025}, author = {Hu, J and Weber, JN and Fuess, LE and Steinel, NC and Bolnick, DI and Wang, M}, title = {A spectral framework to map QTLs affecting joint differential networks of gene co-expression.}, journal = {PLoS computational biology}, volume = {21}, number = {4}, pages = {e1012953}, pmid = {40245036}, issn = {1553-7358}, support = {R01 AI123659/AI/NIAID NIH HHS/United States ; R35 GM142891/GM/NIGMS NIH HHS/United States ; }, mesh = {*Quantitative Trait Loci/genetics ; *Gene Regulatory Networks/genetics ; Animals ; Computational Biology/methods ; *Chromosome Mapping/methods ; Phenotype ; Genotype ; Models, Genetic ; Gene Expression Profiling/methods ; }, abstract = {Studying the mechanisms underlying the genotype-phenotype association is crucial in genetics. Gene expression studies have deepened our understanding of the genotype → expression → phenotype mechanisms. However, traditional expression quantitative trait loci (eQTL) methods often overlook the critical role of gene co-expression networks in translating genotype into phenotype. This gap highlights the need for more powerful statistical methods to analyze genotype → network → phenotype mechanism. Here, we develop a network-based method, called spectral network quantitative trait loci analysis (snQTL), to map quantitative trait loci affecting gene co-expression networks. Our approach tests the association between genotypes and joint differential networks of gene co-expression via a tensor-based spectral statistics, thereby overcoming the ubiquitous multiple testing challenges in existing methods. We demonstrate the effectiveness of snQTL in the analysis of three-spined stickleback (Gasterosteus aculeatus) data. Compared to conventional methods, our method snQTL uncovers chromosomal regions affecting gene co-expression networks, including one strong candidate gene that would have been missed by traditional eQTL analyses. Our framework suggests the limitation of current approaches and offers a powerful network-based tool for functional loci discoveries.}, }
@article {pmid40240877, year = {2025}, author = {Li, W and Chu, C and Zhang, T and Sun, H and Wang, S and Liu, Z and Wang, Z and Li, H and Li, Y and Zhang, X and Geng, Z and Wang, Y and Li, Y and Zhang, H and Fan, W and Wang, Y and Xu, X and Cheng, L and Zhang, D and Xiong, Y and Li, H and Zhou, B and Guan, Q and Deng, CH and Han, Y and Ma, H and Han, Z}, title = {Pan-genome analysis reveals the evolution and diversity of Malus.}, journal = {Nature genetics}, volume = {57}, number = {5}, pages = {1274-1286}, pmid = {40240877}, issn = {1546-1718}, support = {CARS-27//Earmarked Fund for China Agriculture Research System/ ; 32172522//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32422077//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2019M661344//China Postdoctoral Science Foundation/ ; }, mesh = {*Malus/genetics/classification ; *Genome, Plant/genetics ; Phylogeny ; *Genetic Variation ; *Evolution, Molecular ; Polyploidy ; Genomics/methods ; Disease Resistance/genetics ; }, abstract = {Malus Mill., a genus of temperate perennial trees with great agricultural and ecological value, has diversified through hybridization, polyploidy and environmental adaptation. Limited genomic resources for wild Malus species have hindered the understanding of their evolutionary history and genetic diversity. We sequenced and assembled 30 high-quality Malus genomes, representing 20 diploids and 10 polyploids across major evolutionary lineages and geographical regions. Phylogenomic analyses revealed ancient gene duplications and conversions, while six newly defined genome types, including an ancestral type shared by polyploid species, facilitated the detection of strong signals for extensive introgressions. The graph-based pan-genome captured shared and species-specific structural variations, facilitating the development of a molecular marker for apple scab resistance. Our pipeline for analyzing selective sweep identified a mutation in MdMYB5 having reduced cold and disease resistance during domestication. This study advances Malus genomics, uncovering genetic diversity and evolutionary insights while enhancing breeding for desirable traits.}, }
@article {pmid40238767, year = {2025}, author = {Rodrigues, RDS and Cionek, VM and Barreto, AS and Branco, JO}, title = {Seabird strandings on the Brazilian coast: What influences spatial and temporal patterns?.}, journal = {PloS one}, volume = {20}, number = {4}, pages = {e0317335}, pmid = {40238767}, issn = {1932-6203}, mesh = {Animals ; Brazil ; *Animal Migration/physiology ; *Birds/physiology ; Seasons ; Spatio-Temporal Analysis ; Ecosystem ; Biodiversity ; }, abstract = {Seabirds exhibit physiological adaptations that allow them to forage in the marine environment and undertake long-distance migrations during non-reproductive periods. As a result, they face various natural and anthropogenic pressures, which can lead to extreme fatigue and even death. Stranded bodies that float in the sea can wash ashore, providing valuable ecological information. This study aimed to analyze seabird strandings along the south and southeast coasts of Brazil between 2016 and 2019, focusing on spatiotemporal and potential environmental and anthropogenic influences. Using data from the Santos Basin Beach Monitoring Project, we calculated ecological indices of abundance, richness, and diversity for the entire seabird community and separately by migratory behavior (resident, southern migratory, northern migratory). Statistical modeling revealed a strong decreasing trend in strandings from south to north, with higher events on the southern coast (Santa Catarina and Paraná) and lower on the southeast coast (São Paulo). Resident species and northern migratory species showed peak strandings in spring, while southern migratory peaked in winter. These spatial and temporal patterns reflected birds' home ranges, reproductive cycles, and migratory behaviors. Environmental variables influenced strandings differently depending on species migration behavior and ecological indices, highlighting the role of oceanographic processes in carcass drift and the impact of climatic events on species mortality. This study is the first to demonstrate a spatiotemporal pattern of seabird strandings on the Brazilian coast, providing valuable insights into seabird dynamics in the Santos Basin and offering important data for conservation efforts.}, }
@article {pmid40238239, year = {2025}, author = {Sutori, S and Eliasson, ET and Mura, F and Ortiz, V and Catrambonephd, V and Hadlaczky, G and Todorov, I and Alfeo, AL and Cardi, V and Cimino, MGCA and Mioni, G and Raya, MA and Valenza, G and Carli, V and Gentili, C}, title = {Acceptability, Usability, and Insights Into Cybersickness Levels of a Novel Virtual Reality Environment for the Evaluation of Depressive Symptoms: Exploratory Observational Study.}, journal = {JMIR formative research}, volume = {9}, number = {}, pages = {e68132}, pmid = {40238239}, issn = {2561-326X}, mesh = {Humans ; *Virtual Reality ; Male ; Female ; Adult ; *Depression/diagnosis/psychology ; Young Adult ; Italy ; Surveys and Questionnaires ; User-Computer Interface ; Pilot Projects ; Self Report ; }, abstract = {BACKGROUND: There is a clear need for enhanced mental health assessment, depressive symptom (DS) evaluation being no exception. A promising approach to this aim is using virtual reality (VR), which entails the potential of adding a wider set of assessment domains with enhanced ecological validity. However, whilst several studies have used VR for both diagnostic and treatment purposes, its acceptance, in particular how exposure to virtual environments affects populations with psychiatric conditions remains unknown.<br><br>OBJECTIVE: This study aims to report on the acceptability, usability, and cybersickness levels of a pilot VR environment designed for the purpose of differentiating between individuals with DSs.<br><br>METHODS: The exploratory study, conducted in Italy, included 50 healthy controls and 50 young adults with mild-to-moderate DSs (without the need for a formal diagnosis). The study used an observational design with approximately 30 minutes of VR exposure followed by a self-report questionnaire battery. The battery included a questionnaire based on the Theoretical Framework of Acceptability, the System Usability Scale as well as the Simulator Sickness Questionnaire.<br><br>RESULTS: Results indicate that the majority found VR acceptable for the purposes of mental health screening and treatment. However, for diagnostics, there was a clear preference for VR to be used by mental health professionals as a supplementary tool, as opposed to a stand-alone solution. In practice, following exposure to the pilot VR environment, generally, good levels of acceptability and usability were reported, but areas in need of improvement were identified (such as self-efficacy). Self-reported cybersickness levels were comparable to literature averages but were considerably higher among those with DSs.<br><br>CONCLUSIONS: These findings raise questions about the potential interplay between underlying somatic symptoms of depression and VR-induced cybersickness and call for more attention from the scientific community both in terms of methodology as well as potential clinical and theoretical implications. Conclusively, user support indicates a potential for VR to aid mental health assessment, but further research is needed to understand how exposure to virtual environments might affect populations with varying severity and other forms of psychiatric symptoms.<br><br>RR2-10.1186/ISRCTN16396369.}, }
@article {pmid40235568, year = {2025}, author = {Davies, H and Noble, PJ and Fins, IS and Pinchbeck, G and Singleton, D and Pirmohamed, M and Killick, D}, title = {Developing electronic health records as a source of real-world data for veterinary pharmacoepidemiology.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1550468}, pmid = {40235568}, issn = {2297-1769}, abstract = {Spontaneous reporting of adverse events (AEs) by veterinary professionals and the public is the cornerstone of post-marketing safety surveillance for veterinary medicinal products (VMPs). However, studies suggest that most veterinary AEs remain unreported. Veterinary medicine regulators, including the United Kingdom Veterinary Medicines Directorate and the European Medicines Agency, have included the exploration of big data utilization to support pharmacovigilance efforts in their regulatory strategies. In this study, we describe the application of veterinary electronic healthcare records (EHRs) from the SAVSNET veterinary first opinion informatics system to conduct pharmacoepidemiological analyses. Five VMP-AE pairs were selected for investigation in a proof-of-concept study, where drug exposure was identified from semi-structured treatment data and AEs from the unstructured free-text clinical narrative. Dictionaries were developed to identify AEs based on standard terminology. The precision of these dictionaries improved when they were expanded using word vectorization and expert opinion. A key strength of first-opinion EHR datasets is their ability to enable cohort studies and facilitate calculations of absolute incidence and relative risk. Thus, we demonstrate that unstructured free-text clinical narratives can be used to identify outcomes for veterinary pharmacoepidemiological studies and, consequently, support and expand pharmacovigilance efforts based on spontaneous AE reports.}, }
@article {pmid40233751, year = {2025}, author = {McKenzie, PF and Berardi, AE and Hopkins, R}, title = {Delayed flowering phenology of red-flowering plants in response to hummingbird migration.}, journal = {Current biology : CB}, volume = {35}, number = {9}, pages = {2175-2182.e3}, pmid = {40233751}, issn = {1879-0445}, support = {R35 GM142742/GM/NIGMS NIH HHS/United States ; }, mesh = {*Birds ; Animals ; *Flowers/growth &amp; development/physiology ; Animal Migration ; Pollination ; North America ; Datasets as Topic ; Seasons ; Pigmentation ; Time Factors ; *Magnoliopsida/physiology ; Crowdsourcing ; }, abstract = {The radiation of angiosperms is marked by a phenomenal diversity of floral size, shape, color, scent, and reward.[1][,][2][,][3][,][4] The multi-dimensional response to selection to optimize pollination has generated correlated suites of these floral traits across distantly related species, known as "pollination syndromes."[5][,][6][,][7][,][8][,][9] The ability to test the broad utility of pollination syndromes and expand upon the generalities of these syndromes is constrained by limited trait data, creating a need for new approaches that can integrate vast, unstructured records from community-science platforms. Here, we compile the largest North American flower color dataset to date, using GPT-4 with Vision to classify color in over 11,000 species across more than 1.6 million iNaturalist observations. We discover that red- and orange-flowering species (classic "hummingbird pollination" colors) bloom later in eastern North America compared with other colors, corresponding to the arrival of migratory hummingbirds. Our findings reveal how seasonal flowering phenology, in addition to floral color and morphology, can contribute to the hummingbird pollination syndrome in regions where these pollinators are migratory. Our results highlight phenology as an underappreciated dimension of pollination syndromes and underscore the utility of integrating artificial intelligence with community-science data. The potential breadth of analysis offered by community-science datasets, combined with emerging data extraction techniques, could accelerate discoveries about the evolutionary and ecological drivers of biological diversity.}, }
@article {pmid40232549, year = {2025}, author = {Xu, F and Jiang, C and Liu, Q and Yang, R and Li, W and Wei, Y and Bao, L and Tong, H}, title = {Source identification of polycyclic aromatic hydrocarbons (PAHs) in river sediments within a hilly agricultural watershed of Southwestern China: an integrated study based on Pb isotopes and PMF method.}, journal = {Environmental geochemistry and health}, volume = {47}, number = {5}, pages = {174}, pmid = {40232549}, issn = {1573-2983}, support = {NO. 2023YFC3705904//National Key Research and Development Plan of China/ ; NO. 2023YFC3705904//National Key Research and Development Plan of China/ ; NO. 2021-043//Stationing Point Tracking Research of Ecological Barrier Construction in the upper Yangtze River of Sichuan Province/ ; NO. 2021-043//Stationing Point Tracking Research of Ecological Barrier Construction in the upper Yangtze River of Sichuan Province/ ; NO. 41977169//National Natural Science Foundation of China/ ; NO. 41977169//National Natural Science Foundation of China/ ; SKLGP2022Z009//State Key Laboratory of Geohazard Prevention and Geoenvironment Protection Independent Research Project/ ; SKLGP2022Z009//State Key Laboratory of Geohazard Prevention and Geoenvironment Protection Independent Research Project/ ; }, mesh = {China ; *Polycyclic Aromatic Hydrocarbons/analysis ; *Geologic Sediments/chemistry/analysis ; *Rivers/chemistry ; *Water Pollutants, Chemical/analysis ; *Environmental Monitoring/methods ; *Lead/analysis ; Agriculture ; Isotopes/analysis ; Geographic Information Systems ; }, abstract = {Polycyclic aromatic hydrocarbons (PAHs) in sediments represent a pervasive environmental issue that poses significant ecological risks. This study employed a combination of geographic information systems, diagnostic ratios, correlation analysis, Pb isotope ratios, and positive matrix factorization (PMF) to elucidate the potential sources of 16 priority PAHs in river sediments from a hilly agricultural watershed in Southwestern China. The results indicated that PAHs concentrations ranged from 55.9 to 6083.5 ng/g, with a mean value of 1582.1 ± 1528.9 ng/g, reflecting high levels of contamination throughout the watershed. The predominant class of PAHs identified was high molecular weight (HMW) PAHs. Diagnostic ratios and correlation analysis suggested that the presence of PHAs is likely attributed primarily to emissions from industrial dust and combustion of coal and petroleum. Furthermore, correlation analysis revealed a significant association between Pb and PAHs, indicating potential shared sources for both pollutants. Additionally, Pb isotopic analysis demonstrated that aerosols may be the primary contributor to Pb accumulation within this environment. Given the similarity in origins between Pb and PAHs, it can be inferred that PAHs predominantly originate from aerosols associated with coal combustion, industrial dust emissions, and vehicle exhaust. This inference is further supported by PMF results which yielded consistent findings with those derived from Pb isotopes analysis. Moreover, PMF estimated three major sources contributing 57.63%, 23.57%, and 18.80%, respectively. These findings provide novel insights into identifying the sources of PAHs in river sediments within hilly agricultural watersheds in Southwest China, thereby establishing a scientific foundation for enhancing environmental quality in agricultural regions.}, }
@article {pmid40229317, year = {2025}, author = {Sabadel, AJM and Riekenberg, P and Ayala-Diaz, M and Belk, MC and Bennett, J and Bode, A and Bury, SJ and Dabouineau, L and Delgado, J and Finucci, B and García-Seoane, R and Giari, L and Henkens, J and IJsseldijk, LL and Joling, T and Kerr-Hislop, O and MacLeod, CD and Meyer, L and McGill, RAR and Negro, E and Quillfeldt, P and Reed, C and Roberts, C and Sayyaf Dezfuli, B and Schmidt, O and Sturbois, A and Suchomel, AD and Thieltges, DW and van der Lingen, CD and van der Meer, MTJ and Viana, IG and Weston, M and Willis, TJ and Filion, A}, title = {Establishing a comprehensive host-parasite stable isotope database to unravel trophic relationships.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {623}, pmid = {40229317}, issn = {2052-4463}, support = {CAWX2207//Ministry of Business, Innovation and Employment (MBIE)/ ; }, mesh = {*Host-Parasite Interactions ; Animals ; Nitrogen Isotopes/analysis ; Carbon Isotopes ; *Databases, Factual ; Sulfur Isotopes/analysis ; *Parasites ; }, abstract = {Over the past decades, stable isotopes have been infrequently used to characterise host-parasite trophic relationships. This is because we have not yet identified consistent patterns in stable isotope values between parasites and their host tissues across species, which are crucial for understanding host-parasite dynamics. To address this, we initiated a worldwide collaboration to establish a unique database of stable isotope values of novel host-parasite pairs, effectively doubling the existing data in published literature. This database includes nitrogen, carbon, and sulphur stable isotope values. We present 3213 stable isotope data entries, representing 586 previously unpublished host-parasite pairs. Additionally, while existing literature was particularly limited in sulphur isotope values, we tripled information on this crucial element. By publishing unreported host-parasite pairs from previously unsampled areas of the world and using appropriate host tissues, our dataset stands unparalleled. We anticipate that end-users will utilise our database to uncover generalisable patterns, deepening our understanding of the complexities of parasite-host relationships and driving future research efforts in stable isotope parasitology.}, }
@article {pmid40229216, year = {2025}, author = {Zhang, X and Lu, B and Jin, LN and Yang, S and Wang, C and Tai, J and Li, D and Chen, J}, title = {Emission Dynamics and Public Health Implications of Airborne Pathogens and Antimicrobial Resistance from Urban Waste Collection Facilities.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {16}, pages = {8060-8072}, doi = {10.1021/acs.est.4c12108}, pmid = {40229216}, issn = {1520-5851}, mesh = {Humans ; *Air Microbiology ; Bacteria ; Cities ; Drug Resistance, Microbial ; Public Health ; *Waste Disposal Facilities ; }, abstract = {Airborne pathogens and antimicrobial resistance (AMR) present significant global health threats. Household waste collection facilities (WCFs), crucial initial nodes in urban waste management systems, have been understudied in regards to their role in emitting these hazards. This study investigated the abundance, composition, sources, driving mechanisms, and health risks associated with pathogens and AMR originating from WCFs in a major city, using culture-based analysis, high-throughput sequencing, and health risk modeling, respectively. The atmospheric escape rates of culturable bacteria (43.4%), fungi (71.7%), and antibiotic-resistant bacteria (ARB) (43.7%) were estimated based on the concentration differences between the interior and exterior of the WCFs by using SourceTracker2 analysis. Health risk assessments showed that annual infection risks for waste-handling workers ranged from 0.194 to 0.489, far exceeding the World Health Organization's acceptable limit of 10[-4]. Community exposure risks were notable up to 220 m downwind from WCFs, marking the maximum extent of pathogen dispersion. Our analysis suggests that approximately 6.3% of the megacity's area (equivalent to 400 km[2]) is within potential risk zones influenced by WCF emissions. These results underscore the critical need to evaluate and mitigate the public health risks posed by airborne pathogens and AMR emitted from WCFs in megacities globally.}, }
@article {pmid40227267, year = {2025}, author = {Cassaro, A and Pacelli, C and Fanelli, G and Baqué, M and Maturilli, A and Leo, P and Lelli, V and de Vera, JP and Onofri, S and Timperio, A}, title = {Biomarker Preservation in Antarctic Sandstones after Prolonged Space Exposure Outside the International Space Station During the ESA EXPOSE-E Lichens and Fungi Experiment.}, journal = {Astrobiology}, volume = {25}, number = {5}, pages = {331-345}, doi = {10.1089/ast.2024.0068}, pmid = {40227267}, issn = {1557-8070}, mesh = {*Lichens ; Antarctic Regions ; *Biomarkers/analysis ; *Extraterrestrial Environment/chemistry ; *Space Flight ; Mars ; Exobiology ; *Fungi ; Spacecraft ; Spectrum Analysis, Raman ; }, abstract = {A primary aim of current and future space exploration missions is the detection and identification of chemical and biological indicators of life, namely biomarkers, on Mars. The Mars Sample Return NASA-ESA program will bring to Earth samples of martian soil, acquired from up to 7 cm depth. The ESA Rosalind Franklin rover will search for signs of life in the subsurface (down to a depth of 2 meters), given the highly radioactive conditions on Mars' surface, which are not ideal for life as we know it and for the preservation of its traces. In the frame of the Lichens and Fungi Experiment, small fragments of Antarctic sandstones colonized by cryptoendolithic microbial communities were exposed to space and simulated martian conditions in low Earth orbit for 18 months, aboard the EXPOSE-E payload. Through the use of Raman and infrared spectroscopies, as well as a metabolomic approach, we aimed to detect organic compounds in a quartz mineral matrix. The results show that pigments, such as melanin, carotenoids, and chlorophyll, lipids, and amino acids, maintained their stability within minerals under simulated martian conditions in space, which makes them ideal biomarkers for the exploration of putative life on Mars.}, }
@article {pmid40226649, year = {2024}, author = {Tamm, J and Takano, K and Just, L and Ehring, T and Rosenkranz, T and Kopf-Beck, J}, title = {Ecological Momentary Assessment versus Weekly Questionnaire Assessment of Change in Depression.}, journal = {Depression and anxiety}, volume = {2024}, number = {}, pages = {9191823}, pmid = {40226649}, issn = {1520-6394}, mesh = {Humans ; *Ecological Momentary Assessment ; Male ; Female ; Adult ; Middle Aged ; Surveys and Questionnaires/standards ; *Depression/diagnosis/therapy ; *Outcome Assessment, Health Care/methods ; Reproducibility of Results ; Pessimism/psychology ; Psychiatric Status Rating Scales ; Rumination, Cognitive ; }, abstract = {OBJECTIVE: Ecological momentary assessment (EMA) is increasingly used to monitor depressive symptoms in clinical trials, but little is known about the comparability of its outcomes to those of clinical interviews and questionnaires. In our study, we administered EMA and questionnaires to measure change in depressive symptoms and repetitive negative thinking (RNT) in a clinical trial and investigated (a) the size of intervention effects associated with both techniques and (b) their validity in predicting clinical interview outcomes (i.e., global functioning).<br><br>MATERIALS AND METHODS: Seventy-one depressed patients were randomly assigned to one of three psychological interventions. The EMA comprised a concise item set (four items per scale) and was administered three times per day during a 7-week intervention period. Conversely, questionnaires were assessed weekly (WQA), encompassing their full sets of items of depressive symptoms and RNT.<br><br>RESULTS: While EMA excelled in detecting significant intervention effects, WQA demonstrated greater strength in predicting clinician ratings of global functioning. Additionally, we observed significant differences in time effects (slopes) between the two techniques. WQA scores decreased steeper over time and were more extreme, e.g., higher at baseline and lower postintervention, than EMA scores.<br><br>CONCLUSIONS: Although clinical interviews, questionnaires, and EMA outcomes are related, they assess changes in depression differently. EMA may be more sensitive to intervention effects, but all three methods harbor potential bias, raising validity and reliability questions. Therefore, to enhance the validity and reliability of clinical trial assessments, we emphasize the importance of EMA approaches that combine subjective self-reports with objectively measured behavioral markers. This trial is registered with osf.io/9fuhn.}, }
@article {pmid41626904, year = {2025}, author = {Lagisz, M and Yang, Y and Young, S and Nakagawa, S}, title = {A practical guide to evaluating sensitivity of literature search strings for systematic reviews using relative recall.}, journal = {Research synthesis methods}, volume = {16}, number = {1}, pages = {1-14}, pmid = {41626904}, issn = {1759-2887}, support = {//Australian Research Council/ ; }, mesh = {Humans ; *Information Storage and Retrieval/methods ; *Review Literature as Topic ; Reproducibility of Results ; Algorithms ; Databases, Bibliographic ; Research Design ; Benchmarking ; Sensitivity and Specificity ; *Systematic Reviews as Topic ; Mental Recall ; }, abstract = {Systematic searches of published literature are a vital component of systematic reviews. When search strings are not "sensitive," they may miss many relevant studies limiting, or even biasing, the range of evidence available for synthesis. Concerningly, conducting and reporting evaluations (validations) of the sensitivity of the used search strings is rare, according to our survey of published systematic reviews and protocols. Potential reasons may involve a lack of familiarity or inaccessibility of complex sensitivity evaluation approaches. We first clarify the main concepts and principles of search string evaluation. We then present a simple procedure for estimating a relative recall of a search string. It is based on a pre-defined set of "benchmark" publications. The relative recall, that is, the sensitivity of the search string, is the retrieval overlap between the evaluated search string and a search string that captures only the benchmark publications. If there is little overlap (i.e., low recall or sensitivity), the evaluated search string should be improved to ensure that most of the relevant literature can be captured. The presented benchmarking approach can be applied to one or more online databases or search platforms. It is illustrated by five accessible, hands-on tutorials for commonly used online literature sources. Overall, our work provides an assessment of the current state of search string evaluations in published systematic reviews and protocols. It also paves the way to improve evaluation and reporting practices to make evidence synthesis more transparent and robust.}, }
@article {pmid41738821, year = {2024}, author = {Henry, TR and Slipetz, LR and Falk, A and Qiu, J and Chen, M}, title = {Ordinal Outcome State-Space Models for Intensive Longitudinal Data.}, journal = {Psychometrika}, volume = {89}, number = {4}, pages = {1203-1229}, doi = {10.1007/s11336-024-09984-3}, pmid = {41738821}, issn = {1860-0980}, mesh = {Humans ; Longitudinal Studies ; *Models, Statistical ; *Psychometrics/methods ; Data Interpretation, Statistical ; }, abstract = {Intensive longitudinal (IL) data are increasingly prevalent in psychological science, coinciding with technological advancements that make it simple to deploy study designs such as daily diary and ecological momentary assessments. IL data are characterized by a rapid rate of data collection (1+ collections per day), over a period of time, allowing for the capture of the dynamics that underlie psychological and behavioral processes. One powerful framework for analyzing IL data is state-space modeling, where observed variables are considered measurements for underlying states (i.e., latent variables) that change together over time. However, state-space modeling has typically relied on continuous measurements, whereas psychological data often come in the form of ordinal measurements such as Likert scale items. In this manuscript, we develop a general estimation approach for state-space models with ordinal measurements, specifically focusing on a graded response model for Likert scale items. We evaluate the performance of our model and estimator against that of the commonly used "linear approximation" model, which treats ordinal measurements as though they are continuous. We find that our model resulted in unbiased estimates of the state dynamics, while the linear approximation resulted in strongly biased estimates of the state dynamics. Finally, we develop an approximate standard error, termed slice standard errors and show that these approximate standard errors are more liberal than true standard errors (i.e., smaller) at a consistent bias.}, }
@article {pmid41194777, year = {2024}, author = {Boyes, D and Crowley, LM and Wawman, DC and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the September Thorn moth, Ennomos erosaria (Denis &amp; Schiffermüller), 1775.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {287}, pmid = {41194777}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Ennomos erosaria (the September Thorn moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 423.1 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 16.3 kilobases in length.}, }
@article {pmid40800427, year = {2024}, author = {Merritt, H and Faskowitz, J and Gonzalez, MZ and Betzel, RF}, title = {Stability and variation of brain-behavior correlation patterns across measures of social support.}, journal = {Imaging neuroscience (Cambridge, Mass.)}, volume = {2}, number = {}, pages = {}, pmid = {40800427}, issn = {2837-6056}, abstract = {The social environment has a critical influence on human development, cognition, and health. Research in health psychology and social neuroscience indicate an urgent need to understand how social relationships are associated with brain function and organization. To address this, we apply multilayer modeling and modularity maximization-both established tools in network neuroscience-to jointly cluster patterns of brain-behavior associations for seven social support measures. By using network approaches to map and analyze the connectivity between all pairs of brain regions simultaneously, we can clarify how relationships between brain regions (e.g. connectivity) change as a function of social relationships. This multilayer approach enables direct comparison of brain-behavior associations across social contexts for all brain regions and builds on both ecological and developmental neuroscientific findings and network neuroscientific approaches. In particular, we find that subcortical and control systems are especially sensitive to different constructs of perceived social support. Network nodes in these systems are highly flexible; their community affiliations, which reflect groups of nodes with similar patterns of brain-behavior associations, differ across social support measures. Additionally, our application of multilayer modeling to patterns of brain-behavior correlations, as opposed to just functional connectivity, represents an innovation in how multilayer models are used in human neuroscience. More than that, it offers a generalizable technique for studying the stability and variation of brain-behavior associations.}, }
@article {pmid40980745, year = {2024}, author = {Boyes, D and Broad, GR and Sivess, L and Holt, S and Holland, PWH and ,  and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Brown China-mark moth, Elophila nymphaeata (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {155}, pmid = {40980745}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Elophila nymphaeata (the Brown China-mark moth; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 734.1 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,079 protein coding genes.}, }
@article {pmid41625303, year = {2023}, author = {Lohse, K and Vila, R and Hayward, A and Laetsch, DR and Toro-Delgado, E and ,  and ,  and ,  and , }, title = {The genome sequence of the Silver-spotted Skipper, Hesperia comma (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {457}, pmid = {41625303}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Hesperia comma (the Silver-spotted Skipper; Arthropoda; Insecta; Lepidoptera; Hesperiidae). The genome sequence is 525.3 megabases in span. Most of the assembly is scaffolded into 29 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 17.73 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,725 protein coding genes.}, }
@article {pmid40303815, year = {2023}, author = {Wielgus, E and Klamm, A and Conraths, FJ and Dormann, CF and Henrich, M and Kronthaler, F and Heurich, M}, title = {First-Passage Time Analysis Based on GPS Data Offers a New Approach to Estimate Restricted Zones for the Management of Infectious Diseases in Wildlife: A Case Study Using the Example of African Swine Fever.}, journal = {Transboundary and emerging diseases}, volume = {2023}, number = {}, pages = {4024083}, pmid = {40303815}, issn = {1865-1682}, mesh = {Animals ; *African Swine Fever/prevention &amp; control/epidemiology/transmission ; *Geographic Information Systems ; Swine ; Animals, Wild ; *Sus scrofa ; Germany/epidemiology ; Female ; Disease Outbreaks/veterinary/prevention &amp; control ; Male ; African Swine Fever Virus ; }, abstract = {An essential part of any disease containment and eradication policy is the implementation of restricted zones, but determining the appropriate size of these zones can be challenging for managers. We designed a new method, based on animal movement, to help assess how large restricted zones should be after a spontaneous outbreak to successfully control infectious diseases in wildlife. Our approach uses first-passage time (FPT) analysis and Cox proportional hazard (CPH) models to calculate and compare the risk of an animal leaving different-sized areas. We illustrate our approach using the example of the African swine fever (ASF) virus and its wild pig reservoir host species, the wild boar (Sus scrofa), and we investigate the feasibility of applying this method to other systems. Using GPS data from 57 wild boar living in the Hainich National Park, Germany, we calculate the time spent by each individual in areas of different sizes using FPT analysis. We apply CPH models on the derived data to compare the risk of leaving areas of different sizes and to assess the effects of season and the sex of the wild boar on the risk of leaving. We conduct survival analyses to estimate the risk of leaving an area over time. Our results indicate that the risk of leaving an area decreases exponentially by 10% for each 100 m increase in radius size so that the differences were more pronounced for small sizes. Furthermore, the probability of leaving increases exponentially with time. Wild boar had a similar risk of leaving an area of a given size throughout the year, except in spring and winter, when females had a much lower risk of leaving. Our findings are in agreement with the literature on wild boar movement, further validating our method, and repeated analyses with location data resampled at different rates gave similar results. Our results may be applicable only to our study area, but they demonstrate the applicability of the proposed method to any ecosystem where wild boar populations are likely to be infected with ASF and where restricted zones should be established accordingly. The outlined approach relies solely on the analysis of movement data and provides a useful tool to determine the optimal size of restricted zones. It can also be applied to future outbreaks of other diseases.}, }
@article {pmid41000208, year = {2023}, author = {Boyes, D and Holland, PWH and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Brown House-moth, Hofmannophila pseudospretella (Stainton, 1849).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {230}, pmid = {41000208}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Hofmannophila pseudospretella (the Brown House-moth; Arthropoda; Insecta; Lepidoptera; Oecophoridae). The genome sequence is 406.2 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.5 kilobases in length.}, }
@article {pmid41262554, year = {2023}, author = {Boyes, D and Holland, PWH and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Dot Moth, Melanchra persicariae (Linnaeus, 1761).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {190}, pmid = {41262554}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Melanchra persicariae (the Dot Moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 647.9 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length.}, }
@article {pmid41041439, year = {2023}, author = {Boyes, D and ,  and ,  and ,  and ,  and ,  and Hoile, A and , }, title = {The genome sequence of the Brick, Agrochola circellaris (Hufnagel, 1766).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {44}, pmid = {41041439}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Agrochola circellaris (the Brick; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 572 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.5 kilobases in length. Gene annotation of this assembly on Ensembl has identified 18,319 protein coding genes.}, }
@article {pmid40223273, year = {2025}, author = {Yang, SY and Han, SM and Lee, JY and Kim, KS and Lee, JE and Lee, DW}, title = {Advancing Gut Microbiome Research: The Shift from Metagenomics to Multi-Omics and Future Perspectives.}, journal = {Journal of microbiology and biotechnology}, volume = {35}, number = {}, pages = {e2412001}, pmid = {40223273}, issn = {1738-8872}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Metagenomics/trends ; Multiomics/trends ; *Host Microbial Interactions/physiology ; *Translational Research, Biomedical/methods/trends ; Precision Medicine/methods/trends ; }, abstract = {The gut microbiome, a dynamic and integral component of human health, has co-evolved with its host, playing essential roles in metabolism, immunity, and disease prevention. Traditional microbiome studies, primarily focused on microbial composition, have provided limited insights into the functional and mechanistic interactions between microbiota and their host. The advent of multi-omics technologies has transformed microbiome research by integrating genomics, transcriptomics, proteomics, and metabolomics, offering a comprehensive, systems-level understanding of microbial ecology and host-microbiome interactions. These advances have propelled innovations in personalized medicine, enabling more precise diagnostics and targeted therapeutic strategies. This review highlights recent breakthroughs in microbiome research, demonstrating how these approaches have elucidated microbial functions and their implications for health and disease. Additionally, it underscores the necessity of standardizing multi-omics methodologies, conducting large-scale cohort studies, and developing novel platforms for mechanistic studies, which are critical steps toward translating microbiome research into clinical applications and advancing precision medicine.}, }
@article {pmid40222989, year = {2025}, author = {Mu, K and Wang, Z and Tang, J and Zhang, J and Han, W}, title = {The satisfaction of ecological environment in sports public services by artificial intelligence and big data.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {12748}, pmid = {40222989}, issn = {2045-2322}, mesh = {Humans ; *Artificial Intelligence ; *Big Data ; *Sports ; Surveys and Questionnaires ; Neural Networks, Computer ; *Personal Satisfaction ; }, abstract = {In order to gain a more accurate understanding and enhance the relationship between the fitness ecological environment and artificial intelligence (AI)-driven sports public services, this study combines a Convolutional Neural Network (CNN) approach based on residual modules and attention mechanisms with the SERVQUAL evaluation model. The method employed involves the analysis of big data collected from questionnaire surveys, literature reviews, and interviews. This study critically examines the impact of advanced AI technologies on residents' satisfaction with the fitness ecological environment in sports public services and conducts theoretical analysis of the obtained data. The results show that the quality of sports public services empowered by AI significantly influences residents' satisfaction with the fitness ecological environment, such as running, swimming, ball games and other sports with high requirements for sports service quality and ecological environment. Only the good public sports service quality matching with them can meet the needs of the ecological environment for fitness, and stimulate the enthusiasm of the people for fitness. The study also shows that swimming, running and all kinds of ball games account for the largest proportion of all sports. To sum up, the satisfaction of residents' fitness ecological environment is greatly affected by the quality of public sports services, which is mainly reflected in the good and perfect sports environment and facilities that can provide residents with a wealth of fitness options, greatly improving the sports ecological environment. This study is helpful to realize the relationship between sports public service and sports ecological environment. It contributes to understanding the role of AI and deep learning in enhancing the correlation between sports public service and the ecological environment of sports.}, }
@article {pmid40218748, year = {2025}, author = {Meng, J and Wang, Y and Liu, W and Yang, X and He, P}, title = {Research on the Development of an Inland Lake Bathymetry Estimation Model Based on Multispectral Data.}, journal = {Sensors (Basel, Switzerland)}, volume = {25}, number = {7}, pages = {}, pmid = {40218748}, issn = {1424-8220}, support = {41901285//the National Natural Science Foundation of China/ ; }, abstract = {Lakes play a crucial role in regional economic development and ecological construction. The variation in lake water depth has a direct impact on local economic activities, such as agriculture, livestock farming, and fisheries, as well as the stability of hydrological conditions and water ecology. In response to the lack of unified evaluation in the application of remote sensing water-depth estimation models for inland lakes, this study systematically compares the performance of numerical models and machine learning models for water-depth estimation in inland lakes. A machine learning-based water-depth estimation model construction methodology suitable for inland lakes is proposed. This study introduces an innovative approach by integrating machine learning techniques with multispectral remote sensing data, improving the accuracy and applicability of water-depth estimation models for inland lakes. The results show the following: (1) The machine learning models based on random forest (RF), BP neural networks (BP), and AdaBoost demonstrate better performance (R[2] = 0.88, 0.72, and 0.61; MAE = 0.12 m, 0.24 m, and 0.31 m; RMSE = 0.32 m, 0.48 m, and 0.57 m) compared to the multi-band logarithmic ratio (MLR) model (R[2] = 0.59; MAE = 0.32 m; RMSE = 0.58 m); (2) the machine learning water-depth estimation model constructed based on this methodology exhibits improved precision (R[2] = 0.92, 0.89, and 0.80; MAE = 0.11 m, 0.17 m, and 0.25 m; RMSE = 0.25 m, 0.30 m, and 0.41 m). This suggests that the methodology is more suitable for the estimation of water depth in medium- and small-sized lakes; (3) The machine learning model developed in this study, combined with multispectral remote sensing imagery, achieves the accuracy required for the evaluation of water depths for practical water resources. This model enables the rapid acquisition of high-precision underwater three-dimensional topographic maps, providing more accurate and timely hydrological data support for lake water resource management.}, }
@article {pmid40213769, year = {2025}, author = {Yi, S and Liu, Y and Wu, Q and Zhao, D and Li, Z and Peng, X and Liao, G and Wang, S}, title = {Glycosylation of oral bacteria in modulating adhesion and biofilm formation.}, journal = {Journal of oral microbiology}, volume = {17}, number = {1}, pages = {2486650}, pmid = {40213769}, issn = {2000-2297}, abstract = {BACKGROUND: Glycosylation is a ubiquitous biochemical process that covalently attaches glycans to proteins or lipids, which plays a pivotal role in modulating the structure and function of these biomolecules. This post-translational modification is prevalent in living organisms and intricately regulates various biological processes, including signaling transduction, recognition, and immune responses. In the oral environment, bacteria ingeniously use glycosylation to enhance their adhesion to oral surfaces, which is a key step in biofilm formation and subsequent development. This adhesion process is intimately associated with the onset and progression of oral diseases, including dental caries and periodontal disease.<br><br>OBJECTIVE: This review aims to describe the types and mechanisms of glycosylation in oral bacteria, and to understand the role of glycosylation in the adhesion, biofilm formation and virulence of oral bacteria.<br><br>METHODS: We reviewed articles on glycosylation in a variety of oral bacteria.<br><br>CONCLUSION: In cariogenic bacteria and periodontopathic pathogens, glycosylation facilitates adhesion and subsequent biofilm maturation on tooth surface. &#xa0;&#xa0;Distinct glycosylation patterns in oral bacteria shape biofilm structure and function, influencing microbial interactions and community stability. &#xa0;&#xa0;Pathogen-specific glycosylation signatures enhance virulence and ecological competitiveness, contributing to disease progression. Glycosylation plays a critical role in bacterial virulence and community &#xa0;interactions, with significant implications for oral health and disease development.}, }
@article {pmid40213351, year = {2025}, author = {Fehér, &#xc1;M and Bajory, Z and Czimbalmos, N and Burián, K and Lázár, A and Rárosi, F and Köves, B}, title = {Single-dose vs prolonged antibiotic prophylaxis of fosfomycin for transrectal prostate biopsy: a single-center prospective, randomized, controlled trial.}, journal = {Prostate international}, volume = {13}, number = {1}, pages = {28-33}, pmid = {40213351}, issn = {2287-8882}, abstract = {BACKGROUND: Transrectal prostate biopsy is a commonly performed urological procedure in which antibiotic prophylaxis is recommended. Fluoroquinolone-type antibiotics are no longer acceptable in the EU. Fosfomycin-trometamol may be used, but there is no evidence regarding its ideal dose and administration time.<br><br>METHODS: Patients who underwent prostate biopsy between 2021 and 2023 were evaluated prospectively. 204 patients were randomized into two arms: 102 patients (Arm A) received a single-dose of fosfomycin-trometamol one hour before surgery, and 102 patients (Arm B) received one additional dose of fosfomycin-trometamol 48&#xa0;hours after the first dose. Urine tests and questionnaires were administered during the postoperative period and the subsequent four weeks to identify any symptoms, infectious, or other complications.<br><br>RESULTS: There was no statistical difference in the rate of asymptomatic bacteriuria (4.90% (5) vs. 8.82% (9), P&#xa0;=&#xa0;0.27) symptomatic urinary tract infection (0% (0) vs. 1.96% (2), P&#xa0;=&#xa0;0.50), or febrile urinary tract infection (0% (0) vs. 0.98% (1), P&#xa0;=&#xa0;1) between the groups. Only hematuria was significantly more common in Arm B (6.86% (7) vs. 16.67% (17), P&#xa0;=&#xa0;0.03), whereas other complications did not differ significantly. There was no statistical difference in hospitalization (0.98% (1) vs. 2.94 (3), P&#xa0;=&#xa0;0.62) or mortality rate (0 % (0) vs. 0.98% (1), P&#xa0;=&#xa0;1). Sub-group analysis of previous antibiotic users showed no difference in terms of complications.<br><br>CONCLUSION: There is no significant difference in infectious complications between single-dose and prolonged prophylaxis of fosfomycin-trometamol for transrectal prostate biopsy. A single-dose of fosfomycin one hour before biopsy is an ideal choice with a better ecological impact compared with prolonged antibiotic prophylaxis for transrectal prostate biopsy.}, }
@article {pmid40211980, year = {2025}, author = {Elena Schmitz, J and Rahmann, S}, title = {A comprehensive review and evaluation of species richness estimation.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {2}, pages = {}, pmid = {40211980}, issn = {1477-4054}, mesh = {*Biodiversity ; Computer Simulation ; Animals ; Computational Biology/methods ; Algorithms ; }, abstract = {MOTIVATION: The statistical problem of estimating the total number of distinct species in a population (or distinct elements in a multiset), given only a small sample, occurs in various areas, ranging from the unseen species problem in ecology to estimating the diversity of immune repertoires. Accurately estimating the true richness from very small samples is challenging, in particular for highly diverse populations with many rare species. Depending on the application, different estimation strategies have been proposed that incorporate explicit or implicit assumptions about either the species distribution or about the sampling process. These methods are scattered across the literature, and an extensive overview of their assumptions, methodology, and performance is currently lacking.<br><br>RESULTS: We comprehensively review and evaluate a variety of existing methods on real and simulated data with different compositions of rare and abundant species. Our evaluation shows that, depending on species composition, different methods provide the most accurate richness estimates. Simple methods based on the observed number of singletons yield accurate asymptotic lower bounds for several of the tested simulated species compositions, but tend to underestimate the true richness for heterogeneous populations and small samples containing 1% to 5% of the population. When the population size is known, upsampling (extrapolating) estimators such as PreSeq and RichnEst yield accurate estimates of the total species richness in a sample that is up to 10 times larger than the observed sample.<br><br>AVAILABILITY: Source code for data simulation and richness estimation is available at https://gitlab.com/rahmannlab/speciesrichness.}, }
@article {pmid40208899, year = {2025}, author = {Minier, L and Rouch, J and Sabbagh, B and Bertucci, F and Parmentier, E and Lecchini, D and Sèbe, F and Mathevon, N and Emonet, R}, title = {Visualization and quantification of coral reef soundscapes using CoralSoundExplorer software.}, journal = {PLoS computational biology}, volume = {21}, number = {4}, pages = {e1012050}, pmid = {40208899}, issn = {1553-7358}, mesh = {*Coral Reefs ; *Software ; Animals ; Acoustics ; Anthozoa/physiology ; Sound ; Machine Learning ; Computational Biology ; Polynesia ; Ecosystem ; *Environmental Monitoring/methods ; }, abstract = {Despite hosting some of the highest concentrations of biodiversity and providing invaluable goods and services in the oceans, coral reefs are under threat from global change and other local human impacts. Changes in living ecosystems often induce changes in their acoustic characteristics, but despite recent efforts in passive acoustic monitoring of coral reefs, rapid measurement and identification of changes in their soundscapes remains a challenge. Here we present the new open-source software CoralSoundExplorer, which is designed to study and monitor coral reef soundscapes. CoralSoundExplorer uses machine learning approaches and is designed to eliminate the need to extract conventional acoustic indices. To demonstrate CoralSoundExplorer's functionalities, we use and analyze a set of recordings from three coral reef sites, each with different purposes (undisturbed site, tourist site and boat site), located on the island of Bora-Bora in French Polynesia. We explain the CoralSoundExplorer analysis workflow, from raw sounds to ecological results, detailing and justifying each processing step. We detail the software settings, the graphical representations used for visual exploration of soundscapes and their temporal dynamics, along with the analysis methods and metrics proposed. We demonstrate that CoralSoundExplorer is a powerful tool for identifying disturbances affecting coral reef soundscapes, combining visualizations of the spatio-temporal distribution of sound recordings with new quantification methods to characterize soundscapes at different temporal scales.}, }
@article {pmid40205052, year = {2025}, author = {Yoo, D and Rhie, A and Hebbar, P and Antonacci, F and Logsdon, GA and Solar, SJ and Antipov, D and Pickett, BD and Safonova, Y and Montinaro, F and Luo, Y and Malukiewicz, J and Storer, JM and Lin, J and Sequeira, AN and Mangan, RJ and Hickey, G and Monfort Anez, G and Balachandran, P and Bankevich, A and Beck, CR and Biddanda, A and Borchers, M and Bouffard, GG and Brannan, E and Brooks, SY and Carbone, L and Carrel, L and Chan, AP and Crawford, J and Diekhans, M and Engelbrecht, E and Feschotte, C and Formenti, G and Garcia, GH and de Gennaro, L and Gilbert, D and Green, RE and Guarracino, A and Gupta, I and Haddad, D and Han, J and Harris, RS and Hartley, GA and Harvey, WT and Hiller, M and Hoekzema, K and Houck, ML and Jeong, H and Kamali, K and Kellis, M and Kille, B and Lee, C and Lee, Y and Lees, W and Lewis, AP and Li, Q and Loftus, M and Loh, YHE and Loucks, H and Ma, J and Mao, Y and Martinez, JFI and Masterson, P and McCoy, RC and McGrath, B and McKinney, S and Meyer, BS and Miga, KH and Mohanty, SK and Munson, KM and Pal, K and Pennell, M and Pevzner, PA and Porubsky, D and Potapova, T and Ringeling, FR and Rocha, JL and Ryder, OA and Sacco, S and Saha, S and Sasaki, T and Schatz, MC and Schork, NJ and Shanks, C and Smeds, L and Son, DR and Steiner, C and Sweeten, AP and Tassia, MG and Thibaud-Nissen, F and Torres-González, E and Trivedi, M and Wei, W and Wertz, J and Yang, M and Zhang, P and Zhang, S and Zhang, Y and Zhang, Z and Zhao, SA and Zhu, Y and Jarvis, ED and Gerton, JL and Rivas-González, I and Paten, B and Szpiech, ZA and Huber, CD and Lenz, TL and Konkel, MK and Yi, SV and Canzar, S and Watson, CT and Sudmant, PH and Molloy, E and Garrison, E and Lowe, CB and Ventura, M and O'Neill, RJ and Koren, S and Makova, KD and Phillippy, AM and Eichler, EE}, title = {Complete sequencing of ape genomes.}, journal = {Nature}, volume = {641}, number = {8062}, pages = {401-418}, pmid = {40205052}, issn = {1476-4687}, support = {T32 HG012344/HG/NHGRI NIH HHS/United States ; R01 MH120295/MH/NIMH NIH HHS/United States ; UH3 AG064706/AG/NIA NIH HHS/United States ; R35 GM146886/GM/NIGMS NIH HHS/United States ; R01 HG010329/HG/NHGRI NIH HHS/United States ; R01 AG056169/AG/NIA NIH HHS/United States ; R01 GM123312/GM/NIGMS NIH HHS/United States ; T15 LM007093/LM/NLM NIH HHS/United States ; U24 HG007497/HG/NHGRI NIH HHS/United States ; R01 HG002385/HG/NHGRI NIH HHS/United States ; P20 GM139769/GM/NIGMS NIH HHS/United States ; U24 HG010263/HG/NHGRI NIH HHS/United States ; R35 GM133747/GM/NIGMS NIH HHS/United States ; P51 OD011092/OD/NIH HHS/United States ; R56 AG056169/AG/NIA NIH HHS/United States ; P01 AI152999/AI/NIAID NIH HHS/United States ; R35 HG011332/HG/NHGRI NIH HHS/United States ; R35 GM133600/GM/NIGMS NIH HHS/United States ; U19 AG023122/AG/NIA NIH HHS/United States ; R01 HG007352/HG/NHGRI NIH HHS/United States ; R35 GM142916/GM/NIGMS NIH HHS/United States ; R01 HG010169/HG/NHGRI NIH HHS/United States ; U41 HG007234/HG/NHGRI NIH HHS/United States ; R35 GM146926/GM/NIGMS NIH HHS/United States ; R35 GM151348/GM/NIGMS NIH HHS/United States ; R35 GM151945/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Humans ; Centromere/genetics ; Chromosomes, Mammalian/genetics ; Evolution, Molecular ; Genome ; Gorilla gorilla/genetics ; Haplotypes/genetics ; Heterochromatin/genetics ; *Hominidae/genetics/classification ; Pan paniscus/genetics ; Pan troglodytes/genetics ; Phylogeny ; Segmental Duplications, Genomic/genetics ; Telomere/genetics ; *Whole Genome Sequencing ; }, abstract = {The most dynamic and repetitive regions of great ape genomes have traditionally been excluded from comparative studies[1-3]. Consequently, our understanding of the evolution of our species is incomplete. Here we present haplotype-resolved reference genomes and comparative analyses of six ape species: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan and siamang. We achieve chromosome-level contiguity with substantial sequence accuracy (<1 error in 2.7 megabases) and completely sequence 215 gapless chromosomes telomere-to-telomere. We resolve challenging regions, such as the major histocompatibility complex and immunoglobulin loci, to provide in-depth evolutionary insights. Comparative analyses enabled investigations of the evolution and diversity of regions previously uncharacterized or incompletely studied without bias from mapping to the human reference genome. Such regions include newly minted gene families in lineage-specific segmental duplications, centromeric DNA, acrocentric chromosomes and subterminal heterochromatin. This resource serves as a comprehensive baseline for future evolutionary studies of humans and our closest living ape relatives.}, }
@article {pmid40200522, year = {2025}, author = {Dsouza, N and Cohen, E and Ossebaard, H and van Meurs, H and Sijm-Eeken, M}, title = {The Ecological Footprint of Gynecology: Lessons from Dutch Hospitals and Implications for Future Healthcare Management.}, journal = {Studies in health technology and informatics}, volume = {323}, number = {}, pages = {424-428}, doi = {10.3233/SHTI250125}, pmid = {40200522}, issn = {1879-8365}, mesh = {Netherlands ; *Gynecology/organization &amp; administration ; Humans ; Quality Improvement/organization &amp; administration ; Female ; Models, Organizational ; }, abstract = {In 2023, global temperatures reached record-breaking highs, highlighting the urgent need for climate action. Healthcare is responsible for 4-8% of global carbon emissions, contributing to global warming and impacting the health of billions of people. Within healthcare, gynecology has a significant ecological footprint due to its high volume and broad range of care services. However, little is known on how gynecology departments' management structures, information systems and processes can be optimized to reduce the ecological footprint of this specialty. Therefore, a sustainability maturity model based on Donabedian's structure-process-outcome model for quality improvement was used to assess sustainability performance in two gynecology practices with different organizational structures (centralized vs. decentralized). Maturity model scores and interview findings were analyzed to extract lessons and recommendations for optimizing sustainability within gynecology. As the first assessment of its kind, this study provides a foundation for healthcare management seeking to improve environmental performance in gynecological care.}, }
@article {pmid40200140, year = {2025}, author = {Antala, M and Kovar, M and Sporinová, L and Filacek, A and Juszczak, R and Zivcak, M and Shomali, A and Prasad, R and Brestic, M and Rastogi, A}, title = {High-throughput phenotyping of buckwheat (Fagopyrum esculentum Moench.) genotypes under water stress: exploring drought resistance for sustainable agriculture.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {444}, pmid = {40200140}, issn = {1471-2229}, support = {23-04221 L//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 731013//Horizon 2020 Framework Programme/ ; 2021/43/I/NZ9/01356//Narodowym Centrum Nauki/ ; BWS/BIL/2022/1/00120//Narodowa Agencja Wymiany Akademickiej/ ; }, mesh = {*Fagopyrum/genetics/physiology/growth &amp; development ; Genotype ; *Droughts ; Phenotype ; Dehydration ; Crops, Agricultural/genetics/physiology ; Agriculture ; Stress, Physiological ; Plant Breeding ; Drought Resistance ; }, abstract = {BACKGROUND: As global agriculture faces the challenge of climate change, characterized by longer and more severe drought episodes, there is an increasing need for crop diversification and improved plant breeding. Buckwheat is one of the climate-resilient candidates for future important crops with remarkable adaptability to various biotic and abiotic stresses. As an underbred crop, a large number of genotypes should be assessed for the breeding of superior plants. Therefore, this study investigates the response of various buckwheat genotypes to water stress by high-throughput phenotyping and auxiliary plant physiology measurements.<br><br>RESULTS: We assessed six buckwheat genotypes from different regions under mild and severe water stress, focusing on morphological and physiological changes to understand drought tolerance mechanisms. Our findings revealed that reallocation of assimilated carbon from growth to secondary metabolite production is a common response to drought stress. Among the genotypes tested, Panda emerged as the most drought-resistant, with its morphology remaining the most stable under mild water stress and its ability to rapidly accumulate protective pigments in response to drought. Silver Hull also demonstrated resilience, maintaining its aboveground biomass under mild water stress at levels comparable to the control group. Additionally, the response magnitude to drought stress was linked to the biomass production potential of the genotypes, which was higher for those from warmer regions (Bhutan, Zimbabwe) and lower for those from colder regions (Poland, Canada).<br><br>CONCLUSION: The diversity in genotypic responses highlights the significant role of genetic variability in shaping drought resistance strategies in buckwheat. This research not only enhances our understanding of buckwheat's physiological responses to water stress but also holds promise for developing drought-resistant buckwheat varieties. These advancements are crucial for promoting sustainable agriculture in the face of climate change.}, }
@article {pmid40200134, year = {2025}, author = {Hu, X and Pan, L and Fu, C and Zhu, Q and Hao, J and Wang, X and Nawaz, M and Qu, J and Zhang, J and Chen, Y and Zong, J and Liao, L and Tang, M and Wang, Z}, title = {A multi-omics analysis reveals candidate genes for Cd tolerance in Paspalum vaginatum.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {441}, pmid = {40200134}, issn = {1471-2229}, support = {No.321RC475//Hainan Natural Science Foundation high-level Talents Project/ ; No.321RC475//Hainan Natural Science Foundation high-level Talents Project/ ; ZDYF2023XDNY078//the Hainan Province Science and Technology Special Fund/ ; XTCX2022STC10//Collaborative Innovation Center Project of Ecological Civilization in Hainan University/ ; KJRC2023C21//Innovational Fund for Scientific and Technological Personnel of Hainan Province/ ; No.32060409//the National Natural Science Foundation of China/ ; XTCX2022NYB08//Collaborative Innovation Center Project of Nanfan and High-Efficiency Tropical Agriculture in Hainan University/ ; }, mesh = {*Cadmium/toxicity ; *Paspalum/genetics/drug effects/metabolism/physiology ; Genome-Wide Association Study ; *Genes, Plant ; Gene Expression Regulation, Plant ; Multiomics ; }, abstract = {Cadmium (Cd) pollution in the farmland has become a serious global issue threatening both human health and plant biomass production. Seashore paspalum (Paspalum vaginatum Sw.), a halophytic turfgrass, has been recognized as a Cd-tolerant species. However, the underlying genetic basis of natural variations in Cd tolerance still remains unknown. This study is possibly the first to apply genome-wide association studies (GWAS) and selective sweep analysis to identify potential Cd stress-responsive genes in P. vaginatum. We identified a total of 89 candidate genes and 656 putative selective sweeps regions. Based on the correlation analysis of differentially expressed metabolites (DEMs) and differentially expressed genes (DEGs), we identified the 55 key genes associated with metabolic changes induced by Cd treatment as the Cd tolerance-related genes. These genes showed significantly higher expression in Cd-tolerant accessions as compared to Cd-susceptive accessions. Therefore, our multi-omics study revealed the molecular and genetic basis of Cd tolerance, which may help develop Cd tolerant crop varieties.}, }
@article {pmid40199921, year = {2025}, author = {Chaudhary, VB and Nokes, LF and González, JB and Cooper, PO and Katula, AM and Mares, EC and Pehim Limbu, S and Robinson, JN and Aguilar-Trigueros, CA}, title = {TraitAM, a global spore trait database for arbuscular mycorrhizal fungi.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {588}, pmid = {40199921}, issn = {2052-4463}, support = {DEB-2205650//National Science Foundation (NSF)/ ; Feodor Lynen Fellowship//Alexander von Humboldt-Stiftung (Alexander von Humboldt Foundation)/ ; }, mesh = {Databases, Factual ; *Mycorrhizae/genetics ; Phylogeny ; *Spores, Fungal/genetics ; Symbiosis ; }, abstract = {Knowledge regarding organismal traits supports a better understanding of the relationship between form and function and can be used to predict the consequences of environmental stressors on ecological and evolutionary processes. Most plants on Earth form symbioses with mycorrhizal fungi, but our ability to make trait-based inferences for these fungi is limited due to a lack of publicly available trait data. Here, we present TraitAM, a comprehensive database of multiple spore traits for all described species of the most common group of mycorrhizal fungi, the arbuscular mycorrhizal (AM) fungi (subphylum Glomeromycotina). Trait data for 344 species were mined from original species descriptions and used to calculate newly developed fungal trait metrics that can be employed to explore both intra- and inter-specific variation in traits. TraitAM also includes an updated phylogenetic tree that can be used to conduct phylogenetically-informed multivariate analyses of AM fungal traits. TraitAM will aid our further understanding of the biology, ecology, and evolution of these globally widespread, symbiotic fungi.}, }
@article {pmid40198914, year = {2025}, author = {Holmqvist, S and Kaplan, M and Chaturvedi, R and Shou, H and Giovannetti, T}, title = {Longitudinal and Combined Smartwatch and Ecological Momentary Assessment in Racially Diverse Older Adults: Feasibility, Adherence, and Acceptability Study.}, journal = {JMIR human factors}, volume = {12}, number = {}, pages = {e69952}, pmid = {40198914}, issn = {2292-9495}, support = {F31 AG089944/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; *Ecological Momentary Assessment/statistics &amp; numerical data ; Male ; Aged ; Female ; Feasibility Studies ; Middle Aged ; *Patient Compliance/statistics &amp; numerical data ; Aged, 80 and over ; Longitudinal Studies ; *Smartphone ; *Mobile Applications ; *Cognitive Dysfunction/diagnosis ; *Wearable Electronic Devices/statistics &amp; numerical data ; }, abstract = {BACKGROUND: Due to the rising prevalence of Alzheimer disease and related dementias, easily deployable tools to quantify risk are needed. Smartphones and smartwatches enable unobtrusive and continuous monitoring, but there is limited information regarding the feasibility, adherence, and acceptability of digital data collection among racially diverse older adults.<br><br>OBJECTIVE: This paper examined the feasibility, adherence, and acceptability of a 4-week combined smartwatch monitoring and ecological momentary assessment (EMA) study in a racially diverse sample of older adults.<br><br>METHODS: A total of 44 older adults (aged &#x2265;55 y) with either mild cognitive impairment or healthy cognition completed an informed consent comprehension quiz, baseline cognitive testing, training regarding digital data collection, and questionnaires. Participants were instructed to wear a Garmin Vivosmart 4 smartwatch for 23 h/d for 4 weeks, sync 2 smartphone apps (Garmin and Labfront) daily, and complete a daily EMA survey with automated prompts for surveys and charging. Training time, smartwatch adherence (eg, wear time), daily EMA survey response rate, and performance on the consent quiz were quantified. Associations between feasibility and adherence metrics and participant factors were evaluated. Self-reported usability of the apps and smartwatch was collected at study end.<br><br>RESULTS: Consent comprehension quiz scores were high (mean 97.33%, SD 6.86% correct), and training sessions lasted on average 17.93 (SD 6.89) minutes. During the 4-week study, participants wore the smartwatch for an average of 21 h/d (SD 1.53) and showed an average response rate of 94% (SD 9.58%) to daily EMA surveys. In unadjusted bivariate analyses, age, race, and cognition were associated with feasibility and adherence measures, but only age and race remained significant in multivariate models. After accounting for all participant factors, older age was a significant predictor of longer training time, and Black race was a significant predictor of lower daily wear time. On the usability survey, all participants (45/45, 100%) indicated willingness to participate in future smartwatch studies, >80% (37/45) had a positive experience, and >90% (41/45) were satisfied with smartphone app syncing.<br><br>CONCLUSIONS: Smartwatch monitoring, requiring daily wear, smartphone syncing, and daily EMA survey completion, is highly feasible in older adults because adherence to daily wear and EMA surveys was high, as was general satisfaction on usability surveys. Although older participants may require more training on smartwatch and smartphone procedures and automated prompting during the study period, longitudinal monitoring with the Garmin Vivosmart 4 smartwatch and Labfront app is acceptable and feasible for collecting nearly continuous data in Black and White older adults, including those with mild cognitive impairment and those without.}, }
@article {pmid40198742, year = {2025}, author = {Choi, H and Lee, CH}, title = {The impact of climate change on ecology of tick associated with tick-borne diseases.}, journal = {PLoS computational biology}, volume = {21}, number = {4}, pages = {e1012903}, pmid = {40198742}, issn = {1553-7358}, mesh = {*Climate Change ; *Tick-Borne Diseases/transmission/epidemiology/prevention &amp; control ; Animals ; *Ticks/physiology ; Humans ; *Models, Biological ; Population Dynamics ; Computational Biology ; }, abstract = {Infectious diseases have caused significant economic and human losses worldwide. Growing concerns exist regarding climate change potentially exacerbating the spread of these diseases, particularly those transmitted by vectors such as ticks and mosquitoes. Tick-borne diseases, such as Severe Fever with Thrombocytopenia Syndrome (SFTS), can be particularly detrimental to elderly and immunocompromised individuals. This study utilizes a mathematical modeling approach to predict changes in tick populations under climate change scenarios, incorporating tick ecology and climate-sensitive parameters. Sensitivity analysis is performed to investigate the factors influencing tick population dynamics. The study further explores effective tick control strategies and their cost-effectiveness in the context of climate change. The findings indicate that the efficacy of tick population reduction varies greatly depending on the timing of control measure implementation and the effectiveness of the control strategies exhibits a strong dependence on the duration of implementation. Furthermore, as climate change intensifies, tick populations are projected to increase, leading to a rise in control costs and SFTS cases. In light of these findings, identifying and implementing appropriate control measures to manage tick populations under climate change will be increasingly crucial.}, }
@article {pmid40198416, year = {2025}, author = {Huan, F and Gao, S and Gu, Y and Ni, L and Wu, M and Li, Y and Liu, M and Yang, Y and Xiao, A and Liu, G}, title = {Molecular Allergology: Epitope Discovery and Its Application for Allergen-Specific Immunotherapy of Food Allergy.}, journal = {Clinical reviews in allergy &amp; immunology}, volume = {68}, number = {1}, pages = {37}, pmid = {40198416}, issn = {1559-0267}, support = {32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 2022YFF1100103//the grant from the National Key R&amp;D Program of China/ ; 2022YFF1100103//the grant from the National Key R&amp;D Program of China/ ; 2022YFF1100103//the grant from the National Key R&amp;D Program of China/ ; 2022YFF1100103//the grant from the National Key R&amp;D Program of China/ ; 2022YFF1100103//the grant from the National Key R&amp;D Program of China/ ; 2022YFF1100103//the grant from the National Key R&amp;D Program of China/ ; 2022YFF1100103//the grant from the National Key R&amp;D Program of China/ ; 2022YFF1100103//the grant from the National Key R&amp;D Program of China/ ; 2022YFF1100103//the grant from the National Key R&amp;D Program of China/ ; 2022YFF1100103//the grant from the National Key R&amp;D Program of China/ ; }, mesh = {Humans ; *Food Hypersensitivity/therapy/immunology ; *Allergens/immunology/chemistry/genetics ; *Desensitization, Immunologic/methods ; Animals ; *Epitopes, T-Lymphocyte/immunology ; *Epitopes, B-Lymphocyte/immunology ; *Epitopes/immunology ; Computational Biology ; Epitope Mapping ; }, abstract = {The prevalence of food allergy continues to rise, posing a significant burden on health and quality of life. Research on antigenic epitope identification and hypoallergenic agent design is advancing allergen-specific immunotherapy (AIT). This review focuses on food allergens from the perspective of molecular allergology, provides an overview of integration of bioinformatics and experimental validation for epitope identification, highlights hypoallergenic agents designed based on epitope information, and offers a valuable guidance to the application of hypoallergenic agents in AIT. With the development of molecular allergology, the characterization of the amino acid sequence and structure of the allergen at the molecular level facilitates T-/B-cell epitope identification. Alignment of the identified epitopes in food allergens revealed that the amino acid sequence of T-/B-cell epitopes barely overlapped, providing crucial data to design allergen molecules as a promising form for treating (FA) food allergy. Manipulating antigenic epitopes can reduce the allergenicity of allergens to obtain hypoallergenic agents, thereby minimizing the severe side effects associated with AIT. Currently, hypoallergenic agents are mainly developed through synthetic epitope peptides, genetic engineering, or food processing methods based on the identified epitope. New strategies such as DNA vaccines, signaling molecules coupling, and nanoparticles are emerging to improve efficiency. Although significant progress has been made in designing hypoallergenic agents for AIT, the challenge in clinical translation is to determine the appropriate dose and duration of treatment to induce long-term immune tolerance.}, }
@article {pmid40197051, year = {2025}, author = {Shamash, M and Sinha, A and Maurice, CF}, title = {Improving gut virome comparisons using predicted phage host information.}, journal = {mSystems}, volume = {10}, number = {5}, pages = {e0136424}, pmid = {40197051}, issn = {2379-5077}, mesh = {*Bacteriophages/genetics/classification/physiology ; *Virome/genetics ; Humans ; *Gastrointestinal Microbiome/genetics ; Animals ; Mice ; Feces/virology/microbiology ; Metagenomics/methods ; Computational Biology/methods ; Bacteria/virology ; }, abstract = {UNLABELLED: The human gut virome is predominantly made up of bacteriophages (phages), viruses that infect bacteria. Metagenomic studies have revealed that phages in the gut are highly individual specific and dynamic. These features make it challenging to perform meaningful cross-study comparisons. While several taxonomy frameworks exist to group phages and improve these comparisons, these strategies provide little insight into the potential effects phages have on their bacterial hosts. Here, we propose the use of predicted phage host families (PHFs) as a functionally relevant, qualitative unit of phage classification to improve these cross-study analyses. We first show that bioinformatic predictions of phage hosts are accurate at the host family level by measuring their concordance to Hi-C sequencing-based predictions in human and mouse fecal samples. Next, using phage host family predictions, we determined that PHFs reduce intra- and interindividual ecological distances compared to viral contigs in a previously published cohort of 10 healthy individuals, while simultaneously improving longitudinal virome stability. Lastly, by reanalyzing a previously published metagenomics data set with >1,000 samples, we determined that PHFs are prevalent across individuals and can aid in the detection of inflammatory bowel disease-specific virome signatures. Overall, our analyses support the use of predicted phage hosts in reducing between-sample distances and providing a biologically relevant framework for making between-sample virome comparisons.<br><br>IMPORTANCE: The human gut virome consists mainly of bacteriophages (phages), which infect bacteria and show high individual specificity and variability, complicating cross-study comparisons. Furthermore, existing taxonomic frameworks offer limited insight into their interactions with bacterial hosts. In this study, we propose using predicted phage host families (PHFs) as a higher-level classification unit to enhance functional cross-study comparisons. We demonstrate that bioinformatic predictions of phage hosts align with Hi-C sequencing results at the host family level in human and mouse fecal samples. We further show that PHFs reduce ecological distances and improve virome stability over time. Additionally, reanalysis of a large metagenomics data set revealed that PHFs are widespread and can help identify disease-specific virome patterns, such as those linked to inflammatory bowel disease.}, }
@article {pmid40196448, year = {2025}, author = {Rotstein, NM and Cohen, ZD and Welborn, A and Zbozinek, TD and Akre, S and Jones, KG and Null, KE and Pontanares, J and Sanchez, KL and Flanagan, DC and Halavi, SE and Kittle, E and McClay, MG and Bui, AAT and Narr, KL and Welsh, RC and Craske, MG and Kuhn, TP}, title = {Investigating low intensity focused ultrasound pulsation in anhedonic depression-A randomized controlled trial.}, journal = {Frontiers in human neuroscience}, volume = {19}, number = {}, pages = {1478534}, pmid = {40196448}, issn = {1662-5161}, abstract = {INTRODUCTION: Anhedonic depression is a subtype of depression characterized by deficits in reward processing. This subtype of depression is associated with higher suicide risk and longer depressive episodes, underscoring the importance of effective treatments. Anhedonia has also been found to correlate with alterations in activity in several subcortical regions, including the caudate head and nucleus accumbens. Low intensity focused ultrasound pulsation (LIFUP) is an emerging technology that enables non-invasive stimulation of these subcortical regions, which were previously only accessible with surgically-implanted electrodes.<br><br>METHODS: This double-blinded, sham-controlled study aims to investigate the effects of LIFUP to the left caudate head and right nucleus accumbens in participants with anhedonic depression. Participants in this protocol will undergo three sessions of LIFUP over the span of 5-9 days. To investigate LIFUP-related changes, this 7-week protocol collects continuous digital phenotyping data, an array of self-report measures of depression, anhedonia, and other psychopathology, and magnetic resonance imaging (MRI) before and after the LIFUP intervention. Primary self-report outcome measures include Ecological Momentary Assessment, the Positive Valence Systems Scale, and the Patient Health Questionnaire. Primary imaging measures include magnetic resonance spectroscopy and functional MRI during reward-based tasks and at rest. Digital phenotyping data is collected with an Apple Watch and participants' personal iPhones throughout the study, and includes information about sleep, heart rate, and physical activity.<br><br>DISCUSSION: This study is the first to investigate the effects of LIFUP to the caudate head or nucleus accumbens in depressed subjects. Furthermore, the data collected for this protocol covers a wide array of potentially affected modalities. As a result, this protocol will help to elucidate potential impacts of LIFUP in individuals with anhedonic depression.}, }
@article {pmid40194740, year = {2025}, author = {Nieman, DC and Sakaguchi, CA and Williams, JC and Lawson, J and Lambirth, KC and Omar, AM and Mulani, FA and Zhang, Q}, title = {Gut Prevotella copri abundance linked to elevated post-exercise inflammation.}, journal = {Journal of sport and health science}, volume = {14}, number = {}, pages = {101039}, pmid = {40194740}, issn = {2213-2961}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Prevotella/isolation &amp; purification ; *Inflammation/microbiology ; Feces/microbiology ; Male ; Adult ; *Exercise/physiology ; Oxylipins/blood ; *Bicycling/physiology ; Arachidonic Acid/blood ; Young Adult ; }, abstract = {PURPOSE: This study aimed to examine the linkage between gut microbiome taxa and exercise-induced inflammation.<br><br>METHODS: Twenty-five cyclists provided 4 stool samples during a 10-week period and cycled vigorously for 2.25 h at 67% maximal oxygen uptake (VO2max) in a laboratory setting. Blood samples were collected pre- and post-exercise, with additional samples collected at 1.5-h, 3-h, and 24-h post exercise. Primary outcomes included stool microbiome composition and alpha diversity via whole genome shotgun (WGS) sequencing (averaged from 4 stool samples) and a targeted panel of 75 plasma oxylipins. A total of 5719 taxa were identified, and the 339 that were present in more than 20% of stool samples were used in the analysis. Alpha diversity was calculated by evenness, and the Analysis of Composition of Microbiomes (ANCOM) differential abundance analysis was performed using Quantitative Insights Into Microbial Ecology-2 (QIIME2). A composite variable was calculated from 8 pro-inflammatory oxylipins generated from arachidonic acid (ARA) and cytochrome P-450 (CYP).<br><br>RESULTS: ARA-CYP oxylipins were significantly elevated for at least 3-h post-exercise (p < 0.001); they were strongly and positively related to Prevotella copri (P. copri) abundance (R[2]&#x202f;=&#x202f;0.676, p < 0.001) and negatively related to gut microbiome alpha diversity (R[2]&#x202f;=&#x202f;0.771, p < 0.001).<br><br>CONCLUSION: This analysis revealed for the first time a novel, positive relationship between gut microbiome P. copri abundance in cyclists and post-exercise pro-inflammatory oxylipins. These data demonstrate that about two-thirds of the wide variance in inflammation following prolonged and intensive exercise is largely explained by the abundance of a single gut bacterial species: P. copri.}, }
@article {pmid40188731, year = {2025}, author = {Li, Y and Huang, S and Jiang, S and Yang, L and Huang, J and Yang, Q and Jiang, Z and Shi, J and Ma, Z and Li, E and Zhou, F}, title = {Multi-omics insights into antioxidant and immune responses in Penaeus monodon under ammonia-N, low salinity, and combined stress.}, journal = {Ecotoxicology and environmental safety}, volume = {295}, number = {}, pages = {118156}, doi = {10.1016/j.ecoenv.2025.118156}, pmid = {40188731}, issn = {1090-2414}, mesh = {Animals ; *Penaeidae/immunology/physiology/drug effects ; *Ammonia/toxicity ; Salinity ; *Antioxidants/metabolism ; *Water Pollutants, Chemical/toxicity ; Oxidative Stress ; Gastrointestinal Microbiome/drug effects ; Metabolomics ; Stress, Physiological ; Transcriptome ; Nitrogen/toxicity ; Multiomics ; }, abstract = {Ammonia nitrogen and salinity are critical environmental factors that significantly impact marine organisms and present substantial threats to Penaeus monodon species within aquaculture systems. This study utilized a comprehensive multi-omics approach, encompassing transcriptomics, metabolomics, and gut microbiome analysis, to systematically examine the biological responses of shrimp subjected to low salinity, ammonia nitrogen stress, and their combined conditions. Metabolomic analysis demonstrated that exposure to ammonia nitrogen stress markedly influenced the concentrations of antioxidant-related metabolites, such as glutathione, suggesting that shrimp mitigate oxidative stress by augmenting their antioxidant capacity. The transcriptomic analysis revealed an upregulation of genes linked to energy metabolism and immune responses and antioxidant enzymes. Concurrently, gut microbiome analysis demonstrated that ammonia nitrogen stress resulted in a marked increase in Vibrio populations and a significant decrease in Photobacterium, indicating that alterations in microbial community structure are intricately associated with the shrimp stress response. A comprehensive analysis further indicated that the combined stressors of ammonia nitrogen and salinity exert a synergistic effect on the immune function and physiological homeostasis of shrimp by modulating antioxidant metabolic pathways and gut microbial communities. These findings provide critical systematic data for elucidating the mechanisms through which ammonia nitrogen and salinity influence marine ecosystems, offering substantial implications for environmental protection and ecological management.}, }
@article {pmid40186616, year = {2025}, author = {Chen, L and Guo, Y and López-Güell, K and Ma, J and Dong, Y and Xie, J and Alhambra, DP}, title = {Immunity Debt for Seasonal Influenza After the COVID-19 Pandemic and as a Result of Nonpharmaceutical Interventions: An Ecological Analysis and Cohort Study.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {12}, number = {20}, pages = {e2410513}, pmid = {40186616}, issn = {2198-3844}, support = {82373593//National Natural Science Foundation of China/ ; 82103865//National Natural Science Foundation of China/ ; 2022YFC2705300//National Key Research and Development Program of China/ ; 2024YFC3308300//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *COVID-19/epidemiology/prevention &amp; control/immunology ; *Influenza, Human/epidemiology/immunology/prevention &amp; control/transmission ; Seasons ; Pandemics/prevention &amp; control ; SARS-CoV-2 ; Cohort Studies ; Europe/epidemiology ; }, abstract = {Non-pharmaceutical interventions (NPIs) during the COVID-19 pandemic significantly reduced influenza transmission. This study explores the hypothesis of "immunity debt" which suggests increased vulnerability to influenza following reduced exposure during the pandemic. World Health Organization aggregated data on influenza from 116 countries and its association with NPI intensity as measured by the COVID-19 Stringency Index is analyzed. Where individual-level data available (France, the United Kingdom, Spain, Italy, Belgium, and Romania), the analyses of influenza monthly rates in six European countries (France, the United Kingdom, Spain, Italy, Belgium, and Romania) are replicated. The results indicate globally a 46.3% (95% CI: 15.79-70.78%) reduction in influenza cases during COVID-19 restrictions in the winter season, followed by a 131.7% (95% CI: 34.95-255.78%) increase in the first postrelaxation winter and a 161.2% (95% CI: 31.88-382.16%) increase in the summer as compared to the predicted level based on historical influenza epidemic trends. In addition, a positive association between the Stringency Index and post-relaxation influenza surge is observed globally (R[2] = 0.14-0.17) and replicated regionally. The findings support the population immunity debt hypothesis for influenza and call for proactive preparations against its consequences in future pandemics.}, }
@article {pmid40185844, year = {2025}, author = {Amin, NU and Islam, F and Umar, M and Muhammad, W and Rahman, SU and Gaafar, AZ and Shah, TA and Dauelbait, M and Bourhia, M}, title = {Evaluation of crop phenology using remote sensing and decision support system for agrotechnology transfer.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {11582}, pmid = {40185844}, issn = {2045-2322}, mesh = {*Remote Sensing Technology/methods ; *Crops, Agricultural/growth &amp; development ; Biomass ; *Agriculture/methods ; *Decision Support Techniques ; Plant Leaves/growth &amp; development ; Seasons ; }, abstract = {The decision support system for agro-technology transfer (DSSAT) is a worldwide crop modeling platform used for crops growth, yield, leaf area index (LAI), and biomass estimation under varying climatic, soil and management conditions. This study integrates DSSAT with satellite remote sensing (RS) data to estimates canopy state variables like LAI and biomass. For LAI estimation, Moderate Resolution Imaging Spectroradiometer (MODIS) product (MCD15A3H for LAI and MOD17A2 / MOD17A3 products for biomass) are used. Field data for Sheikhupura district is provided by National Agriculture Research Council (NARC) and used for the calibration and validation of the model. The results indicate strong agreement between the DSSAT and RS derived estimates. Correlation coefficients (R[2]) for LAI varied from 0.82 to 0.90, while for biomass ranged from 0.92 to 0.99 over two farms and two growing seasons (2012-2014). The index of agreement (D-index) ranged from 0.79 to 0.96 across the two farms and two growing seasons (2012-2014) affirming the model's durability. However, the biomass estimated from RS data is underestimated due to saturation phenomenon in the optical RS. The performance metrics, comprising the coefficient of residual mass (CRM) and normalized root mean square error (nRMSE), further substantiate the approach utilized. This study will help decision and policymakers and researchers to apply geospatial techniques for the sustainable agriculture practices.}, }
@article {pmid40181527, year = {2025}, author = {Mills, MB and Shenkin, A and Wilkes, P and Disney, M and Page, S and Berrio, JC and Kaduk, J and Malhi, Y and Robert, R and Nilus, R and Riutta, T}, title = {Investigating the accuracy of tropical woody stem CO2 efflux estimates: scaling methods, and vertical and diel variation.}, journal = {The New phytologist}, volume = {246}, number = {5}, pages = {2004-2014}, pmid = {40181527}, issn = {1469-8137}, support = {CA20118//European Cooperation in Science and Technology/ ; PRA 11.23//Royal Geographical Society/ ; NE/P011780/1//Natural Environment Research Council/ ; NE/Y006216/1//National Centre for Earth Observation/ ; NE/S007350/1//Central England NERC Training Alliance/ ; }, mesh = {*Plant Stems/metabolism/anatomy &amp; histology ; *Carbon Dioxide/metabolism ; *Tropical Climate ; *Wood/metabolism ; Trees/metabolism ; Borneo ; Malaysia ; }, abstract = {Stem CO2 efflux (EA) significantly contributes to autotrophic and ecosystem respiration in tropical forests, but field methodologies often introduce biases and uncertainty. This study evaluates these biases and their impact on scaling EA at the stand-level. Diel and vertical patterns of EA were investigated, along with the accuracy of estimating stem surface area from allometric equations vs terrestrial light dection and ranging (LiDAR) scanning (TLS) in Maliau Basin Conservation Area, Sabah, Malaysian Borneo. Diel EA exhibited no uniform pattern due to inter-tree variability, but results suggest measuring EA before 15:00 h. EA was significantly higher on buttresses and above the first major branching point, but vertical variations in EA did not impact stand-level EA when stem surface area was accurately estimated. Allometric equations underestimated total stem surface area by c. 40% compared with TLS, but applying a site-specific correction factor yielded a similar stand-level EA and total stem surface area to TLS. This study provides guidance for measuring EA in the field and suggests that measuring at one time point and one height along the stem can produce accurate results if conducted using the correct time frame and if stem surface area is accurately estimated.}, }
@article {pmid40180992, year = {2025}, author = {González, AL and Merder, J and Andraczek, K and Brose, U and Filipiak, M and Harpole, WS and Hillebrand, H and Jackson, MC and Jochum, M and Leroux, SJ and Nessel, MP and Onstein, RE and Paseka, R and Perry, GLW and Rugenski, A and Sitters, J and Sperfeld, E and Striebel, M and Zandona, E and Aymes, JC and Blanckaert, A and Bluhm, SL and Doi, H and Eisenhauer, N and Farjalla, VF and Hood, J and Kratina, P and Labonne, J and Lovelock, CE and Moody, EK and Mozsár, A and Nash, L and Pollierer, MM and Potapov, A and Romero, GQ and Roussel, JM and Scheu, S and Scheunemann, N and Seeber, J and Steinwandter, M and Susanti, WI and Tiunov, A and Dézerald, O}, title = {StoichLife: A Global Dataset of Plant and Animal Elemental Content.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {569}, pmid = {40180992}, issn = {2052-4463}, support = {DFG HI848/26-2//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; FOR 5000//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG 493345801//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; RGPIN-2020-04132//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology)/ ; 310119/2018-9//Ministry of Science, Technology and Innovation | Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (National Council for Scientific and Technological Development)/ ; NAF\R2\180791//Royal Society/ ; DP0986179//Department of Education and Training | Australian Research Council (ARC)/ ; DP160103669//Department of Education and Training | Australian Research Council (ARC)/ ; 22-14-00363)//Russian Science Foundation (RSF)/ ; }, mesh = {*Plants/chemistry ; Animals ; Ecosystem ; Phosphorus/analysis ; Nitrogen/analysis ; Carbon/analysis ; }, abstract = {The elemental content of life is a key trait shaping ecology and evolution, yet organismal stoichiometry has largely been studied on a case-by-case basis. This limitation has hindered our ability to identify broad patterns and mechanisms across taxa and ecosystems. To address this, we present StoichLife, a global dataset of 28,049 records from 5,876 species spanning terrestrial, freshwater, and marine realms. Compiled from published and unpublished sources, StoichLife documents elemental content and stoichiometric ratios (%C, %N, %P, C:N, C:P, and N:P) for individual plants and animals. The dataset is standardized and, where available, includes information on taxonomy, habitat, body mass (for animals), geography, and environmental conditions such as temperature, solar radiation, and nutrient availability. By providing an unprecedented breadth of organismal stoichiometry, StoichLife enables the exploration of global patterns, ecological and evolutionary drivers, and context-dependent variations. This resource advances our understanding of the chemical makeup of life and its responses to environmental change, supporting progress in ecological stoichiometry and related fields.}, }
@article {pmid40180917, year = {2025}, author = {Schmitz, MA and Dimonaco, NJ and Clavel, T and Hitch, TCA}, title = {Lineage-specific microbial protein prediction enables large-scale exploration of protein ecology within the human gut.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {3204}, pmid = {40180917}, issn = {2041-1723}, support = {460129525//Massachusetts Department of Fish and Game (DFG)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Metagenome/genetics ; *Metagenomics/methods ; *Bacterial Proteins/genetics/metabolism ; *Bacteria/genetics/classification/metabolism ; Phylogeny ; Computational Biology/methods ; }, abstract = {Microbes use a range of genetic codes and gene structures, yet these are often ignored during metagenomic analysis. This causes spurious protein predictions, preventing functional assignment which limits our understanding of ecosystems. To resolve this, we developed a lineage-specific gene prediction approach that uses the correct genetic code based on the taxonomic assignment of genetic fragments, removes incomplete protein predictions, and optimises prediction of small proteins. Applied to 9634 metagenomes and 3594 genomes from the human gut, this approach increased the landscape of captured expressed microbial proteins by 78.9%, including previously hidden functional groups. Optimised small protein prediction captured 3,772,658 small protein clusters, which form an improved microbial protein catalogue of the human gut (MiProGut). To enable the ecological study of a protein's prevalence and association with host parameters, we developed InvestiGUT, a tool which integrates both the protein sequences and sample metadata. Accurate prediction of proteins is critical to providing a functional understanding of microbiomes, enhancing our ability to study interactions between microbes and hosts.}, }
@article {pmid40179878, year = {2025}, author = {Li, Y and Liu, X and Guo, L and Han, K and Fang, S and Wan, X and Wang, D and Xu, X and Jiang, L and Fan, G and Xu, M}, title = {SpaGRN: Investigating spatially informed regulatory paths for spatially resolved transcriptomics data.}, journal = {Cell systems}, volume = {16}, number = {4}, pages = {101243}, doi = {10.1016/j.cels.2025.101243}, pmid = {40179878}, issn = {2405-4720}, mesh = {Animals ; *Transcriptome/genetics ; *Gene Expression Profiling/methods ; Humans ; *Gene Regulatory Networks/genetics ; Drosophila/genetics ; Computational Biology/methods ; }, abstract = {Cells spatially organize into distinct cell types or functional domains through localized gene regulatory networks. However, current spatially resolved transcriptomics analyses fail to integrate spatial constraints and proximal cell influences, limiting the mechanistic understanding of tissue organization. Here, we introduce SpaGRN, a statistical framework that reconstructs cell-type- or functional-domain-specific, dynamic, and spatial regulons by coupling intracellular spatial regulatory causality with extracellular signaling path information. Benchmarking across synthetic and real datasets demonstrates SpaGRN's superior precision over state-of-the-art tools in identifying context-dependent regulons. Applied to diverse spatially resolved transcriptomics platforms (Stereo-seq, STARmap, MERFISH, CosMx, Slide-seq, and 10x Visium), complex cancerous samples, and 3D datasets of developing Drosophila embryos and larvae, SpaGRN not only provides a versatile toolkit for decoding receptor-mediated spatial regulons but also reveals spatiotemporal regulatory mechanisms underlying organogenesis and inflammation.}, }
@article {pmid40179423, year = {2025}, author = {Dejeante, R and Valeix, M and Chamaillé-Jammes, S}, title = {Do Mixed-Species Groups Travel as One? An Investigation on Large African Herbivores Monitored Using Animal-Borne Video Collars.}, journal = {The American naturalist}, volume = {205}, number = {4}, pages = {451-458}, doi = {10.1086/734410}, pmid = {40179423}, issn = {1537-5323}, mesh = {Animals ; Video Recording ; *Herbivory ; *Giraffes/physiology ; *Equidae/physiology ; *Antelopes/physiology ; Social Behavior ; Geographic Information Systems ; Ecosystem ; }, abstract = {AbstractAlthough prey foraging in mixed-species groups benefit from a reduced risk of predation, whether heterospecific groupmates move together in the landscape, and more generally to what extent mixed-species groups remain cohesive over time and space, remains unknown. Here, we used GPS collars with video cameras to investigate the movements of plains zebras (Equus quagga) in mixed-species groups. Blue wildebeest (Connochaetes taurinus), impalas (Aepyceros melampus), and giraffes (Giraffa camelopardalis) commonly form mixed-species groups with zebras in savanna ecosystems. We found that zebras adjust their movement decisions solely on the basis of the presence of giraffes, being more likely to move in zebra-giraffe herds, and this was correlated with a higher cohesion of such groups. Additionally, zebras moving with giraffes spent more time grazing, suggesting that zebras benefit from foraging in the proximity of giraffes. Our results provide new insights into animal movements in mixed-species groups, contributing to a better consideration of mutualism in movement ecology.}, }
@article {pmid40179162, year = {2025}, author = {Davín, AA and Woodcroft, BJ and Soo, RM and Morel, B and Murali, R and Schrempf, D and Clark, JW and Álvarez-Carretero, S and Boussau, B and Moody, ERR and Szánthó, LL and Richy, E and Pisani, D and Hemp, J and Fischer, WW and Donoghue, PCJ and Spang, A and Hugenholtz, P and Williams, TA and Szöllősi, GJ}, title = {A geological timescale for bacterial evolution and oxygen adaptation.}, journal = {Science (New York, N.Y.)}, volume = {388}, number = {6742}, pages = {eadp1853}, doi = {10.1126/science.adp1853}, pmid = {40179162}, issn = {1095-9203}, support = {/ERC_/European Research Council/International ; }, mesh = {*Oxygen/metabolism ; Phylogeny ; *Biological Evolution ; Oxidation-Reduction ; *Bacteria/metabolism/classification/genetics ; Machine Learning ; Photosynthesis ; Adaptation, Physiological ; Cyanobacteria/genetics/metabolism ; }, abstract = {Microbial life has dominated Earth's history but left a sparse fossil record, greatly hindering our understanding of evolution in deep time. However, bacterial metabolism has left signatures in the geochemical record, most conspicuously the Great Oxidation Event (GOE). We combine machine learning and phylogenetic reconciliation to infer ancestral bacterial transitions to aerobic lifestyles, linking them to the GOE to calibrate the bacterial time tree. Extant bacterial phyla trace their diversity to the Archaean and Proterozoic, and bacterial families prior to the Phanerozoic. We infer that most bacterial phyla were ancestrally anaerobic and adopted aerobic lifestyles after the GOE. However, in the cyanobacterial ancestor, aerobic metabolism likely predated the GOE, which may have facilitated the evolution of oxygenic photosynthesis.}, }
@article {pmid40178345, year = {2025}, author = {Riobueno-Naylor, A and Gomez, I and Quan, S and Hutt Vater, C and Montes, M and Hoskova, B and Lai, BS}, title = {Methods for integrating public datasets: insights from youth disaster mental health research.}, journal = {European journal of psychotraumatology}, volume = {16}, number = {1}, pages = {2481699}, pmid = {40178345}, issn = {2000-8066}, mesh = {Humans ; Adolescent ; *Disasters ; United States/epidemiology ; *Mental Health/statistics &amp; numerical data ; Male ; Female ; *Depression/epidemiology ; *Datasets as Topic ; Databases, Factual ; }, abstract = {Introduction: Weather-related disasters pose significant risks to youth mental health. Exposure to multiple disasters is becoming more common; however, the effects of such exposure remain understudied. This study demonstrates the application of integrative data approaches and FAIR (Findable, Accessible, Interoperable, Reusable) data principles to evaluate the relationship between cumulative disaster exposure and youth depression and suicidality in the United States, taking into account contextual factors across levels of social ecology.Methods: We combined data from five public sources, including the Youth Risk Behavior Surveillance System (YRBS), Federal Emergency Management Agency (FEMA), United States Census Bureau, Center for Homeland Defense and Security School Shooting Safety Compendium, and Global Terrorism Database. The integrative dataset included 415,701 youth from 37 districts across the United States who completed the YRBS between 1999 and 2021. The YRBS served as the core dataset.Results: This data note highlights strategies for harmonizing diverse data formats, addressing geographic and temporal inconsistencies, and validating integrated datasets. Automated data cleaning and visualization techniques enhance accuracy and efficiency. Planning for sensitivity analyses before data cleaning is recommended to improve the data integration process and enhance the robustness of findings.Discussion: This integrative approach demonstrates how leveraging FAIR principles can advance trauma research by facilitating large-scale analyses of complex public health questions. The methods provide a replicable framework for examining population-level impacts of phenomena and highlight opportunities for expanding trauma research.}, }
@article {pmid40175550, year = {2025}, author = {Pärtel, M and Tamme, R and Carmona, CP and Riibak, K and Moora, M and Bennett, JA and Chiarucci, A and Chytrý, M and de Bello, F and Eriksson, O and Harrison, S and Lewis, RJ and Moles, AT and Öpik, M and Price, JN and Amputu, V and Askarizadeh, D and Atashgahi, Z and Aubin, I and Azcárate, FM and Barrett, MD and Bashirzadeh, M and Bátori, Z and Beenaerts, N and Bergholz, K and Birkeli, K and Biurrun, I and Blanco-Moreno, JM and Bloodworth, KJ and Boisvert-Marsh, L and Boldgiv, B and Brancalion, PHS and Brearley, FQ and Brown, C and Bueno, CG and Buffa, G and Cahill, JF and Campos, JA and Cangelmi, G and Carbognani, M and Carcaillet, C and Cerabolini, BEL and Chevalier, R and Clavel, JS and Costa, JM and Cousins, SAO and Čuda, J and Dairel, M and Dalle Fratte, M and Danilova, A and Davison, J and Deák, B and Del Vecchio, S and Dembicz, I and Dengler, J and Dolezal, J and Domene, X and Dvorsky, M and Ejtehadi, H and Enrico, L and Epikhin, D and Eskelinen, A and Essl, F and Fan, G and Fantinato, E and Fazlioglu, F and Fernández-Pascual, E and Ferrara, A and Fidelis, A and Fischer, M and Flagmeier, M and Forte, TGW and Fraser, LH and Fujinuma, J and Furquim, FF and Garris, B and Garris, HW and Giorgis, MA and Giusso Del Galdo, G and González-Robles, A and Good, MK and Guardiola, M and Guarino, R and Guerrero, I and Guillemot, J and Güler, B and Guo, Y and Haesen, S and Hejda, M and Heleno, RH and Høye, TT and Hrivnák, R and Huang, Y and Hunter, JT and Iakushenko, D and Ibáñez, R and Ingerpuu, N and Irl, SDH and Janíková, E and Jansen, F and Jeltsch, F and Jentsch, A and Jiménez-Alfaro, B and Jõks, M and Jouri, MH and Karami, S and Katal, N and Kelemen, A and Khairullin, BI and Khuroo, AA and Komatsu, KJ and Konečná, M and Kook, E and Korell, L and Koroleva, N and Korznikov, KA and Kozhevnikova, MV and Kozub, &#x141; and Laanisto, L and Lager, H and Lanta, V and Lasagno, RG and Lembrechts, JJ and Li, L and Lisner, A and Liu, H and Liu, K and Liu, X and Lucas-Borja, ME and Ludewig, K and Lukács, K and Luther-Mosebach, J and Macek, P and Marignani, M and Michalet, R and Miglécz, T and Moeslund, JE and Moeys, K and Montesinos, D and Moreno-Jiménez, E and Moysiyenko, I and Mucina, L and Muñoz-Rojas, M and Murillo, RA and Nambahu, SM and Neuenkamp, L and Normand, S and Nowak, A and Nuche, P and Oja, T and Onipchenko, VG and Pachedjieva, KL and Paganeli, B and Peco, B and Peralta, AML and Pérez-Haase, A and Peri, PL and Petraglia, A and Peyre, G and Plaza-Álvarez, PA and Plue, J and Prentice, HC and Prokhorov, VE and Radujković, D and Rahmanian, S and Reitalu, T and Ristow, M and Robin, AA and Robles, AB and Rodríguez Ginart, DA and Román, R and Roos, RE and Rosati, L and Sádlo, J and Salimbayeva, K and Sánchez de Dios, R and Sanchir, K and Sattler, C and Scasta, JD and Schmiedel, U and Schrader, J and Schultz, NL and Sellan, G and Serra-Diaz, JM and Silan, G and Skálová, H and Skobel, N and Sonkoly, J and Štajerová, K and Svitková, I and Świerszcz, S and Tanentzap, AJ and Tanentzap, FM and Tarifa, R and Tejero, P and Tekeev, DK and Tholin, M and Thormodsæter, RS and Tian, Y and Tokaryuk, A and Tölgyesi, C and Tomaselli, M and Tordoni, E and Török, P and Tóthmérész, B and Toussaint, A and Touzard, B and Trindade, DPF and Tsakalos, JL and Türkiş, S and Valencia, E and Valerio, M and Valkó, O and Van Meerbeek, K and Vandvik, V and Villellas, J and Virtanen, R and Vítková, M and Vojík, M and von Hessberg, A and von Oppen, J and Wagner, V and Wan, JZ and Wang, CJ and Wani, SA and Weiss, L and Wevill, T and Xiao, S and Zárate Martínez, O and Zobel, M}, title = {Global impoverishment of natural vegetation revealed by dark diversity.}, journal = {Nature}, volume = {641}, number = {8064}, pages = {917-924}, pmid = {40175550}, issn = {1476-4687}, mesh = {*Biodiversity ; *Plants/classification ; *Conservation of Natural Resources ; *Anthropogenic Effects ; Humans ; Human Activities ; Ecosystem ; }, abstract = {Anthropogenic biodiversity decline threatens the functioning of ecosystems and the many benefits they provide to humanity[1]. As well as causing species losses in directly affected locations, human influence might also reduce biodiversity in relatively unmodified vegetation if far-reaching anthropogenic effects trigger local extinctions and hinder recolonization. Here we show that local plant diversity is globally negatively related to the level of anthropogenic activity in the surrounding region. Impoverishment of natural vegetation was evident only when we considered community completeness: the proportion of all suitable species in the region that are present at a site. To estimate community completeness, we compared the number of recorded species with the dark diversity-ecologically suitable species that are absent from a site but present in the surrounding region[2]. In the sampled regions with a minimal human footprint index, an average of 35% of suitable plant species were present locally, compared with less than 20% in highly affected regions. Besides having the potential to uncover overlooked threats to biodiversity, dark diversity also provides guidance for nature conservation. Species in the dark diversity remain regionally present, and their local populations might be restored through measures that improve connectivity between natural vegetation fragments and reduce threats to population persistence.}, }
@article {pmid40175491, year = {2025}, author = {Zhang, H and Guo, G and Li, H and Wang, T and Ni, J and Meng, H}, title = {A new numerical method for calculating residual deformation in mined-out areas considering water-rock interaction and its application.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {11207}, pmid = {40175491}, issn = {2045-2322}, support = {2023YFC3804201//National Key R&amp;D Program of China/ ; }, abstract = {Globally, extensive land regions have fallen victim to coal mining subsidence, rendering the reuse of goaf sites a crucial concern. The residual deformation amount of these sites is the linchpin for determining their reusability. Presently, numerical computations of residual deformation in goafs, which overlook water-rock coupling, breed significant errors, posing severe threats to the safety of on-site structures. To remedy the situation, this research hinges on the mechanical experiment results of fractured rock masses under water-rock interaction within the goaf. By leveraging an embedded programming language, it pinpoints the irregular damage range of overlying strata due to water-rock effects. Then, corresponding mechanical parameters are allocated to the surrounding rocks at diverse spatial positions, with the erosive impact of water-soaked coal pillars also factored in. This gives rise to a novel numerical method that more precisely gauges groundwater's influence on strata movement and surface subsidence. Using the 01 working face of a Shandong mine as a practical backdrop, the new method verifies its reliability and accuracy. When contrasted with traditional approaches, be it neglecting water filling or assuming full saturation in the goaf, it slashes the calculation error by 20%, furnishing new approaches for residual deformation calculation and novel perspectives for evaluating site stability under complex geological conditions.}, }
@article {pmid40173850, year = {2025}, author = {Vivien, R and Martin, P}, title = {Maintaining taxonomic accuracy in genetic databases: A duty for taxonomists-Reanalysis of the DNA sequences from Mercan et al. (2024) on the genus Potamothrix (Annelida, Clitellata) in Turkish lakes.}, journal = {Zootaxa}, volume = {5575}, number = {4}, pages = {555-562}, doi = {10.11646/zootaxa.5575.4.5}, pmid = {40173850}, issn = {1175-5334}, mesh = {Turkey ; Animals ; Lakes ; Phylogeny ; *Databases, Genetic/standards ; *Databases, Nucleic Acid/standards ; Sequence Analysis, DNA ; *Polychaeta/classification/genetics ; }, abstract = {Public DNA sequence databases such as GenBank are widely used for identification of organisms in ecological and taxonomic studies. It is important that these public databases contain as few mistakes as possible and that any errors detected in these databases are reported. Here, we reanalyzed the COI sequences of Mercan et al. (2024) and showed that they were mistakenly considered by these authors as belonging to different populations (haplotypes) within the species Potamothrix hammoniensis (Tubificinae). We found that they corresponded to four distinct Tubificinae lineages (species), Pothamothrix alatus paravanicus, Potamothrix bavaricus, Tubifex sp. and Potamothrix sp. Despite these identification errors, the data from Mercan et al. (2024) remain interesting as they provide new information on the diversity of the genus Potamothrix in Turkey. Prompt measures must be taken to correct these errors and prevent them from being detrimental to future studies.}, }
@article {pmid40173380, year = {2025}, author = {Zagorščak, M and Abdelhakim, L and Rodriguez-Granados, NY and Široká, J and Ghatak, A and Bleker, C and Blejec, A and Zrimec, J and Novák, O and Pěnčík, A and Baebler, &#x160; and Perez Borroto, L and Schuy, C and Županič, A and Afjehi-Sadat, L and Wurzinger, B and Weckwerth, W and Pompe Novak, M and Knight, MR and Strnad, M and Bachem, C and Chaturvedi, P and Sonnewald, S and Sasidharan, R and Panzarová, K and Gruden, K and Teige, M}, title = {Integration of multi-omics data and deep phenotyping provides insights into responses to single and combined abiotic stress in potato.}, journal = {Plant physiology}, volume = {197}, number = {4}, pages = {}, pmid = {40173380}, issn = {1532-2548}, support = {//H2020-SFS-2019-2/ ; P4-0165//Slovenian Research Agency/ ; //Ministry of Education, Youth and Sports of the Czech Republic/ ; CZ.02.1.01/0.0/0.0/16_026/0008446//European Regional Development Fund-Project/ ; }, mesh = {*Solanum tuberosum/physiology/genetics/metabolism ; *Stress, Physiological/genetics ; Phenotype ; Droughts ; Proteomics ; Metabolomics ; Gene Expression Regulation, Plant ; Transcriptome ; Plant Leaves/physiology ; Plant Tubers ; Multiomics ; }, abstract = {Potato (Solanum tuberosum) is highly water and space efficient but susceptible to abiotic stresses such as heat, drought, and flooding, which are severely exacerbated by climate change. Our understanding of crop acclimation to abiotic stress, however, remains limited. Here, we present a comprehensive molecular and physiological high-throughput profiling of potato (Solanum tuberosum, cv. Désirée) under heat, drought, and waterlogging applied as single stresses or in combinations designed to mimic realistic future scenarios. Stress responses were monitored via daily phenotyping and multi-omics analyses of leaf samples comprising proteomics, targeted transcriptomics, metabolomics, and hormonomics at several timepoints during and after stress treatments. Additionally, critical metabolites of tuber samples were analyzed at the end of the stress period. We performed integrative multi-omics data analysis using a bioinformatic pipeline that we established based on machine learning and knowledge networks. Waterlogging produced the most immediate and dramatic effects on potato plants, interestingly activating ABA responses similar to drought stress. In addition, we observed distinct stress signatures at multiple molecular levels in response to heat or drought and to a combination of both. In response to all treatments, we found a downregulation of photosynthesis at different molecular levels, an accumulation of minor amino acids, and diverse stress-induced hormones. Our integrative multi-omics analysis provides global insights into plant stress responses, facilitating improved breeding strategies toward climate-adapted potato varieties.}, }
@article {pmid40171777, year = {2025}, author = {Zhao, W and Han, Q and Yang, F and Zhao, Y}, title = {Enhancing Enzyme Commission Number Prediction With Contrastive Learning and Agent Attention.}, journal = {Proteins}, volume = {93}, number = {9}, pages = {1507-1517}, doi = {10.1002/prot.26822}, pmid = {40171777}, issn = {1097-0134}, support = {32101590//National Outstanding Youth Science Fund Project of National Natural Science Foundation of China/ ; 32071838//Foundation for Innovative Research Groups of the National Natural Science Foundation of China/ ; }, mesh = {*Enzymes/chemistry/metabolism/classification ; Databases, Protein ; *Machine Learning ; *Computational Biology/methods ; Algorithms ; Software ; Data Mining ; Proteins/chemistry ; }, abstract = {The accurate prediction of enzyme function is crucial for elucidating disease mechanisms and identifying drug targets. Nevertheless, existing enzyme commission (EC) number prediction methods are limited by database coverage and the depth of sequence information mining, hindering the efficiency and precision of enzyme function annotation. Therefore, this study introduces ProteEC-CLA (Protein EC number prediction model with Contrastive Learning and Agent Attention). ProteEC-CLA utilizes contrastive learning to construct positive and negative sample pairs, which not only enhances sequence feature extraction but also improves the utilization of unlabeled data. This process helps the model learn the differences in sequence features, thereby enhancing its ability to predict enzyme function. Integrating the pre-trained protein language model ESM2, the model generates informative sequence embeddings for deep functional correlation analysis, significantly enhancing prediction accuracy. With the incorporation of the Agent Attention mechanism, ProteEC-CLA's ability to comprehensively capture local details and global features is enhanced, ensuring high-accuracy predictions on complex sequences. The results demonstrate that ProteEC-CLA performs exceptionally well on two independent and representative datasets. In the standard dataset, it achieves 98.92% accuracy at the EC4 level. In the more challenging clustered split dataset, ProteEC-CLA achieves 93.34% accuracy and an F1-score of 94.72%. With only enzyme sequences as input, ProteEC-CLA can accurately predict EC numbers up to the fourth level, significantly enhancing annotation efficiency and accuracy, which makes it a highly efficient and precise functional annotation tool for enzymology research and applications.}, }
@article {pmid40171521, year = {2025}, author = {Boyes, D and Hutchinson, F and Crowley, LM and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Large Birch Bell moth, Large Birch Roller, Epinotia brunnichana (Linnaeus, 1767).}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {101}, pmid = {40171521}, issn = {2398-502X}, abstract = {We present a genome assembly from a female Epinotia brunnichana (Large Birch Bell, Large Birch Roller; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence has a total length of 943.10 megabases. Most of the assembly (99.68%) is scaffolded into 29 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.7 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,003 protein-coding genes.}, }
@article {pmid40170100, year = {2025}, author = {Sato, K and Watanabe, S and Noda, T and Koizumi, T and Yoda, K and Watanabe, YY and Sakamoto, KQ and Isokawa, T and Yoshida, MA and Aoki, K and Takahashi, A and Iwata, T and Nishizawa, H and Maekawa, T and Kawabe, R and Watanuki, Y}, title = {Biologging intelligent Platform (BiP): an integrated and standardized platform for sharing, visualizing, and analyzing biologging data.}, journal = {Movement ecology}, volume = {13}, number = {1}, pages = {23}, pmid = {40170100}, issn = {2051-3933}, abstract = {Sharing biologging data can facilitate collaborative research and biological conservation by providing maps showing animals' distribution and movements. It is a critical social mission to preserve not only horizontal position data, but also behavioral data such as diving depth, flight altitude, speed, and acceleration, as well as physiological data such as body temperature, along with related metadata, ensuring their preservation for future generation. Moreover, although biologging was initially developed in the field of biology, it now contributes to diverse fields such as meteorology and oceanography, leading to expanded opportunities for secondary data utilization. In light of social and academic requirements, we developed "Biologging intelligent Platform (BiP)", which adheres to internationally recognized standards for sensor data and metadata storage. As a result, BiP not only stores sensor data along with metadata but also standardizes this information to facilitate secondary data analysis, facilitating broader applications of biologging data across various disciplines. By visiting the website (https://www.bip-earth.com) and completing the user registration, data owners can interactively upload sensor data, input metadata associated with individual animals, devices, and deployments, standardize data formats, and choose between open and private settings for sharing data. Anyone interested in utilizing the data can access metadata and visualized route maps, irrespective of the data's open or private status. Users can freely download open datasets that are available under the CC BY 4.0 license, which permits copying, redistribution, and modification while adhering to the metadata's credit requirements. To use private datasets, users can contact the data owner to request permission. A unique feature of BiP is the Online Analytical Processing (OLAP) tools that calculate environmental parameters, such as surface currents, ocean winds, and waves from data collected by animals. Algorithms published in some previous studies are integrated into the OLAP which can estimate the environmental and behavioral parameters. To enhance data accessibility, BiP allows users to search for datasets using the DOI of the paper in which the data was used. We believe that linking with other databases for data exchange and multi-repository storage could enhance the sustainability of the data itself.}, }
@article {pmid40169791, year = {2025}, author = {Ding, DY and Tang, Z and Zhu, B and Ren, H and Shalek, AK and Tibshirani, R and Nolan, GP}, title = {Quantitative characterization of tissue states using multiomics and ecological spatial analysis.}, journal = {Nature genetics}, volume = {57}, number = {4}, pages = {910-921}, pmid = {40169791}, issn = {1546-1718}, support = {P01 AI177687/AI/NIAID NIH HHS/United States ; U54 HG010426/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; *Spatial Analysis ; *Genomics/methods ; Single-Cell Analysis/methods ; Multiomics ; }, abstract = {The spatial organization of cells in tissues underlies biological function, and recent advances in spatial profiling technologies have enhanced our ability to analyze such arrangements to study biological processes and disease progression. We propose MESA (multiomics and ecological spatial analysis), a framework drawing inspiration from ecological concepts to delineate functional and spatial shifts across tissue states. MESA introduces metrics to systematically quantify spatial diversity and identify hot spots, linking spatial patterns to phenotypic outcomes, including disease progression. Furthermore, MESA integrates spatial and single-cell multiomics data to facilitate an in-depth, molecular understanding of cellular neighborhoods and their spatial interactions within tissue microenvironments. Applying MESA to diverse datasets demonstrates additional insights it brings over prior methods, including newly identified spatial structures and key cell populations linked to disease states. Available as a Python package, MESA offers a versatile framework for quantitative decoding of tissue architectures in spatial omics across health and disease.}, }
@article {pmid40168108, year = {2025}, author = {Wang, TY and Wu, YW and Lu, HJ and Liao, TY and Tai, JH and Huang, SP and Wang, FY and Yu, TH and Ting, CT and Chaw, SM and Wang, HY}, title = {Chromosome-Level Genome Assembly of the Loach Goby Rhyacichthys aspro Offers Insights Into Gobioidei Evolution.}, journal = {Molecular ecology resources}, volume = {25}, number = {7}, pages = {e14110}, pmid = {40168108}, issn = {1755-0998}, support = {23-23//Biodiversity Research Center, Academia Sinica/ ; MOST 102-2311-B-001-019//National Science and Technology Council/ ; MOST 108-2621-B-001-002//National Science and Technology Council/ ; MOST 109-2311-B-002-023-MY3//National Science and Technology Council/ ; 113L7223//National Taiwan University/ ; }, mesh = {Animals ; DNA Transposable Elements ; *Perciformes/genetics/classification ; *Genome ; *Evolution, Molecular ; *Chromosomes/genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The percomorph fish clade Gobioidei is a suborder that comprises over 2200 species distributed in nearly all aquatic habitats. To understand the genetics underlying their species diversification, we sequenced and annotated the genome of the loach goby, Rhyacichthys aspro, an early-diverging group, and compared it with nine additional Gobioidei species. Within Gobioidei, the loach goby possesses the smallest genome at 594 Mb, and a rise in species diversity from early-diverging to more recently diverged lineages is mirrored by enlarged genomes and a higher presence of transposable elements (TEs), particularly DNA transposons. These DNA transposons are enriched in genic and regulatory regions and their copy number increase is strongly correlated with substitution rate, suggesting that DNA repair after transposon excision/insertion leads to nearby mutations. Consequently, the proliferation of DNA transposons might be the crucial driver of Gobioidei diversification and adaptability. The loach goby genome also points to mechanisms of ecological adaptation. It contains relatively few genes for lateral line development but an overrepresentation of synaptic function genes, with genes putatively under selection linked to synapse organisation and calcium signalling, implicating a sensory system distinct from other Gobioidei species. We also see an overabundance of genes involved in neurocranium development and renal function, adaptations likely connected to its flat morphology suited for strong currents and an amphidromous life cycle. Comparative analyses with hill-stream loaches and the European eel reveal convergent adaptations in body shape and saltwater balance. These findings shed new light on the loach goby's survival mechanisms and the broader evolutionary trends within Gobioidei.}, }
@article {pmid40167332, year = {2025}, author = {Curto, M and Veríssimo, A and Riccioni, G and Santos, CD and Ribeiro, F and Jentoft, S and Alves, MJ and Gante, HF}, title = {Improving Whole Biodiversity Monitoring and Discovery With Environmental DNA Metagenomics.}, journal = {Molecular ecology resources}, volume = {25}, number = {6}, pages = {e14105}, pmid = {40167332}, issn = {1755-0998}, support = {CEEC/0482/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; DL 57/2016/CP1440/CP1646/CT0001//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; LA/P/0069/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PTDC/BIA-CBI/31644/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UID/04292/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UID/BIA/00329/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDP/50027/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; LA/P/0048/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 857251//Horizon 2020 Framework Programme/ ; STG/21/044//KU Leuven/ ; }, mesh = {*Metagenomics/methods ; *Biodiversity ; *DNA, Environmental/genetics ; *Computational Biology/methods ; DNA Barcoding, Taxonomic/methods ; Metagenome ; }, abstract = {Environmental DNA (eDNA) metagenomics sequences all DNA molecules present in environmental samples and has the potential of identifying virtually any organism from which they are derived. However, due to unacceptable levels of false positives and negatives, this approach is underexplored as a tool for biodiversity monitoring across the tree of life, particularly for non-microscopic eukaryotes. We present SeqIDist, a framework that combines multilocus BLAST matches against several reference databases followed by an analysis of sequence identity distribution patterns to disentangle false positives while revealing new biodiversity and increasing the accuracy of metagenomic approaches. We tested SeqIDist on an eDNA metagenomic dataset from a riverine site and compared the results to those obtained with an eDNA metabarcoding approach for benchmarking purposes. We start by characterising the biological community (~2000 taxa) across the tree of life at low taxonomic levels and show that eDNA metagenomics has a higher sensitivity than eDNA metabarcoding in discovering new diversity. We show that limited representation of whole genome sequences in reference databases can lead to false positives. For non-microscopic eukaryotes, eDNA metagenomic data often consist of a few sparse, anonymous sequences scattered across the genome, making metagenome assembly methods unfeasible. Finally, we infer eDNA source and residency time using read length distributions as a measure of decay status. The higher accuracy of SeqIDist opens the discussion of the potential of eDNA metagenomics for archived samples and its implementation in long-term biodiversity monitoring at a planetary scale.}, }
@article {pmid40165685, year = {2025}, author = {Gu, Y and Meng, L and Wang, Y and Wu, Z and Pan, Y and Zhao, Y and Detto, M and Wu, J}, title = {Uncovering the role of solar radiation and water stress factors in constraining decadal intra-site spring phenology variability in diverse ecosystems across the Northern Hemisphere.}, journal = {The New phytologist}, volume = {246}, number = {5}, pages = {1986-2003}, pmid = {40165685}, issn = {1469-8137}, support = {#2017804//Carbon Mitigation Initiative of Princeton University and NSF grant/ ; //HKU Seed Funding for Strategic Interdisciplinary Research Scheme/ ; #17305321//Hong Kong Research Grant Council General Research Fund/ ; #C5062-21GF//Hong Kong Research Grant Council Collaborative Research Fund/ ; #31922090//National Natural Science Foundation of China/ ; //Innovation and Technology Fund (funding support to State Key Laboratories of Agrobiotechnology)/ ; //HKU Science Faculty RAE Improvement Fund 2023-24/ ; }, mesh = {*Ecosystem ; *Seasons ; *Sunlight ; *Water ; *Stress, Physiological ; Soil/chemistry ; Rain ; }, abstract = {The spring phenology has advanced significantly over recent decades with climate change, impacting large-scale biogeochemical cycles, climate feedback, and other essential ecosystem processes. Although numerous prognostic models have been developed for spring phenology, regional analyses of the optimality (OPT) strategy model that incorporate environmental variables beyond temperature and photoperiod remain lacking. We investigated the roles of solar radiation (SR) and three water stress factors (precipitation (P), soil moisture, and vapor pressure deficit (VPD)) on spring phenology from 1982 to 2015 using the OPT model with Global Inventory Modeling and Mapping Studies NDVI3g dataset and environmental data from TerraClimate, CRU_TS, and Global Land Data Assimilation System across the Northern Hemisphere (> 30°N). Our results show that SR and water stress factors significantly impacted intrasite decadal spring phenology variability, with water stress factors dominant in grassland ecosystems while SR dominated in the rest of the ecosystem types. Enhanced models incorporating SR (OPT-S) and VPD (OPT-VPD) outperformed the original OPT model, likely due to improved representation of the adaptive strategy of spring phenology to optimize photosynthetic carbon gain while minimizing frost risk. Our research enhances the understanding of the key environmental drivers influencing decadal spring phenology variation in the Northern Hemisphere and contributes to more accurate forecasts of ecological responses to global environmental change.}, }
@article {pmid40163742, year = {2025}, author = {Ghassemi Nedjad, C and Bolteau, M and Bourneuf, L and Paulevé, L and Frioux, C}, title = {Seed2LP: seed inference in metabolic networks for reverse ecology applications.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {4}, pages = {}, pmid = {40163742}, issn = {1367-4811}, support = {//French National Research Agency/ ; }, mesh = {*Metabolic Networks and Pathways ; *Software ; *Computational Biology/methods ; Models, Biological ; Algorithms ; }, abstract = {MOTIVATION: A challenging problem in microbiology is to determine nutritional requirements of microorganisms and culture them, especially for the microbial dark matter detected solely with culture-independent methods. The latter foster an increasing amount of genomic sequences that can be explored with reverse ecology approaches to raise hypotheses on the corresponding populations. Building upon genome-scale metabolic networks (GSMNs) obtained from genome annotations, metabolic models predict contextualized phenotypes using nutrient information.<br><br>RESULTS: We developed the tool Seed2LP, addressing the inverse problem of predicting source nutrients, or seeds, from a GSMN and a metabolic objective. The originality of Seed2LP is its hybrid model, combining a scalable and discrete Boolean approximation of metabolic activity, with the numerically accurate flux balance analysis (FBA). Seed inference is highly customizable, with multiple search and solving modes, exploring the search space of external and internal metabolites combinations. Application to a benchmark of 107 curated GSMNs highlights the usefulness of a logic modelling method over a graph-based approach to predict seeds, and the relevance of hybrid solving to satisfy FBA constraints. Focusing on the dependency between metabolism and environment, Seed2LP is a computational support contributing to address the multifactorial challenge of culturing possibly uncultured microorganisms.<br><br>Seed2LP is available on https://github.com/bioasp/seed2lp.}, }
@article {pmid40156461, year = {2025}, author = {Sharma, G and Deuis, JR and Jia, X and Crawford, T and Rahnama, S and Undheim, EAB and Vetter, I and Chin, YK and Mobli, M}, title = {Refining the NaV1.7 pharmacophore of a class of venom-derived peptide inhibitors via a combination of in silico screening and rational engineering.}, journal = {FEBS letters}, volume = {599}, number = {12}, pages = {1717-1732}, pmid = {40156461}, issn = {1873-3468}, support = {FTl10100925//Australian Research Council/ ; DE160101142//Australian Research Council/ ; APP1102267//National Health and Medical Research Council/ ; APP1080405//National Health and Medical Research Council/ ; 2017086//National Health and Medical Research Council/ ; APP1034958//National Health and Medical Research Council/ ; //University of Queensland/ ; 101039862/ERC_/European Research Council/International ; }, mesh = {*NAV1.7 Voltage-Gated Sodium Channel/chemistry/metabolism/genetics ; Humans ; *Peptides/chemistry/pharmacology ; Animals ; *Voltage-Gated Sodium Channel Blockers/chemistry/pharmacology ; Structure-Activity Relationship ; Amino Acid Sequence ; Computer Simulation ; Protein Engineering ; *Scorpion Venoms/chemistry/pharmacology ; Computational Biology ; Pharmacophore ; }, abstract = {Ion channels are among the main targets of venom peptides. Extensive functional screening has identified a number of these peptides as modulators of the voltage-gated sodium channel subtype NaV1.7, a potential target for the treatment of chronic pain. In this study, we used a bioinformatic approach that can automatically identify NaV1.7 gating modifier toxins from sequence information alone. The method further enables the incorporation of evolutionarily accessible sequence space in structure-activity relationship studies. The in silico method identified a putative NaV1.7 inhibitor, μ-theraphotoxin Cg4a, which we produced recombinantly and confirmed as a NaV1.7 inhibitor. Using structural and mutagenesis studies, we propose an improved definition of the pharmacophore of this class of NaV1.7 inhibitors, aiding future in silico screening and classification of NaV1.7 inhibitors.}, }
@article {pmid40155956, year = {2025}, author = {van Kessel, SAM and Wielders, CCH and Schoffelen, AF and Verbon, A}, title = {Enhancing antimicrobial resistance surveillance and research: a systematic scoping review on the possibilities, yield and methods of data linkage studies.}, journal = {Antimicrobial resistance and infection control}, volume = {14}, number = {1}, pages = {25}, pmid = {40155956}, issn = {2047-2994}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Drug Resistance, Bacterial ; Antimicrobial Stewardship ; *Information Storage and Retrieval/methods ; *Epidemiological Monitoring ; }, abstract = {BACKGROUND: Surveillance data on antimicrobial resistance (AMR) determinants such as antibiotic use, prevalence of AMR, antimicrobial stewardship, and infection prevention and control are mostly analysed and reported separately, although they are inextricably linked to each other. The impact of surveillance and research can be enhanced by linking these data. This systematic scoping review aims to summarize the studies that link AMR data and evaluate whether they yield new results, implications, or recommendations for practice.<br><br>METHODS: For this review, data linkage is defined as the process of linking records, from at least two independent data sources on either (I) at least two AMR determinants or (II) one AMR determinant and one or more general population characteristics. Data linkage should be performed on the level of a certain entity which, in the context of this review, can encompass persons, healthcare institutes, geographical regions or countries. A systematic literature search was performed on February 7th 2025 in Embase.com, PubMed and Scopus to identify AMR data linkage studies.<br><br>RESULTS: Forty-eight articles were included in our review. Most data linkage studies used two data sources, and most studies were published in the last 5 years (n&#x2009;=&#x2009;23 in 2020-2024). A predominance of studies linked data on geographical location, and thirteen studies linked data on individual patient level. Findings demonstrate that the majority of studies (43/48) had added value and provided recommendations for clinical practice and future policies or had suggestions for further research and surveillance. Additionally, data linkage studies appeared to be suitable for hypothesis generating. Several limitations were identified. Most studies had ecological designs, which are prone to ecological fallacy and unobserved confounding, making it hard to establish causality.<br><br>CONCLUSION: This systematic scoping review showed that AMR data linkage studies are increasingly performed. They have potential to gain a more comprehensive understanding of AMR dynamics by generating hypotheses, assisting in optimisation of surveillance, and interpretation of data in the context of guideline/policy development. To increase the added value of data linkage, more studies should be performed to improve knowledge on methodological approaches, data access, data management, and governance issues.<br><br>CLINICAL TRIAL NUMBER: Not applicable.}, }
@article {pmid40155652, year = {2025}, author = {Rehbein, M and Escobari, B and Fischer, S and Güntsch, A and Haas, B and Matheisen, G and Perschl, T and Wieshuber, A and Engel, T}, title = {Quantitative and qualitative Data on historical Vertebrate Distributions in Bavaria 1845.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {525}, pmid = {40155652}, issn = {2052-4463}, support = {442032008//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {*Vertebrates ; Animals ; *Biodiversity ; Germany ; History, 19th Century ; Ecosystem ; *Animal Distribution ; }, abstract = {Archival collections contain an underutilized wealth of biodiversity data, encapsulated in government files and other historical documents. In 1845, the Bavarian government conducted a comprehensive national survey on the occurrence of 44 selected vertebrate species across the country. The detailed expert responses from 119 forestry offices, totalling 520 handwritten pages, have been preserved in the Bavarian State Archives. In this study, we digitized, annotated, geographically referenced, and published these historical records, making them widely available as data for research and conservation planning. Our dataset, openly accessible through the Global Biodiversity Information Facility (GBIF) and Zenodo, contains 5,467 species occurrence records from 1845. Besides the binary presence/absence data, we have also published the original textual survey responses, which contain rich qualitative information, such as species abundances, population trends, habitats, forest management practices, and human-nature relationships. This information can be further processed and interpreted to address a range of questions in historical and contemporary ecology.}, }
@article {pmid40147302, year = {2025}, author = {Keneally, C and Chilton, D and Dornan, TN and Kidd, SP and Gaget, V and Toomes, A and Lassaline, C and Petrovski, R and Wood, L and Brookes, JD}, title = {Multi-omics reveal microbial succession and metabolomic adaptations to flood in a hypersaline coastal lagoon.}, journal = {Water research}, volume = {280}, number = {}, pages = {123511}, doi = {10.1016/j.watres.2025.123511}, pmid = {40147302}, issn = {1879-2448}, mesh = {*Floods ; Salinity ; RNA, Ribosomal, 16S/genetics ; Geologic Sediments/microbiology ; Metabolomics ; Microbiota ; Multiomics ; }, abstract = {Microorganisms drive essential biogeochemical processes in aquatic ecosystems and are sensitive to both salinity and hydrological changes. As climate change and anthropogenic activities alter hydrology and salinity worldwide, understanding microbial ecology and metabolism becomes increasingly important for managing aquatic ecosystems. Biogeochemical processes were investigated on sediment microbial communities during a significant flood event in the hypersaline Coorong lagoon, South Australia (the largest in the Murray-Darling Basin since 1956). Samples from six sites across a salinity gradient were collected before and during flooding in 2022. To assess changes in microbial taxonomy and metabolic function, 16S rRNA amplicon sequencing was employed alongside untargeted liquid chromatography-mass spectrometry (LC-MS) to assess changes in microbial taxonomy and metabolic function. Results showed a decrease in microbial richness and diversity during flooding, especially in hypersaline conditions. Pre-flood communities were enriched with osmolyte-degrading and methanogenic taxa, alongside osmoprotectant metabolites, such as glycine betaine and choline. Flood conditions favored taxa such as Halanaerobiaceae and Beggiatoaceae, inducing inferred metagenomic shifts indicative of sulfur cycling and nitrogen reduction pathways, while also enriching a greater diversity of metabolites including Gly-Phe dipeptides and guanine. This study demonstrates that integrating metabolomics with microbial community analysis enhances understanding of ecosystem responses to disturbance. These findings suggest microbial communities rapidly change in response to salinity reductions while maintaining key biogeochemical functions. Such insights are valuable for ecosystem management and predictive modelling under environmental stressors such as flooding.}, }
@article {pmid40144399, year = {2021}, author = {Boyes, D and Holland, PWH and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the poplar hawk-moth, Laothoe populi (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {6}, number = {}, pages = {237}, pmid = {40144399}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Laothoe populi (the poplar hawk-moth; Arthropoda; Insecta; Lepidoptera; Sphingidae). The genome sequence is 576 megabases in span. Most of the assembly is scaffolded into 29 chromosomal pseudomolecules, with the W and Z sex chromosome assembled.}, }
@article {pmid40143245, year = {2025}, author = {Culot, A and Abriat, G and Furlong, KP}, title = {High-Performance Genome Annotation for a Safer and Faster-Developing Phage Therapy.}, journal = {Viruses}, volume = {17}, number = {3}, pages = {}, pmid = {40143245}, issn = {1999-4915}, mesh = {*Genome, Viral ; *Bacteriophages/genetics ; *Molecular Sequence Annotation/methods ; *Computational Biology/methods ; *Phage Therapy/methods ; Humans ; }, abstract = {Phage therapy, which uses phages to decrease bacterial load in an ecosystem, introduces a multitude of gene copies (bacterial and phage) into said ecosystem. While it is widely accepted that phages have a significant impact on ecology, the mechanisms underlying their impact are not well understood. It is therefore paramount to understand what is released in the said ecosystem, to avoid alterations with difficult-to-predict-but potentially huge-consequences. An in-depth annotation of therapeutic phage genomes is therefore essential. Currently, the average published phage genome has only 20-30% functionally annotated genes, which represents a hurdle to overcome to deliver safe phage therapy, for both patients and the environment. This study aims to compare the effectiveness of manual versus automated phage genome annotation methods. Twenty-seven phage genomes were annotated using SEA-PHAGE and Rime Bioinformatics protocols. The structural (gene calling) and functional annotation results were compared. The results suggest that during the structural annotation step, the SEA-PHAGE method was able to identify an average of 1.5 more genes per phage (typically a frameshift gene) and 5.3 gene start sites per phage. Despite this difference, the impact on functional annotation appeared to be limited: on average, 1.2 genes per phage had erroneous functions, caused by the structural annotation. Rime Bioinformatics' tool (rTOOLS, v2) performed better at assigning functions, especially where the SEA-PHAGE methods assigned hypothetical proteins: 7.0 genes per phage had a better functional annotation on average, compared to SEA PHAGE's 1.7. The method comparison detailed in this article indicate that (1) manual structural annotation is marginally superior to rTOOLS automated structural annotation; (2) rTOOLS automated functional annotation is superior to manual functional annotation. Previously, the only way to obtain a high-quality annotation was by using manual protocols, such as SEA-PHAGES. In the relatively new field of phage therapy, which requires support to advance, manual work can be problematic due to its high cost. Rime Bioinformatics' rTOOLS software allows for time and money to be saved by providing high-quality genome annotations that are comparable to manual results, enabling a safer and faster-developing phage therapy.}, }
@article {pmid40140737, year = {2025}, author = {Tahir Ul Qamar, M and Fatima, K and Rao, MJ and Tang, Q and Sadaqat, M and Ding, B and Chen, LL and Zhu, XT}, title = {Comparative genomics profiling of Citrus species reveals the diversity and disease responsiveness of the GLP pangenes family.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {388}, pmid = {40140737}, issn = {1471-2229}, mesh = {*Citrus/genetics/microbiology ; Genomics ; *Genome, Plant ; *Plant Diseases/microbiology/genetics ; Genetic Variation ; *Multigene Family ; Phylogeny ; *Plant Proteins/genetics/metabolism ; Genes, Plant ; }, abstract = {Citrus is an important nutritional fruit globally; however, its yield is affected by various stresses. This study presents the draft pangenome of Citrus, developed using 11 species to examine their genetic diversity and identify members of the germin-like proteins (GLPs) gene family involved in disease responsiveness. The developed sequence-based pangenome contains 954 Mb sequence and 74,755 genes. The comparative genomics analysis revealed the presence-absence variations (PAVs) among the Citrus genomes and species-specific protein-coding genes. Gene-based pangenome analysis revealed 4,936 new genes missing in the reference genome and highlighted the core and shell genes with putative functions in stress regulation. The pangenome-wide identification of GLP gene family members indicated the intraspecies diversity among the members across 11 genomes by analyzing their gene structure, motifs, and chromosomal distribution patterns. The synteny and evolutionary constraints analyses of Citrus GLPs provide detailed evidence of their evolutionary conservation and divergence. Further, the interaction, functional enrichment, and promoter analysis revealed their involvement in abiotic-, biotic-stress, signaling, and development-related pathways. The expression patterns of C. sinensis GLPs were studied in Huanglongbing (HLB) and Citrus canker disease. Several genes including CsGLPs1-2 and CsGLPs8-4 showed changes in expression patterns under both disease conditions. The qRT-PCR analysis revealed that these two genes were highly expressed in leaves infected with HLB disease across seven HLB-tolerant and susceptible citrus species. This Citrus pangenome and pangenes family study offers a comprehensive resource and new insights into the structural and functional diversity, identifying candidate genes that are important for future research to understand the stress-responsive mechanisms in Citrus.}, }
@article {pmid40139213, year = {2025}, author = {Tam, CC and Young, SD and Harrison, S and Li, X and Litwin, AH}, title = {Theory-Based Social Media Intervention for Nonmedical Use of Prescription Opioids in Young Adults: Protocol for a Randomized Controlled Trial.}, journal = {JMIR research protocols}, volume = {14}, number = {}, pages = {e65847}, pmid = {40139213}, issn = {1929-0748}, mesh = {Humans ; *Social Media ; Young Adult ; Male ; Female ; *Analgesics, Opioid/adverse effects ; *Opioid-Related Disorders/prevention &amp; control/psychology/therapy ; Randomized Controlled Trials as Topic ; Peer Group ; Adult ; Adolescent ; *Prescription Drug Misuse/prevention &amp; control ; Pragmatic Clinical Trials as Topic ; }, abstract = {BACKGROUND: The nonmedical use of prescription opioids (NMUPO) in young adults in the United States is concerning and is robustly influenced by many psychosocial factors. Given the advantages of flexibility, wide coverage, and real-time responses and assessment, using social media appears to be a promising and innovative approach to delivering psychosocial intervention to young adults. However, few theory-based social media interventions are available for NMUPO targeting this at-risk population.<br><br>OBJECTIVE: Guided by the information-motivation-behavioral skills model, the proposed research aims to address critical gaps by theoretically exploring psychosocial content associated with NMUPO among young adults via formative assessment. These findings will then be used to develop and evaluate the feasibility and preliminary efficacy of a peer-led social media intervention to reduce NMUPO among young adults.<br><br>METHODS: The proposed study will comprise serial research activities. First, formative research will be conducted through semistructured interviews among 30 young adults engaged in NMUPO. Qualitative data will be synthesized using a pragmatic approach for identifying psychosocial content associated with NMUPO. Second, qualitative findings will be used for developing a peer-led social media intervention to reduce NMUPO among young adults by integrating promising psychotherapy principles and incorporating them with well-trained recovery coaches. Third, the social media intervention will be evaluated through a 12-week randomized controlled trial among 70 young adults (n=35, 50% in the intervention group and control group) engaged in NMUPO via mixed methods, including pre- and postintervention surveys, social media paradata (eg, time-series reactions to posts) collection, and ecological momentary assessment during the intervention. The control group will not receive an intervention but will complete the pre- and postintervention surveys. The primary outcomes will be feasibility, usability, and acceptability, while the secondary outcomes will be psychosocial and behavioral measures, such as past-3-month NMUPO, intention, psychological distress, self-efficacy, resilience, and coping strategies.<br><br>RESULTS: The proposed study was funded in May 2024. Social media campaigns have received responses from a total of 379 individuals, with 24 (6.3%) identified as eligible. As of February 10, 2025, we have completed formative interviews with 8 eligible participants.<br><br>CONCLUSIONS: The proposed study will be one of the first efforts to develop and deliver a theory-based peer-led intervention on social media, incorporating empirical findings on the psychosocial mechanism of NMUPO. The findings of the proposed study will provide valuable insights into opioid risk reduction for young adults through an innovative approach. If the tested trial is found to be feasible, the proposed study will contribute to future scaled-up and fully powered psychosocial interventions among young adults and other key populations at risk for NMUPO.<br><br>TRIAL REGISTRATION: ClincialTrials.gov NCT06469749; https://clinicaltrials.gov/study/NCT06469749.<br><br>DERR1-10.2196/65847.}, }
@article {pmid40139065, year = {2025}, author = {Sfriso, AA and Juhmani, AS and Tomio, Y and Wedyan, M and Cunsolo, F and Forlani, G and Sfriso, A and Ferretti, G and Coltorti, M and Munari, C and Mistri, M}, title = {Microbial dynamics in seagrass restoration: Unveiling hidden indicators of ecological success.}, journal = {Marine environmental research}, volume = {208}, number = {}, pages = {107089}, doi = {10.1016/j.marenvres.2025.107089}, pmid = {40139065}, issn = {1879-0291}, mesh = {*Geologic Sediments/microbiology ; *Zosteraceae/physiology ; *Microbiota ; *Environmental Restoration and Remediation ; Ecosystem ; }, abstract = {Seagrass transplantation significantly alters sediment microbial communities, shaping their composition and metabolic functions. One year after Zostera marina transplantation, the microbial community structure and functions at the recipient site began shifting toward those of the donor site. Key microbial taxa associated with seagrass meadow sediment, such as Firmicutes (Hungateiclostridiaceae, Defluviitaleaceae) and Campylobacterota (Sulfurovum), increased in abundance, correlating with sediment organic matter content and carbon availability. Four functional groups were identified, each with distinct metabolic roles: (1) Opportunistic Anaerobic Degraders, (2) Seagrass-Driven Carbon Recyclers, (3) Anaerobic Fermenters and Hydrocarbon Recyclers and (4) Oxygen-Linked Carbon and Sulfur Cyclers. The sediments of transplanted Z. marina meadows exhibited increased cellulolysis and aerobic chemoheterotrophy, along with a reduction in nitrogen metabolism one year post transplant. Despite these microbial shifts, sediment isotopic signatures remained indicative of algal biomass, suggesting an incomplete transition toward a mature seagrass environment. Multivariate analysis further confirmed that the microbial community at the recipient site had not yet fully converged with that of the donor meadow, indicating that complete sediment maturation may require longer timescales. These findings demonstrate that microbial community composition and functional annotations serve as early indicators of seagrass restoration success. Long-term monitoring is essential to track ecosystem recovery and assess the stabilization of sediment conditions.}, }
@article {pmid40136166, year = {2025}, author = {Ferrari, YAC and Jesus, CVF and Batista, JFC and Silva, BEBD and Cavalcante, AB and Lima, CA}, title = {Secular trend of cervical cancer mortality in Brazil and regions.}, journal = {Ciencia &amp; saude coletiva}, volume = {30}, number = {3}, pages = {e09962023}, doi = {10.1590/1413-81232025303.09962023}, pmid = {40136166}, issn = {1678-4561}, mesh = {Humans ; Brazil/epidemiology ; Female ; *Uterine Cervical Neoplasms/mortality/epidemiology ; Middle Aged ; Adult ; Aged ; Young Adult ; Age Distribution ; Adolescent ; Mortality/trends ; Age Factors ; }, abstract = {The scope of this study was to describe the secular trend of cervical cancer mortality in Brazil and its various regions from 1980 to 2021. It involved a populational and ecological study, based on data available at the Department of Informatics of the Unified Health System, using codes 180 and C53. Crude rates, age-specific rates, and age-standardized rates were calculated for the Brazilian and world population. The Average Annual Percent Change (AAPC) was obtained by trend analysis using the Joinpoint Regression Program, with a significance level of 0.05 and 95% confidence intervals (95%CI). There were 171,793 deaths from cervical cancer. In Brazil (AAPC -0.3; CI95%-1.0; 0.4), North (AAPC 0.6; 95%CI -0.1; 1.3) and South (AAPC 0.0; 95%CI -0.5; 0.5) the trends were stationary, increasing in the Northeast (AAPC 0.6; 95%CI 0.3; 0.8) and in the Midwest (AAPC -1.3; 95%CI -1.5; -1.1), and decreasing in the Southeast (AAPC -0.9; 95%CI -1.4; -0.5). Regional differences indicate that public policies need to be improved regarding women's access to a health system that offers adequate prevention, screening and treatment through management strategies that include the most vulnerable population.}, }
@article {pmid40136165, year = {2025}, author = {Aquino, &#xc9;C and Borowicc, SL and Alves-Souza, SN and Teixeira, RA and Ishitani, LH and Malta, DC and Morais Neto, OL}, title = {Distribution of garbage codes in the Mortality Information System, Brazil, 2000 to 2020.}, journal = {Ciencia &amp; saude coletiva}, volume = {30}, number = {3}, pages = {e09442023}, doi = {10.1590/1413-81232025303.09442023}, pmid = {40136165}, issn = {1678-4561}, mesh = {Brazil/epidemiology ; Humans ; *Information Systems/statistics &amp; numerical data ; Cause of Death/trends ; Time Factors ; Linear Models ; *Mortality/trends ; }, abstract = {The analysis of the causes of death is essential to understand the main problems that affect the health level of the population of a region or country. The garbage codes (GC) provide little useful information about causes of death. This study aims to identify the proportion of GC among the deaths registered and to analyze their temporal distribution in Brazil from 2000 to 2020. It's an ecological time-series study of the evolution of the proportion of GC in Brazil. Time series analysis was performed using segmented linear regression models (joinpoint). Between 2000 and 2020, 39.9% of deaths that occurred in Brazil were coded with GC. Between 2000 and 2007, there was a continuous and persistent reduction in the proportion of GC (APC -2.1; P < 0.001). Between 2007 and 2015, there continued to be a reduction, albeit to a lesser extent (APC = -0.7; P = 0.013). Between 2015 and 2018, there was no significant trend of the proportion of GC (APC = -2.3; P = 0.172), which persisted from 2018 (APC 3.2; P < 0.079). Although a reduction in the proportion of GC in Brazil was observed until 2018, this trend did not persist after that year. Reducing the proportion of GC allows managers to plan health policies more adequately for the population.}, }
@article {pmid40133528, year = {2025}, author = {Pekar, JE and Wang, Y and Wang, JC and Shao, Y and Taki, F and Forgione, LA and Amin, H and Clabby, T and Johnson, K and Torian, LV and Braunstein, SL and Pathela, P and Omoregie, E and Hughes, S and Suchard, MA and Vasylyeva, TI and Lemey, P and Wertheim, JO}, title = {Transmission dynamics of the 2022 mpox epidemic in New York City.}, journal = {Nature medicine}, volume = {31}, number = {5}, pages = {1464-1473}, pmid = {40133528}, issn = {1546-170X}, support = {U19 AI135995/AI/NIAID NIH HHS/United States ; R01 AI153044/AI/NIAID NIH HHS/United States ; AI135995//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI153044//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI135992//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; PS21-2102//U.S. Department of Health &amp; Human Services | Centers for Disease Control and Prevention (CDC)/ ; R01 AI135992/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; New York City/epidemiology ; Male ; Female ; *Epidemics ; *HIV Infections/epidemiology/transmission/virology ; Phylogeny ; HIV-1/genetics ; Phylogeography ; Homosexuality, Male ; Disease Outbreaks ; Sexual Behavior ; Mpox, Monkeypox ; }, abstract = {The 2022 global mpox epidemic was caused by transmission of MPXV clade IIb, lineage B.1 through sexual contact networks, with New York City (NYC) experiencing the first and largest outbreak in the United States. By performing phylogeographic analysis of MPXV genomes sampled from 757 individuals in NYC between April 2022 and April 2023, and 3,287 MPXV genomes sampled around the world, we identify over 200 introductions of MPXV into NYC with at least 84 leading to onward transmission. These infections primarily occurred among men who have sex with men, transgender women and nonbinary individuals. Through a comparative analysis with HIV in NYC, we find that both MPXV and HIV genomic cluster sizes are best fit by scale-free distributions, and that people in MPXV clusters are more likely to have previously received an HIV diagnosis and be a member of a recently growing HIV transmission cluster. We model MPXV transmission through sexual contact networks and show that highly connected individuals would be disproportionately infected at the start of an epidemic, which would likely result in the exhaustion of the most densely connected parts of the network, and, therefore, explain the rapid expansion and decline of the NYC outbreak. By coupling the genomic epidemiology of MPXV and HIV with epidemic modeling, we demonstrate that the transmission dynamics of MPXV in NYC can be understood by general principles of sexually transmitted pathogens.}, }
@article {pmid40132633, year = {2025}, author = {Liu, X and Milesi, E and Fontsere, C and Owens, HL and Heinsohn, R and Gilbert, MTP and Crates, R and Nogués-Bravo, D and Morales, HE}, title = {Time-lagged genomic erosion and future environmental risks in a bird on the brink of extinction.}, journal = {Proceedings. Biological sciences}, volume = {292}, number = {2043}, pages = {20242480}, pmid = {40132633}, issn = {1471-2954}, support = {//The European Molecular Biology Organization/ ; //Mohamed bin Zayed Species Conservation Fund/ ; //Danish National Research Foundation/ ; /ERC_/European Research Council/International ; 25925//Villum Fonden/ ; }, mesh = {Animals ; *Extinction, Biological ; Endangered Species ; *Genome ; *Genetic Variation ; Conservation of Natural Resources ; Ecosystem ; Australia ; Genomics ; Biodiversity ; Population Dynamics ; *Passeriformes/genetics ; }, abstract = {Global biodiversity is rapidly declining due to habitat degradation and genomic erosion, highlighting the urgent need to monitor endangered species and their genetic health. Temporal genomics and ecological modelling offer finer resolution than single-time-point measurements, providing a comprehensive view of species' recent and future trajectories. We investigated genomic erosion and environmental suitability in the critically endangered regent honeyeater (Anthochaera phrygia) by sequencing whole genomes of historical and modern specimens and building multi-temporal species distribution models (SDMs) across the last century. The species has declined from hundreds of thousands of individuals to fewer than 300 over the past 100 years. SDMs correctly predicted known patterns of local extinction in southeast Australia. Our demographic reconstructions revealed a gradual population decline from 2000 to 2500 years ago, sharply accelerating in the last 500 years due to climate variability and habitat loss. Despite this substantial demographic collapse, the regent honeyeater has lost only 9% of its genetic diversity, with no evidence of inbreeding or connectivity loss. Also, it exhibits higher diversity than many other threatened bird species. Forward-in-time genomic simulations indicate that this time lag between population decline and genetic diversity loss conceals the risk of ongoing genomic erosion into a future of rapidly degrading environmental suitability. Our work underscores the need for targeted conservation efforts and continuous genetic monitoring to prevent species extinction.}, }
@article {pmid40132265, year = {2025}, author = {Gu, J and Shen, Y and Guo, L and Chen, Z and Zhou, D and Ji, G and Gu, A}, title = {Investigation of the mechanisms of liver injury induced by emamectin benzoate exposure at environmental concentrations in zebrafish: A multi-omics approach to explore the role of the gut-liver axis.}, journal = {Journal of hazardous materials}, volume = {491}, number = {}, pages = {138008}, doi = {10.1016/j.jhazmat.2025.138008}, pmid = {40132265}, issn = {1873-3336}, mesh = {Animals ; Zebrafish ; *Ivermectin/analogs &amp; derivatives/toxicity ; *Liver/drug effects/metabolism/pathology ; Gastrointestinal Microbiome/drug effects ; *Chemical and Drug Induced Liver Injury/metabolism/pathology/etiology ; *Water Pollutants, Chemical/toxicity ; Metabolomics ; Lipid Metabolism/drug effects ; *Insecticides/toxicity ; RNA, Ribosomal, 16S/genetics ; Multiomics ; }, abstract = {Emamectin benzoate (EMB) is a lipophilic pesticide that enters aquatic systems and adversely affects non-target organisms. This study investigated the long-term effects of EMB on zebrafish, exposing them to concentrations of 0, 0.1, 1, and 10 μg/L from the 4-hour post-fertilization (hpf) embryo stage to the 120-day post-fertilisation (dpf) adult stage. We found that exposure to 1 μg/L EMB induced liver damage, manifested as impaired liver function (elevated aspartate aminotransferase (AST) and alanine aminotransferase (ALT)), histopathological damage (lipid accumulation), as well as inflammatory and oxidative damage, with a dose - dependent effect. Non-targeted metabolomic analysis revealed an increase in lipid molecules in the liver, affecting the pathways related to glycerophospholipid metabolism. In addition, EMB exposure resulted in damage to the intestinal barrier and inflammatory responses in zebrafish. 16S rRNA sequencing demonstrated that EMB exposure resulted in notable alterations in the gut microbiota composition. Notably, the abundance of Plesiomonas and Cetobacterium increased in the EMB exposure group and exhibited a positive correlation with the majority of liver lipid metabolites. In contrast, reductions in Muribaculaceae and Alloprevotella were negatively correlated. The results of this study indicate that long-term exposure to EMB disrupts the gut microbiota, leading to the dysregulation of hepatic phospholipid metabolism. These findings provide new insights into the health risks associated with EMB and highlight its potential threats to higher organisms, including mammals.}, }
@article {pmid40125978, year = {2025}, author = {Bailey, N and Stevison, L and Samuk, K}, title = {Correcting for Bias in Estimates of θ w and Tajima's D From Missing Data in Next-Generation Sequencing.}, journal = {Molecular ecology resources}, volume = {25}, number = {6}, pages = {e14104}, pmid = {40125978}, issn = {1755-0998}, support = {R35 GM147501/GM/NIGMS NIH HHS/United States ; R35GM147501/GM/NIGMS NIH HHS/United States ; }, mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Genetics, Population/methods ; *Genetic Variation ; Software ; *Computational Biology/methods ; Bias ; }, abstract = {Population genetic analyses use information from the site frequency spectrum to infer evolutionary processes. Two summary statistics, Watterson's estimator (θ w) of genetic diversity, and Tajima's D , used for detecting non-neutral evolution, are among the most frequently computed statistics utilising this information. However, missing information in genomic data, particularly as encoded in the Variant Call Format (VCF), can bias these estimates, leading to incorrect evolutionary inferences. We assessed the impact of missing data on the estimation of these statistics using various population genetic software packages (VCFtools, PopGenome, pegas and scikit-allel). By simulating neutral genomic data with varying levels of missing genotypes and sites, we found consistent underestimation of θ w across programs. We found a consequent bias in estimates of Tajima's D , though the direction varied by software. We developed and implemented correction methods as functions in an update of the popular pixy software, significantly reducing these biases. Our findings highlight the need for accurate data handling in population genomics to avoid misinterpretations of evolutionary phenomena.}, }
@article {pmid40125538, year = {2025}, author = {Broad, GR and Holt, S and Sivess, L and Boyes, D and ,  and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Scorched Wing moth, Plagodis dolabraria (Linnaeus, 1767).}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {111}, pmid = {40125538}, issn = {2398-502X}, abstract = {We present a genome assembly from a male specimen of Plagodis dolabraria (Scorched Wing; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 939.07 megabases. Most of the assembly (99.59%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.97 kilobases in length.}, }
@article {pmid40123484, year = {2025}, author = {Poulin, R}, title = {To bin or not to bin: why parasite abundance data should not be lumped into categories for statistical analysis.}, journal = {Parasitology}, volume = {152}, number = {3}, pages = {338-345}, pmid = {40123484}, issn = {1469-8161}, mesh = {Animals ; *Host-Parasite Interactions ; *Parasites/physiology ; *Parasitology/methods ; Data Interpretation, Statistical ; *Parasitic Diseases/parasitology ; }, abstract = {The impact of macroparasites on their hosts is proportional to the number of parasites per host, or parasite abundance. Abundance values are count data, i.e. integers ranging from 0 to some maximum number, depending on the host-parasite system. When using parasite abundance as a predictor in statistical analysis, a common approach is to bin values, i.e. group hosts into infection categories based on abundance, and test for differences in some response variable (e.g. a host trait) among these categories. There are well-documented pitfalls associated with this approach. Here, I use a literature review to show that binning abundance values for analysis has been used in one-third of studies published in parasitological journals over the past 15 years, and half of the studies in ecological and behavioural journals, often without any justification. Binning abundance data into arbitrary categories has been much more common among studies using experimental infections than among those using naturally infected hosts. I then use simulated data to demonstrate that true and significant relationships between parasite abundance and host traits can be missed when abundance values are binned for analysis, and vice versa that when there is no underlying relationship between abundance and host traits, analysis of binned data can create a spurious one. This holds regardless of the prevalence of infection or the level of parasite aggregation in a host sample. These findings argue strongly for the practice of binning abundance data as a predictor variable to be abandoned in favour of more appropriate analytical approaches.}, }
@article {pmid40121238, year = {2025}, author = {Kelliher, JM and Rodriguez, FE and Johnson, LYD and Roux, S and Smith, M and Clum, A and Lynch, W and Bias, CH and Finks, SS and Keenum, I and Kiledal, EA and Lin, HA and Longley, R and McDonald, R and Pitot, TM and Rodríguez-Ramos, J and Shen, J and Sprockett, DD and Swift, J and Yadav, A and Eloe-Fadrosh, EA}, title = {Quantifying the impact of workshops promoting microbiome data standards and data stewardship.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {9887}, pmid = {40121238}, issn = {2045-2322}, support = {The work conducted by the National Microbiome Data Collaborative (https://ror.org/05cwx3318) is supported by the Genomic Science Program in the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research (BER) under contract numbers DE-AC02-05CH11231 (LBNL), 89233218CNA000001 (LANL), and DE-AC05-76RL01830 (PNNL).//U.S. Department of Energy/ ; }, mesh = {*Microbiota ; Humans ; Surveys and Questionnaires ; Education ; Research Personnel/education ; }, abstract = {The field of microbiome research continues to grow at a rapid pace, with multi-omics approaches becoming widely used to interrogate diverse microbiome samples. However, due to lagging awareness and implementation of standards and data stewardship, many datasets are produced that are not comparable, reproducible, or reusable. In 2021, the National Microbiome Data Collaborative launched its Ambassador Program, which utilizes a community-learning model to annually train a cohort of early-career researchers in microbiome data stewardship best practices. These Ambassadors then host workshops and other events to communicate these themes to their respective microbiome research communities. To quantify the impact of this learning model for promoting awareness of and experience with microbiome data, we conducted a survey of workshop participants from events hosted by the 2023 Ambassador cohort. The 2023 cohort of 13 National Microbiome Data Collaborative Ambassadors collectively hosted 21 events, reaching over 550 researchers. The Ambassadors distributed an anonymous post-workshop survey to their event participants to quantify the effectiveness of the training materials, the workshop format, and the thematic content. From the 21 events, survey results were successfully collected for 15 of those events from a total of 122 researchers. Overall, 122 participants working with a range of microbiome types and from a variety of institutions responded to the survey and reported overwhelmingly positive experiences with the workshop content and materials, with 98% of respondents reporting that they gained knowledge from the event. Participants across the events also reported an increase in their post-workshop understanding of metadata standards, principles for microbiome data management and reporting, and the importance of standardization in microbiome data processing. Participants also expressed a willingness to apply what they learned about microbiome data stewardship to their own research. The results of this study demonstrate the effectiveness of hands-on workshops and community-learning for communicating data stewardship best practices to microbiome researchers. The lessons learned and details about the implementation of this cohort-based learning model contained herein are intended to assist other groups in their efforts to create or improve similar learning strategies.}, }
@article {pmid40121181, year = {2025}, author = {Eaton, WD and McGee, KM and Glahn, A and Lemenze, A and Soteropoulos, P}, title = {Use of a logging road in a Costa Rican forest changes the composition and stability of soil microbial decomposer communities, and the conversion of organic carbon into biomass.}, journal = {Journal of applied microbiology}, volume = {136}, number = {4}, pages = {}, doi = {10.1093/jambio/lxaf075}, pmid = {40121181}, issn = {1365-2672}, support = {//Pace University Dyson College Office of the Dean/ ; }, mesh = {*Soil Microbiology ; Costa Rica ; *Forests ; Biomass ; *Carbon/metabolism/analysis ; *Fungi/metabolism/classification/genetics/isolation &amp; purification ; Soil/chemistry ; Actinobacteria/metabolism/genetics/isolation &amp; purification ; Nitrogen/analysis/metabolism ; Acidobacteria/metabolism/genetics/isolation &amp; purification ; *Forestry ; Trees ; }, abstract = {AIMS: The effects of a tropical forest logging road on soil C and N, and the compositions of Actinobacteria, Acidobacteria, and wood rot/lignin-degrading fungal (WRT/LD) decomposer communities were evaluated.<br><br>METHODS AND RESULTS: Soils from a healthy Costa Rican old growth forest before Hurricane Otto and from an adjacent, recently formed logging road built after Hurricane Otto were collected over 4 years and assessed for C and N metrics, and characteristics of the three decomposer communities determined by Illumina amplicon sequencing methods. The Logging Road negatively impacted the soil total organic C, respiration, biomass C, qCO2, and total N, while the Actinobacterial and Acidobacterial communities changed from stable compositions of copiotrophic taxa in the rich forest soil to stable compositions of oligotrophic taxa in the poor logging road soil, and the WRT/LD community changed from stable compositions of copiotrophic taxa in the forest soils to an unstable community of oligotrophic taxa with almost no overlap in genera between logging road soils.<br><br>CONCLUSIONS: The logging road negatively influenced 3 decomposer communities and associated C and N metrics, with the two bacterial communities taxonomically stabilizing, but the fungal community taxonomically diverging into an unstable composition over time. Monitoring efforts are on-going to provide local forest land managers with potential indicators of soil ecosystem damage and recovery.}, }
@article {pmid40121109, year = {2025}, author = {Hanly, J and Anon,  and Perret, J and Khan, A}, title = {Disability in ecology and evolution.}, journal = {Trends in ecology &amp; evolution}, volume = {40}, number = {4}, pages = {309-314}, doi = {10.1016/j.tree.2025.02.005}, pmid = {40121109}, issn = {1872-8383}, }
@article {pmid40120582, year = {2025}, author = {Pinkert, S and Reuber, V and Krug, LM and Heidrich, L and Rehling, F and Brandl, R and Farwig, N}, title = {Burrowing facilitated the survival of mammals in harsh and fluctuating climates.}, journal = {Current biology : CB}, volume = {35}, number = {8}, pages = {1779-1790.e3}, doi = {10.1016/j.cub.2025.02.064}, pmid = {40120582}, issn = {1879-0445}, mesh = {Animals ; *Mammals/physiology ; *Climate Change ; Biological Evolution ; Biodiversity ; Phylogeny ; *Climate ; Ecosystem ; *Behavior, Animal ; }, abstract = {Species' ability to cope with climatic instability varies greatly, influenced by factors such as dispersal, physiological adaptations, and phylogenetic conservatism. Here, we investigate how burrowing behavior, a key component of species' endurance strategies and ecosystem functioning, shaped the contemporary patterns of species richness and range size as well as the diversification of mammalian lineages. Analyzing 4,407 terrestrial mammal species, excluding bats, combined with novel trait data on 3,096 species, we reveal contrasting responses to climatic factors between burrowing and non-burrowing species. Burrowing lineages are disproportionately species-rich at lower temperatures and productivity. Both range size and species richness steeply increase with climate seasonality in burrowing species as opposed to non-burrowing species. The proportion of burrowing species increases with latitude, with regions above 20°, especially those exhibiting greater Pleistocene temperature changes, being almost exclusively composed of burrowing species. Trait conservatism, higher net diversification rates, and Eocene peak diversification provide the evolutionary context for these contemporary patterns, underscoring the role of burrowing for mammalian radiations into temperate climates. Moreover, the lower extinction rate of burrowing species and peak diversification at the Cretaceous-Paleogene (K-Pg) boundary support the longstanding hypothesis that burrowing behavior promoted survival during the "impact winter" that marks the replacement of non-avian dinosaurs by mammals. Our study highlights the potential of readily available trait information for understanding the ecological and evolutionary processes that shape species distributions through space and time. The careful integration of divergent environmental constraints bears vast improvements for forecasts of species' responses to climatic changes and global models of biodiversity patterns.}, }
@article {pmid40120189, year = {2025}, author = {Sun, Q and Li, D and He, Y and Ping, Q and Wang, L and Li, Y}, title = {Improved anaerobic digestion of waste activated sludge under ammonia stress by nanoscale zero-valent iron/peracetic acid pretreatment and hydrochar regulation: Insights from multi-omics analyses.}, journal = {Water research}, volume = {279}, number = {}, pages = {123497}, doi = {10.1016/j.watres.2025.123497}, pmid = {40120189}, issn = {1879-2448}, mesh = {*Sewage ; *Ammonia ; Anaerobiosis ; Iron/chemistry ; Methane ; *Peracetic Acid/chemistry ; Multiomics ; }, abstract = {This study developed a novel strategy combining a nanoscale zero-valent iron (nZVI)/peracetic acid (PAA) pretreatment and hydrochar regulation to enhance anaerobic digestion of waste activated sludge (WAS) under ammonia-stressed conditions. The strategy significantly enhanced methane production at ammonia concentrations below 3000 mg/L, with the regulation groups (AN3000/REG) achieving a 50.1 % increase in cumulative methane yield. Metagenomic analysis demonstrated a 14.2 % enrichment of key functional microorganisms, including syntrophic fatty acid-oxidizing bacteria and hydrogenotrophic methanogens, in the AN3000/REG groups. Some of them promote the conversion of butyrate and valerate to acetate through the upregulation of key genes in the fatty acid β-oxidation pathway, thereby supplying sufficient substrates for acetoclastic methanogenesis. Beyond enhancing acetoclastic methanogenesis, the AN3000/REG groups exhibited significant upregulation of other metabolic pathways, with a 34.2 % increase in syntrophic acetate oxidation-hydrogenotrophic methanogenesis genes and a 17.1 % increase in methanol/methylotrophic methanogenesis-related genes. These findings were further validated by the metatranscriptomic and metaproteomic combination analyses. Furthermore, the AN3000/REG groups exhibited a significant enhancement in direct interspecies electron transfer, with functional microbes (e.g., Geobacter, Methanosarcina, and Methanobacterium), pili, and cytochrome c showing significant increases of 1.38-fold, 12.7-fold, and 5.6-fold, respectively. This might be due to the synergistic effects of nZVI and hydrochar in the regulation groups. Additionally, metabolomic analyses revealed that the regulation strategy improved the microbial adaptability to ammonia stress by modulating metabolic products, such as alkaloids. Our study not only provides a promising strategy for alleviating ammonia inhibition during the anaerobic digestion of WAS but also provides a strong basis for understanding the underlying mechanism under ammonia-stressed conditions.}, }
@article {pmid40117176, year = {2025}, author = {Zielińska, K and Udekwu, KI and Rudnicki, W and Frolova, A and Łabaj, PP}, title = {Healthy microbiome-moving towards functional interpretation.}, journal = {GigaScience}, volume = {14}, number = {}, pages = {}, pmid = {40117176}, issn = {2047-217X}, support = {2020/38/E/NZ2/00598//NCN/ ; PLG/2023/016234//Jagiellonian University in Krakow/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Inflammatory Bowel Diseases/microbiology ; *Metagenomics/methods ; Dysbiosis/microbiology ; Phylogeny ; *Microbiota ; Principal Component Analysis ; Computational Biology/methods ; }, abstract = {BACKGROUND: Microbiome-based disease prediction has significant potential as an early, noninvasive marker of multiple health conditions linked to dysbiosis of the human gut microbiota, thanks in part to decreasing sequencing and analysis costs. Microbiome health indices and other computational tools currently proposed in the field often are based on a microbiome's species richness and are completely reliant on taxonomic classification. A resurgent interest in a metabolism-centric, ecological approach has led to an increased understanding of microbiome metabolic and phenotypic complexity, revealing substantial restrictions of taxonomy-reliant approaches.<br><br>FINDINGS: In this study, we introduce a new metagenomic health index developed as an answer to recent developments in microbiome definitions, in an effort to distinguish between healthy and unhealthy microbiomes, here in focus, inflammatory bowel disease (IBD). The novelty of our approach is a shift from a traditional Linnean phylogenetic classification toward a more holistic consideration of the metabolic functional potential underlining ecological interactions between species. Based on well-explored data cohorts, we compare our method and its performance with the most comprehensive indices to date, the taxonomy-based Gut Microbiome Health Index (GMHI), and the high-dimensional principal component analysis (hiPCA) methods, as well as to the standard taxon- and function-based Shannon entropy scoring. After demonstrating better performance on the initially targeted IBD cohorts, in comparison with other methods, we retrain our index on an additional 27 datasets obtained from different clinical conditions and validate our index's ability to distinguish between healthy and disease states using a variety of complementary benchmarking approaches. Finally, we demonstrate its superiority over the GMHI and the hiPCA on a longitudinal COVID-19 cohort and highlight the distinct robustness of our method to sequencing depth.<br><br>CONCLUSIONS: Overall, we emphasize the potential of this metagenomic approach and advocate a shift toward functional approaches to better understand and assess microbiome health as well as provide directions for future index enhancements. Our method, q2-predict-dysbiosis (Q2PD), is freely available (https://github.com/Kizielins/q2-predict-dysbiosis).}, }
@article {pmid40115327, year = {2025}, author = {Hesson, JC and Haba, Y and McBride, CS and Sheerin, E and Mathers, TC and Paulini, M and Pointon, DB and Torrance, JW and Sadasivan Baby, C and Wood, JMD and ,  and ,  and McCarthy, SA and Lawniczak, MKN and Makunin, A}, title = {A chromosomal reference genome sequence for the northern house mosquito, Culex pipiens form pipiens, Linnaeus, 1758.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {107}, pmid = {40115327}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Culex pipiens sensu stricto (the northern house mosquito; Arthropoda; Insecta; Diptera; Culicidae), from a wild population in Sweden. The genome sequence is 533 megabases in span. Most of the assembly is scaffolded into three chromosomal pseudomolecules. The complete mitochondrial genome was also assembled and is 15.6 kilobases in length.}, }
@article {pmid40112992, year = {2025}, author = {Wei, L and Luo, Z and Wu, X and Liu, C and Shi, Y and Zhang, Q and Chen, M and Qin, W}, title = {Multi-omics analysis provided insights into the fruit softening of postharvest okra under carboxymethyl chitosan treatment.}, journal = {International journal of biological macromolecules}, volume = {307}, number = {Pt 3}, pages = {142149}, doi = {10.1016/j.ijbiomac.2025.142149}, pmid = {40112992}, issn = {1879-0003}, mesh = {*Chitosan/analogs &amp; derivatives/pharmacology ; *Fruit/drug effects/metabolism/genetics ; *Abelmoschus/genetics/metabolism/drug effects ; Gene Expression Regulation, Plant/drug effects ; Transcriptome/drug effects ; *Metabolomics/methods ; Metabolome/drug effects ; Gene Expression Profiling ; Pectins/metabolism ; Multiomics ; }, abstract = {To understand the potential regulatory mechanism of carboxymethyl chitosan (CMCS) treatment on postharvest softening of okra, a joint analysis of physiologic index, transcriptome and metabolome was used. The results showed that CMCS could delay the deterioration of the apparent quality of okra and reduce the degradation of chlorophyll. CMCS can reduce the accumulation of WSP and CSP and the decrease of NSP, and inhibit the enzyme activities of pectin degradation (PE, PG, PL). The results of metabolic pathways related to quality and texture showed that CMCS could increase the metabolic level of pentose phosphate pathway (PPP), inhibit the expression of membrane lipid degradation-related genes, and balance the expression of antioxidant-related genes. Ethylene and abscisic acid (ABA) are two important phytohormones. CMCS down-regulates the biosynthesis of ethylene and increases the expression of ABA. The combined analysis of transcriptome and metabolome showed that CMCS could significantly up-regulate flavonoid biosynthesis metabolites and transcriptional expression levels. Cellulose and pectin are important polymers to maintain the rigidity of okra cell wall. CMCS treatment can slow down the accumulation of cellulose by regulating the expression of DEGs related to cellulose synthesis (CesA) and degradation (EGase). CMCS slowed down the degradation of pectin by down-regulating the expression of pectin degradation-related genes. These results indicate that the quality of okra is deteriorated and the fruit is softened during cold storage. CMCS treatment can improve the nutritional quality of okra and slow down its texture decline. In this study, the regulatory effect of CMCS on softening and quality deterioration of okra during cold storage was discussed at the molecular level, which provided a reference for improving the quality of postharvest okra.}, }
@article {pmid40111995, year = {2025}, author = {Eales, O and Shearer, FM and McCaw, JM}, title = {How immunity shapes the long-term dynamics of influenza H3N2.}, journal = {PLoS computational biology}, volume = {21}, number = {3}, pages = {e1012893}, pmid = {40111995}, issn = {1553-7358}, mesh = {Humans ; *Influenza, Human/immunology/epidemiology/transmission/virology ; *Influenza A Virus, H3N2 Subtype/immunology/genetics ; Computational Biology ; *Models, Immunological ; Adult ; Aged ; Middle Aged ; Adolescent ; }, abstract = {Since its emergence in 1968, influenza A H3N2 has caused yearly epidemics in temperate regions. While infection confers immunity against antigenically similar strains, new antigenically distinct strains that evade existing immunity regularly emerge ('antigenic drift'). Immunity at the individual level is complex, depending on an individual's lifetime infection history. An individual's first infection with influenza typically elicits the greatest response with subsequent infections eliciting progressively reduced responses ('antigenic seniority'). The combined effect of individual-level immune responses and antigenic drift on the epidemiological dynamics of influenza are not well understood. Here we develop an integrated modelling framework of influenza transmission, immunity, and antigenic drift to show how individual-level exposure, and the build-up of population level immunity, shape the long-term epidemiological dynamics of H3N2. Including antigenic seniority in the model, we observe that following an initial decline after the pandemic year, the average annual attack rate increases over the next 80 years, before reaching an equilibrium, with greater increases in older age-groups. Our analyses suggest that the average attack rate of H3N2 is still in a growth phase. Further increases, particularly in the elderly, may be expected in coming decades, driving an increase in healthcare demand due to H3N2 infections.}, }
@article {pmid40108281, year = {2025}, author = {Dong, J and Dai, W and Xu, J and Zhang, H and Li, Y and Xie, F}, title = {Impact and elastic modulus of coal mining on terrestrial ecosystems.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {9454}, pmid = {40108281}, issn = {2045-2322}, support = {CSC202306420029//China Scholarship Council/ ; Lumeidike (2022) No.14//Key Research Projects of Shandong Bureau of Coal Geology/ ; }, abstract = {The energy consumption structure is gradually evolving into a "diversified energy structure" against the backdrop of the global implementation of energy-saving and low-carbon policies. Coal, as the main energy source in China, is difficult to change in the short term, given the characteristics of China's energy and resource endowments, as well as the actual social and economic development at the present stage. Nevertheless, coal mining inevitably leads to a range of ecological issues. Identifying the impact of coal mining on terrestrial ecosystems and adopting resilient recovery measures are crucial prerequisites for advancing green coal mining efforts and attaining carbon peaking and carbon neutrality goals. Using China's open-pit coal mining as a case study: (1) the research examines the fundamental attributes and evolving patterns of spatial distribution among these mines within the country. Furthermore, it delineates the life cycle stages and distinctive features of the five principal open-pit coal mines. The life cycle of a coal mining area is divided into four distinct development phases: the initial phase, the accelerated phase, the stable phase, and the declining phase. The spatial relationship between the life cycle stages of coal mining and ecosystem succession is elucidated by examining the evolutionary types of ecosystems within coal mine area. In the accelerated and stable development phase, the adverse effects of coal mining on the ecosystem are in a long-term increasing trend, causing the key elements of the ecosystem to gradually surpass their threshold values. The ecosystem is out of balance, severely damaged, and gradually undergoing degradation or extreme degradation. The types of ecological succession in coal mining areas can be categorized as follows: terrestrial succession leading to a new terrestrial ecosystem, terrestrial to aquatic ecosystem transitions, or the development of an amphibious symbiotic ecosystem. (2) The research quantitatively assessed the impact of surface coal mining on terrestrial ecosystems by utilizing remote sensing data in conjunction with coal production information. In 2022, the affected areas of the five major open-pit coal mines due to coal mining activities amounted to approximately 0.02% of China's total land area. Meanwhile, the nationwide affected areas of all open-pit coal mines combined reached to approximately 0.13% of China's land area. Open-pit coal mining activities have a significant impact on the surface. (3) By incorporating the ecological resilience theory, we establish a model for the ecosystem's elastic modulus in coal mining areas, taking into account landscape diversity, vegetation coverage, land type, and climate factors, which are based on the concepts of elastic strength and elastic limit. A conceptual model for recognizing ecological thresholds in coal mining areas is developed by incorporating the comprehensive integrity index of the ecosystem. The comprehensive integrity of the ecosystem within a coal mining area undergoes significant alterations as it crosses three distinct ecological thresholds: the elastic point, the yield point, and the mutational point. There should be a corresponding constant (or constant interval) at the three ecological thresholds of ecosystem resilience, the elastic point, the yield point, and the mutational point, which is closely related to the scale of mining operations, mining technology, and the service life in coal mining areas. The established models for identifying ecological thresholds and the resilience modulus degree serve as both theoretical references and practical bases for managing the progress and trends of ecosystem changes during coal resource extraction, making ecological restoration in coal mine areas more target-oriented and specific.}, }
@article {pmid40108248, year = {2025}, author = {Mammides, C and Ieronymidou, C and Papadopoulos, H}, title = {An ecoacoustic dataset collected on the island of Cyprus in the Mediterranean Basin biodiversity hotspot.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {461}, pmid = {40108248}, issn = {2052-4463}, support = {101090273//European Commission (EC)/ ; }, mesh = {Cyprus ; *Biodiversity ; *Acoustics ; Animals ; *Vocalization, Animal ; Islands ; }, abstract = {There is growing interest in using novel technologies for large-scale biodiversity monitoring. Passive acoustic monitoring (PAM) represents a promising approach for surveying vocalizing animals. However, further development of PAM methods is needed to improve their accuracy. The availability of extensive ecoacoustic datasets from biodiverse areas can facilitate this development. In this study, we present a large ecoacoustic dataset (1.58 TB) collected at sixty-one study sites on the island of Cyprus between March and May 2023. The dataset comprises >313,000 audio files, representing over 5,200 hours of recordings. It can be used for a range of applications, such as developing and refining species identification algorithms, acoustic indices, and protocols for processing acoustic data to exclude non-focal sounds, e.g., those produced by human activities. It can also be used to explore fundamental ecological questions. To facilitate its use, the complete dataset has been made available on the Hugging Face repository and the ARBIMON platform, operated by Rainforest Connection[TM], which offers a range of free tools for ecoacoustic analyses.}, }
@article {pmid40102961, year = {2025}, author = {Hinojosa-Alvarez, S and Mendoza-Portillo, V and Chavez-Santoscoy, RA and Hernández-Pérez, J and Felix-Ceniceros, A and Magallón-Gayón, E and Mar-Silva, AF and Ochoa-Zavala, M and Díaz-Jaimes, P}, title = {The draft genome assembly of the cosmopolitan pelagic fish dolphinfish Coryphaena hippurus.}, journal = {G3 (Bethesda, Md.)}, volume = {15}, number = {5}, pages = {}, pmid = {40102961}, issn = {2160-1836}, support = {CF-2023-G-493//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; }, mesh = {Animals ; *Genome ; Molecular Sequence Annotation ; *Genomics/methods ; *Perciformes/genetics ; Sequence Analysis, DNA ; High-Throughput Nucleotide Sequencing ; *Fishes/genetics ; Whole Genome Sequencing ; Computational Biology/methods ; }, abstract = {For the first time, the complete genome assembly of the dolphinfish (Coryphaena hippurus), a tropical cosmopolitan species with commercial fishing importance was sequenced. Using a combination of Illumina and Nanopore sequencing technologies, a draft genome of 497.8 Mb was assembled into 6,044 contigs, with an N50 of 200.9 kb and a BUSCO genome completeness score of 89%. This high-quality genome assembly provides a valuable resource to study adaptive evolutionary processes and supports conservation and management strategies for this ecologically and economically significant species.}, }
@article {pmid40102641, year = {2026}, author = {Kalvapalle, PB and Staubus, A and Dysart, MJ and Gambill, L and Reyes Gamas, K and Lu, LC and Silberg, JJ and Stadler, LB and Chappell, J}, title = {Information storage across a microbial community using universal RNA barcoding.}, journal = {Nature biotechnology}, volume = {44}, number = {2}, pages = {269-276}, pmid = {40102641}, issn = {1546-1696}, support = {2021-33522-35356//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; W911NF-24-2-0073//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; 1805901//National Science Foundation (NSF)/ ; 1828869//National Science Foundation (NSF)/ ; 2227526//National Science Foundation (NSF)/ ; 2237052//National Science Foundation (NSF)/ ; 2237512//National Science Foundation (NSF)/ ; FWP 78814//U.S. Department of Energy (DOE)/ ; A23-0202-004//Robert J. Kleberg, Jr. and Helen C. Kleberg Foundation/ ; }, mesh = {*Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; *DNA Barcoding, Taxonomic/methods ; Escherichia coli/genetics ; Plasmids/genetics ; *Information Storage and Retrieval/methods ; RNA, Bacterial/genetics ; RNA, Catalytic/genetics ; Wastewater/microbiology ; }, abstract = {Gene transfer can be studied using genetically encoded reporters or metagenomic sequencing but these methods are limited by sensitivity when used to monitor the mobile DNA host range in microbial communities. To record information about gene transfer across a wastewater microbiome, a synthetic catalytic RNA was used to barcode a highly conserved segment of ribosomal RNA (rRNA). By writing information into rRNA using a ribozyme and reading out native and modified rRNA using amplicon sequencing, we find that microbial community members from 20 taxonomic orders participate in plasmid conjugation with an Escherichia coli donor strain and observe differences in 16S rRNA barcode signal across amplicon sequence variants. Multiplexed rRNA barcoding using plasmids with pBBR1 or ColE1 origins of replication reveals differences in host range. This autonomous RNA-addressable modification provides information about gene transfer without requiring translation and will enable microbiome engineering across diverse ecological settings and studies of environmental controls on gene transfer and cellular uptake of extracellular materials.}, }
@article {pmid40102624, year = {2025}, author = {Rank, M and Kather, A and Wilke, D and Steib-Bauert, M and Kern, WV and Röder, I and de With, K}, title = {Limitations of estimating antibiotic resistance using German hospital consumption data - a comprehensive computational analysis.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {9244}, pmid = {40102624}, issn = {2045-2322}, mesh = {Germany ; Humans ; *Anti-Bacterial Agents/therapeutic use ; *Hospitals/statistics &amp; numerical data ; Neural Networks, Computer ; *Drug Resistance, Microbial ; *Drug Resistance, Bacterial ; }, abstract = {For almost a century, antibiotics have played an important role in the treatment of infectious diseases. However, the efficacy of these very drugs is now threatened by the development of resistances, which pose major challenges to medical professionals and decision-makers. Thereby, the consumption of antibiotics in hospitals is an important driver that can be targeted directly. To illuminate the relation between consumption and resistance depicts a very important step in this procedure. With the help of comprehensive ecological and clinical data, we applied a variety of different computational approaches ranging from classical linear regression to artificial neural networks to analyze antibiotic resistance in Germany. These mathematical and statistical models demonstrate that the amount and particularly the structure of currently available data sets lead to contradictory results and do, therefore, not allow for profound conclusions. More effort and attention on both data collection and distribution is necessary to overcome this problem. In particular, our results suggest that at least monthly or quarterly antibiotic use and resistance data at the department and ward level for each hospital (including application route and type of specimen) are needed to reliably determine the extent to which antibiotic consumption influences resistance development.}, }
@article {pmid40099017, year = {2025}, author = {Sivell, O and Sivell, D and Mitchell, R and Webb, J and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Small Red Damselfly, Ceriagrion tenellum (de Villers, 1789).}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {79}, pmid = {40099017}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from a male specimen of Ceriagrion tenellum (Small Red Damselfly; Arthropoda; Insecta; Odonata; Coenagrionidae). The genome sequence has a total length of 2,077.00 megabases. Most of the assembly (99.28%) is scaffolded into 14 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 17.21 kilobases in length.}, }
@article {pmid40096239, year = {2025}, author = {Dinnage, R and Kleineberg, M}, title = {Generative AI extracts ecological meaning from the complex three dimensional shapes of bird bills.}, journal = {PLoS computational biology}, volume = {21}, number = {3}, pages = {e1012887}, pmid = {40096239}, issn = {1553-7358}, mesh = {Animals ; *Birds/anatomy &amp; histology ; *Imaging, Three-Dimensional/methods ; Computational Biology ; *Beak/anatomy &amp; histology ; *Artificial Intelligence ; Deep Learning ; }, abstract = {Data on the three dimensional shape of organismal morphology is becoming increasingly available, and forms part of a new revolution in high-throughput phenomics that promises to help understand ecological and evolutionary processes that influence phenotypes at unprecedented scales. However, in order to meet the potential of this revolution we need new data analysis tools to deal with the complexity and heterogeneity of large-scale phenotypic data such as 3D shapes. In this study we explore the potential of generative Artificial Intelligence to help organize and extract meaning from complex 3D data. Specifically, we train a deep representational learning method known as DeepSDF on a dataset of 3D scans of the bills of 2,020 bird species. The model is designed to learn a continuous vector representation of 3D shapes, along with a 'decoder' function, that allows the transformation from this vector space to the original 3D morphological space. We find that approach successfully learns coherent representations: particular directions in latent space are associated with discernible morphological meaning (such as elongation, flattening, etc.). More importantly, learned latent vectors have ecological meaning as shown by their ability to predict the trophic niche of the bird each bill belongs to with a high degree of accuracy. Unlike existing 3D morphometric techniques, this method has very little requirements for human supervised tasks such as landmark placement, increasing it accessibility to labs with fewer labour resources. It has fewer strong assumptions than alternative dimension reduction techniques such as PCA. Once trained, 3D morphology predictions can be made from latent vectors very computationally cheaply. The trained model has been made publicly available and can be used by the community, including for finetuning on new data, representing an early step toward developing shared, reusable AI models for analyzing organismal morphology.}, }
@article {pmid40091737, year = {2025}, author = {Slipetz, LR and Falk, A and Henry, TR}, title = {Missing Data in Discrete Time State-Space Modeling of Ecological Momentary Assessment Data: A Monte-Carlo Study of Imputation Methods.}, journal = {Multivariate behavioral research}, volume = {60}, number = {4}, pages = {695-710}, doi = {10.1080/00273171.2025.2469055}, pmid = {40091737}, issn = {1532-7906}, mesh = {*Ecological Momentary Assessment ; Humans ; *Monte Carlo Method ; *Models, Statistical ; Data Interpretation, Statistical ; Bias ; Computer Simulation ; Time Factors ; }, abstract = {When using ecological momentary assessment data (EMA), missing data is pervasive as participant attrition is a common issue. Thus, any EMA study must have a missing data plan. In this paper, we discuss missingness in time series analysis and the appropriate way to handle missing data when the data is modeled as an idiographic discrete time continuous measure state-space model. We found that Missing Completely at Random, Missing At Random, and Time-dependent Missing At Random data have less bias and variability than Autoregressive Time-dependent Missing At Random and Missing Not At Random. The Kalman filter excelled at handling missing data under most conditions. Contrary to the literature, we found that using a variety of methods, multiple imputations struggled to recover the parameters.}, }
@article {pmid40091604, year = {2025}, author = {Tu, M and Liu, N and He, ZS and Dong, XM and Gao, TY and Zhu, A and Yang, JB and Zhang, SB}, title = {Integrative omics reveals mechanisms of biosynthesis and regulation of floral scent in Cymbidium tracyanum.}, journal = {Plant biotechnology journal}, volume = {23}, number = {6}, pages = {2162-2181}, pmid = {40091604}, issn = {1467-7652}, support = {202403AC100032//Key Research and Development Program of Yunnan Province/ ; YNWR-CYJS-2020-023//High-level Talent Support Plan of Yunnan Province/ ; XDB31000000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 32170393//National Natural Science Foundation of China/ ; 2024YFF1306703//National Key Research and Development Program of China/ ; 202201AU070123//Yunnan Fundamental Research Project/ ; 202301AT070306//Yunnan Fundamental Research Project/ ; }, mesh = {*Flowers/metabolism/genetics ; *Orchidaceae/genetics/metabolism ; *Odorants/analysis ; Terpenes/metabolism ; Gene Expression Regulation, Plant ; Transcriptome ; Volatile Organic Compounds/metabolism ; Genomics ; Plant Proteins/metabolism/genetics ; Multiomics ; }, abstract = {Flower scent is a crucial determiner in pollinator attraction and a significant horticultural trait in ornamental plants. Orchids, which have long been of interest in evolutionary biology and horticulture, exhibit remarkable diversity in floral scent type and intensity. However, the mechanisms underlying floral scent biosynthesis and regulation in orchids remain largely unexplored. In this study, we focus on floral scent in Cymbidium tracyanum, a wild species known for its strong floral fragrance and as a primary breeding parent of commercial Cymbidium hybrids. We present a chromosome-level genome assembly of C. tracyanum, totaling 3.79 Gb in size. Comparative genomic analyses reveal significant expansion of gene families associated with terpenoid biosynthesis and related metabolic pathways in C. tracyanum. Integrative analysis of genomic, volatolomic and transcriptomic data identified terpenoids as the predominant volatile components in the flowers of C. tracyanum. We characterized the spatiotemporal patterns of these volatiles and identified CtTPS genes responsible for volatile terpenoid biosynthesis, validating their catalytic functions in vitro. Dual-luciferase reporter assays, yeast one-hybrid assays and EMSA experiments confirmed that CtTPS2, CtTPS3, and CtTPS8 could be activated by various transcription factors (i.e., CtAP2/ERF1, CtbZIP1, CtMYB2, CtMYB3 and CtAP2/ERF4), thereby regulating the production of corresponding monoterpenes and sesquiterpenes. Our study elucidates the biosynthetic and regulatory mechanisms of floral scent in C. tracyanum, which is of great significance for the breeding of fragrant Cymbidium varieties and understanding the ecological adaptability of orchids. This study also highlights the importance of integrating multi-omics data in deciphering key horticultural traits in orchids.}, }
@article {pmid40089216, year = {2025}, author = {Torres-Roman, JS and Quispe-Vicuña, C and Benavente-Casas, A and Julca-Marin, D and Rios-Garcia, W and Challapa-Mamani, MR and Rio-Muñiz, LD and Ybaseta-Medina, J}, title = {Trends in stroke mortality in Latin America and the Caribbean from 1997 to 2020 and predictions to 2035: An analysis of gender, and geographical disparities.}, journal = {Journal of stroke and cerebrovascular diseases : the official journal of National Stroke Association}, volume = {34}, number = {6}, pages = {108286}, doi = {10.1016/j.jstrokecerebrovasdis.2025.108286}, pmid = {40089216}, issn = {1532-8511}, mesh = {Humans ; Latin America/epidemiology ; Female ; Male ; *Stroke/mortality/diagnosis ; Caribbean Region/epidemiology ; Risk Factors ; Sex Factors ; Middle Aged ; Sex Distribution ; Time Factors ; Databases, Factual ; Aged ; Adult ; *Health Status Disparities ; Age Distribution ; Forecasting ; Risk Assessment ; Age Factors ; Young Adult ; Aged, 80 and over ; }, abstract = {BACKGROUND: Stroke is a leading cause of death and disability globally, with significant public health implications. In Latin America, while mortality rates have declined, the number of stroke cases has increased due to prevalent risk factors like high blood pressure and obesity. Unlike Europe, recent trends in stroke mortality in this region remain underreported.<br><br>OBJECTIVE: This study evaluates stroke mortality rates in Latin America Latin American and Caribbean (LAC) countries from 1997 to 2020 and predictions to 2035.<br><br>METHODS: This ecological observational study utilized mortality data from the World Health Organization database. Trends were analyzed using Joinpoint regression to evaluate the annual percent change (APC) by sex and country. Predicted mortality rates through 2035 were calculated using the Nordpred package in R. Changes in stroke mortality were assessed by disentangling the effects of population growth, aging, and risk factor modifications, based on age-specific rates and projections. Results were presented as absolute case numbers and relative percentages.<br><br>RESULTS: From 1997 to 2020, twelve countries presented significant reductions in stroke mortality rates for men in LAC, the main ones being Chile (-4.2 %), El Salvador (-4.2 %), and Puerto Rico (-4.0 %). Thirteen countries reported a reduction in their mortality for women, mainly in Puerto Rico (-4.3 %), Chile (-3.7 %), Argentina, El Salvador, and Uruguay (-3.5 %). By 2035, an increase in deaths among men and women is expected, mainly due to the increase in population structure and size. However, a decrease in the mortality rate will be reported, mainly due to the reduction of risk factors.<br><br>CONCLUSION: Our final findings show a reduction in stroke mortality trends in LAC countries between 1997 and 2020, due to creating public awareness about vascular risk factors by authorities and the implementation of effective health policies. By 2035, an overall increase in mortality is expected, mainly due to population change in each country.}, }
@article {pmid40088887, year = {2025}, author = {Hartley, GA and Okhovat, M and Hoyt, SJ and Fuller, E and Pauloski, N and Alexandre, N and Alexandrov, I and Drennan, R and Dubocanin, D and Gilbert, DM and Mao, Y and McCann, C and Neph, S and Ryabov, F and Sasaki, T and Storer, JM and Svendsen, D and Troy, W and Wells, J and Core, L and Stergachis, A and Carbone, L and O'Neill, RJ}, title = {Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon.}, journal = {Cell genomics}, volume = {5}, number = {4}, pages = {100808}, pmid = {40088887}, issn = {2666-979X}, support = {R01 HG007352/HG/NHGRI NIH HHS/United States ; }, mesh = {*Centromere/genetics ; Animals ; *DNA Transposable Elements/genetics ; *Epigenesis, Genetic ; DNA Methylation/genetics ; *Hylobates/genetics ; Karyotype ; CpG Islands/genetics ; Evolution, Molecular ; }, abstract = {Great apes have maintained a stable karyotype with few large-scale rearrangements; in contrast, gibbons have undergone a high rate of chromosomal rearrangements coincident with rapid centromere turnover. Here, we characterize fully assembled centromeres in the eastern hoolock gibbon, Hoolock leuconedys (HLE), finding a diverse group of transposable elements (TEs) that differ from the canonical alpha-satellites found across centromeres of other apes. We find that HLE centromeres contain a CpG methylation centromere dip region, providing evidence that this epigenetic feature is conserved in the absence of satellite arrays. We uncovered a variety of atypical centromeric features, including protein-coding genes and mismatched replication timing. Further, we identify duplications and deletions in HLE centromeres that distinguish them from other gibbons. Finally, we observed differentially methylated TEs, topologically associated domain boundaries, and segmental duplications at chromosomal breakpoints, and thus propose that a combination of multiple genomic attributes with propensities for chromosome instability shaped gibbon centromere evolution.}, }
@article {pmid40087979, year = {2025}, author = {Van den Wyngaert, S and Cerbin, S and Garzoli, L and Grossart, HP and Gsell, AS and Kraberg, A and Lepère, C and Neuhauser, S and Stupar, M and Tarallo, A and Cunliffe, M and Gachon, C and Gavrilović, A and Masigol, H and Rasconi, S and Selmeczy, GB and Schmeller, DS and Scholz, B and Timoneda, N and Trbojević, I and Wilk-Woźniak, E and Reñé, A}, title = {ParAquaSeq, a Database of Ecologically Annotated rRNA Sequences Covering Zoosporic Parasites Infecting Aquatic Primary Producers in Natural and Industrial Systems.}, journal = {Molecular ecology resources}, volume = {25}, number = {6}, pages = {e14099}, pmid = {40087979}, issn = {1755-0998}, support = {PID2020-112978GB-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; CA20125//European Cooperation in Science and Technology/ ; 451-03-66/2024-03/200178//Ministarstvo Prosvete, Nauke i Tehnolo&#x161;kog Razvoja/ ; 239548-051//RANNIS Icelandic Research Fund/ ; 340659//Research Council of Finland/ ; 346387//Research Council of Finland/ ; 101086521//European Commission/ ; IR0000005//European Commission/ ; NKFIH KKP 144068//National Laboratory for Water Science and Water Security/ ; RRF-2.3.1-21-2022-00008//National Laboratory for Water Science and Water Security/ ; Y0801-B16//Austrian Science Fund/ ; //AXA Research Fund/ ; ANR-21-BIRE-0002-01//Agence Nationale de la Recherche/ ; 101052342//Biodiversa+/ ; CIR-01_00028//Italian Ministry of University and Research/ ; GR1540/33-1//Deutsche Forschungsgemeinschaft/ ; GR1540/47-1//Deutsche Forschungsgemeinschaft/ ; GR1540/48-1//Deutsche Forschungsgemeinschaft/ ; GR1540/51-1//Deutsche Forschungsgemeinschaft/ ; CEX2019-000928-S//AEI/ ; }, mesh = {*Aquatic Organisms/parasitology ; *RNA, Ribosomal/genetics ; Microalgae/parasitology ; *Parasites/genetics/classification ; *Databases, Genetic ; }, abstract = {Amplicon sequencing tools such as metabarcoding are commonly used for thorough characterisation of microbial diversity in natural samples. They mostly rely on the amplification of conserved universal markers, mainly ribosomal genes, allowing the taxonomic assignment of barcodes. However, linking taxonomic classification with functional traits is not straightforward and requires knowledge of each taxonomic group to confidently assign taxa to a given functional trait. Zoosporic parasites are highly diverse and yet understudied, with many undescribed species and host associations. However, they can have important impacts on host populations in natural ecosystems (e.g., controlling harmful algal blooms), as well as on industrial-scale algae production, e.g. aquaculture, causing their collapse or economic losses. Here, we present ParAquaSeq, a curated database of available molecular ribosomal sequences belonging to zoosporic parasites infecting aquatic vascular plants, macroalgae and photosynthetic microorganisms, i.e. microalgae and cyanobacteria. These sequences are aligned with ancillary data and other information currently available, including details on their hosts, occurrence, culture availability and associated bibliography. The database includes 1131 curated sequences from marine, freshwater and industrial or artificial environments, and belonging to 13 different taxonomic groups, including Chytridiomycota, Oomycota, Phytomyxea, and Syndiniophyceae. The curated database will allow a comprehensive analysis of zoosporic parasites in molecular datasets to answer questions related to their occurrence and distribution in natural communities. Especially through meta-analysis, the database serves as a valuable tool for developing effective mitigation and sustainable management strategies in the algae biomass industry, but it will also help to identify knowledge gaps for future research.}, }
@article {pmid40087683, year = {2025}, author = {Mbuba, E and Mañas-Chavernas, N and Moore, SJ and Ruzige, PD and Kobe, D and Moore, J and Philipo, R and Kisoka, N and Pontiggia, G and Chacky, F and Mwalimu, CD and Cattin, PC and Wolleb, J and Sandkuehler, R and Ross, A}, title = {Estimating the hole surface area of insecticide-treated nets using image analysis, manual hole counting and exact hole measurements.}, journal = {Malaria journal}, volume = {24}, number = {1}, pages = {82}, pmid = {40087683}, issn = {1475-2875}, mesh = {*Insecticide-Treated Bednets/standards ; *Image Processing, Computer-Assisted/methods ; *Mosquito Control/methods ; Animals ; Humans ; }, abstract = {BACKGROUND: The physical integrity of insecticidal-treated nets (ITNs) is important for creating a barrier against host-seeking mosquitoes and, therefore, influences people's perception of the net's effectiveness and their willingness to use it. Monitoring the physical integrity of ITNs over time provides information for replenishment schedules and purchasing decisions. Currently, the assessment of physical integrity of ITNs is conducted by manually counting holes and estimating their size to class the net as functional or not. This approach is laborious to routinely conduct during field surveys of ITNs. Automated image analysis may provide a rapid assessment of the physical integrity of ITNs but it is not known if the images can capture sufficient information. As a first step, this study aimed to assess the agreement between estimated hole surface areas derived from (1) manually segmented images, (2) manual hole counting compared to (3) ground truth obtained by calibrated close-up shots of individual holes.<br><br>METHODS: The physical integrity of 75 ITNs purposely selected from an ongoing study was assessed by manual hole counting, image analysis and ground truth. For the image analysis, a graphical user interface was developed and used for the segmentation of holes visible in photographs taken from each side of the net. The hole surface area was then computed from this data. The agreement between the estimates from image analysis and manual hole counting was compared to the ground truth using the Bland-Altman method.<br><br>RESULTS: There was substantial agreement between the manually segmented image analysis estimates and the ground truth hole surface areas. The overall bias was small, with a mean ratio of the hole surface area from image analysis to the ground truth of 0.70, and the 95% limits of agreement ranging from 0.35 to 1.38. Manual hole counting underestimated the hole surface area compared to the ground truth, particularly among nets with holes above 10&#xa0;cm in diameter.<br><br>CONCLUSION: Images coupled with manual segmentation contain sufficient information to calculate hole surface area. This lays the groundwork for incorporating automatic hole detection, and then assessing whether this method will offer a fast and objective method for routine assessment of physical integrity of ITNs. While the WHO method underestimated the hole surface area, it remains useful in classifying nets as either serviceable or too torn because the cut-off is specific to this method.}, }
@article {pmid40086783, year = {2025}, author = {Yang, JZ and Li, JH and Liu, JL and Zhou, AD and Wang, H and Xie, XL and Zhang, KK and Wang, Q}, title = {Multiomics analysis revealed the effects of polystyrene nanoplastics at different environmentally relevant concentrations on intestinal homeostasis.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {372}, number = {}, pages = {126050}, doi = {10.1016/j.envpol.2025.126050}, pmid = {40086783}, issn = {1873-6424}, mesh = {Animals ; Mice ; *Polystyrenes/toxicity ; Homeostasis/drug effects ; *Microplastics/toxicity ; Gastrointestinal Microbiome/drug effects ; *Intestines/drug effects ; Male ; Metabolomics ; Multiomics ; }, abstract = {Nanoplastics pollution is a global issue, with the digestive tract being one of the first affected organs, requiring further research on its impact on intestinal health. This study involved orally exposing mice to polystyrene nanoplastics (PS-NPs) at doses of 0.1, 0.5, or 2.5 mg/d for 42 days. The effects on intestinal health were thoroughly assessed via microbiomics, metabolomics, transcriptomics, and molecular biology. Our study demonstrated that the administration of all three doses of PS-NPs resulted in increased colonic permeability, heightened colonic and peripheral inflammation, reduced levels of antimicrobial peptides, and shortened colonic length. These effects may be attributed to a reduction in the abundance of probiotic bacteria, such as Clostridia_UCG-014, Roseburia, and Akkermansia, alongside an increase in the abundance of the pathogenic bacterium Desulfovibrionaceae induced by PS-NPs. Furthermore, we underscored the crucial role of histidine metabolism in PS-NPs-induced colonic injury, characterized by a significant reduction of L-histidine, which is closely related to microbial ecological dysregulation. Corresponding to microbiota deterioration and metabolic dysregulation, transcriptome analysis revealed that PS-NPs may disrupt colonic immune homeostasis by activating the TLR4/MyD88/NF-κB/NLRP3 signaling pathway. In conclusion, this study provided novel insights into the mechanisms by which PS-NPs disrupt intestinal homeostasis through integrated multiomics analysis, revealing critical molecular pathway and providing a scientific basis for future risk assessment of nanoplastics exposure.}, }
@article {pmid40086213, year = {2025}, author = {Dong, L and Mu, L and Huang, X}, title = {Exploring lipid remodeling and antioxidant responses in Chlorella pyrenoidosa exposed to streptomycin sulfate stress.}, journal = {Food chemistry}, volume = {478}, number = {}, pages = {143565}, doi = {10.1016/j.foodchem.2025.143565}, pmid = {40086213}, issn = {1873-7072}, mesh = {*Chlorella/metabolism/drug effects/genetics ; *Streptomycin/pharmacology ; *Antioxidants/metabolism ; *Lipid Metabolism/drug effects ; Superoxide Dismutase/metabolism/genetics ; *Anti-Bacterial Agents/pharmacology ; Plant Proteins/metabolism/genetics ; Ascorbate Peroxidases/metabolism/genetics ; Stress, Physiological/drug effects ; Microalgae/drug effects/metabolism ; }, abstract = {Microalgae, particularly Chlorella pyrenoidosa, are valuable for bioactive compounds and biofuel production, but antibiotic use in large-scale cultivation can impact growth and biochemical productivity. This study examines the physiological and molecular responses of C. pyrenoidosa to streptomycin sulfate (STRS) stress. STRS exposure significantly reduced cell density (15.31 × 10[6] to 11.20 × 10[6] cells/mL, p < 0.001) and photosynthetic efficiency (Fv/fm from 0.45 to 0.15). Multi-omics analysis revealed a dual adaptive strategy: (1) activation of antioxidant defenses, including upregulated superoxide dismutase (SOD, 19-fold) and ascorbate peroxidase (APX, 32-fold); (2) lipid remodeling, with increased α-linolenic acid (ALA) content (17.43 % to 21.25 %, p < 0.001) due to β-oxidation downregulation. These findings enhance understanding of microalgal stress adaptation and highlight potential applications in biofuel and food/feed industries. Future studies should optimize genetic and cultivation strategies to enhance these adaptive traits while ensuring ecological sustainability.}, }
@article {pmid40079420, year = {2025}, author = {Jurburg, SD}, title = {Short Read Lengths Recover Ecological Patterns in 16S rRNA Gene Amplicon Data.}, journal = {Molecular ecology resources}, volume = {25}, number = {6}, pages = {e14102}, pmid = {40079420}, issn = {1755-0998}, mesh = {*RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; *Metagenomics/methods ; Microbiota ; Animals ; *DNA Barcoding, Taxonomic/methods ; Biodiversity ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; }, abstract = {16S rRNA gene metabarcoding, the study of amplicon sequences of the 16S rRNA gene from mixed environmental samples, is an increasingly popular and accessible method for assessing bacterial communities across a wide range of environments. As metabarcoding sequence data archives continue to grow, data reuse will likely become an important source of novel insights into the ecology of microbes. While recent work has demonstrated the benefits of longer read lengths for the study of microbial communities from 16S rRNA gene segments, no studies have explored the use of shorter (< 200 bp) read lengths in the context of data reuse. Nevertheless, this information is essential to improve the reuse and comparability of metabarcoding data across existing datasets. This study reanalyzed nine 16S rRNA datasets targeting aquatic, animal-associated and soil microbiomes, and evaluated how processing the sequence data across a range of read lengths affected the resulting taxonomic assignments, biodiversity metrics and differential (i.e., before-after treatment) analyses. Short read lengths successfully recovered ecological patterns and allowed for the use of more sequences. Limited increases in resolution were observed beyond 150 bp reads across environments. Furthermore, abundance-weighted diversity metrics (e.g., Inverse Simpson index, Morisita-Horn dissimilarities or weighted Unifrac distances) were more robust to variation in read lengths. Read lengths alone contributed to consistent increases in the total number of ASVs detected, highlighting the need to consider metabarcoding-derived diversity estimates within the context of the bioinformatics parameters selected. This study provides evidence-based guidelines for the processing of short reads.}, }
@article {pmid40074806, year = {2025}, author = {Tang, Y and Hu, H and Chen, S and Hao, B and Xu, X and Zhu, H and Zhan, W and Zhang, T and Hu, H and Chen, G}, title = {Multi-omics analysis revealed the novel role of NQO1 in microenvironment, prognosis and immunotherapy of hepatocellular carcinoma.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {8591}, pmid = {40074806}, issn = {2045-2322}, support = {24B0413//the Scientific Research Project of the Hunan Provincial Department of Education/ ; 2024JJ7455//Natural Science Foundation of Hunan Province/ ; 20224310NHYCG04//University of South China Clinical Research 4310 Program/ ; 20224310NHYCG01//University of South China Clinical Research 4310 Program/ ; 82473965//National Natural Science Foundation of China/ ; 2023JJ50156//the Natural Science Foundation of Hunan Province/ ; 202250045223//Science and technology innovation Program of Hengyang City/ ; ZYYD2024CG17//Central Government Guided Local Science and Technology Development Fund Project in Xinjiang Uygur Autonomous Region/ ; 2024WK4008//Hunan Province Innovation Ecological Construction Plan Science and Technology Assistance Project in Xinjiang Uygur Autonomous Region/ ; SYTG-Y202429//Health Technology Promotion Project in Xinjiang Uygur Autonomous Region/ ; }, mesh = {Humans ; *Carcinoma, Hepatocellular/therapy/genetics/pathology/mortality/immunology/metabolism ; *NAD(P)H Dehydrogenase (Quinone)/genetics/metabolism ; *Liver Neoplasms/therapy/genetics/pathology/mortality/immunology/metabolism ; *Tumor Microenvironment/genetics ; *Immunotherapy/methods ; Prognosis ; Male ; Gene Expression Regulation, Neoplastic ; Female ; Tumor-Associated Macrophages/immunology/metabolism ; Middle Aged ; Cell Line, Tumor ; Nomograms ; Multiomics ; }, abstract = {NAD(P)H dehydrogenase quinone 1 (NQO1) is overexpressed in various cancers and is strongly associated with an immunosuppressive microenvironment and poor prognosis. In this study, we explored the role of NQO1 in the microenvironment, prognosis and immunotherapy of Hepatocellular carcinoma (HCC) using multi-omics analysis and machine learning. The results revealed that NQO1 was significantly overexpressed in HCC cells. NQO1[+]HCC cells were correlated with poor prognosis and facilitated tumor-associated macrophages (TAMs) polarization to M2 macrophages. We identified core NQO1-related genes (NRGs) and developed the NRGs-related risk-scores in hepatocellular carcinoma (NRSHC). The comprehensive nomogram integrating NRSHC, age, and pathological tumor-node-metastasis (pTNM) Stage achieved an area under the curve (AUC) above 0.7, demonstrating its accuracy in predicting survival outcomes and immunotherapy responses of HCC patients. High-risk patients exhibited worse prognoses but greater sensitivity to immunotherapy. Additionally, a web-based prediction tool was designed to enhance clinical utility. In conclusion, NQO1 may play a critical role in M2 polarization and accelerates HCC progression. The NRSHC model and accompanying tools offer valuable insights for personalized HCC treatment.}, }
@article {pmid40074756, year = {2025}, author = {Wei, P and Song, Y and Tian, R and Wang, Y and Chen, J and Yuan, Z and Zhou, W}, title = {CaecilianTraits, an individual level trait database of Caecilians worldwide.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {428}, pmid = {40074756}, issn = {2052-4463}, support = {32170445//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; *Amphibians/anatomy &amp; histology/classification ; *Databases, Factual ; Biological Evolution ; Biodiversity ; }, abstract = {Functional traits differ among species, which determine the ecological niche a species occupies and its ability to adapt to environment. However, differences in traits also exist at intraspecific level. Such variations shape differences in individual survival capabilities. Investigating intraspecific differences of functional traits is important for ecology, evolutionary biology and biodiversity conservation. Individual trait-based approaches have been applied in plant ecology. But for animals, most databases only provide data at the species level. In this study, we presented a global database of morphological traits for caecilians (Amphibia, Gymnophiona) at both species and individual level. Caecilians are a unique group of amphibians characterized by their secretive habits, which have limited our understanding of this taxon. We compiled the most comprehensive database covering 218 out of 222 known species, with 215 of them have individual level data. This database will facilitate research in the ecology, evolutionary biology, conservation biology, and taxonomy of caecilians. Furthermore, this dataset can be utilized to test ecological and evolutionary hypotheses at the individual level.}, }
@article {pmid40073274, year = {2025}, author = {Aucello, R and Pernice, S and Tortarolo, D and Calogero, RA and Herrera-Rincon, C and Ronchi, G and Geuna, S and Cordero, F and Lió, P and Beccuti, M}, title = {UnifiedGreatMod: a new holistic modelling paradigm for studying biological systems on a complete and harmonious scale.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {3}, pages = {}, pmid = {40073274}, issn = {1367-4811}, support = {//Ministero dell'Univerisita' e della Ricerca/ ; }, mesh = {*Models, Biological ; *Software ; *Systems Biology/methods ; Escherichia coli/metabolism/genetics ; Computer Simulation ; Clostridioides difficile ; *Computational Biology/methods ; }, abstract = {MOTIVATION: Computational models are crucial for addressing critical questions about systems evolution and deciphering system connections. The pivotal feature of making this concept recognizable from the biological and clinical community is the possibility of quickly inspecting the whole system, bearing in mind the different granularity levels of its components. This holistic view of system behaviour expands the evolution study by identifying the heterogeneous behaviours applicable, e.g. to the cancer evolution study.<br><br>RESULTS: To address this aspect, we propose a new modelling paradigm, UnifiedGreatMod, which allows modellers to integrate fine-grained and coarse-grained biological information into a unique model. It enables functional studies by combining the analysis of the system's multi-level stable states with its fluctuating conditions. This approach helps to investigate the functional relationships and dependencies among biological entities. This is achieved, thanks to the hybridization of two analysis approaches that capture a system's different granularity levels. The proposed paradigm was then implemented into the open-source, general modelling framework GreatMod, in which a graphical meta-formalism is exploited to simplify the model creation phase and R languages to define user-defined analysis workflows. The proposal's effectiveness was demonstrated by mechanistically simulating the metabolic output of Escherichia coli under environmental nutrient perturbations and integrating a gene expression dataset. Additionally, the UnifiedGreatMod was used to examine the responses of luminal epithelial cells to Clostridium difficile infection.<br><br>GreatMod https://qbioturin.github.io/epimod/, epimod_FBAfunctions https://github.com/qBioTurin/epimod_FBAfunctions, first case study E. coli &#xa0;https://github.com/qBioTurin/Ec_coli_modelling, second case study C. difficile &#xa0;https://github.com/qBioTurin/EpiCell_CDifficile.}, }
@article {pmid40070804, year = {2025}, author = {Vršanský, P and Sendi, H and Kotulová, J and Szwedo, J and Havelcová, M and Palková, H and Vršanská, L and Sakala, J and Puškelová, L and Golej, M and Biroň, A and Peyrot, D and Quicke, D and Néraudeau, D and Uher, P and Maksoud, S and Azar, D}, title = {Jurassic Park approached: a coccid from Kimmeridgian cheirolepidiacean Aintourine Lebanese amber.}, journal = {National science review}, volume = {12}, number = {3}, pages = {nwae200}, pmid = {40070804}, issn = {2053-714X}, abstract = {With the exception of a fly and a mite from the Triassic of Italy, all Mesozoic amber arthropods are from the Cretaceous. Late Jurassic Lebanese amber from Aintourine revealed a completely preserved adult coccid male (wing length 0.8 mm), Jankotejacoccus libanogloria gen. et sp. n., the earliest record of a plant sucking scale insect. Associated plant material included the cheirolepidiaceans Protopodocarpoxylon, Brachyphyllum and Classostrobus, plus Classopolis pollen, suggesting a forested temporary swamp habitat with ferns, tree ferns, water ferns, tall araucarian and ginkgoacean trees and shrubs. (Sub)tropic lateritic soil with vegetation debris underwent incomplete microbial decomposition in an anoxic water environment of peat swamp development. Strata-associated marine organisms support the Kimmeridgian age revealed by zircons. The discovery opens a new field of research in Jurassic amber fossils.}, }
@article {pmid40069723, year = {2025}, author = {Pieroni, A and Zocchi, DM and Alrhmoun, M and Sulaiman, N and Bavorova, M and Sõukand, R}, title = {Not "just necessity"? Two-x-eco-cultural dilemmas and the ethnobiological importance of the informal grannies' markets in Moldova.}, journal = {Journal of ethnobiology and ethnomedicine}, volume = {21}, number = {1}, pages = {17}, pmid = {40069723}, issn = {1746-4269}, support = {714874/ERC_/European Research Council/International ; }, mesh = {Humans ; Moldova ; Female ; Middle Aged ; *Food Supply ; Aged ; Agriculture ; Biodiversity ; *Commerce ; Male ; Adult ; Conservation of Natural Resources ; Rural Population ; Culture ; }, abstract = {Informal food markets, particularly those managed by (elderly) women in post-communist Eastern Europe, represent a biocultural phenomenon of profound significance since globalisation and increasingly strict legal frameworks often threaten these reservoirs of biocultural food heritage. In the fall of 2022 and 2023, a preliminary field study was conducted by visiting the informal markets of six Moldovan centres: Chișinău, Orhei, Bălți, Călărași, Comrat, and Taraclia, and conversing with approximately 40 mid-aged and elderly sellers. We argue that these markets are crucial in sustaining small-scale farming, preserving biodiversity, and maintaining a connection between urban communities and rural communities and, ultimately, between these rural citizens and their nature, keeping small-scale family farming and domestic traditional gastronomic activities alive. By trading fresh, homegrown, and homemade food and goods (including handicrafts), these mid-aged and elderly vendors support local economies, promote environmental sustainability, and safeguard traditional ecological knowledge and cultural heritage. This paper explores how grannies' markets contribute to biocultural diversity and sustainable food practices, especially amid the country's recent turbulent political, socioeconomic, and demographic challenges. The analysis advocates for the survival rights of these ecological, economic, and cultural (2-x-eco-cultural) refugia and invites ethnobiologists, food studies and cultural heritage scholars, rural sociologists, and agricultural economists to defend the biocultural diversity of informal food markets, moving them from an "out of necessity" status to a solid pillar of a possible future, new, family farming and small-scale ecological and gastronomic (conscientious) tourism. Policymakers should protect and enhance these informal spaces, especially the socioecological farming systems behind them, as essential socioeconomic and environmental assets. They should emphasise their importance as hubs for biological diversity, cultural preservation, community cohesion, and ecological sustainability.}, }
@article {pmid40067093, year = {2025}, author = {Zhang, G and Ristola, P and Su, H and Kumar, B and Zhang, B and Hu, Y and Elliot, MG and Drobot, V and Zhu, J and Staal, J and Larralde, M and Wang, S and Yi, Y and Yu, H}, title = {BioArchLinux: community-driven fresh reproducible software repository for life sciences.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {3}, pages = {}, pmid = {40067093}, issn = {1367-4811}, mesh = {*Software ; *Computational Biology/methods ; *Biological Science Disciplines ; Programming Languages ; Reproducibility of Results ; }, abstract = {MOTIVATION: The BioArchLinux project was initiated to address challenges in bioinformatics software reproducibility and freshness. Relying on Arch Linux's user-driven ecosystem, we aim to create a comprehensive and continuously updated repository for life sciences research.<br><br>RESULTS: BioArchLinux provides a PKGBUILD-based system for seamless software packaging and maintenance, enabling users to access the latest bioinformatics tools across multiple programming languages. The repository includes Docker images, Windows Subsystem for Linux (WSL) support, and Junest for nonroot environments, enhancing accessibility across platforms. Although being developed and maintained by a small core team, BioArchLinux is a fast-growing bioinformatics repository that offers a participatory and community-driven environment.<br><br>The repository, documentation, and tools are freely available at https://bioarchlinux.org and https://github.com/BioArchLinux. Users and developers are encouraged to contribute and expand this open-source initiative.}, }
@article {pmid40066908, year = {2025}, author = {Weeks, F and Myerson, R and Gangnon, R and Dykema, J and Cornelius, C and Green, T}, title = {Intrapartum Care Experiences Associated With Postpartum Visit Attendance.}, journal = {Birth (Berkeley, Calif.)}, volume = {52}, number = {4}, pages = {652-658}, pmid = {40066908}, issn = {1523-536X}, support = {//Wisconsin Alumni Research Foundation/ ; }, mesh = {Humans ; Female ; Pregnancy ; Adult ; Wisconsin ; *Postnatal Care/statistics &amp; numerical data ; Young Adult ; *Patient Acceptance of Health Care/statistics &amp; numerical data ; *Quality of Health Care ; *Perinatal Care/statistics &amp; numerical data ; Postpartum Period ; Surveys and Questionnaires ; Patient Satisfaction ; }, abstract = {INTRODUCTION: The postpartum visit is an important opportunity to prevent pregnancy-related morbidity and mortality; however, about 1 in 10 birthing people do not attend this visit. Intrapartum care experiences are an understudied factor that may contribute to postpartum healthcare engagement.<br><br>MATERIALS AND METHODS: We analyze data from a novel survey supplement on intrapartum care experiences administered to a probability-based population sample of people who have recently given birth through the Wisconsin Pregnancy Risk Assessment Monitoring System.<br><br>RESULTS: In regression models adjusting for a robust set of individual characteristics and birth hospital clustering, we find that lower provider responsiveness during intrapartum care is associated with increased odds of forgoing the postpartum visit (aOR 1.4, 95% CI 1.0-2.0).<br><br>DISCUSSION: The quality of care received during the birth hospitalization may shape how birthing people feel about health care providers and their willingness to attend future visits. Experiences of care during the intrapartum period may contribute to future health care utilization. Improving these experiences is an opportunity to promote long-term health.}, }
@article {pmid40064850, year = {2025}, author = {Roman, J and Abraham, AJ and Kiszka, JJ and Costa, DP and Doughty, CE and Friedlaender, A and Hückstädt, LA and Marcondes, M and Wetsel, E and Pershing, AJ}, title = {Migrating baleen whales transport high-latitude nutrients to tropical and subtropical ecosystems.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2125}, pmid = {40064850}, issn = {2041-1723}, mesh = {Animals ; *Ecosystem ; *Whales/physiology ; *Animal Migration/physiology ; Tropical Climate ; *Nutrients/metabolism ; Seasons ; Nitrogen/metabolism ; Biomass ; Oceans and Seas ; Female ; Urea/metabolism ; }, abstract = {Baleen whales migrate from productive high-latitude feeding grounds to usually oligotrophic tropical and subtropical reproductive winter grounds, translocating limiting nutrients across ecosystem boundaries in their bodies. Here, we estimate the latitudinal movement of nutrients through carcasses, placentas, and urea for four species of baleen whales that exhibit clear annual migration, relying on spatial data from publicly available databases, present and past populations, and measurements of protein catabolism and other sources of nitrogen from baleen whales and other marine mammals. Migrating gray, humpback, and North Atlantic and southern right whales convey an estimated 3784 tons N yr[-1] and 46,512 tons of biomass yr[-1] to winter grounds, a flux also known as the "great whale conveyor belt"; these numbers might have been three times higher before commercial whaling. We discuss how species recovery might help restore nutrient movement by whales in global oceans and increase the resilience and adaptative capacity of recipient ecosystems.}, }
@article {pmid40064777, year = {2025}, author = {Crespo-Bellido, A and Martin, DP and Duffy, S}, title = {Recombination Analysis of Geminiviruses Using Recombination Detection Program (RDP).}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2912}, number = {}, pages = {125-143}, pmid = {40064777}, issn = {1940-6029}, mesh = {*Geminiviridae/genetics ; *Recombination, Genetic ; *Software ; Genome, Viral ; Algorithms ; Sequence Alignment ; *Computational Biology/methods ; Evolution, Molecular ; }, abstract = {Geminiviruses are recombination-prone, and characterizing this evolutionary process within their genomes is a frequent goal of researchers. RDP is a stand-alone Windows program combining many algorithms that detect and characterize recombination. It has been widely used by the geminivirus community (and beyond). Here we describe the use of RDP4 and RDP5 for analysis of geminiviral nucleotide sequences including: (i) obtaining a reasonable dataset for analysis, (ii) making a credible multiple sequence alignment and (iii) analyzing an alignment with RDP on that alignment. RDP to both characterize recombination events and to produce statistically recombination-free datasets for other molecular evolution analyses.}, }
@article {pmid40063696, year = {2025}, author = {Smith, LB and Ahlich, E and Lang, B and Bollepalli, S and Prioleau, T and Bartolome, A and Hughes Lansing, A and Rancourt, D}, title = {Glycemic variability and weight-focused eating behaviors among adolescents and young adults with type 1 diabetes†.}, journal = {Journal of pediatric psychology}, volume = {50}, number = {4}, pages = {326-334}, doi = {10.1093/jpepsy/jsaf009}, pmid = {40063696}, issn = {1465-735X}, support = {//Dexcom, Inc/ ; }, mesh = {Humans ; Female ; *Diabetes Mellitus, Type 1/blood/psychology/physiopathology ; Adolescent ; Young Adult ; Male ; *Feeding Behavior/physiology/psychology ; *Feeding and Eating Disorders ; *Hunger/physiology ; *Blood Glucose/metabolism/analysis ; Adult ; Weight Loss ; }, abstract = {OBJECTIVE: Type 1 diabetes (T1D) disease management and associated glycemic fluctuations can disrupt experiences of hunger and satiety, which may increase risk for disordered eating behaviors. Glycemic variability may be a useful trigger for just-in-time interventions for disordered eating behaviors. In this exploratory study, we hypothesized that two metrics of glycemic variability would be associated with greater hunger and predict eating behaviors for weight loss or maintenance in adolescents and young adults with T1D.<br><br>METHODS: Individuals with T1D were recruited from a university diabetes clinic (N&#x2009;=&#x2009;34; 50% female, Mage&#x2009;=&#x2009;19.53&#x2009;years, MHbA1c&#x2009;=&#x2009;7.98%; 29% Hispanic/Latinx; 79% White). Participants wore a blinded continuous glucose monitor for 5&#xa0;days, and completed ecological momentary assessments (four prompts per day) that included measures of hunger and eating behaviors for weight loss or maintenance purposes. Generalized and linear mixed models were used to test hypotheses.<br><br>RESULTS: Approximately 30% of participants were at risk for an eating disorder based on Diabetes Eating Problem Survey-Revised scores. Greater glycemic variability did not predict hunger, but was associated with increased odds of endorsing any eating behavior for weight loss or maintenance purposes within-person (ps<.05). Greater hunger was associated with increased odds of endorsing disordered eating behavior within-person (p<.05).<br><br>CONCLUSIONS: This exploratory study provides some preliminary evidence that times of greater hunger and glycemic variability may be when individuals with T1D may be at higher risk of engaging in behaviors to lose or maintain weight.}, }
@article {pmid40062320, year = {2025}, author = {Boyes, D and Davis, J and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Sandy Carpet moth, Perizoma flavofasciatum (Thunberg, 1792).}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {40}, pmid = {40062320}, issn = {2398-502X}, abstract = {We present a genome assembly from a male specimen of Perizoma flavofasciatum (Sandy Carpet; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 369.30 megabases. Most of the assembly (99.88%) is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.61 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,915 protein-coding genes.}, }
@article {pmid40062319, year = {2025}, author = {Boyes, D and Boyes, C and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Alder Moth, Acronicta alni (Linnaeus, 1767).}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {68}, pmid = {40062319}, issn = {2398-502X}, abstract = {We present a genome assembly from a male Acronicta alni (Alder Moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The assembly contains two haplotypes with total lengths of 470.37 megabases and 472.86 megabases. Most of haplotype 1 (98.95%) is scaffolded into 31 chromosomal pseudomolecules, including the Z chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled and is 15.38 kilobases in length.}, }
@article {pmid40061226, year = {2025}, author = {Ab Kadir, MA and Abdul Manaf, R and Mokhtar, SA and Ismail, LI}, title = {Identifying leptospirosis hotspots in Selangor: uncovering climatic connections using remote sensing and developing a predictive model.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e18851}, pmid = {40061226}, issn = {2167-8359}, mesh = {*Leptospirosis/epidemiology ; Humans ; Malaysia/epidemiology ; Cross-Sectional Studies ; Geographic Information Systems ; *Remote Sensing Technology ; Incidence ; Climate Change ; Climate ; }, abstract = {BACKGROUND: Leptospirosis is an endemic disease in countries with tropical climates such as South America, Southern Asia, and Southeast Asia. There has been an increase in leptospirosis incidence in Malaysia from 1.45 to 25.94 cases per 100,000 population between 2005 and 2014. With increasing incidence in Selangor, Malaysia, and frequent climate change dynamics, a study on the disease hotspot areas and their association with the hydroclimatic factors could enhance disease surveillance and public health interventions.<br><br>METHODS: This ecological cross-sectional study utilised a geographic information system (GIS) and remote sensing techniques to analyse the spatiotemporal distribution of leptospirosis in Selangor from 2011 to 2019. Laboratory-confirmed leptospirosis cases (n&#xa0;= 1,045) were obtained from the Selangor State Health Department. Using ArcGIS Pro, spatial autocorrelation analysis (Moran's I) and Getis-Ord Gi* (hotspot analysis) was conducted to identify hotspots based on the monthly aggregated cases for each subdistrict. Satellite-derived rainfall and land surface temperature (LST) data were acquired from NASA's Giovanni EarthData website and processed into monthly averages. These data were integrated into ArcGIS Pro as thematic layers. Machine learning algorithms, including support vector machine (SVM), Random Forest (RF), and light gradient boosting machine (LGBM) were employed to develop predictive models for leptospirosis hotspot areas. Model performance was then evaluated using cross-validation and metrics such as accuracy, precision, sensitivity, and F1-score.<br><br>RESULTS: Moran's I analysis revealed a primarily random distribution of cases across Selangor, with only 20 out of 103 observed having a clustered distribution. Meanwhile, hotspot areas were mainly scattered in subdistricts throughout Selangor with clustering in the central region. Machine learning analysis revealed that the LGBM algorithm had the best performance scores compared to having a cross-validation score of 0.61, a precision score of 0.16, and an F1-score of 0.23. The feature importance score indicated river water level and rainfall contributes most to the model.<br><br>CONCLUSIONS: This GIS-based study identified a primarily sporadic occurrence of leptospirosis in Selangor with minimal spatial clustering. The LGBM algorithm effectively predicted leptospirosis hotspots based on the analysed hydroclimatic factors. The integration of GIS and machine learning offers a promising framework for disease surveillance, facilitating targeted public health interventions in areas at high risk for leptospirosis.}, }
@article {pmid40055331, year = {2025}, author = {Guerrero, PC and Contador, T and Díaz, A and Escobar, C and Orlando, J and Marín, C and Medina, P}, title = {Southern Islands Vascular Flora (SIVFLORA) dataset: A global plant database from Southern Ocean islands.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {397}, pmid = {40055331}, issn = {2052-4463}, mesh = {Islands ; *Biodiversity ; *Plants/classification ; Climate Change ; Ecosystem ; Oceans and Seas ; Databases, Factual ; }, abstract = {The Southern Islands Vascular Flora (SIVFLORA) dataset is a globally significant, open-access resource that compiles essential biodiversity data on vascular plants from islands across the Southern Ocean. The SIVFLORA dataset was generated through five steps: study area delimitation, compiling the dataset, validating and harmonizing taxonomy, structuring dataset attributes, and establishing file format and open access. Covering major taxonomic divisions, SIVFLORA offers a comprehensive overview of plant occurrences, comprising 14,589 records representing 886 species, 95 families, and 42 orders. This dataset documents that 58.62% of the taxa are native, 9.61% are endemic, and 31.77% are alien species. The Falkland/Malvinas Archipelago, the most species-rich, contrast sharply with less diverse islands like the South Orkney Archipelago. SIVFLORA serves as a taxonomically harmonized, interoperable resource for investigating plant diversity patterns, ecosystem responses to climate change in extreme environments, island biogeography, endemism, and the effects of anthropogenic pressures on Southern Ocean flora.}, }
@article {pmid40055329, year = {2025}, author = {Ferrer-Paris, JR and Sánchez-Mercado, A and Cornwell, WK and Ooi, M and Tozer, M and Mackenzie, BDE and Woodward, R and Denham, AJ and Auld, TD and Keith, DA}, title = {Fire ecology database for documenting plant responses to fire events in Australia.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {399}, pmid = {40055329}, issn = {2052-4463}, mesh = {*Fires ; *Plants ; *Databases, Factual ; Australia ; Biodiversity ; New South Wales ; *Plant Physiological Phenomena ; }, abstract = {An understanding of fire-response traits is essential for predicting how fire regimes structure plant communities and for informing fire management strategies for biodiversity conservation. Quantification of these traits is complex, encompassing several levels of data abstraction scaling up from field observations of individuals, to general categories of species responses. We developed the Fire Ecology Database to accommodate this complexity. Its conceptual framework is underpinned by a flexible data pipeline enabling links between fire-related trait data and event information at individual, population, and community levels. Key features include: (a) concise and documented trait and method vocabularies; (b) documented uncertainty in observations and aggregation; and (c) documented origin of data including field observations, laboratory experiments, and expert elicitation. We demonstrated application of our framework using data from new field surveys and existing data sets in New South Wales, Australia. The database includes 14 traits for 6,287 plant species derived from 8,936 field work records from 2007 to 2018, 7,054 field records from surveys after 2019, and 48,306 records from 301 existing sources.}, }
@article {pmid40054299, year = {2025}, author = {Guarischi, M and Montagnani, E and Catalano, G and Saligari, E and Signorini, S and Gori, M}, title = {From motion to interaction: How multisensory information shapes motor behaviors in children with visual impairment.}, journal = {Research in developmental disabilities}, volume = {159}, number = {}, pages = {104956}, doi = {10.1016/j.ridd.2025.104956}, pmid = {40054299}, issn = {1873-3379}, mesh = {Humans ; Female ; Male ; Child ; *Social Interaction ; Cues ; *Vision Disorders/physiopathology/psychology ; Biomechanical Phenomena ; Child, Preschool ; Attention ; *Auditory Perception ; Visual Perception ; }, abstract = {BACKGROUND: The ability to move independently enables children to develop perceptual, cognitive, and social interaction skills. Concerning this, vision holds a key role. As a result, children with visual impairment (VI) might be more challenged in their ability to move within their surroundings and interact with their caregivers.<br><br>AIM: This study investigated whether the use of multisensory stimuli could influence the motor exploration of children with VI and shape their interaction with the caregivers. For this, the present work examined the variability of children's motor trajectory and the distance between children and caregivers in a setting with and without multisensory cues.<br><br>METHODS AND PROCEDURES: A Motion Capture System was used within an ecological playroom environment. The Strange Situation paradigm was simplified and adapted by placing three TechARMs in the corners of the playroom to deliver audio-visual stimuli, used instead of the stranger.<br><br>OUTCOMES AND RESULTS: Children with VI showed larger variability within their motor trajectory and kept a shorter distance from the caregivers when multisensory cues were introduced in the playroom.<br><br>CONCLUSIONS AND IMPLICATIONS: Multisensory signals were considered unusual and influenced the kinematic parameters. Motor control of the environment was achieved by managing attention flexibility. WHAT DOES THIS PAPER ADD?: This study enriches available evidence about the study of motor and social interaction in children with VI, highlighting how multisensory stimuli could either support or hinder social and motor behaviors. Moreover, enhancing ecological validity could drive progress in the development and application of technological devices to clinical and research setting.}, }
@article {pmid40053082, year = {2025}, author = {Alibardi, L}, title = {Immunoreactivity of flexible and inflexible scales in different lizards indicates that the mature beta-layer contains different corneous proteins.}, journal = {Protoplasma}, volume = {262}, number = {5}, pages = {1129-1149}, pmid = {40053082}, issn = {1615-6102}, mesh = {Animals ; *Lizards/anatomy &amp; histology/genetics/immunology/metabolism ; Immunohistochemistry ; *Animal Scales/cytology/immunology/metabolism ; *Reptilian Proteins/chemistry/genetics/immunology/metabolism ; Computational Biology ; Amino Acid Sequence ; Epitopes/immunology ; Peptides/chemistry/metabolism ; Keratins/chemistry/metabolism ; }, abstract = {We have analyzed by immunohistochemical methods the Oberhautchen-beta layer, here abbreviated as beta-layer, of lizards with hard scales and lizards with softer scales. Different antibodies for detecting Corneous Beta Proteins (CBPs) have been utilized. The agamid beta-corneous layer is generally 3-4 times thicker than in geckos, and the surface microornamentation forms a honeycomb pattern. Geckos feature thinner beta-layers and a spinulated pattern and show immunolocalization for CBPs and isopeptide bonds, a product of transglutaminase catalysis, in their thin beta-layer. CBPs and isopeptide-bonds are detected in the superficial Oberhautchen and alpha-layer of agamids while the beta-layer is immuno-negative. Considering the limitations of immunolabeling methods, the unexpected result might derive from inaccessibility of antibodies to epitopes that are masked within the packed corneous material of the agamid beta-layer. However, bioinformatics analysis for CBPs sequenced in the few species of agamids so far known indicates that these proteins have low identity with those of other lizards. This suggests that agamids possess peculiar CBPs but low isopeptide bonds in their inflexible beta-layer. In contrast, the thinner and pliable beta-corneous layers of geckos may derive from the presence of isopeptide bonds mixed with lower amounts of CBPs. The differences in material properties of lizard scales, inflexibility versus pliability, are adaptive for the different ecological conditions of the species here analyzed.}, }
@article {pmid40053042, year = {2025}, author = {Duarte, T and Martin, GM and Anjos-Santos, D and Pessacq, P}, title = {Unraveling Plecoptera Diversity in Two Protected Areas of Argentine Patagonia.}, journal = {Anais da Academia Brasileira de Ciencias}, volume = {97}, number = {1}, pages = {e20240085}, doi = {10.1590/0001-3765202520240085}, pmid = {40053042}, issn = {1678-2690}, mesh = {Animals ; Argentina ; *Biodiversity ; *Neoptera/classification ; Forests ; Population Density ; Cluster Analysis ; *Animal Distribution ; *Insecta/classification ; Conservation of Natural Resources ; Parks, Recreational ; Geographic Information Systems ; }, abstract = {The Plecoptera taxonomy in Patagonia is well-documented, yet their distribution remains poorly understood, hindering comprehensive ecological and biogeographical studies. This study enhances knowledge of stonefly distribution in two Patagonian national parks: Nahuel Huapi and Los Alerces. Extensive fieldwork, georeferenced species records, and geographic information system data integration were conducted. Species richness was calculated using polygons (0.1° x 0.1° pixels) across ecoregions, with species indexed from rare to ubiquitous. Cluster analyses revealed faunal affinities across ecosystem complexes, and richness estimators (Jack1, Jack2, and Chao2) highlighted knowledge gaps. Results showed uneven species distribution, with the highest richness polygon (n = 19) in Los Alerces. The Northern Moist Forests hosted the most species, followed by the Transitional Cypress-Beech Forests. The rarest species were also found in these two complexes, as well as the Ecotone Steppe-Forest. Cluster analysis revealed strong affinities between the Northern Moist Forests of Nahuel Huapi and Ecotone Steppe-Forest. Richness estimators suggested up to 23 undocumented species. Though much remains to be learned about Plecoptera distribution in Patagonia, this study emphasizes the critical role of national parks in conserving biodiversity and provides a foundation for future conservation strategies, identifying new taxa records, including southernmost distributions.}, }
@article {pmid40051336, year = {2025}, author = {Birchard, K and Boccia, C and Lounder, H and Colston-Nepali, L and Friesen, VL}, title = {Popfinder: A Highly Effective Artificial Neural Network Package for Genetic Population Assignment.}, journal = {Molecular ecology resources}, volume = {25}, number = {6}, pages = {e14096}, pmid = {40051336}, issn = {1755-0998}, support = {//Environment and Climate Change Canada/ ; }, mesh = {*Neural Networks, Computer ; Animals ; *Genetics, Population/methods ; *Computational Biology/methods ; *Software ; *Birds/genetics/classification ; }, abstract = {The ability to assign biological samples to source populations with high accuracy and precision based on genetic variation is important for numerous applications from ecological studies through wildlife conservation to epidemiology. However, population assignment when genetic differentiation is low is challenging, and methods to address this problem are lacking. The application of artificial neural networks to population assignment using genomic data is highly promising. Here we present popfinder: a new, easy-to-use Python-based artificial neural network pipeline for genetic population assignment. We tested popfinder both with simulated genetic data from populations connected by varying levels of gene flow and with reduced-representation sequence data for three species of seabirds with weak to no population genetic structure. Popfinder was able to assign individuals to their source populations with high accuracy, precision and recall in most cases, including both simulated and empirical data sets, except in the empirical data set with the weakest population structure, where the comparator programs also performed poorly. Compared to other available software, popfinder was slower on the simulated data sets due to hyperparameter tuning and the fact that it does not reduce the dimensionality of the data set; however, all programs ran in seconds on empirical data sets. Additionally, popfinder provides a perturbation ranking method to help develop optimised SNP panels for genetic population assignment and is designed to be user-friendly. Finally, we caution users of all assignment programs to watch both for leakage of data during model training, which can lead to overfitting and inflation of performance metrics, and for unequal detection probabilities.}, }
@article {pmid40049043, year = {2025}, author = {Huang, JN and Gao, CC and Ren, HY and Wen, B and Wang, ZN and Gao, JZ and Chen, ZZ}, title = {Multi-omics association pattern between gut microbiota and host metabolism of a filter-feeding fish in situ exposed to microplastics.}, journal = {Environment international}, volume = {197}, number = {}, pages = {109360}, doi = {10.1016/j.envint.2025.109360}, pmid = {40049043}, issn = {1873-6750}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Carps/microbiology/metabolism ; *Water Pollutants, Chemical/toxicity ; *Microplastics/toxicity ; Multiomics ; }, abstract = {Microplastics (MPs) are widespread in water environments and can affect gut microbiota and host metabolism of fish, but whether changes in host metabolism under MPs are mediated by gut microbiota remains unclear. Here, silver carp, a filter-feeding fish with important ecological functions, was in-situ exposure to environmentally relevant MPs. Multi-omics analysis and fecal microbiota transplantation were used to reveal the metabolic responses of carp along gut-liver-muscle axis. After three months of in situ exposure to MPs, community structure of gut microbiota of carp was reshaped, and five dominate phyla were significantly changed, including increased Cyanobacteria, Chloroflexi and Planctomycetota but decreased Firmicutes and Fusobacteriota. Weighted gene co-expression network analysis was further performed between these phyla and liver transcription spectrum, showing that the hub gene module contained up-regulated hppD, maiA and plg and activated ubiquinone and other terpenoid-quinone biosynthesis and phenylalanine metabolism. By fecal microbiota transplantation, the key gene module associated with core microbiota phyla of carp was verified in germ-free zebrafish. Interestingly, up-regulated hppD, maiA and plg and enriched phenylalanine metabolism were also observed in this module. Subsequently, metabolome performed in carp liver also shared activated phenylalanine metabolism, including increased trans-cinnamic acid and L-tyrosine. Furthermore, high-associated mapping showed that the differentially expressed metabolites (gamma-aminobutyric acid, ornithine and L-serine) related to amino acid metabolism in carp muscle were significantly accompanied with increased L-tyrosine in its liver. Overall, MPs exposure could change gut microbiome of silver carp and alter host metabolism especially amino acid metabolism along the gut-liver-muscle axis.}, }
@article {pmid40048849, year = {2025}, author = {Bargheet, A and Noordzij, HT and Ponsero, AJ and Jian, C and Korpela, K and Valles-Colomer, M and Debelius, J and Kurilshikov, A and Pettersen, VK}, title = {Dynamics of gut resistome and mobilome in early life: a meta-analysis.}, journal = {EBioMedicine}, volume = {114}, number = {}, pages = {105630}, pmid = {40048849}, issn = {2352-3964}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant ; Metagenomics/methods ; Infant, Newborn ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Metagenome ; Female ; Interspersed Repetitive Sequences ; *Drug Resistance, Bacterial/genetics ; Computational Biology/methods ; }, abstract = {BACKGROUND: The gut microbiota of infants harbours a higher proportion of antibiotic resistance genes (ARGs) compared to adults, even in infants never exposed to antibiotics. Our study aims to elucidate this phenomenon by analysing how different perinatal factors influence the presence of ARGs, mobile genetic elements (MGEs), and their bacterial hosts in the infant gut.<br><br>METHODS: We searched MEDLINE and Embase up to April 3rd, 2023, for studies reporting infant cohorts with shotgun metagenomic sequencing of stool samples. The systematic search identified 14 longitudinal infant cohorts from 10 countries across three continents, featuring publicly available sequencing data with corresponding metadata. For subsequent integrative bioinformatic analyses, we used 3981 high-quality metagenomic samples from 1270 infants and 415 mothers.<br><br>FINDINGS: We identified distinct trajectories of the resistome and mobilome associated with birth mode, gestational age, antibiotic use, and geographical location. Geographical variation was exemplified by differences between cohorts from Europe, Southern Africa, and Northern America, which showed variation in both diversity and abundance of ARGs. On the other hand, we did not detect a significant impact of breastfeeding on the infants' gut resistome. More than half of detected ARGs co-localised with plasmids in key bacterial hosts, such as Escherichia coli and Enterococcus faecalis. These ARG-associated plasmids were gradually lost during infancy. We also demonstrate that E.&#xa0;coli role as a primary modulator of the infant gut resistome and mobilome is facilitated by its increased abundance and strain diversity compared to adults.<br><br>INTERPRETATION: Birth mode, gestational age, antibiotic exposure, and geographical location significantly influence the development of the infant gut resistome and mobilome. A reduction in E. coli relative abundance over time appears as a key factor driving the decrease in both resistome and plasmid relative abundance as infants grow.<br><br>FUNDING: Centre for Advanced Study in Oslo, Norway. Centre for New Antibacterial Strategies through the Troms&#xf8; Research Foundation, Norway.}, }
@article {pmid40045231, year = {2025}, author = {Agyapong, D and Propster, JR and Marks, J and Hocking, TD}, title = {Cross-validation for training and testing co-occurrence network inference algorithms.}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {74}, pmid = {40045231}, issn = {1471-2105}, support = {2125088//National Science Foundation/ ; }, mesh = {*Algorithms ; *Microbiota ; *Computational Biology/methods ; }, abstract = {BACKGROUND: Microorganisms are found in almost every environment, including soil, water, air and inside other organisms, such as animals and plants. While some microorganisms cause diseases, most of them help in biological processes such as decomposition, fermentation and nutrient cycling. Much research has been conducted on the study of microbial communities in various environments and how their interactions and relationships can provide insight into various diseases. Co-occurrence network inference algorithms help us understand the complex associations of micro-organisms, especially bacteria. Existing network inference algorithms employ techniques such as correlation, regularized linear regression, and conditional dependence, which have different hyper-parameters that determine the sparsity of the network. These complex microbial communities form intricate ecological networks that are fundamental to ecosystem functioning and host health. Understanding these networks is crucial for developing targeted interventions in both environmental and clinical settings. The emergence of high-throughput sequencing technologies has generated unprecedented amounts of microbiome data, necessitating robust computational methods for network inference and validation.<br><br>RESULTS: Previous methods for evaluating the quality of the inferred network include using external data, and network consistency across sub-samples, both of which have several drawbacks that limit their applicability in real microbiome composition data sets. We propose a novel cross-validation method to evaluate co-occurrence network inference algorithms, and new methods for applying existing algorithms to predict on test data. Our method demonstrates superior performance in handling compositional data and addressing the challenges of high dimensionality and sparsity inherent in real microbiome datasets. The proposed framework also provides robust estimates of network stability.<br><br>CONCLUSIONS: Our empirical study shows that the proposed cross-validation method is useful for hyper-parameter selection (training) and comparing the quality of inferred networks between different algorithms (testing). This advancement represents a significant step forward in microbiome network analysis, providing researchers with a reliable tool for understanding complex microbial interactions. The method's applicability extends beyond microbiome studies to other fields where network inference from high-dimensional compositional data is crucial, such as gene regulatory networks and ecological food webs. Our framework establishes a new standard for validation in network inference, potentially accelerating discoveries in microbial ecology and human health.}, }
@article {pmid40045055, year = {2025}, author = {Shi, J and Gong, J and Zhang, Y and Kan, G}, title = {Spatiotemporal change in ecological quality of the Qinghai-Tibetan Plateau based on an improved remote sensing ecological index and Google Earth Engine platform.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {4}, pages = {355}, pmid = {40045055}, issn = {1573-2959}, mesh = {*Remote Sensing Technology ; *Environmental Monitoring/methods ; *Ecosystem ; China ; Tibet ; Spatio-Temporal Analysis ; Conservation of Natural Resources ; Geographic Information Systems ; }, abstract = {The Qinghai-Tibetan Plateau (QTP) serves as a vital ecological security barrier in China and globally. Evaluating changes in ecological quality on the QTP provides critical insights for regional conservation initiatives. This study, tailored to the unique characteristics of the region, develops an Improved Remote Sensing Ecological Index (IRSEI) framework by integrating Gross Primary Productivity (GPP) with the Normalized Difference Vegetation Index (NDVI), humidity (WET), Land Surface Temperature (LST), and the Negative Drought Index (NDBSI). This comprehensive index aims to provide a more precise assessment of the environmental quality of the alpine ecosystem. It investigates spatial and temporal variations in ecological quality across the QTP, as well as within individual geographic subregions from 2000 to 2020. The first principal component accounts for an average variance of 63.69%. Over the past 20 years, the spatial distribution pattern of IRSEI on the QTP has shown lower values in the northwest, higher values in the southeast, and predominantly poor grades throughout the region. The mean trend coefficient for IRSEI was 0.002, indicating a gradual improvement in ecological quality on the QTP over time. Among 11 influencing factors examined, NDVI and GPP exhibit significant positive correlation with ecological quality, with q statistics of 0.942 and 0.932, respectively, underscoring the substantial impact of vegetation cover on ecosystem quality. These findings provide a robust theoretical foundation for supporting ecological management, restoration efforts, and the evaluation of ecological restoration within the QTP, thereby promoting ecosystem balance.}, }
@article {pmid40044867, year = {2025}, author = {Aguirre-Gutiérrez, J and Rifai, SW and Deng, X and Ter Steege, H and Thomson, E and Corral-Rivas, JJ and Guimaraes, AF and Muller, S and Klipel, J and Fauset, S and Resende, AF and Wallin, G and Joly, CA and Abernethy, K and Adu-Bredu, S and Alexandre Silva, C and de Oliveira, EA and Almeida, DRA and Alvarez-Davila, E and Asner, GP and Baker, TR and Benchimol, M and Bentley, LP and Berenguer, E and Blanc, L and Bonal, D and Bordin, K and Borges de Lima, R and Both, S and Cabezas Duarte, J and Cardoso, D and de Lima, HC and Cavalheiro, L and Cernusak, LA and Dos Santos Prestes, NCC and da Silva Zanzini, AC and da Silva, RJ and Dos Santos Alves da Silva, R and de Andrade Iguatemy, M and De Sousa Oliveira, TC and Dechant, B and Derroire, G and Dexter, KG and Rodrigues, DJ and Espírito-Santo, M and Silva, LF and Domingues, TF and Ferreira, J and Simon, MF and Girardin, CAJ and Hérault, B and Jeffery, KJ and Kalpuzha Ashtamoorthy, S and Kavidapadinjattathil Sivadasan, A and Klitgaard, B and Laurance, WF and Dan, ML and Magnusson, WE and Campos-Filho, EM and Manoel Dos Santos, R and Manzatto, AG and Silveira, M and Marimon-Junior, BH and Martin, RE and Vieira, DLM and Metzker, T and Milliken, W and Moonlight, P and Moraes de Seixas, MM and Morandi, PS and Muscarella, R and Nava-Miranda, MG and Nyirambangutse, B and Silva, JO and Oliveras Menor, I and Francisco Pena Rodrigues, PJ and Pereira de Oliveira, C and Pereira Zanzini, L and Peres, CA and Punjayil, V and Quesada, CA and Réjou-Méchain, M and Riutta, T and Rivas-Torres, G and Rosa, C and Salinas, N and Bergamin, RS and Marimon, BS and Shenkin, A and Silva Rodrigues, PM and Figueiredo, AES and Garcia, QS and Spósito, T and Storck-Tonon, D and Sullivan, MJP and Svátek, M and Vieira Santiago, WT and Arn Teh, Y and Theruvil Parambil Sivan, P and Nascimento, MT and Veenendaal, E and Zo-Bi, IC and Dago, MR and Traoré, S and Patacca, M and Badouard, V and de Padua Chaves E Carvalho, S and White, LJT and Zhang-Zheng, H and Zibera, E and Zwerts, JA and Burslem, DFRP and Silman, M and Chave, J and Enquist, BJ and Barlow, J and Phillips, OL and Coomes, DA and Malhi, Y}, title = {Canopy functional trait variation across Earth's tropical forests.}, journal = {Nature}, volume = {641}, number = {8061}, pages = {129-136}, pmid = {40044867}, issn = {1476-4687}, mesh = {Africa ; Asia ; Biodiversity ; *Earth, Planet ; *Forests ; Plant Leaves/physiology/chemistry/anatomy &amp; histology ; Soil/chemistry ; *Trees/physiology/anatomy &amp; histology/chemistry/classification ; Tropical Climate ; Uncertainty ; }, abstract = {Tropical forest canopies are the biosphere's most concentrated atmospheric interface for carbon, water and energy[1,2]. However, in most Earth System Models, the diverse and heterogeneous tropical forest biome is represented as a largely uniform ecosystem with either a singular or a small number of fixed canopy ecophysiological properties[3]. This situation arises, in part, from a lack of understanding about how and why the functional properties of tropical forest canopies vary geographically[4]. Here, by combining field-collected data from more than 1,800 vegetation plots and tree traits with satellite remote-sensing, terrain, climate and soil data, we predict variation across 13 morphological, structural and chemical functional traits of trees, and use this to compute and map the functional diversity of tropical forests. Our findings reveal that the tropical Americas, Africa and Asia tend to occupy different portions of the total functional trait space available across tropical forests. Tropical American forests are predicted to have 40% greater functional richness than tropical African and Asian forests. Meanwhile, African forests have the highest functional divergence-32% and 7% higher than that of tropical American and Asian forests, respectively. An uncertainty analysis highlights priority regions for further data collection, which would refine and improve these maps. Our predictions represent a ground-based and remotely enabled global analysis of how and why the functional traits of tropical forest canopies vary across space.}, }
@article {pmid40041564, year = {2025}, author = {Zhang, J and Qian, H and Wang, X}, title = {An online version and some updates of R package U.Taxonstand for standardizing scientific names in plant and animal species.}, journal = {Plant diversity}, volume = {47}, number = {1}, pages = {166-168}, pmid = {40041564}, issn = {2468-2659}, abstract = {•We present 'U.Taxonstand Online', a user-friendly web application for scientific name matching of both plants and animals.•U.Taxonstand Online provides a solution for the users with limited abilities of programming and data mining.•We add several new functions to clean and format the data for R package U.Taxonstand.}, }
@article {pmid40038315, year = {2025}, author = {Chen, Y and Chen, S and Tao, J and Li, M and Wang, W and Chen, M and Fang, X and Kong, L and Wang, Y and Pereira, O and Zhang, C}, title = {Multi-omic stock of surface ocean microbiome built by monthly, weekly and daily sampling in Dapeng Bay, China.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {378}, pmid = {40038315}, issn = {2052-4463}, support = {32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; RCBS20221008093229035//Shenzhen Science and Technology Innovation Commission/ ; 92351301//&#xc9;cole Nationale d'Ing&#xe9;nieurs de Saint-Etienne (National Engineering School of Saint-&#xc9;tienne)/ ; }, mesh = {China ; *Microbiota ; *Bays/microbiology ; Archaea/genetics/classification ; Metagenome ; Bacteria/classification/genetics ; Oceans and Seas ; Metagenomics ; *Seawater/microbiology ; Multiomics ; }, abstract = {The coastal ocean is the dynamic interface where terrestrial, atmospheric, and marine systems converge, acting as a hotspot for microbial activity, which underpins the intricate web of carbon and nitrogen cycling. Dapeng Bay, a typical semi-enclosed bay along the southern coastline of China, is strongly influenced by monsoon climates and human activities. Despite its ecological importance, long-term observations and investigations into the microbial community structure in this region are notably lacking. To address this gap, we conducted a two-year continuous sampling from May 2021 to June 2023 to explore shifts in nearshore surface microbial communities and assess the long-term effects of environmental stressors. This study presents comprehensive amplicon, metagenomic, and metatranscriptomic information. We identified 3,600 amplicon sequence variants and recovered 1,216 high-quality metagenome-assembled MAGs, representing 17 bacterial and 3 archaeal phyla. Additionally, 587 MAGs were correlated with transcriptional activity, comprising 539 bacterial and 48 archaeal populations. This dataset is anticipated to provide a multi-dimensional perspective, enhancing our understanding of the complexity, dynamics, and adaptability of microbial communities in coastal environments.}, }
@article {pmid40038157, year = {2025}, author = {Prescott, J and Keyser, AJ and Litwin, P and Dunbar, MD and McClelland, R and Ruple, A and Ernst, H and Butler, BL and Kauffman, M and Avery, A and Harrison, BR and Partida-Aguilar, M and McCoy, BM and Slikas, E and Greenier, AK and Muller, E and Algavi, YM and Bamberger, T and Creevy, KE and ,  and Borenstein, E and Snyder-Mackler, N and Promislow, DEL}, title = {Rationale and design of the Dog Aging Project precision cohort: a multi-omic resource for longitudinal research in geroscience.}, journal = {GeroScience}, volume = {47}, number = {4}, pages = {5725-5748}, pmid = {40038157}, issn = {2509-2723}, support = {U19 AG057377/AG/NIA NIH HHS/United States ; AG057377/AG/NIA NIH HHS/United States ; USDA/ARS 58-8050-9-004//U.S. Department of Agriculture/ ; AG057377/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; *Dogs/physiology ; Female ; Male ; *Aging/physiology ; Immunophenotyping ; Life Expectancy ; *Multiomics/methods/organization &amp; administration/standards ; Pets/physiology ; Research Design ; Longitudinal Studies ; *Geroscience/methods ; }, abstract = {A significant challenge in multi-omic geroscience research is the collection of high quality, fit-for-purpose biospecimens from a diverse and well-characterized study population with sufficient sample size to detect age-related changes in physiological biomarkers. The Dog Aging Project designed the precision cohort to study the mechanisms underlying age-related change in the metabolome, microbiome, and epigenome in companion dogs, an emerging model system for translational geroscience research. One thousand dog-owner pairs were recruited into cohort strata based on life stage, sex, size, and geography. We designed and built a novel implementation of the REDCap electronic data capture system to manage study participants, logistics, and biospecimen and survey data collection in a secure online platform. In collaboration with primary care veterinarians, we collected and processed blood, urine, fecal, and hair samples from 976 dogs. The resulting data include complete blood count, chemistry profile, immunophenotyping by flow cytometry, metabolite quantification, fecal microbiome characterization, epigenomic profile, urinalysis, and associated metadata characterizing sample conditions at collection and during lab processing. The project, which has already begun collecting second- and third-year samples from precision cohort dogs, demonstrates that scientifically useful biospecimens can be collected from a geographically dispersed population through collaboration with private veterinary clinics and downstream labs. The data collection infrastructure developed for the precision cohort can be leveraged for future studies. Most important, the Dog Aging Project is an open data project. We encourage researchers around the world to apply for data access and utilize this rich, constantly growing dataset in their own work.}, }
@article {pmid40036964, year = {2025}, author = {Jyoti, J and Hütt, MT}, title = {Evaluating changes in attractor sets under small network perturbations to infer reliable microbial interaction networks from abundance patterns.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {4}, pages = {}, pmid = {40036964}, issn = {1367-4811}, mesh = {Algorithms ; *Microbial Interactions ; Humans ; *Microbiota ; *Computational Biology/methods ; }, abstract = {MOTIVATION: Inferring microbial interaction networks from microbiome data is a core task of computational ecology. An avenue of research to create reliable inference methods is based on a stylized view of microbiome data, starting from the assumption that the presences and absences of microbiomes, rather than the quantitative abundances, are informative about the underlying interaction network. With this starting point, inference algorithms can be based on the notion of attractors (asymptotic states) in Boolean networks. Boolean network framework offers a computationally efficient method to tackle this problem. However, often existing algorithms operating under a Boolean network assumption, fail to provide networks that can reproduce the complete set of initial attractors (abundance patterns). Therefore, there is a need for network inference algorithms capable of reproducing the initial stable states of the system.<br><br>RESULTS: We study the change of attractors in Boolean threshold dynamics on signed undirected graphs under small changes in network architecture and show, how to leverage these relationships to enhance network inference algorithms. As an illustration of this algorithmic approach, we analyse microbial abundance patterns from stool samples of humans with inflammatory bowel disease (IBD), with colorectal cancer and from healthy individuals to study differences between the interaction networks of the three conditions. The method reveals strong diversity in IBD interaction networks. The networks are first partially deduced by an earlier inference method called ESABO, then we apply the new algorithm developed here, EDAME, to this result to generate a network that comes nearest to satisfying the original attractors.<br><br>Implementation code is freely available at https://github.com/Jojo6297/edame.git.}, }
@article {pmid40034275, year = {2025}, author = {Veneros, J and Hansen, AJ and Jantz, P and Roberts, D and Noguera-Urbano, E and García, L}, title = {Analysis of changes in temperature and precipitation in South American countries and ecoregions: Comparison between reference conditions and three representative concentration pathways for 2050.}, journal = {Heliyon}, volume = {11}, number = {4}, pages = {e42459}, pmid = {40034275}, issn = {2405-8440}, abstract = {Climate change is a global concern, and its impact on environmental variables such as temperature and annual precipitation is unknown spatially in the desert, andes, and rainforest ecoregions of Peru, Ecuador, and Colombia. In this study, we conducted a general review of climate drivers for South America (SA) and explored climate data using the GCM compareR package (General Circulation Models) and average ensembles for temperature and precipitation. Our results showed that all GCMs demonstrated increases in the annual mean temperature (BIO1) and in the mean temperature of the driest quarter (BIO9) for Peru, Ecuador, and Colombia for 2050 in three RCPs (2.6, 4.5, and 8.5). Also, most of the GCMs showed increases in the annual precipitation (BIO12) and the precipitation in the driest quarter (BIO17). We conducted non-parametric tests (Kruskal-Wallis Test) to assess if the medians of temperature and precipitation in the three ecoregions are equal for both the baseline and the climate change scenarios. We rejected the null hypothesis that the medians are equal for both temperatures and precipitation in the baseline vs. 2050 RCPs (2.6, 4.5, and 8.5). A spatial analysis was conducted to visualize the variations in temperature and precipitation between the RCPs versus the baseline, and the spatial variation at the country or ecoregion level can be observed. The annual mean temperature (°C) or annual precipitation (mm) divided by its standard deviation for each ecoregion (M metric) was analyzed to see how much the average temperature or the annual precipitation is relatively large compared to the variability or dispersion of temperatures or precipitation respectively; the average temperature and the annual precipitation for the baseline and the three RCPs are relatively large and associated with the variability or dispersion of their temperatures in the Napo moist forest compared to the other ecoregions. Our study provides important insights into the potential impacts of climate change on these ecosystems. Prospects in the Napo moist forest ecoregion, where significant changes in temperature and humidity have already occurred, and new species have invaded or evolved in the western Amazon rainforest, are particularly highlighted and reflected in terms of risk mitigation, ecosystem restoration, surveillance, and monitoring.}, }
@article {pmid40033715, year = {2025}, author = {Gorné, LD and Hendry, AP and Pelletier, F and Sanderson, S and Correa, C and Arias, C and Beausoleil, MO and Boisjoly, M and Crispo, E and Berner, D and De León, LF and DiBattista, JD and Haines, GE and Haller, BC and Kinnison, MT and Muttalib, S and McKellar, AE and O'Dea, RE and Reyes-Corral, WD and Ritchot, Y and Oke, KB and Wood, ZT and Farrugia, T and Gotanda, KM}, title = {PROCEED v6.1: Phenotypic rates of change evolutionary and ecological database.}, journal = {Ecology}, volume = {106}, number = {3}, pages = {e70009}, pmid = {40033715}, issn = {1939-9170}, support = {//Natural Sciences and Engineering Research Council of Canada/ ; //Le Fonds Qu&#xe9;b&#xe9;cois de la Recherche sur la Nature et les Technologies/ ; //McGill University/ ; //National Science Foundation/ ; //Brock University/ ; }, mesh = {*Phenotype ; *Biological Evolution ; Animals ; *Databases, Factual ; *Ecosystem ; *Ecology ; }, abstract = {Populations must continuously respond to environmental change or risk extinction. These responses can be measured as phenotypic rates of change, which allow researchers to predict their contemporary evolutionary responses. In 1999, a database of phenotypic rates of change in wild populations was compiled. Since then, researchers have used (and expanded) this database to examine the phenotypic responses as a function of the features of the study system (i.e., the population or set of populations, of a given species, that experienced a specific driver or disturbance), the measured traits, and methodological approaches. Therefore, PROCEED (Phenotypic Rates of Change Evolutionary and Ecological Database) is an ongoing compilation of rates of phenotypic change, typically calculated as Haldanes and Darwins, published in peer-reviewed literature (but also including data from theses and technical reports). Studies in this database measure the intraspecific change in quantitative (continuous or discrete) traits and report either the time elapsed from the onset of environmental novelty, or reference a historical or biological event reported in other sources (e.g., a mine opening or a well-documented biological invasion). Included studies either follow a single population through time (allochronic design) or compare two or more populations that diverged at a known time (synchronic design). Some included studies account for the total phenotypic variability in the field (i.e., phenotypic studies), while others employed common-garden or other quantitative genetic approaches to account for the heritable component of the phenotypic change (i.e., genetic studies). PROCEED includes systems in both natural and experimental conditions, provided that reproduction was not manipulated (i.e., artificial selection experiments were excluded). In the included experimental systems, the environment of the focal populations was manipulated (e.g., an herbivory exclusion experiment, where the type and load of herbivory are manipulated) but the studies did not deliberately select for trait values in the study population (e.g., the plant height). PROCEED does not include systems where the phenotypic change is presumably due to interspecific hybridization, polyploidy, or other chromosomal alterations. Here, we present the most recently updated PROCEED (Version 6.1). This new, curated version has 9263 records (n) collated from 326 studies, 1801 systems, and 428 species. The database includes records belonging to mammals (n = 686), birds (n = 1475), reptiles (n = 96), amphibians (n = 23), fishes (n = 3671), invertebrates (n = 1141, mostly arthropods), and plants (n = 2171). The maximum elapsed time between the environmental change and the sampling is 500 years but is typically less than 100 years (third quartile 89.5; median 45 years). The database also includes a set of variables describing biological and methodological aspects of the study system and measured traits, along with features of the sampling design in the primary source of information. This new version of PROCEED also includes a time series dataset comprising a subset of records included in the general dataset. These are allochronic studies with three or more sampling times throughout the entire study period. The time series dataset contains 655 time series (s)-belonging to 61 studies, from 156 systems, and 77 species-including mammals (s = 140), birds (s = 77), reptiles (s = 4), amphibians (s = 8), fishes (s = 404), and plants (s = 22). The data are released under a Creative Commons CC0 1.0 Universal Public Domain Dedication license.}, }
@article {pmid40030035, year = {2025}, author = {Jin, J and Zhang, R and Li, J and Gao, F and Liao, Z and Yu, Y and Wang, Y and Bucci, D and Xiao, M and Ma, R and Ma, Q and Gao, S and Lio, J and Novais, F and Huang, SC and Zhu, J and Ghoneim, H and Wen, H and Li, Z and Sun, N and Xin, G}, title = {The NAE1-mediated neddylation operates as an essential post-translational modification checkpoint for effector CD8[+] T cells.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {10}, pages = {e2424061122}, pmid = {40030035}, issn = {1091-6490}, support = {1R01CA269984//HHS | NIH | National Cancer Institute (NCI)/ ; R01 AI162711/AI/NIAID NIH HHS/United States ; R01 CA269984/CA/NCI NIH HHS/United States ; RSG-23-1036499-01//American Cancer Society (ACS)/ ; CCR231013713//Susan G. Komen (SGK)/ ; }, mesh = {*CD8-Positive T-Lymphocytes/immunology/metabolism ; Animals ; *Protein Processing, Post-Translational ; Humans ; Mice ; *NEDD8 Protein/metabolism ; *Ubiquitin-Activating Enzymes/metabolism/genetics ; Receptors, Antigen, T-Cell/metabolism ; Lymphocyte Activation ; NFATC Transcription Factors/metabolism/genetics ; Colonic Neoplasms/immunology/pathology/metabolism ; Proteomics ; Mice, Inbred C57BL ; }, abstract = {Optimal activation of CD8+ T cells is crucial for immunity-mediated destruction of cancer, requiring a substantial amount of proteins involved in metabolism, proliferation, and effector function. Despite extensive studies emphasizing the role of transcriptional regulation in this process, paired transcriptomic and proteomic analyses reveal that the RNA profile is poorly correlated with protein levels. This discrepancy underscores the importance of post-translational modifications (PTMs) in controlling protein abundance during activation. However, the impact of PTMs on the CD8+ T cell protein dynamic remains underexplored. We identify that neddylation, a recently discovered PTM, is activated in response to T cell receptor (TCR) stimulation and enriched in effector CD8+ T cells from colon cancer patients. Mechanistically, we found the rate-limiting enzyme of neddylation, neural precursor cell expressed developmentally down-regulated protein 8 activating enzyme E1 (NAE1), is induced by the NFATc1, a critical transcription factor downstream of TCR signaling. Our observation revealed that genetic ablation of NAE1 significantly disturbed the proteomic landscape related to activation and mitochondrial function. As a result, CD8+ T cells lacking NAE1 exhibited severely compromised activation, proliferation, and survival, which was accompanied by impaired mitochondrial function. Consistently, deletion of NAE1 in CD8+ T cells abolished their antitumor function and promoted tumor progression. By contrast, the overexpression of NAE1 significantly improved the function of tumor-infiltrating CD8+ T cells. Overall, we uncovered neddylation, a previously underappreciated PTM, as a proteomic checkpoint for CD8+ T cell activation. Enforced expression of NAE1 offers promising therapeutic potential for boosting the antitumor CD8+ T cell responses.}, }
@article {pmid40029426, year = {2025}, author = {Zhang, J and Wang, Q and Gao, H and Qi, Q and He, W and Li, J and Yao, S and Li, W}, title = {Ecological suitability distribution of hop based on MaxEnt modeling.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {4}, pages = {346}, pmid = {40029426}, issn = {1573-2959}, mesh = {China ; *Humulus/growth &amp; development ; *Environmental Monitoring/methods ; Geographic Information Systems ; *Ecosystem ; Models, Theoretical ; Conservation of Natural Resources ; }, abstract = {Hop has been widely utilized in both food production and traditional medicine owing to their distinctive flavor and various pharmacological effects. In recent years, the increasing demand for hop has led to their cultivation in many regions across China. However, hops require specific ecological conditions, including climate, soil, precipitation, and temperature, which significantly affect their distribution and growth. To facilitate the standardization and scientific cultivation of hops, it is essential to clarify the distribution of their ecological suitability. In this study, we collected data from 95 hops distribution locations and 115 ecological factors to determine the areas suitable for hops cultivation using the Maximum Entropy (MaxEnt) model and Geographic Information System (GIS). The highly suitable areas are primarily located in the northwestern part of the Xinjiang Uygur Autonomous Region, the eastern part of Gansu Province, Shaanxi Province, the southwestern part of Shanxi Province, and parts of Ningxia Hui Autonomous Region and Yunnan Province. These findings provide valuable guidance for the scientific cultivation of hops, ensuring the efficient use of ecological resources and promoting sustainable cultivation practices.}, }
@article {pmid40028774, year = {2025}, author = {Fuzessy, L and Pizo, MA}, title = {NeoFrugivory: A comprehensive database for frugivory interactions and functional traits in the Neotropics.}, journal = {Ecology}, volume = {106}, number = {3}, pages = {e70049}, doi = {10.1002/ecy.70049}, pmid = {40028774}, issn = {1939-9170}, support = {2023/12469-5//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 21/02943-6//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 151167/2023-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 304742/2019-8//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Animals ; *Fruit/physiology ; *Vertebrates/physiology ; *Databases, Factual ; Ecosystem ; *Herbivory ; *Feeding Behavior/physiology ; Plants/classification ; South America ; }, abstract = {Frugivory plays a crucial role in shaping Neotropical ecosystems, influencing plant dispersal, community dynamics, and ecosystem function. Despite its ecological significance, a systematic understanding of frugivore-fruit interactions spanning the entire Neotropical realm has been lacking. Therefore, we compiled the NeoFrugivory database, which addresses this gap by synthesizing data from a wide range of sources, including peer-reviewed literature, field studies, and existing databases. NeoFrugivory represents a comprehensive compilation of 10,175 unique frugivory interactions across the Neotropical region, the most diverse in terms of vertebrate frugivores, and consolidates information from 419 studies spanning from 1967 to 2023. It includes 2375 plant species and 758 terrestrial vertebrate species. In addition to documenting frugivory interactions, NeoFrugivory includes information on functional traits for both plants and vertebrates, such as body mass, diet, fruit morphology, and seed characteristics. The database encompasses diverse terrestrial vertebrate taxa, including species belonging to taxonomic groups such as Primates, Chiroptera, Birds, Artiodactyla/Perissodactyla, Reptilia, Carnivora, Marsupialia, and Rodentia. By providing a centralized repository of frugivory interactions, NeoFrugivory facilitates comprehensive analyses of ecological networks, evolutionary patterns, and ecosystem dynamics across the Neotropics, and NeoFrugivory provides a unique resource for researchers interested in exploring the intricate dynamics of plant-animal frugivory interactions in the Neotropics. This database enables researchers to explore the ecological roles of different frugivore taxa, identify keystone species, assess the resilience of mutualistic networks, and evaluate the impacts of environmental change on fruit-frugivore interactions. Furthermore, NeoFrugivory serves as a valuable resource for conservation practitioners, supporting the design and implementation of targeted conservation strategies aimed at preserving biodiversity and ecosystem function in the Neotropical region. Overall, NeoFrugivory represents a significant advancement in our understanding of frugivory dynamics in the Neotropics and provides a foundation for future research and conservation efforts in this ecologically diverse and critically important region. There are no copyright restrictions on the data; this paper should be cited when data are used in publications.}, }
@article {pmid40027489, year = {2025}, author = {Bai, D and Chen, T and Xun, J and Ma, C and Luo, H and Yang, H and Cao, C and Cao, X and Cui, J and Deng, YP and Deng, Z and Dong, W and Dong, W and Du, J and Fang, Q and Fang, W and Fang, Y and Fu, F and Fu, M and Fu, YT and Gao, H and Ge, J and Gong, Q and Gu, L and Guo, P and Guo, Y and Hai, T and Liu, H and He, J and He, ZY and Hou, H and Huang, C and Ji, S and Jiang, C and Jiang, GL and Jiang, L and Jin, LN and Kan, Y and Kang, D and Kou, J and Lam, KL and Li, C and Li, C and Li, F and Li, L and Li, M and Li, X and Li, Y and Li, ZT and Liang, J and Lin, Y and Liu, C and Liu, D and Liu, F and Liu, J and Liu, T and Liu, T and Liu, X and Liu, Y and Liu, B and Liu, M and Lou, W and Luan, Y and Luo, Y and Lv, H and Ma, T and Mai, Z and Mo, J and Niu, D and Pan, Z and Qi, H and Shi, Z and Song, C and Sun, F and Sun, Y and Tian, S and Wan, X and Wang, G and Wang, H and Wang, H and Wang, H and Wang, J and Wang, J and Wang, K and Wang, L and Wang, SK and Wang, X and Wang, Y and Xiao, Z and Xing, H and Xu, Y and Yan, SY and Yang, L and Yang, S and Yang, Y and Yao, X and Yousuf, S and Yu, H and Lei, Y and Yuan, Z and Zeng, M and Zhang, C and Zhang, C and Zhang, H and Zhang, J and Zhang, N and Zhang, T and Zhang, YB and Zhang, Y and Zhang, Z and Zhou, M and Zhou, Y and Zhu, C and Zhu, L and Zhu, Y and Zhu, Z and Zou, H and Zuo, A and Dong, W and Wen, T and Chen, S and Li, G and Gao, Y and Liu, YX}, title = {EasyMetagenome: A user-friendly and flexible pipeline for shotgun metagenomic analysis in microbiome research.}, journal = {iMeta}, volume = {4}, number = {1}, pages = {e70001}, pmid = {40027489}, issn = {2770-596X}, abstract = {Shotgun metagenomics has become a pivotal technology in microbiome research, enabling in-depth analysis of microbial communities at both the high-resolution taxonomic and functional levels. This approach provides valuable insights of microbial diversity, interactions, and their roles in health and disease. However, the complexity of data processing and the need for reproducibility pose significant challenges to researchers. To address these challenges, we developed EasyMetagenome, a user-friendly pipeline that supports multiple analysis methods, including quality control and host removal, read-based, assembly-based, and binning, along with advanced genome analysis. The pipeline also features customizable settings, comprehensive data visualizations, and detailed parameter explanations, ensuring its adaptability across a wide range of data scenarios. Looking forward, we aim to refine the pipeline by addressing host contamination issues, optimizing workflows for third-generation sequencing data, and integrating emerging technologies like deep learning and network analysis, to further enhance microbiome insights and data accuracy. EasyMetageonome is freely available at https://github.com/YongxinLiu/EasyMetagenome.}, }
@article {pmid40025088, year = {2025}, author = {Kim, SY and Cheon, S and Park, C and Soh, HY}, title = {Integrating DNA metabarcoding and morphological analysis improves marine zooplankton biodiversity assessment.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {7283}, pmid = {40025088}, issn = {2045-2322}, support = {RS-2018-KS181192//Korea Institute of Marine Science &amp; Technology Promotion (KIMST) funded by the Ministry of Oceans and Fisheries, Korea/ ; No. RS-2024-00442775)//Global-Learning &amp; Academic research institution for Master's &#xb7; PhD students, and Postdocs (LAMP) Program of the National Research Foundation of Korea (NRF) grant funded by the Ministry of Education/ ; Grant number: 2018-3416//Chonnam National University/ ; }, mesh = {Animals ; *Zooplankton/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; *Biodiversity ; *Copepoda/genetics/classification ; Ecosystem ; China ; Oceans and Seas ; }, abstract = {Marine copepod communities play crucial roles in ocean ecosystems. However, their accurate assessment remains challenging due to taxonomic complexities. This study combines morphological and DNA metabarcoding approaches to evaluate copepod diversity and community structure in the northern East China Sea. Zooplankton samples were collected from 10 stations along a coastal-offshore gradient in August 2019. Morphological analysis identified 34 species from 25 genera, while DNA metabarcoding detected 31 species from 20 genera. Both methods revealed distinct coastal and offshore assemblages, with Paracalanus parvus s.l. as the dominant species across all stations. A significant positive correlation was found between morphology-based individual counts and metabarcoding sequence reads (Spearman's Rho = 0.58, p < 0.001), improving at the genus level (Rho = 0.70, p < 0.001). Redundancy analysis revealed that salinity, temperature, and phytoplankton density significantly influenced copepod distribution. Although both approaches captured similar broad-scale patterns, they provided complementary insights into community structure. Morphological identification was more effective for detecting Cyclopoida diversity, whereas DNA metabarcoding had greater sensitivity for specific Calanoid species. This study underscores the value of integrating traditional and molecular methods for marine biodiversity assessment, especially in the context of global environmental changes.}, }
@article {pmid40023237, year = {2025}, author = {Munteanu, A and Bortolini, M and Feltracco, M and Alterio, A and Cairns, WRL and Turetta, C and Barbaro, E and Barbante, C and Gambaro, A and Azzaro, M}, title = {Contamination by benzothiazoles in the Arctic: First evidence in the seawater of the Greenland Sea.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {371}, number = {}, pages = {125943}, doi = {10.1016/j.envpol.2025.125943}, pmid = {40023237}, issn = {1873-6424}, mesh = {*Benzothiazoles/analysis ; *Seawater/chemistry ; *Water Pollutants, Chemical/analysis ; *Environmental Monitoring ; Greenland ; Arctic Regions ; Water Pollution, Chemical/statistics &amp; numerical data ; }, abstract = {Benzothiazoles (BTHs), used in industrial chemistry, consumer products, and pharmaceuticals, are emerging contaminants due to their environmental presence and toxicological risks to aquatic life and human health. However, their environmental fate in seawater remains poorly investigated. This study reports for the first time the occurrence and distribution of six BTHs in the sub-Arctic seawater of the Greenland Sea. Using solid-phase extraction combined with ultrahigh performance liquid chromatography tandem mass spectrometry, total BTHs were detected at concentrations ranging from 0.2 to 1043 ng L[-1]. Benzothiazole, 2-hydroxy-benzothiazole, 2-methylthio-benzothiazole, and 2-methyl-benzothiazole exhibited higher mean concentrations (355 ± 335, 114 ± 80, 34 ± 7, 15 ± 8 ng L[-1], respectively) compared to 2-thiocyanomethylthio-benzothiazole (0.5 ± 0.9 ng L[-1]) and 2-amino-benzothiazole (0.3 ± 0.2 ng L[-1]). Local emissions and both short- and long-range transport may account for BTHs presence in the Greenland Sea. The spatial distribution of BTHs along the 75° N transect and in the water column appears influenced by the Greenland Sea Gyre circulation and deep convection processes. Total BTHs distribution showed no significant differences between superficial and water column concentrations or between the outermost and innermost transect zones, as determined by the Mann-Whitney test, although concentrations were generally higher in the zone influenced by the Norwegian Atlantic Current. The ecological risks of BTHs, assessed using the risk quotient methodology, indicate a low threat to aquatic life. This research underscores the need for monitoring BTHs in the Arctic to understand their sources, transport, and environmental fate, providing a foundation for future studies.}, }
@article {pmid40022802, year = {2025}, author = {Wang, H and Liu, C and Li, L and Kong, Y and Akbar, A and Zhou, X}, title = {High-precision inversion of urban river water quality via integration of riparian spatial structures and river spectral signatures.}, journal = {Water research}, volume = {278}, number = {}, pages = {123378}, doi = {10.1016/j.watres.2025.123378}, pmid = {40022802}, issn = {1879-2448}, mesh = {*Rivers/chemistry ; *Water Quality ; *Environmental Monitoring/methods ; Phosphorus/analysis ; Remote Sensing Technology ; Urbanization ; Cities ; China ; }, abstract = {With the ongoing process of urbanization, it poses challenges to the monitoring of water quality in urban rivers. The mainstream methods for remote sensing water quality monitoring rely on the optical characteristics of water to achieve water quality inversion, while overlooking the correlation between water quality and riparian zones. The spatial arrangement and scale fluctuation of the riparian zones exert a substantial influence on water quality as it serves as an intermediary region connecting riverine and terrestrial ecosystems. Therefore, this study firstly employed unmanned aerial vehicle (UAV)-borne multispectral remote sensing technology to capture the subtle variations in urban river water quality and obtain detailed spatial information of the riparian zone. The Liang-Kleeman information flow was subsequently employed to quantitatively assess the causal responses of the spatial composition of riparian zone to water quality parameters across various spatial scales. Finally, we developed a hierarchical ensemble learning model for water quality assessment by integrating the spatial characteristics of the riparian zone with the spectral properties of the water body. The result demonstrates that this model accurately delineated water quality grades for three key parameters: ammonia nitrogen (NH3N), chemical oxygen demand (COD), and total phosphorus (TP), achieving accuracies of 94.87 %, 92.31 %, and 89.74 %, respectively. Our study presents a water quality inversion method for urban rivers, which holds significant guidance for the monitoring and management of urban rivers and contributes to further promoting the sustainable development of cities.}, }
@article {pmid40021550, year = {2025}, author = {Post, AK and Richardson, AD}, title = {Predicting end-of-season timing across diverse North American grasslands.}, journal = {Oecologia}, volume = {207}, number = {3}, pages = {44}, pmid = {40021550}, issn = {1432-1939}, support = {EF-1065029//National Science Foundation/ ; EF-1702697//National Science Foundation/ ; DESC0016011//U.S. Department of Energy/ ; }, mesh = {*Grassland ; *Seasons ; *Climate Change ; North America ; Ecosystem ; }, abstract = {Climate change is altering the timing of seasonal vegetation cycles (phenology), with cascading consequences on larger ecosystem processes. Therefore, understanding the drivers of vegetation phenology is critical to predicting ecological impacts of climate change. While numerous phenology models exist to predict the timing of the start of the growing season (SOS), there are fewer end-of-season (EOS) models, and most perform poorly in grasslands, since they were made for forests. Our objective was to develop an improved EOS grassland phenology model. We used repeat digital imagery from the PhenoCam Network to extract EOS dates for 44 diverse North American grassland sites (212 site-years) that we fit to 20 new and 3 existing EOS models. All new EOS models (RMSE = 22-33 days between observed and predicted dates) performed substantially better than existing ones (RMSE = 43-46 days). The top model predicted EOS after surpassing a threshold of either accumulated cold temperatures or dryness, but only after a certain number of days following SOS. Including SOS date improved all model fits, indicating a strong correlation between start- and end-of-season timing. Model performance was further improved by independently optimizing parameters for six distinct climate regions (RMSE = 4-19 days). While the best model varied slightly by region, most included similar drivers as the top all-sites model. Thus, across diverse grassland sites, EOS is influenced by both weather (temperature, moisture) and SOS timing. Incorporating these new EOS models into Earth System Models should improve predictions of grassland dynamics and associated ecosystem processes.}, }
@article {pmid40017036, year = {2025}, author = {Han, Y and Du, Q and Dai, Y and Gu, S and Lei, M and Liu, W and Zhang, W and Zhu, M and Feng, L and Si, H and Liu, J and Zan, Y}, title = {EasyOmics: A graphical interface for population-scale omics data association, integration, and visualization.}, journal = {Plant communications}, volume = {6}, number = {5}, pages = {101293}, pmid = {40017036}, issn = {2590-3462}, mesh = {*Software ; *Genomics/methods ; Genome-Wide Association Study ; *Computational Biology/methods ; User-Computer Interface ; Computer Graphics ; Quantitative Trait Loci ; Proteomics ; Metabolomics ; }, abstract = {The rapid growth of population-scale whole-genome resequencing, RNA sequencing, bisulfite sequencing, and metabolomic and proteomic profiling has led quantitative genetics into the era of big omics data. Association analyses of omics data, such as genome-, transcriptome-, proteome-, and methylome-wide association studies, along with integrative analyses of multiple omics datasets, require various bioinformatics tools, which rely on advanced programming skills and command-line interfaces and thus pose challenges for wet-lab biologists. Here, we present EasyOmics, a stand-alone R Shiny application with a user-friendly interface that enables wet-lab biologists to perform population-scale omics data association, integration, and visualization. The toolkit incorporates multiple functions designed to meet the increasing demand for population-scale omics data analyses, including data quality control, heritability estimation, genome-wide association analysis, conditional association analysis, omics quantitative trait locus mapping, omics-wide association analysis, omics data integration, and visualization. A wide range of publication-quality graphs can be prepared in EasyOmics by pointing and clicking. EasyOmics is a platform-independent software that can be run under all operating systems, with a docker container for quick installation. It is freely available to non-commercial users at Docker Hub https://hub.docker.com/r/yuhan2000/easyomics.}, }
@article {pmid40016792, year = {2025}, author = {Mendoza, JN and Prūse, B and Ciriaco, A and Mendoza, A and Ciriaco, H and Buen, C and Pua, JJ and Primavera, F and Mattalia, G and Sõukand, R}, title = {Correction: Fishery and ecology-related knowledge about plants among fishing communities along Laguna Lake, Philippines.}, journal = {Journal of ethnobiology and ethnomedicine}, volume = {21}, number = {1}, pages = {11}, doi = {10.1186/s13002-025-00763-7}, pmid = {40016792}, issn = {1746-4269}, }
@article {pmid40014700, year = {2025}, author = {Chen, Z and Baeza, JA and Chen, C and Gonzalez, MT and González, VL and Greve, C and Kocot, KM and Arbizu, PM and Moles, J and Schell, T and Schwabe, E and Sun, J and Wong, NLWS and Yap-Chiongco, M and Sigwart, JD}, title = {A genome-based phylogeny for Mollusca is concordant with fossils and morphology.}, journal = {Science (New York, N.Y.)}, volume = {387}, number = {6737}, pages = {1001-1007}, doi = {10.1126/science.ads0215}, pmid = {40014700}, issn = {1095-9203}, mesh = {Animals ; Biological Evolution ; *Fossils ; *Genome ; *Mollusca/genetics/anatomy &amp; histology/classification ; Phylogeny ; }, abstract = {Extreme morphological disparity within Mollusca has long confounded efforts to reconstruct a stable backbone phylogeny for the phylum. Familiar molluscan groups-gastropods, bivalves, and cephalopods-each represent a diverse radiation with myriad morphological, ecological, and behavioral adaptations. The phylum further encompasses many more unfamiliar experiments in animal body-plan evolution. In this work, we reconstructed the phylogeny for living Mollusca on the basis of metazoan BUSCO (Benchmarking Universal Single-Copy Orthologs) genes extracted from 77 (13 new) genomes, including multiple members of all eight classes with two high-quality genome assemblies for monoplacophorans. Our analyses confirm a phylogeny proposed from morphology and show widespread genomic variation. The flexibility of the molluscan genome likely explains both historic challenges with their genomes and their evolutionary success.}, }
@article {pmid40012989, year = {2024}, author = {Boyes, D and Holland, PWH and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Olive Crescent, Trisateles emortualis (Denis &amp; Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {178}, pmid = {40012989}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Trisateles emortualis (the Olive Crescent; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 565.5 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.01 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,176 protein coding genes.}, }
@article {pmid40012987, year = {2024}, author = {McGregor, AP and Sumner-Rooney, L and Burkmar, R and Schoenauer, A and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the silver stretch spider, Tetragnatha montana (Simon, 1874) (Araneae: Tetragnathidae).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {288}, pmid = {40012987}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Tetragnatha montana (the silver stretch spider; Arthropoda; Arachnida; Araneae; Tetragnathidae). The genome sequence is 784.7 megabases in span. Most of the assembly is scaffolded into 13 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 15.49 kilobases in length.}, }
@article {pmid40011724, year = {2025}, author = {Brodie, JF and Mohd-Azlan, J and Chen, C and Wearn, OR and Deith, MCM and Ball, JGC and Slade, EM and Burslem, DFRP and Teoh, SW and Williams, PJ and Nguyen, A and Moore, JH and Goetz, SJ and Burns, P and Jantz, P and Hakkenberg, CR and Kaszta, Z and Cushman, S and Coomes, D and Helmy, OE and Reynolds, G and Rodríguez, JP and Jetz, W and Luskin, MS}, title = {Reply to: Causal claims, causal assumptions and protected area impact.}, journal = {Nature}, volume = {638}, number = {8052}, pages = {E42-E44}, pmid = {40011724}, issn = {1476-4687}, }
@article {pmid40007820, year = {2024}, author = {Grieco, F and Parisi, S and Simmenroth, A and Eichinger, M and Zirkel, J and König, S and Jünger, J and Geck, E and Schwienhorst-Stich, EM}, title = {Planetary health education in undergraduate medical education in Germany: results from structured interviews and an online survey within the national PlanetMedEd Project.}, journal = {Frontiers in medicine}, volume = {11}, number = {}, pages = {1507515}, pmid = {40007820}, issn = {2296-858X}, abstract = {BACKGROUND: In light of the accumulating evidence, awareness and urgency to act upon the three planetary crises - climate change, biodiversity loss, and pollution - the concept of Planetary Health underscores their profound implications for health and promotes actionable solutions to advance both wellbeing and ecological sustainability. Despite (inter)national calls to integrate Planetary Health into health workers' curricula, the current status of Planetary Health Education in undergraduate medical education in Germany is unclear. This study therefore aimed (a) to assess the current implementation of Planetary Health in undergraduate medical education in Germany and (b) to explore its characteristics as a foundation to develop evidence-informed recommendations for mainstreaming Planetary Health Education in medical schools in Germany.<br><br>METHODS: The study comprised structured interviews followed by an online survey, both targeting all 39 medical schools in Germany. In 2021, structured interviews were conducted with students, educators and deanery staff at medical schools. In 2023, educators and deanery staff participated in an online survey based on the findings from the interviews.<br><br>FINDINGS: In total, 80% of the 39 medical schools participated in the interviews, while 90% took part in the online survey. Based on integrated findings, 35 medical schools (90%) offered Planetary Health Education, with a median of two educational activities, including both stand-alone courses and lectures integrated into other courses. Despite an overall increase since winter semester 2021/2022, most educational activities were electives and not part of the mandatory curriculum. Innovative educational approaches and learning objectives differed significantly between mandatory and elective formats. In contrast to mandatory educational activities, student involvement was reported for the majority of electives and was significantly associated with transformative learning objectives.<br><br>INTERPRETATION: Despite a steady rise in teaching activities, mandatory Planetary Health Education remains insufficiently integrated into undergraduate medical education in Germany. Key criteria defining high-quality Planetary Health Education, such as innovative educational approaches, practical skills, and transformative learning, were primarily reflected in electives, that reach only a minority of students. To adequately equip the future healthcare workforce, the current barriers to successfully integrating Planetary Health into medical education must be systematically addressed and overcome.}, }
@article {pmid40007688, year = {2025}, author = {Boyes, D and Lees, DC and Coates, BS and ,  and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the European Corn Borer, Ostrinia nubilalis Hübner, 1796.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {12}, pmid = {40007688}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female specimen of Ostrinia nubilalis (European Corn Borer; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence has a total length of 495.50 megabases. Most of the assembly (99.87%) is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.24 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,780 protein-coding genes.}, }
@article {pmid40007687, year = {2025}, author = {Boyes, D and Lewis, OT and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of Red Underwing, Catocala nupta Linnaeus, 1767.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {36}, pmid = {40007687}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female specimen of Catocala nupta (Red Underwing; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence has a total length of 930.40 megabases. Most of the assembly (99.82%) is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.57 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,889 protein-coding genes.}, }
@article {pmid40004070, year = {2025}, author = {Brzhozovskiy, AG and Semenov, SD and Zherebker, AY and Bugrova, AE and Yurova, MN and Zhernov, YV and Kovaleva, OA and Semenov, AL and Abroskin, DP and Kruglov, SS and Fedoros, EI and Kononikhin, AS and Nikolaev, EN}, title = {Hepatoprotective Activity of Nature-Derived Polyphenols Studied by Mass Spectrometry Based Multi-OMICS Approach.}, journal = {International journal of molecular sciences}, volume = {26}, number = {4}, pages = {}, pmid = {40004070}, issn = {1422-0067}, support = {22-75-10140//Russian Science Foundation/ ; }, mesh = {Animals ; *Polyphenols/pharmacology/chemistry ; Mice ; Metabolomics/methods ; Proteomics/methods ; *Liver/drug effects/metabolism/pathology ; Mice, Inbred BALB C ; Mass Spectrometry/methods ; *Protective Agents/pharmacology/chemistry ; Pueraria/chemistry ; Carbon Tetrachloride/toxicity ; Metabolome/drug effects ; Male ; Plant Extracts/pharmacology/chemistry ; Disease Models, Animal ; Chemical and Drug Induced Liver Injury/metabolism/drug therapy ; Plant Roots/chemistry ; Multiomics ; }, abstract = {The aim of this study was to examine the hepatoprotective activity of multicomponent mixtures of natural origin in the BALB/C mouse model, with subacute liver failure (SALF) induced by the administration of toxin carbon tetrachloride (CCl4). The hepatoprotective activity of activated hydrolytic lignin (BP-Cx-1), humic acid peloids (HA), and isoflavones from kudzu Pueraria lobata roots (IFL) was evaluated using mass spectrometry (MS)-based omics technologies. Our MS-based approach revealed new insights into the molecular mechanisms of the hepatoprotective activity of multicomponent mixtures of natural origin. Significant differences were observed in the proteome and metabolome profiles of the urine and liver of BALB/c mice with SALF between a control group with CCl4 administration, intact controls, and groups receiving potential hepatoprotectors of natural origin (BP-Cx-1, HA, IFL). Proteomic and metabolomics analyses demonstrated that among the hepatoprotectors, IFL possessed the highest hepatoprotective potential, which correlated well with the relative effectiveness of the drugs recorded during in vitro studies. These results correlate with the relative effectiveness of the drugs recorded in previous in vitro and in vivo studies. The leading IFL activity may be attributed to a higher content of active polyphenolic components compared to heterogeneous HA and BP-Cx-1. Enrichment with active components by fractionation is a direction that can be explored for developing hepatoprotective agents based on natural complex polyphenols.}, }
@article {pmid39996333, year = {2025}, author = {Medeiros, W and Kralova, S and Oliveira, V and Ziemert, N and Sehnal, L}, title = {Antarctic bacterial natural products: from genomic insights to drug discovery.}, journal = {Natural product reports}, volume = {42}, number = {5}, pages = {774-787}, doi = {10.1039/d4np00045e}, pmid = {39996333}, issn = {1460-4752}, mesh = {*Biological Products/chemistry/pharmacology/metabolism ; Antarctic Regions ; *Drug Discovery ; *Bacteria/genetics/chemistry/metabolism ; Genomics ; Molecular Structure ; }, abstract = {Covering: up to the end of 2024Microbial life dominates the extreme continent Antarctica, playing a pivotal role in ecosystem functioning and serving as a reservoir of specialized metabolites known as natural products (NPs). NPs not only contribute to microbial adaptation to harsh conditions but also modulate microbial community structure. Long-term isolation and environmental pressures have shaped the genomes of Antarctic bacteria, suggesting that they also encode unique NPs. Since NPs are also an important source of drugs, we argue that investigating Antarctic bacterial NPs is essential not only for understanding their ecological role and evolution, but also for discovering new chemical structures, biosynthetic mechanisms, and potential new drugs. Yet, despite advances in omics technologies and increased scientific activities in Antarctica, relatively few new bacterial NPs have been discovered. The lack of systematic research activities focused on the exploration of Antarctic bacteria and their NPs constitutes a big problem considering the climate change issue, to which ecosystems in polar regions are the most sensitive areas on the Earth. Here, we highlight the currently available data on Antarctic bacteria, their biosynthetic potential, and the successful NP discoveries, while addressing the challenges in NP research and advocating for systematic, collaborative efforts aligned with the Antarctic Treaty System and the Antarctic Conservation Biogeographic Regions.}, }
@article {pmid39995465, year = {2025}, author = {Huang, J and Bibri, SE and Keel, P}, title = {Generative spatial artificial intelligence for sustainable smart cities: A pioneering large flow model for urban digital twin.}, journal = {Environmental science and ecotechnology}, volume = {24}, number = {}, pages = {100526}, pmid = {39995465}, issn = {2666-4984}, abstract = {Rapid urbanization, alongside escalating resource depletion and ecological degradation, underscores the critical need for innovative urban development solutions. In response, sustainable smart cities are increasingly turning to cutting-edge technologies-such as Generative Artificial Intelligence (GenAI), Foundation Models (FMs), and Urban Digital Twin (UDT) frameworks-to transform urban planning and design practices. These transformative tools provide advanced capabilities to analyze complex urban systems, optimize resource management, and enable evidence-based decision-making. Despite recent progress, research on integrating GenAI and FMs into UDT frameworks remains scant, leaving gaps in our ability to capture complex urban flows and multimodal dynamics essential to achieving environmental sustainability goals. Moreover, the lack of a robust theoretical foundation and real-world operationalization of these tools hampers comprehensive modeling and practical adoption. This study introduces a pioneering Large Flow Model (LFM), grounded in a robust foundational framework and designed with GenAI capabilities. It is specifically tailored for integration into UDT systems to enhance predictive analytics, adaptive learning, and complex data management functionalities. To validate its applicability and relevance, the Blue City Project in Lausanne City is examined as a case study, showcasing the ability of the LFM to effectively model and analyze urban flows-namely mobility, goods, energy, waste, materials, and biodiversity-critical to advancing environmental sustainability. This study highlights how the LFM addresses the spatial challenges inherent in current UDT frameworks. The LFM demonstrates its novelty in comprehensive urban modeling and analysis by completing impartial city data, estimating flow data in new locations, predicting the evolution of flow data, and offering a holistic understanding of urban dynamics and their interconnections. The model enhances decision-making processes, supports evidence-based planning and design, fosters integrated development strategies, and enables the development of more efficient, resilient, and sustainable urban environments. This research advances both the theoretical and practical dimensions of AI-driven, environmentally sustainable urban development by operationalizing GenAI and FMs within UDT frameworks. It provides sophisticated tools and valuable insights for urban planners, designers, policymakers, and researchers to address the complexities of modern cities and accelerate the transition towards sustainable urban futures.}, }
@article {pmid39995103, year = {2025}, author = {Campbell, IH and Needham, N and Grossi, H and Kamenska, I and Luz, S and Sheehan, S and Thompson, G and Thrippleton, MJ and Gibbs, MC and Leitao, J and Moses, T and Burgess, K and Rigby, BP and Simpson, SA and McIntosh, E and Brown, R and Meadowcroft, B and Creasy, F and Mitchell-Grigorjeva, M and Norrie, J and McLellan, A and Fisher, C and Zieliński, T and Gaggioni, G and Campbell, H and Smith, DJ}, title = {A pilot study of a ketogenic diet in bipolar disorder: clinical, metabolic and magnetic resonance spectroscopy findings.}, journal = {BJPsych open}, volume = {11}, number = {2}, pages = {e34}, pmid = {39995103}, issn = {2056-4724}, abstract = {BACKGROUND: Preliminary evidence suggests that a ketogenic diet may be effective for bipolar disorder.<br><br>AIMS: To assess the impact of a ketogenic diet in bipolar disorder on clinical, metabolic and magnetic resonance spectroscopy outcomes.<br><br>METHOD: Euthymic individuals with bipolar disorder (N = 27) were recruited to a 6- to 8-week single-arm open pilot study of a modified ketogenic diet. Clinical, metabolic and MRS measures were assessed before and after the intervention.<br><br>RESULTS: Of 27 recruited participants, 26 began and 20 completed the ketogenic diet. For participants completing the intervention, mean body weight fell by 4.2 kg (P < 0.001), mean body mass index fell by 1.5 kg/m[2] (P < 0.001) and mean systolic blood pressure fell by 7.4 mmHg (P < 0.041). The euthymic participants had average baseline and follow-up assessments consistent with them being in the euthymic range with no statistically significant changes in Affective Lability Scale-18, Beck Depression Inventory and Young Mania Rating Scale. In participants providing reliable daily ecological momentary assessment data (n = 14), there was a positive correlation between daily ketone levels and self-rated mood (r = 0.21, P < 0.001) and energy (r = 0.19 P < 0.001), and an inverse correlation between ketone levels and both impulsivity (r = -0.30, P < 0.001) and anxiety (r = -0.19, P < 0.001). From the MRS measurements, brain glutamate plus glutamine concentration decreased by 11.6% in the anterior cingulate cortex (P = 0.025) and fell by 13.6% in the posterior cingulate cortex (P = <0.001).<br><br>CONCLUSIONS: These findings suggest that a ketogenic diet may be clinically useful in bipolar disorder, for both mental health and metabolic outcomes. Replication and randomised controlled trials are now warranted.}, }
@article {pmid39990470, year = {2025}, author = {Edwards, SV and Fang, B and Khost, D and Kolyfetis, GE and Cheek, RG and DeRaad, DA and Chen, N and Fitzpatrick, JW and McCormack, JE and Funk, WC and Ghalambor, CK and Garrison, E and Guarracino, A and Li, H and Sackton, TB}, title = {Comparative population pangenomes reveal unexpected complexity and fitness effects of structural variants.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39990470}, issn = {2692-8205}, support = {R01 GM123489/GM/NIGMS NIH HHS/United States ; R01 HG011485/HG/NHGRI NIH HHS/United States ; R35 GM133412/GM/NIGMS NIH HHS/United States ; U01 DA047638/DA/NIDA NIH HHS/United States ; }, abstract = {Structural variants (SVs) are widespread in vertebrate genomes, yet their evolutionary dynamics remain poorly understood. Using 45 long-read de novo genome assemblies and pangenome tools, we analyze SVs within three closely related species of North American jays (Aphelocoma, scrub-jays) displaying a 60-fold range in effective population size. We find rapid evolution of genome architecture, including ~100 Mb variation in genome size driven by dynamic satellite landscapes with unexpectedly long (> 10 kb) repeat units and widespread variation in gene content, influencing gene expression. SVs exhibit slightly deleterious dynamics modulated by variant length and population size, with strong evidence of adaptive fixation only in large populations. Our results demonstrate how population size shapes the distribution of SVs and the importance of pangenomes to characterizing genomic diversity.}, }
@article {pmid39990132, year = {2025}, author = {Keet, JH and Hui, C}, title = {One-hectare fine-scale dataset of a fynbos plant community in the Cape Floristic Region.}, journal = {Data in brief}, volume = {59}, number = {}, pages = {111334}, pmid = {39990132}, issn = {2352-3409}, abstract = {Cape fynbos, which forms part of the Cape Floristic Region (CFR) of South Africa, a global biodiversity hotspot, is renowned for its high levels of plant species endemism and diversity. This extraordinary ecosystem, characterised by nutrient-poor soils and fire-adapted vegetation, is a treasure trove of endemic flora. However, this fragile system faces increasing threats from habitat loss, climate change, and invasive species. Pristine fynbos, naturally high in plant diversity and which forms a large part of the CFR, presents an ideal opportunity to gather fine-scale data on community assembly patterns. Most fynbos vegetation surveys use a plot size of about 100 m[2], with no spatial structures within plots to demarcate individual subplots. Here, a groundbreaking dataset is presented that fully covers 1-hectare of pristine fynbos, systematically gridded into 50 × 50 subplots, each measuring 2 × 2 m, arranged evenly within a square-shaped survey site. Each plot was assigned a unique Y-X coordinate combination. For each plot, all plant species present were recorded, along with their total percentage covers and maximum height values. Total percentage covers were also recorded for bare soil, rock, and termite mounds. This dataset provides a valuable contribution to the field of fynbos ecology, as well as plant community ecology in general, and establishes a benchmark for future one-hectare surveys of similar fynbos vegetation types, delineating the fine-scale composition and structure of fynbos in the CFR. The dataset will be useful for a wide audience, including community and spatial ecologists, plant and environmental scientists, and biodiversity informaticians and statistical ecologists, offering ideal data for testing new metrics of diversity and compositional turnover.}, }
@article {pmid39987271, year = {2025}, author = {Wuyun, D and Sun, L and Chen, Z and Li, Y and Han, M and Shi, Z and Ren, T and Zhao, H}, title = {A 10-meter resolution dataset of abandoned and reclaimed cropland from 2016 to 2023 in Inner Mongolia, China.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {317}, pmid = {39987271}, issn = {2052-4463}, abstract = {Amid growing global food security concerns and frequent armed conflicts, real-time monitoring of abandoned cropland is essential for strategic planning and crisis management. This study develops a method to map abandoned cropland accurately, crucial for maintaining the food supply chain and ecological balance. Utilizing Sentinel-1/2 satellite data, we employed multi-feature stacking and machine learning to create the ARCC10-IM (Abandoned and Reclaimed Cropland Classification at 10-meter resolution in Inner Mongolia) dataset, which tracks annual cropland activity. A novel temporal segmentation algorithm was developed to extract cropland abandonment and reclamation patterns annually, using sliding time windows over several years. This research differentiates cropland states-active cultivation, unstable fallowing, continuous abandonment, and reclamation-providing continuous, regional-scale maps with 10-meter resolution. ARCC10-IM is crucial for land planning, environmental monitoring, and agricultural management in arid areas like Inner Mongolia, enhancing decision-making and technology in land use tracking.}, }
@article {pmid39986902, year = {2025}, author = {Lee, S and Kaufmann, CN and Lippi, CA and Ryan, SJ and Guo, Y}, title = {Untreated insomnia as a contributor to geographic disparities in risk for Alzheimer's disease and related dementias.}, journal = {Sleep health}, volume = {11}, number = {2}, pages = {131-132}, pmid = {39986902}, issn = {2352-7226}, support = {K01 AG061239/AG/NIA NIH HHS/United States ; R01 AG079391/AG/NIA NIH HHS/United States ; R01 HL163226/HL/NHLBI NIH HHS/United States ; R56 AG065251/AG/NIA NIH HHS/United States ; }, }
@article {pmid39982558, year = {2025}, author = {Li, L and Gupta, A and Zhu, C and Xu, K and Watanabe, Y and Tanaka, M and Seki, M and Mochida, K and Kanno, Y and Seo, M and Nguyen, KH and Tran, CD and Chu, HD and Yin, H and Jia, KP and Tran, LP and Yin, X and Li, W}, title = {Strigolactone and karrikin receptors regulate phytohormone biosynthetic and catabolic processes.}, journal = {Plant cell reports}, volume = {44}, number = {3}, pages = {60}, pmid = {39982558}, issn = {1432-203X}, support = {XDA28110100//State Key Laboratory of Microbial Resources, Chinese Academy of Sciences/ ; 2022YFD1500505//National Key Research and Development Program of China/ ; 32370321//Natural Science Foundation of Jilin Province/ ; }, mesh = {*Furans/metabolism ; *Pyrans/metabolism ; *Lactones/metabolism ; *Heterocyclic Compounds, 3-Ring/metabolism ; *Plant Growth Regulators/genetics/metabolism ; Metabolism ; Gene Expression Regulation, Plant ; *Arabidopsis Proteins/genetics/metabolism ; Gene Expression Profiling ; Abscisic Acid/metabolism ; Indoleacetic Acids/metabolism ; Cyclopentanes/metabolism ; Genes, Plant ; *Arabidopsis/genetics/metabolism ; Genotype ; Cytokinins/genetics/metabolism ; Receptors, Cell Surface ; Hydrolases ; Oxylipins ; }, abstract = {Karrikin plays a more critical role in affecting the homeostasis of ABA and cytokinins, while strigolactones play a more critical role in influencing the homeostasis of jasmonic acid and gibberellins. Strigolactones (SLs) and karrikins (KARs) regulate plant growth and development through their crosstalk, and through the crosstalk between them and other phytohormones, such as abscisic acid (ABA) and auxin. However, how SL and KAR signaling pathways influence the levels of other phytohormones is still unknown. Here, we performed a comparative transcriptome analysis of the Arabidopsis thaliana double mutant dwarf14 karrikin-insensitive 2 (d14 kai2), deficient in SL and KAR perception, and the wild-type (WT) using their rosette leaves. Ten gene ontology terms related to phytohormones were enriched with differentially expressed genes derived from the 'd14 kai2 vs WT' comparison. Our data revealed that the levels of auxin, ABA and salicylic acid (SA) were higher in d14 and kai2 single and d14 kai2 mutant plants than in WT, which was consistent with the results of previous investigations. In contrast, the levels of cytokinins (CKs) were found to be lower in all single and double mutants than in WT. The levels of active gibberellins were lower in d14 and d14 kai2 mutants than in WT, while they were comparable in kai2 and WT plants. Similarly, the levels of jasmonic acid (JA) were lower in d14 and d14 kai2 plants, but higher in kai2 plants than in WT. Both transcriptome and qRT-PCR analyses indicated that SL and KAR signaling pathways affect the levels of auxin, SA, CKs, gibberellin 4 (GA4) and ABA by influencing the expression of their biosynthetic (in case of auxin, SA, GA4 and CKs) and catabolic (in case of ABA) genes. Collectively, our data demonstrated that KAI2 plays a more critical role in the homeostasis of ABA and CKs, while D14 plays a more critical role in the homeostasis of JA and gibberellins. Findings of this study indicate a complex and broad crosstalk among various phytohormones in plants, which can be considered for future exogenous applications and hormone engineering.}, }
@article {pmid39982516, year = {2025}, author = {Elkin-Frankston, S and McIntyre, J and Brunyé, TT and Gardony, AL and Hancock, CL and O'Donovan, MP and Bode, VG and Miller, EL}, title = {Beyond boundaries: a location-based toolkit for quantifying group dynamics in diverse contexts.}, journal = {Cognitive research: principles and implications}, volume = {10}, number = {1}, pages = {10}, pmid = {39982516}, issn = {2365-7464}, support = {W911QY1920003//U.S. Army Combat Capabilities Development Command Soldier Center/ ; 1934553//National Science Foundation/ ; 1931978//National Science Foundation/ ; }, mesh = {Humans ; *Group Processes ; Military Personnel ; Geographic Information Systems ; Movement/physiology ; Group Dynamics ; }, abstract = {Existing toolkits for analyzing movement dynamics in animal ecology primarily focus on individual or group behavior in habitats without predefined boundaries, while methods for studying human activity often cater to bounded environments, such as team sports played on defined fields. This leaves a gap in tools for modeling and analyzing human group dynamics in large-scale, unbounded, or semi-constrained environments. Examples of such contexts include tourist groups, cycling teams, search and rescue teams, and military units. To address this issue, we survey existing methods and metrics for characterizing individual and collective movement in humans and animals. Using a rich GPS dataset from groups of military personnel engaged in a foot march, we develop a comprehensive, general-purpose toolkit for quantifying group dynamics using location-based metrics during goal-directed movement in open environments. This toolkit includes a repository of Python functions for extracting and analyzing movement data, integrating cognitive factors such as decision-making, situational awareness, and group coordination. By extending location-based analytics to non-traditional domains, this toolkit enhances the understanding of collective movement, group behavior, and emergent properties shaped by cognitive processes. To demonstrate its practical utility, we present a use case utilizing metrics derived from the foot march data to predict group performance during a subsequent strategic and tactical exercise, highlighting the influence of cognitive and decision-making behaviors on team effectiveness.}, }
@article {pmid39982380, year = {2025}, author = {Blumenstiel, JP and Kingan, SB and Garrigan, D and Hill, T and Vedanayagam, J}, title = {Nested likelihood-ratio testing of the nonsynonymous:synonymous ratio suggests greater adaptation in the piRNA machinery of Drosophila melanogaster compared with Drosophila ananassae and Drosophila willistoni, two species with higher repeat content.}, journal = {G3 (Bethesda, Md.)}, volume = {15}, number = {4}, pages = {}, pmid = {39982380}, issn = {2160-1836}, support = {//KU Medical Center Genome Sequencing Facility/ ; P20 GM103638/GM/NIGMS NIH HHS/United States ; UL1TR002366//Frontiers CTSA/ ; NIH U54 HD090216/GF/NIH HHS/United States ; //University of Kansas/ ; R00 GM137077/GM/NIGMS NIH HHS/United States ; S10 OD036343/OD/NIH HHS/United States ; UL1 TR002366/TR/NCATS NIH HHS/United States ; P30 GM145499/GM/NIGMS NIH HHS/United States ; P20GM103418//NIH-NIGMS/KINBRE/ ; DEB1209536//NSF-DDIG/ ; //University of Texas at San Antonio/ ; P20 GM103418/GM/NIGMS NIH HHS/United States ; 1413532//NSF MCB/ ; P20GM103638//NIH-NIGMS/COBRE/ ; R00GM137077//NIH-NIGMS/ ; }, mesh = {Animals ; *RNA, Small Interfering/genetics ; *Drosophila melanogaster/genetics ; DNA Transposable Elements ; Evolution, Molecular ; *Drosophila/genetics ; Likelihood Functions ; *Repetitive Sequences, Nucleic Acid ; *Adaptation, Physiological/genetics ; Piwi-Interacting RNA ; }, abstract = {Numerous studies have revealed a signature of strong adaptive evolution in the piwi-interacting RNA (piRNA) machinery of Drosophila melanogaster, but the cause of this pattern is not understood. Several hypotheses have been proposed. One hypothesis is that transposable element (TE) families and the piRNA machinery are co-evolving under an evolutionary arms race, perhaps due to antagonism by TEs against the piRNA machinery. A related, though not co-evolutionary, hypothesis is that recurrent TE invasion drives the piRNA machinery to adapt to novel TE strategies. A third hypothesis is that ongoing fluctuation in TE abundance leads to adaptation in the piRNA machinery that must constantly adjust between sensitivity for detecting new elements and specificity to avoid the cost of off-target gene silencing. Rapid evolution of the piRNA machinery may also be driven independently of TEs, and instead from other functions such as the role of piRNAs in suppressing sex-chromosome meiotic drive. We sought to evaluate the impact of TE abundance on adaptive evolution of the piRNA machinery in D. melanogaster and 2 species with higher repeat content-Drosophila ananassae and Drosophila willistoni. This comparison was achieved by employing a likelihood-based hypothesis testing framework based on the McDonald-Kreitman test. We show that we can reject a faster rate of adaptive evolution in the piRNA machinery of these 2 species. We propose that the high rate of adaptation in D. melanogaster is either driven by a recent influx of TEs that have occurred during range expansion or selection on other functions of the piRNA machinery.}, }
@article {pmid39981105, year = {2025}, author = {Plaitano, EG and McNeish, D and Bartels, SM and Bell, K and Dallery, J and Grabinski, M and Kiernan, M and Lavoie, HA and Lemley, SM and Lowe, MR and MacKinnon, DP and Metcalf, SA and Onken, L and Prochaska, JJ and Sand, CL and Scherer, EA and Stoeckel, LE and Xie, H and Marsch, LA}, title = {Adherence to a digital therapeutic mediates the relationship between momentary self-regulation and health risk behaviors.}, journal = {Frontiers in digital health}, volume = {7}, number = {}, pages = {1467772}, pmid = {39981105}, issn = {2673-253X}, support = {P30 CA023108/CA/NCI NIH HHS/United States ; UH3 DA041713/DA/NIDA NIH HHS/United States ; P30 DA029926/DA/NIDA NIH HHS/United States ; R37 DA009757/DA/NIDA NIH HHS/United States ; T32 DA037202/DA/NIDA NIH HHS/United States ; }, abstract = {INTRODUCTION: Smoking, obesity, and insufficient physical activity are modifiable health risk behaviors. Self-regulation is one fundamental behavior change mechanism often incorporated within digital therapeutics as it varies momentarily across time and contexts and may play a causal role in improving these health behaviors. However, the role of momentary self-regulation in achieving behavior change has been infrequently examined. Using a novel momentary self-regulation scale, this study examined how targeting self-regulation through a digital therapeutic impacts adherence to the therapeutic and two different health risk behavioral outcomes.<br><br>METHODS: This prospective interventional study included momentary data for 28 days from 50 participants with obesity and binge eating disorder and 50 participants who smoked regularly. An evidence-based digital therapeutic, called Laddr&#x2122;, provided self-regulation behavior change tools. Participants reported on their momentary self-regulation via ecological momentary assessments and health risk behaviors were measured as steps taken from a physical activity tracker and breathalyzed carbon monoxide. Medical regimen adherence was assessed as daily Laddr usage. Bayesian dynamic mediation models were used to examine moment-to-moment mediation effects between momentary self-regulation subscales, medical regimen adherence, and behavioral outcomes.<br><br>RESULTS: In the binge eating disorder sample, the perseverance [&#x3b2; 1&#x2009;=&#x2009;0.17, 95% CI&#x2009;=&#x2009;(0.06, 0.45)] and emotion regulation [&#x3b2; 1&#x2009;=&#x2009;0.12, 95% CI&#x2009;=&#x2009;(0.03, 0.27)] targets of momentary self-regulation positively predicted Laddr adherence on the following day, and higher Laddr adherence was subsequently a positive predictor of steps taken the same day for both perseverance [&#x3b2; 2&#x2009;=&#x2009;0.335, 95% CI&#x2009;=&#x2009;(0.030, 0.717)] and emotion regulation [&#x3b2; 2&#x2009;=&#x2009;0.389, 95% CI&#x2009;=&#x2009;(0.080, 0.738)]. In the smoking sample, the perseverance target of momentary self-regulation positively predicted Laddr adherence on the following day [&#x3b2;&#x2009;=&#x2009;0.91, 95% CI&#x2009;=&#x2009;(0.60, 1.24)]. However, higher Laddr adherence was not a predictor of CO values on the same day [&#x3b2; 2&#x2009;=&#x2009;-0.09, 95% CI&#x2009;=&#x2009;(-0.24, 0.09)].<br><br>CONCLUSIONS: This study provides evidence that a digital therapeutic targeting self-regulation can modify the relationships between momentary self-regulation, medical regimen adherence, and behavioral health outcomes. Together, this work demonstrated the ability to digitally assess the transdiagnostic mediating effect of momentary self-regulation on medical regimen adherence and pro-health behavioral outcomes.<br><br>CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov, identifier (NCT03774433).}, }
@article {pmid39980689, year = {2025}, author = {Su, Z and Liu, L and Zhang, J and Guo, J and Wang, G and Zeng, X}, title = {A scientometric visualization analysis of the gut microbiota and gestational diabetes mellitus.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1485560}, pmid = {39980689}, issn = {1664-302X}, abstract = {BACKGROUND: The prevalence of gestational diabetes mellitus (GDM), a condition that is widespread globally, is increasing. The relationship between the gut microbiota and GDM has been a subject of research for nearly two decades, yet there has been no bibliometric analysis of this correlation. This study aimed to use bibliometrics to explore the relationship between the gut microbiota and GDM, highlighting emerging trends and current research hotspots in this field.<br><br>RESULTS: A total of 394 papers were included in the analysis. China emerged as the preeminent nation in terms of the number of publications on the subject, with 128 papers (32.49%), whereas the United States had the most significant impact, with 4,874 citations. The University of Queensland emerged as the most prolific institution, contributing 18 publications. Marloes Dekker Nitert was the most active author with 16 publications, and Omry Koren garnered the most citations, totaling 154. The journal Nutrients published the most studies (28 publications, 7.11%), whereas PLoS One was the most commonly co-cited journal, with a total of 805 citations. With respect to keywords, research focuses can be divided into 4 clusters, namely, "the interrelationship between the gut microbiota and pregnancy, childbirth," "the relationship between adverse metabolic outcomes and GDM," "the gut microbiota composition and metabolic mechanisms" and "microbiota and ecological imbalance." Key areas of focus include the interactions between the gut microbiota and individuals with GDM, as well as the formation and inheritance of the gut microbiota. Increasing attention has been given to the impact of probiotic supplementation on metabolism and pregnancy outcomes in GDM patients. Moreover, ongoing research is exploring the potential of the gut microbiota as a biomarker for GDM. These topics represent both current and future directions in this field.<br><br>CONCLUSION: This study provides a comprehensive knowledge map of the gut microbiota and GDM, highlights key research areas, and outlines potential future directions.}, }
@article {pmid39980161, year = {2025}, author = {Smith, AR and Mueller, ER and Lewis, CE and Markland, A and Smerdon, C and Smith, AL and Sutcliffe, S and Wyman, JF and Low, LK and Miller, JM and , }, title = {Assessment of Environmental, Sociocultural, and Physiological Influences on Women's Toileting Decisions and Behaviors Using "Where I Go": Pilot Study of a Mobile App.}, journal = {JMIR mHealth and uHealth}, volume = {13}, number = {}, pages = {e56533}, pmid = {39980161}, issn = {2291-5222}, support = {P30 CA046592/CA/NCI NIH HHS/United States ; U24 DK106786/DK/NIDDK NIH HHS/United States ; U01 DK106858/DK/NIDDK NIH HHS/United States ; U01 DK106892/DK/NIDDK NIH HHS/United States ; U01 DK106893/DK/NIDDK NIH HHS/United States ; U01 DK106827/DK/NIDDK NIH HHS/United States ; U01 DK106908/DK/NIDDK NIH HHS/United States ; U01 DK106898/DK/NIDDK NIH HHS/United States ; U01 DK126045/DK/NIDDK NIH HHS/United States ; U01 DK106853/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; Female ; *Mobile Applications/standards/statistics &amp; numerical data ; Adult ; Pilot Projects ; Middle Aged ; Aged ; *Decision Making ; Aged, 80 and over ; Surveys and Questionnaires ; *Urination ; }, abstract = {BACKGROUND: Little is known about women's decisions around toileting for urination and how those decisions influence moment-to-moment behaviors to manage bladder needs. The new smartphone app "Where I Go" captures such nuanced and granular data in real-world environments.<br><br>OBJECTIVE: This study aims to describe participant engagement with "Where I Go", variation in novel parameters collected, and readiness for the data collection tool's use in population-based studies.<br><br>METHODS: "Where I Go" has three components: (1) real-time data, (2) short look-back periods (3-4 h), and (3) event location (GPS recorded at each interaction). The sample size was 44 women. Recording of real-time toileting events and responding to look-back questions was measured over 2 days of data collection. The participant's self-entered location descriptions and the automatic GPS recordings were compared.<br><br>RESULTS: A total of 44 women with an average age of 44 (range 21-85) years interacted with the app. Real-time reporting of at least 1 toileting event per day was high (38/44, 86%, on day 1 and 40/44, 91%, on day 2) with a median of 5 (IQR 3-7 on day 1 and IQR 3-8 on day 2) toileting events recorded each day. Toileting most commonly occurred at home (85/140, 61%, on day 1 and 129/171, 75%, on day 2) due to a need to go (114/140, 66%, on day 1 and 153/171, 74%, on day 2). The most common reasons for delaying toileting were "work duties" (33/140, 21%, on day 1 and 21/171, 11%, on day 2) and "errands or traveling" (19/140, 12%, on day 1 and 19/171, 10%, on day 2). Response to at least 1 look-back notification was similarly high (41/44, 93%, on day 1 and 42/44, 95%, on day 2), with number of responses higher on average on day 2 compared with day 1 (mean on day 1=3.2, 95% CI 3.0-3.5; mean on day 2=4.3, 95% CI 3.9-4.7; P<.001). Median additional toileting events reported on the look-back survey were 1 (IQR 1-2) and 2 (IQR 1-2) on days 1 and 2, respectively. Overall concordance between self-reported location recording and GPS was 76% (188/247). Participants reported lower urge ratings when at home versus away when reporting real-time toileting (median rating 61, IQR 41-84 vs 72, IQR 56-98), and daily fluid intake showed a small to medium positive correlation with toileting frequency (day 1 r=0.3, day 2 r=0.24). Toileting frequency reported in "Where I Go" showed a small positive correlation with the frequency item from the International Consultation on Incontinence Questionnaire (r=0.31 with day 1 toileting frequency and r=0.21 with day 2 toileting frequency).<br><br>CONCLUSIONS: "Where I Go" has potential to increase the understanding of factors that affect women's toileting decisions and long-term bladder health. We anticipate its use as a data collection tool in population-based studies.}, }
@article {pmid39975655, year = {2025}, author = {Gutiérrez, ME and Lahoz-Beltrá, R and Donayre-Torres, AJ}, title = {Editorial: Towards the embedding of artificial intelligence into synthetic organisms: engineering intelligence in microorganisms.}, journal = {Frontiers in genetics}, volume = {16}, number = {}, pages = {1562092}, doi = {10.3389/fgene.2025.1562092}, pmid = {39975655}, issn = {1664-8021}, }
@article {pmid39974046, year = {2025}, author = {Slack, SD and Esquinca, E and Arehart, CH and Boorgula, MP and Szczesny, B and Romero, A and Campbell, M and Chavan, S and Rafaels, N and Watson, H and Landis, RC and Hansel, NN and Rotimi, CN and Olopade, CO and Figueiredo, CA and Ober, C and Liu, AH and Kenny, EE and Kammers, K and Ruczinski, I and Taub, MA and Daya, M and Gignoux, CR and Kechris, K and Barnes, KC and Mathias, RA and Johnson, RK}, title = {Prediction and Characterization of Genetically Regulated Expression of Target Tissues in Asthma.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {39974046}, support = {R01 AI132476/AI/NIAID NIH HHS/United States ; R01 HL104608/HL/NHLBI NIH HHS/United States ; }, abstract = {BACKGROUND: Genetic control of gene expression in asthma-related tissues is not well-characterized, particularly for African-ancestry populations, limiting advancement in our understanding of the increased prevalence and severity of asthma in those populations.<br><br>OBJECTIVE: To create novel transcriptome prediction models for asthma tissues (nasal epithelium and CD4+ T cells) and apply them in transcriptome-wide association study (TWAS) to discover candidate asthma genes.<br><br>METHODS: We developed and validated gene expression prediction databases for unstimulated CD4+ T cells (CD4+T) and nasal epithelium using an elastic net framework. Combining these with existing prediction databases (N=51), we performed TWAS of 9,284 individuals of African-ancestry to identify tissue-specific and cross-tissue candidate genes for asthma. For detailed Methods, please see the Supplemental Methods.<br><br>RESULTS: Novel databases for CD4+T and nasal epithelial gene expression prediction contain 8,351 and 10,296 genes, respectively, including four asthma loci (SCGB1A1, MUC5AC, ZNF366, LTC4S) not predictable with existing public databases. Prediction performance was comparable to existing databases and was most accurate for populations sharing ancestry with the training set (e.g. African ancestry). From TWAS, we identified 17 candidate causal asthma genes (adjusted P<0.1), including genes with tissue-specific (IL33 in nasal epithelium) and cross-tissue (CCNC and FBXW7) effects.<br><br>CONCLUSIONS: Expression of IL33, CCNC, and FBXW7 may affect asthma risk in African ancestry populations by mediating inflammatory responses. The addition of CD4+T and nasal epithelium prediction databases to the public sphere will improve ancestry representation and power to detect novel gene-trait associations from TWAS.}, }
@article {pmid39973193, year = {2025}, author = {Beltran, RS and Kilpatrick, AM and Adamczak, SK and Beumer, LT and Czapanskiy, MF and Davidson, SC and McLean, BS and Mueller, T and Payne, AR and Soria, CD and Weeks, BC and Williams, TM and Salguero-Gómez, R}, title = {Integrating animal tracking and trait data to facilitate global ecological discoveries.}, journal = {The Journal of experimental biology}, volume = {228}, number = {Suppl_1}, pages = {}, pmid = {39973193}, issn = {1477-9145}, support = {IOS 2052497//National Science Foundation/ ; //Office of Naval Research/ ; //David and Lucile Packard Foundation/ ; //Arnold and Mabel Beckman Foundation/ ; //Elysea Fund/ ; NE/X013766/1//Natural Environment Research Council/ ; 101044740//European Union/ ; //University of California/ ; 80NSSC21K1182/NASA/NASA/United States ; }, mesh = {Animals ; *Ecology/methods ; Locomotion ; *Animal Migration ; Databases, Factual ; }, abstract = {Understanding animal movement is at the core of ecology, evolution and conservation science. Big data approaches for animal tracking have facilitated impactful synthesis research on spatial biology and behavior in ecologically important and human-impacted regions. Similarly, databases of animal traits (e.g. body size, limb length, locomotion method, lifespan) have been used for a wide range of comparative questions, with emerging data being shared at the level of individuals and populations. Here, we argue that the proliferation of both types of publicly available data creates exciting opportunities to unlock new avenues of research, such as spatial planning and ecological forecasting. We assessed the feasibility of combining animal tracking and trait databases to develop and test hypotheses across geographic, temporal and biological allometric scales. We identified multiple research questions addressing performance and distribution constraints that could be answered by integrating trait and tracking data. For example, how do physiological (e.g. metabolic rates) and biomechanical traits (e.g. limb length, locomotion form) influence migration distances? We illustrate the potential of our framework with three case studies that effectively integrate trait and tracking data for comparative research. An important challenge ahead is the lack of taxonomic and spatial overlap in trait and tracking databases. We identify critical next steps for future integration of tracking and trait databases, with the most impactful being open and interlinked individual-level data. Coordinated efforts to combine trait and tracking databases will accelerate global ecological and evolutionary insights and inform conservation and management decisions in our changing world.}, }
@article {pmid39973045, year = {2025}, author = {Panayi, P and Contreras, A and Peters, E and Bentall, R and Hardy, A and Berry, K and Sellwood, W and Dudley, R and Longden, E and Underwood, R and Steel, C and Jafari, H and Mason, L and Varese, F}, title = {A temporal network analysis of complex post-traumatic stress disorder and psychosis symptoms.}, journal = {Psychological medicine}, volume = {55}, number = {}, pages = {e43}, pmid = {39973045}, issn = {1469-8978}, support = {2488414//Economic and Social Research Council/ ; NIHR128623//Health Technology Assessment Programme/ ; //NIHR Maudsley Biomedical Research Centre/ ; }, mesh = {Humans ; *Stress Disorders, Post-Traumatic/epidemiology/psychology/physiopathology ; *Psychotic Disorders/epidemiology/psychology/physiopathology ; Male ; Adult ; Female ; Middle Aged ; Young Adult ; Comorbidity ; Ecological Momentary Assessment ; }, abstract = {BACKGROUND: Symptoms of complex post-traumatic stress disorder (cPTSD) may play a role in the maintenance of psychotic symptoms. Network analyses have shown interrelationships between post-traumatic sequelae and psychosis, but the temporal dynamics of these relationships in people with psychosis and a history of trauma remain unclear. We aimed to explore, using network analysis, the temporal order of relationships between symptoms of cPTSD (i.e. core PTSD and disturbances of self-organization [DSOs]) and psychosis in the flow of daily life.<br><br>METHODS: Participants with psychosis and comorbid PTSD (N&#xa0;=&#xa0;153) completed an experience-sampling study involving multiple daily assessments of psychosis (paranoia, voices, and visions), core PTSD (trauma-related intrusions, avoidance, hyperarousal), and DSOs (emotional dysregulation, interpersonal difficulties, negative self-concept) over six consecutive days. Multilevel vector autoregressive modeling was used to estimate three complementary networks representing different timescales.<br><br>RESULTS: Our between-subjects network suggested that, on average over the testing period, most cPTSD symptoms related to at least one positive psychotic symptom. Many average relationships persist in the contemporaneous network, indicating symptoms of cPTSD and psychosis co-occur, especially paranoia with hyperarousal and negative self-concept. The temporal network suggested that paranoia reciprocally predicted, and was predicted by, hyperarousal, negative self-concept, and emotional dysregulation from moment to moment. cPTSD did not directly relate to voices in the temporal network.<br><br>CONCLUSIONS: cPTSD and positive psychosis symptoms mutually maintain each other in trauma-exposed people with psychosis via the maintenance of current threat, consistent with cognitive models of PTSD. Current threat, therefore, represents a valuable treatment target in phased-based trauma-focused psychosis interventions.}, }
@article {pmid39969985, year = {2025}, author = {Zhang, J and Gao, X and Liang, C and Zhang, M and Zhang, S}, title = {Spatiotemporal pattern evolution analysis of ecological networks based on morphological spatial pattern analysis: a case study of Ningbo City, China.}, journal = {Integrated environmental assessment and management}, volume = {21}, number = {3}, pages = {540-554}, doi = {10.1093/inteam/vjaf027}, pmid = {39969985}, issn = {1551-3793}, support = {202148/WT_/Wellcome Trust/United Kingdom ; }, mesh = {China ; *Environmental Monitoring/methods ; Spatio-Temporal Analysis ; *Ecosystem ; Cities ; *Conservation of Natural Resources/methods ; Geographic Information Systems ; Biodiversity ; Urbanization ; }, abstract = {The exponential expansion of urban areas has precipitated a concomitant deterioration in the natural environment. Constructing ecological networks is vital in improving landscape connectivity, protecting biodiversity, and maintaining regional sustainable development. Ningbo, China, was set as the research area. Geographic information system and morphological spatial pattern analysis (MSPA) were used to determine the ecological source area. Subsequently, the corridor design model Linkage Mapper was used to ascertain and assess the linkages between the designated ecological source areas. The results showed that from 2000-2020, there was a large-scale change in land use type in Ningbo, with increasing complexity of patches and landscape fragmentation. The ecological sources of the three periods in Ningbo were primarily situated in the western, southern, and Hangzhou Bay coastal regions, exhibiting an uneven distribution in the eastern and western areas. The number of primary ecological corridors in Ningbo underwent a significant reduction, from 26 to 17, between the years 2000-2020. In terms of the distribution of ecological corridors, the primary corridors were concentrated in the central, southern, and western regions of the study area in 2000. By 2020, however, the primary ecological corridors within the study region were distributed mainly in a southerly direction. The interaction between north and south ecological sources was weakened, which adversely affected the species spread and ecosystem stability. After optimization, 12 ecological corridors and four ecological nodes were incorporated into Ningbo, 67 ecological breakpoints were identified, and four stepping stone patches were added. The study used spatiotemporal change trends, including land use type and landscape pattern, to examine the ecological network of Ningbo. In conclusion, the proposed optimization strategy is aligned with the current urban development context, offering a particularly pertinent reference point for Ningbo's ecological protection initiatives.}, }
@article {pmid39969100, year = {2025}, author = {Miller, L and Beaney, T and Hope, R and Cunningham, M and Robotham, JV and Pouwels, KB and Costelloe, CE}, title = {General practice antibiotic prescriptions attributable to respiratory syncytial virus by age and antibiotic class: an ecological analysis of the English population.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {80}, number = {4}, pages = {1116-1126}, pmid = {39969100}, issn = {1460-2091}, support = {//University of Oxford/ ; NIHR200915//UK Health Security Agency (UKHSA)/ ; //National Institute for Health and Care Research (NIHR) Royal Marsden/ ; //Institute of Cancer Research Biomedical Research Centre/ ; //Healthcare Associated Infections and Antimicrobial Resistance/ ; 2016-10-95//NIHR/ ; MRF-145-0004-TPG-AVISO//Medical Research Foundation National PhD Training Programme in Antimicrobial Resistance Research/ ; /WT_/Wellcome Trust/United Kingdom ; //National Institute for Health Research Health Protection Research Unit (NIHR HPRU)/ ; //National Institute for Health Research Health Protection Research Unit/ ; }, mesh = {Humans ; *Anti-Bacterial Agents/therapeutic use/classification ; *Respiratory Syncytial Virus Infections/drug therapy/epidemiology ; Infant ; Child, Preschool ; Aged ; England/epidemiology ; Adult ; Middle Aged ; *Respiratory Tract Infections/drug therapy/virology ; *General Practice/statistics &amp; numerical data ; Young Adult ; Child ; Male ; Female ; Adolescent ; *Drug Prescriptions/statistics &amp; numerical data ; Age Factors ; Infant, Newborn ; Respiratory Syncytial Virus, Human ; Practice Patterns, Physicians'/statistics &amp; numerical data ; Aged, 80 and over ; }, abstract = {BACKGROUND: Respiratory syncytial virus (RSV) may contribute to a substantial volume of antibiotic prescriptions in primary care. However, data on the type of antibiotics prescribed for such infections are only available for children <5 years in the UK. Understanding the contribution of RSV to antibiotic prescribing would facilitate predicting the impact of RSV preventative measures on antibiotic use and resistance. The objective of this study was to estimate the proportion of antibiotic prescriptions in English general practice attributable to RSV by age and antibiotic class.<br><br>METHODS: Generalized additive models examined associations between weekly counts of general practice antibiotic prescriptions and laboratory-confirmed respiratory infections from 2015 to 2018, adjusting for temperature, practice holidays and remaining seasonal confounders. We used general practice records from the Clinical Practice Research Datalink and microbiology tests for RSV, influenza, rhinovirus, adenovirus, parainfluenza, human metapneumovirus, Mycoplasma pneumoniae and Streptococcus pneumoniae from England's Second Generation Surveillance System.<br><br>RESULTS: An estimated 2.1% of antibiotics were attributable to RSV, equating to an average of 640 000 prescriptions annually. Of these, adults &#x2265;75&#x2005;years contributed to the greatest volume, with an annual average of 149&#x200a;078 (95% credible interval: 93&#x200a;733-206&#x200a;045). Infants 6-23&#x2005;months had the highest average annual rate at 6580 prescriptions per 100&#x200a;000 individuals (95% credible interval: 4522-8651). Most RSV-attributable antibiotic prescriptions were penicillins, macrolides or tetracyclines. Adults &#x2265;65&#x2005;years had a wider range of antibiotic classes associated with RSV compared with younger age groups.<br><br>CONCLUSIONS: Interventions to reduce the burden of RSV, particularly in older adults, could complement current strategies to reduce antibiotic use in England.}, }
@article {pmid39968615, year = {2025}, author = {Klarevas-Irby, JA and Nyaguthii, B and Farine, DR}, title = {Moving as a group imposes constraints on the energetic efficiency of movement.}, journal = {Proceedings. Biological sciences}, volume = {292}, number = {2041}, pages = {20242760}, pmid = {39968615}, issn = {1471-2954}, support = {//Centre for the Advanced Study of Collective Behaviour/ ; //Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; //Association for the Study of Animal Behaviour/ ; //H2020 European Research Council/ ; //Max Planck Society/ ; //Deutsche Forschungsgemeinschaft/ ; //Max Planck-Yale Center for Biodiversity Movement and Global Change/ ; }, mesh = {Animals ; *Energy Metabolism ; Movement ; *Galliformes/physiology ; Geographic Information Systems ; }, abstract = {Movement is a key part of life for many species. In solitary animals, the energetic costs of movement can be mitigated through energetically efficient strategies that produce faster, straighter movements. However, little is known about whether moving as part of a collective enhances or limits the ability of individual group members to express such strategies. Drawing on 6 years of population-level, high-resolution (1 Hz) GPS tracking of group-living vulturine guineafowl (Acryllium vulturinum), we detected 886 events from 94 tagged individuals where their groups made large, range-shifting displacements in response to changing environmental conditions. We contrasted these movements with data from 94 similarly large displacement events by 19 lone, dispersing individuals. Our results suggest that individuals in groups can significantly reduce their energetic cost of transport when making large displacements (15.3% more efficient relative to their normal daily ranging) by increasing the speed and straightness of their movements. However, even during their most efficient movements, individuals in groups could not achieve or maintain comparable increases in speed to lone individuals, resulting in significantly limited efficiency gains (35.7% less efficient than solitary individuals). Overall, this study provides evidence for a substantial energetic cost arising from collective movement.}, }
@article {pmid39963945, year = {2025}, author = {Giglio, VJ and Adelir-Alves, J and Balzaretti Merino, N and Bravo-Olivas, ML and Camp, EF and Casoli, E and Chávez-Dagostino, RM and Ferretti, E and Fraser, D and Grillo, AC and Jiménez-Guiérrez, S and Leite, KL and Lucrezi, S and Luiz, OJ and Luna-Pérez, B and McBride, J and Milanese, M and Moity, N and Pinheiro, JV and Renfro, B and Roche, R and Saliba, BM and Sara, A and Schiavetti, A and Toso, Y and Valle-Pérez, C and Ferreira, CEL}, title = {DiverReef: A global database of the behavior of recreational divers and their interactions with reefs over 20 years.}, journal = {Ecology}, volume = {106}, number = {2}, pages = {e4519}, doi = {10.1002/ecy.4519}, pmid = {39963945}, issn = {1939-9170}, support = {17/22273-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 111.210/2014//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; }, mesh = {*Diving ; *Coral Reefs ; Animals ; *Databases, Factual ; *Recreation ; Humans ; Time Factors ; }, abstract = {Recreational diving is an important activity in reef environments worldwide, providing income and employment for coastal communities and connecting visiting divers to these ecosystems promoting conservation and stewardship. However, if poorly managed, diving has the potential to cause detrimental effects on benthic communities via mechanical damage caused by physical contact of divers with the reef, often in the form of unintentional fin kicks resulting from poor buoyancy. Understanding diver-reef interaction patterns is important to elucidate the potential impacts of diving tourism on the reef biota. The DiverReef database provides the first public dataset on the underwater behavior of recreational divers in shallow reef environments (<25 m depth) globally and their interactions with the reef seascape and/or reef benthic sessile organisms. The dataset comprises 20 years of data (2004-2023) by observing the behavior of 2311 recreational divers in nine countries at 19 diving destinations and 176 diving sites; 93% of the observations were in marine protected areas. The data were collected through on-site observations of divers' behavior during tourism activities and their physical interactions with the reef structure and/or benthic sessile reef organisms. Observers discreetly followed divers and recorded their behavior and interactions with the reef over set periods. Interactions were described as "contact" or "damage," the latter referring to when physical damage to a benthic organism or the reef structure was observed. Besides behavior, observers also recorded data on the type of diving activity (scuba or snorkeling), profiles of the divers (gender and experience), use of cameras by the divers, visibility, type of reef formation, and marine protection status of the dive site. The authors of this research expect that the data provided will be useful in advancing knowledge of how divers interact with reefs and in developing strategies to mitigate the potential detrimental effects of the diving industry on reef biota. Part of the data has already been used in reports and scientific articles. This dataset can be freely used for noncommercial purposes; we request that users of these data cite this data paper in all publications resulting from the use of this dataset.}, }
@article {pmid39963041, year = {2025}, author = {Lima-Cordón, R and Mohabir, JT and Sooklall, M and Zurita, AM and Shieh, M and Knox, C and Gobran, S and Johnson, Z and Laws, M and Panchal, R and Niles-Robin, R and Cox, H and Grillet, ME and Moreno, JE and Herrera, S and Quinones, M and Early, AM and Tennessen, JA and Neafsey, DE}, title = {A Short-Read Amplicon Sequencing Protocol and Bioinformatic Pipeline for Ecological Surveillance of Dipteran Disease Vectors.}, journal = {Molecular ecology resources}, volume = {25}, number = {6}, pages = {e14088}, pmid = {39963041}, issn = {1755-0998}, support = {U19 AI110818/AI/NIAID NIH HHS/United States ; U19AI110818//National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services/ ; INV-009416/GATES/Gates Foundation/United States ; INV-009416/GATES/Gates Foundation/United States ; }, mesh = {Animals ; *Computational Biology/methods ; *DNA Barcoding, Taxonomic/methods ; *Sequence Analysis, DNA/methods ; *Diptera/genetics/classification ; *Insect Vectors/classification/genetics/parasitology ; Anopheles/genetics/parasitology/classification ; Humans ; *Disease Vectors ; }, abstract = {Vector control remains an important strategy worldwide to prevent human infection with pathogens transmitted by arthropods. Vector control strategies rely on accurate identification of vector taxa along with vector-specific biological indicators such as feeding ecology, infection prevalence and insecticide resistance. Multiple 'DNA barcoding' protocols have been published over the past several decades to support these applications, generally relying on informal manual approaches such as BLAST to assign taxonomic identity to the resulting sequences. We present a standardised informatic pipeline for analysis of DNA barcoding data from dipteran vectors, VecTreeID, that uses short-read amplicon sequencing (AmpSeq) coupled with sequence similarity assessment (BLAST) and an evolutionary placement algorithm (EPA-ng) to achieve vector taxonomic identification, capture bionomic features (blood and plant meal sources), determine Plasmodium infection status (for anopheline mosquitoes) and detect target-site insecticide resistance mutations. The VecTreeID pipeline provides uncertainty in assignment through identifications at varying levels of taxonomic rank, a feature missing from many approaches to DNA barcoding, but important given gaps and labelling problems in public sequence databases. We validated an Illumina-based implementation of VecTreeID on laboratory and field samples, and find that the blood meal amplicons can detect vertebrate DNA sequences up to 36 h post-feeding, and that short-read sequencing data are capable of sensitively detecting minor sequences in DNA mixtures representing multi-species blood or nectar meals. This high-throughput VecTreeID approach empowers researchers and public health professionals to survey and control arthropod disease vectors consistently and effectively.}, }
@article {pmid39960184, year = {2025}, author = {Ferdousee, S and Alam, MS and Hwangbo, M and Kim, J}, title = {Visualizing Methane-Cycling Microbial Dynamics in Coastal Wetlands.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {215}, pages = {}, doi = {10.3791/67715}, pmid = {39960184}, issn = {1940-087X}, mesh = {*Methane/metabolism ; *Wetlands ; Texas ; Geographic Information Systems ; Seashore ; }, abstract = {Coastal wetlands are the largest biotic source of methane, where methanogens convert organic matter into methane and methanotrophs oxidize methane, thus playing a critical role in regulating the methane cycle. The wetlands in South Texas, which are subject to frequent weather events, fluctuating salinity levels, and anthropogenic activities due to climate change, influence methane cycling. Despite the ecological importance of these processes, methane cycling in South Texas coastal wetlands remains insufficiently explored. To address this gap, we developed and optimized a method for detecting genes related to methanogens and methanotrophs, including mcrA as a biomarker for methanogens and pmoA1, pmoA2, and mmoX as biomarkers for methanotrophs. Additionally, this study aimed to visualize the spatial and temporal distribution patterns of methanogen and methanotroph abundance utilizing the geographic information system (GIS) software ArcGIS Pro. The integration of these molecular techniques with advanced geospatial visualization provided critical insights into the spatial and temporal distribution of methanogen and methanotroph communities across South Texas wetlands. Thus, the methodology established in this study offers a robust framework for mapping microbial dynamics in wetlands, enhancing our understanding of methane cycling under varying environmental conditions, and supporting broader ecological and environmental change studies.}, }
@article {pmid39957502, year = {2025}, author = {Latini, L and Burini, G and Mazza, V and Grignani, G and De Donno, R and Bello, E and Tricarico, E and Malavasi, S and Nascetti, G and Canestrelli, D and Carere, C}, title = {Early-life environment shapes claw bilateral asymmetry in the European lobster (Homarus gammarus).}, journal = {Biology open}, volume = {14}, number = {3}, pages = {}, pmid = {39957502}, issn = {2046-6390}, support = {//Universite degli Studi della Tuscia/ ; //Universite degli Studi di Firenze/ ; //Universite Ca' Foscari Venezia/ ; //University of Florence/ ; }, mesh = {Animals ; *Nephropidae/growth &amp; development/anatomy &amp; histology/physiology ; *Environment ; *Hoof and Claw/anatomy &amp; histology/growth &amp; development ; }, abstract = {Developmental plasticity refers to an organism's ability to adjust its development in response to changing environmental conditions, leading to changes in behaviour, physiology, or morphology. This adaptability is crucial for survival and helps organisms to cope with environmental challenges throughout their lives. Understanding the mechanisms underlying developmental plasticity, particularly how environmental and ontogenetic factors shape functional traits, is fundamental for both evolutionary biology and conservation efforts. In this study we investigated the effects of early-life environmental conditions on the development of claw asymmetry in juvenile European lobsters (Homarus gammarus, N=244), a functional trait essential for survival and ecological success. Juveniles were randomly divided between four different rearing conditions characterized by the presence or absence of physical enrichments (e.g. substrate and shelters), which were introduced at different developmental stages in separated groups to assess the timing and nature of their effect. Results revealed that exposure to substrate alone, without additional stimuli, consistently promoted claw asymmetry, regardless of the timing of its introduction, while the 6th developmental stage emerged as the critical period for claw differentiation. By identifying the environmental factors that influence developmental outcomes in lobsters, and the timing of these effects, this study improves our understanding of developmental plasticity and offers valuable insights for optimizing conservation aquaculture and reintroduction strategies.}, }
@article {pmid39955351, year = {2025}, author = {Yang, Y and Yang, Y and Yang, S and Zhang, J}, title = {Pollution control mechanism of national water network with water quality differences based on differential game and case study.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {5588}, pmid = {39955351}, issn = {2045-2322}, support = {51679089//National Nature Science Foundation of China/ ; 51679089//National Nature Science Foundation of China/ ; 51679089//National Nature Science Foundation of China/ ; 51679089//National Nature Science Foundation of China/ ; GXJD004//Intelligent Water Conservancy Project of the Discipline Innovation Introduction Base of Henan Province, China/ ; GXJD004//Intelligent Water Conservancy Project of the Discipline Innovation Introduction Base of Henan Province, China/ ; GXJD004//Intelligent Water Conservancy Project of the Discipline Innovation Introduction Base of Henan Province, China/ ; GXJD004//Intelligent Water Conservancy Project of the Discipline Innovation Introduction Base of Henan Province, China/ ; }, abstract = {The construction of the national water network optimizes water resource allocation but also causes a redistribution of pollutants due to water quality differences, posing urgent challenges for water pollution management. Taking the South-to-North Water Diversion Project and Yangtze-to-Hanjiang River Water Diversion Project (YHRWDP) as an example and considering the pressure brought by the redistribution of pollutants to the polluting enterprises (PE) and water diversion enterprises (WDE) situated in areas where pollution is aggravated, a differential game model of pollution control among the central government, water-supply area (WSA), PE and WDE is constructed based on the cost-sharing mechanism. The results show that: (1) The pressure coefficient has an apparent negative correlation with the effort level of the affected subject. (2) An increase in the amount of pollution elimination per unit of pollution control effort of WSA and PE will lead to their own investment in more efforts to improve the ecology of the basin, thus benefiting all participants in the system. (3) The cost-sharing rate of the central government on the WSA of the YHRWDP, the PE, and the WDE is influenced by several factors, which shows a stable monotonically increasing or decreasing relation. The results are an useful supplement to the research on natural river pollution control, and can also provide a reference for designing pollution control mechanisms of national water network.}, }
@article {pmid39952648, year = {2025}, author = {Siddiqui, JA and Fan, R and Liu, Y and Syed, AH and Benlin, Y and Chu, Q and Ding, Z and Ghani, MI and Liu, X and Wakil, W and Liu, DD and Chen, X and Cernava, T and Smagghe, G}, title = {The larval gut of Spodoptera frugiperda harbours culturable bacteria with metabolic versatility after insecticide exposure.}, journal = {Insect molecular biology}, volume = {34}, number = {3}, pages = {452-469}, doi = {10.1111/imb.12983}, pmid = {39952648}, issn = {1365-2583}, support = {32360705//National Natural Science Foundation of China/ ; 31960555//National Natural Science Foundation of China/ ; GCC[2023]070//Guizhou Provincial Science and Technology Program/ ; HZJD[2022]001//Guizhou Provincial Science and Technology Program/ ; 2019-1410//Guizhou Provincial Science and Technology Program/ ; [2023]1-4//Guiyang Science and Technology Program/ ; D20023//Program for Introducing Talents to Chinese Universities/ ; }, mesh = {Animals ; *Spodoptera/microbiology/growth &amp; development/drug effects ; *Gastrointestinal Microbiome/drug effects ; Larva/microbiology/drug effects/growth &amp; development ; *Insecticides/pharmacology ; *Bacteria/drug effects/genetics/classification/metabolism/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Spodoptera frugiperda (fall armyworm) poses a substantial risk to crops worldwide, resulting in considerable economic damage. The gut microbiota of insects plays crucial roles in digestion, nutrition, immunity, growth and, sometimes, the degradation of insecticides. The current study examines the effect of synthetic insecticides on the gut microbiome of third instar S. frugiperda larvae using both culture-dependent techniques and 16S rRNA gene sequencing for bacterial community profiling and diversity analysis. In untreated larvae, the sequencing approach revealed a diverse microbiome dominated by the phyla Firmicutes, Proteobacteria and Bacteroidota, with key genera including Bacteroides, Faecalibacterium and Pelomonas. In parallel, 323 bacterial strains were isolated and assigned to the orders Bacillales, Burkholderiales, Enterobacterales, Flavobacteriales, Lactobacillales, Micrococcales, Neisseriaies, Pseudomonadales, Sphingobacteriales and Xanthomonadales. The prevailing culturable species included Serratia marcescens, Klebsiella variicola and Enterobacter quasiroggenkampii. Treatment with sublethal concentrations of three insecticides (broflanilide, spinosad and indoxacarb) caused significant changes in gut microbiome diversity and composition. Treated larvae showed a shift towards increased Proteobacteria abundance and decreased Firmicutes. Specifically, Acinetobacter and Rhodococcus were dominant in treated samples. Functional predictions highlighted significant metabolic versatility involving nutrient processing, immune response, detoxification, xenobiotic metabolism, and stress response, suggesting microbial adaptation to insecticide exposure. Network correlation analysis highlighted disrupted microbial interactions and altered community structures under insecticide treatment. These findings enhance our understanding of how insecticides impact the gut microbiota in S. frugiperda and may inform future strategies for managing pest resistance through microbiome-based approaches.}, }
@article {pmid39952543, year = {2025}, author = {Chaemsaithong, P and Romero, R and Pongchaikul, P and Warintaksa, P and Mongkolsuk, P and Bhuwapathanapun, M and Kotchompoo, K and Nimsamer, P and Kruasuwan, W and Amnuaykiatlert, O and Vivithanaporn, P and Meyyazhagan, A and Awonuga, A and Settacomkul, R and Singhsnaeh, A and Laolerd, W and Santanirand, P and Thaipisuttikul, I and Wongsurawat, T and Jenjaroenpun, P}, title = {The rapid diagnosis of intraamniotic infection with nanopore sequencing.}, journal = {American journal of obstetrics and gynecology}, volume = {233}, number = {3}, pages = {193.e1-193.e18}, doi = {10.1016/j.ajog.2025.02.011}, pmid = {39952543}, issn = {1097-6868}, mesh = {Humans ; Pregnancy ; Female ; *Amniotic Fluid/microbiology/chemistry ; *Chorioamnionitis/diagnosis/microbiology ; Prospective Studies ; Adult ; RNA, Ribosomal, 16S/genetics ; *Nanopore Sequencing ; Interleukin-6/analysis/metabolism ; Premature Rupture of Fetal Membranes/microbiology ; Obstetric Labor, Premature/microbiology ; Polymerase Chain Reaction ; *Pregnancy Complications, Infectious/diagnosis/microbiology ; }, abstract = {BACKGROUND: Intraamniotic infection (defined as intraamniotic inflammation with microorganisms) is an important cause of the preterm labor syndrome. Methods for the detection of microorganisms in amniotic fluid are culture and/or polymerase chain reaction assay. However, both methods take time, and the results are rarely available for clinical decision-making. Nanopore sequencing technology offers real-time, long-read sequencing that can produce rapid results.<br><br>OBJECTIVE: To determine 1) the diagnostic performance of the 16S rDNA nanopore sequencing method for the identification of microorganisms in patients with intraamniotic inflammation and 2) the relationship between microbial burden and the intensity of the amniotic fluid inflammatory response.<br><br>STUDY DESIGN: We performed a prospective cohort study that included singleton pregnancies presenting with symptoms of preterm labor with intact membranes or of preterm prelabor rupture of the membranes. Amniotic fluid samples were obtained for the evaluation of bacteria in the amniotic cavity using cultivation and polymerase chain reaction-based 16S Sanger sequencing methods. Participants were classified into 4 groups according to the results of an amniotic fluid culture, 16S Sanger sequencing, and an amniotic fluid interleukin 6 concentration: 1) no intraamniotic infection and intraamniotic inflammation (interleukin 6 <2.6 ng/mL, and no microorganisms in the amniotic cavity, as determined by culture or 16S Sanger sequencing); 2) microbial invasion of the amniotic cavity without intraamniotic inflammation, defined by the presence of bacteria detected by culture or 16S Sanger sequencing; 3) sterile intraamniotic inflammation (interleukin 6 &#x2265;2.6 ng/mL without microbial invasion of the amniotic cavity); and 4) intraamniotic infection (interkeukin 6 &#x2265;2.6 ng/mL with microbial invasion of the amniotic cavity). Patients who underwent a mid-trimester amniocentesis, had no intraamniotic infection or intraamniotic inflammation, and delivered at term represented the control group. 16S rDNA nanopore sequencing was performed and the diagnostic indices for the identification of intraamniotic infection were determined. Bioinformatic analysis was carried out to identify microorganisms, and a read count of at least 100 or a read count exceeding that of the background species from the control group, along with a relative abundance of no less than 1%, was used.<br><br>RESULTS: 1) The 16S nanopore sequencing had a sensitivity of 88.9% (8/9), specificity of 95.4% (41/43), positive predictive value of 80.0% (8/10), negative predictive value of 97.6% (41/42), positive likelihood ratio of 19.1 (95% confidence interval, 4.8-75.4), negative likelihood ratio of 0.1 (95% confidence interval, 0.02-0.7), and an accuracy of 94.2% (49/52) for the identification of intraamniotic infection (prevalence, 17% [9/52]); 2) the microbial load determined by the 16S nanopore sequencing had a strong positive correlation with the intensity of an intraamniotic inflammatory response (amniotic fluid interleukin 6 concentration; Spearman's correlation 0.9; P=.002); and 3) a subgroup of patients with intraamniotic inflammation did not have bacteria determined by culture, Sanger sequencing, or nanopore 16S, thus confirming the existence of sterile intraamniotic inflammation.<br><br>CONCLUSION: The 16S nanopore sequencing has high diagnostic indices, predictive values, likelihood ratios, and accuracy in the diagnosis of intraamniotic infection.}, }
@article {pmid39952461, year = {2025}, author = {Shi, W and Lu, P and Yang, H and Han, J and Wang, Q}, title = {Quantifying the relative importance of natural and human factors on vegetation dynamics in China's western frontiers during 2010-2021.}, journal = {Environmental research}, volume = {271}, number = {}, pages = {121120}, doi = {10.1016/j.envres.2025.121120}, pmid = {39952461}, issn = {1096-0953}, mesh = {China ; *Conservation of Natural Resources ; Humans ; *Ecosystem ; *Environmental Monitoring ; *Plant Development ; }, abstract = {Vegetation is a core component of terrestrial ecosystems, thus understanding the drivers of its dynamics is crucial for ecological conservation and management, especially in regions rich in natural resources but ecologically fragile. Here, we examined vegetation cover changes in China's western frontiers and quantified the relative importance of key drivers of vegetation dynamics. First, we employed the Dimidiate Pixel Model (DPM) via Google Earth Engine (GEE) to estimate fractional vegetation cover (FVC), followed by trend analysis using the Theil-Sen median and Mann-Kendall methods to examine FVC dynamics from 2010 to 2021. Next, we applied the optimal parameter-based geographic detector (OPGD) to further assess the impact of natural (ie., temperature, precipitation, and elevation) and human (ie., land use and population density) factors on FVC. Our results revealed that approximately 61.26% of the vegetation-covered regions in China's western frontiers have shown improvement. In Xinjiang, population density, land use, and precipitation were the primary drivers of FVC changes, with Q values exceeding 0.20. In Xizang, precipitation, elevation, temperature, and land use changes were the dominant drivers, with Q values greater than 0.30. Furthermore, interactions between natural and human factors significantly influenced FVC variation. Our findings have the potential to provide references for promoting sustainable vegetation management in western China.}, }
@article {pmid39948527, year = {2025}, author = {Rakshasa-Loots, AM and Steyn, C and Swiffen, D and Marwick, KFM and Semple, RK and Reynolds, RM and Burgess, K and Lawrie, SM and Lightman, SL and Luz, S and Smith, DJ}, title = {Metabolic biomarkers of clinical outcomes in severe mental illness (METPSY): protocol for a prospective observational study in the Hub for metabolic psychiatry.}, journal = {BMC psychiatry}, volume = {25}, number = {1}, pages = {122}, pmid = {39948527}, issn = {1471-244X}, support = {MR/Z503563/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adolescent ; Adult ; Female ; Humans ; Male ; Young Adult ; Biomarkers/blood ; *Bipolar Disorder/metabolism/blood ; *Major Depressive Disorder/metabolism/blood ; Metabolomics ; Prospective Studies ; *Schizophrenia/metabolism/blood ; Scotland ; Observational Studies as Topic ; }, abstract = {People with severe mental illness have high rates of obesity, type 2 diabetes, and cardiovascular disease. Emerging evidence suggests that metabolic dysfunction may be causally linked to the risk of severe mental illness. However, more research is needed to identify reliable metabolic markers which may have an impact on mental health outcomes, and to determine the mechanisms behind their impact. In the METPSY research study, we will investigate the relationship between metabolic markers and clinical outcomes of severe mental illness in young adults. We will recruit 120 young adults aged 16-25 years living in Scotland with major depressive disorder, bipolar disorder, schizophrenia, or no severe mental illness (controls) for a prospective observational study. We will assess clinical symptoms at three in-person visits (baseline, 6 months, and 12 months) using the Structured Clinical Interview for DSM-5, and collect blood samples at each of these visits for agnostic profiling of metabolic biomarkers through an untargeted metabolomic screen, using the rapid hydrophilic interaction liquid chromatography ion mobility mass spectrometry method (RHIMMS). Participants will also complete remote assessments at 3 and 9 months after the baseline visit: Ecological Momentary Assessments to measure mental health, wrist actigraphy to measure rhythms of rest and activity, and continuous glucose monitoring to measure metabolic changes. Throughout the 12-month enrolment period, we will also measure objective markers of sleep using a radar sleep monitor (Somnofy). Using advanced statistical techniques and machine learning analysis, we will seek to better understand the mechanisms linking metabolic health with mental health in young adults with schizophrenia, bipolar disorder, and severe depression. Clinical trial number: Not applicable.}, }
@article {pmid39945053, year = {2025}, author = {Tittes, S and Lorant, A and McGinty, SP and Holland, JB and de Jesus Sánchez-González, J and Seetharam, A and Tenaillon, M and Ross-Ibarra, J}, title = {The population genetics of convergent adaptation in maize and teosinte is not locally restricted.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {39945053}, issn = {2050-084X}, support = {1822330//National Science Foundation/ ; 1238014//National Science Foundation/ ; CA-D-PLS-2066-H 548//U.S. Department of Agriculture/ ; }, mesh = {*Genetics, Population ; *Zea mays/genetics ; *Adaptation, Physiological/genetics ; Gene Flow ; Genetic Variation ; Inbreeding ; Mutation ; Selection, Genetic ; Sympatry/genetics ; }, abstract = {What is the genetic architecture of local adaptation and what is the geographic scale over which it operates? We investigated patterns of local and convergent adaptation in five sympatric population pairs of traditionally cultivated maize and its wild relative teosinte (Zea mays subsp. parviglumis). We found that signatures of local adaptation based on the inference of adaptive fixations and selective sweeps are frequently exclusive to individual populations, more so in teosinte compared to maize. However, for both maize and teosinte, selective sweeps are also frequently shared by several populations, and often between subspecies. We were further able to infer that selective sweeps were shared among populations most often via migration, though sharing via standing variation was also common. Our analyses suggest that teosinte has been a continued source of beneficial alleles for maize, even after domestication, and that maize populations have facilitated adaptation in teosinte by moving beneficial alleles across the landscape. Taken together, our results suggest local adaptation in maize and teosinte has an intermediate geographic scale, one that is larger than individual populations but smaller than the species range.}, }
@article {pmid39943576, year = {2025}, author = {Cleveland, P and Morrison, A}, title = {Sông Sài Gòn: Extreme Plastic Pollution Pathways in Riparian Waterways.}, journal = {Sensors (Basel, Switzerland)}, volume = {25}, number = {3}, pages = {}, pmid = {39943576}, issn = {1424-8220}, support = {2023//Annual Award, School of Future Environments, Auckland University of Techolology/ ; }, mesh = {*Plastics/analysis ; *Rivers/chemistry ; *Environmental Monitoring/methods ; Vietnam ; Geographic Information Systems ; *Water Pollutants, Chemical/analysis ; }, abstract = {Plastic pollution in waterways poses a significant global challenge, largely stemming from land-based sources and subsequently transported by rivers to marine environments. With a substantial percentage of marine plastic waste originating from land-based sources, comprehending the trajectory and temporal experience of single-use plastic bottles assumes paramount importance. This project designed, developed, and released a plastic pollution tracking device, coinciding with Vietnam's annual Plastic Awareness Month. By mapping the plastic tracker's journey through the Saigon River, this study generated high-fidelity data for comprehensive analysis and bolstered public awareness through regular updates on the Re-Think Plastics Vietnam website. The device, equipped with technologies such as drone flight controller, open-source software, embedded computing, and cellular networking effectively captured GPS position, track, and localized conditions experienced by the plastic bottle tracker on its journey. This amalgamation of data contributes to the understanding of plastic pollution behaviors and serves as a data set for future initiatives aimed at plastic prevention in the ecologically sensitive Mekong Delta. By illuminating the transportation of single-use plastic bottles in the riparian waterways of Ho Chi Minh City and beyond, this study plays a role in collective efforts to understand plastic pollution and preserve aquatic ecosystems. By deploying a GPS-enabled plastic tracker, this study provides novel, high-resolution empirical data on plastic transport in urban tidal systems. These findings contribute to improving waste interception strategies and informing environmental policies aimed at reducing plastic accumulation in critical retention zones.}, }
@article {pmid39938845, year = {2025}, author = {Rakkannan, G and Mohanty, AK and Das, II and Nayak, S and Sahoo, L and Kumar, R and Rasal, A and Rather, MA and Ahmad, I and Sundaray, JK}, title = {Triflumezopyrim induced oxidative stress, DNA damage and apoptosis on Labeo rohita: Insights from Bioinformatics, Histopathological and Molecular approaches.}, journal = {International journal of biological macromolecules}, volume = {304}, number = {Pt 2}, pages = {140911}, doi = {10.1016/j.ijbiomac.2025.140911}, pmid = {39938845}, issn = {1879-0003}, mesh = {Animals ; *Oxidative Stress/drug effects ; *DNA Damage/drug effects ; *Apoptosis/drug effects ; *Computational Biology/methods ; Molecular Docking Simulation ; *Carps/metabolism/genetics ; Liver/drug effects/pathology/metabolism ; Cyprinidae ; 8-Hydroxy-2'-Deoxyguanosine ; Water Pollutants, Chemical/toxicity ; }, abstract = {Triflumezopyrim is a novel mesoionic pesticide used in Asian rice fields to control brown plant hopper, which can reach aquatic environments through drift during application or surface runoff. Thus, this study aimed to investigate the effect of chronic exposure of sub-lethal concentrations of triflumezopyrim (2.468 ppm, 1.480 ppm, and 0.740 ppm) on freshwater carp, Labeo rohita.This study encompassed a multi-pronged approach, including molecular docking studies to elucidate the interactions between triflumezopyrim and selected proteins, an assessment of 8-OHdG (8-hydroxy-2-deoxyguanosine) activity to gauge DNA damage, histopathological examinations to identify cellular alterations, and expression of genes involved in oxidative stress, DNA repair, and apoptosis in L. rohita. We observed dose-dependent responses in 8-OHdG activity and the expression of select genes, with higher concentrations of triflumezopyrim yielding more pronounced transcriptional alterations. Notably, histopathological examinations of liver and brain tissues vividly portrayed the impact of triflumezopyrim on L. rohita. These findings contribute to the assessment of biological toxicity and the environmental footprint left by chemical pollutants such as triflumezopyrim. The study emphasizes the crucial role of monitoring histopathological alterations, 8-OHdG activity and gene expression changes as potential biomarkers for assessing exposures to triflumezopyrim. This research provides valuable insights into the ecological implications of triflumezopyrim in aquatic ecosystems.}, }
@article {pmid39938295, year = {2025}, author = {Zhuo, W and Wu, N and Shi, R and Cui, Y and Zhang, C and Liu, S and Zhu, F and Zhang, B and Liu, P}, title = {Assessing the impacts of reclamation and invasion on ecological dynamics of coastal wetland vegetation in the Yangtze Estuary from 1985 to 2019:A case study of Chongming Island, China.}, journal = {Journal of environmental management}, volume = {376}, number = {}, pages = {124505}, doi = {10.1016/j.jenvman.2025.124505}, pmid = {39938295}, issn = {1095-8630}, mesh = {*Wetlands ; China ; *Estuaries ; *Introduced Species ; Ecosystem ; *Conservation of Natural Resources ; Humans ; Climate Change ; }, abstract = {The distribution of coastal wetland vegetation is influenced by biological invasions, human reclamations and climate changes, which continually reshape vegetation structures. However, limited attention has been given to the impact of biological invasion on native vegetation and tidal wetlands. This study focuses on the wetlands of Chongming Island, employing a multi-feature dataset combining spectral, phenological, and temporal information on the Google Earth Engine (GEE) platform. Using the Random Forest (RF) classification method, we analyzed annual vegetation distribution changes and examined the distinct effects of natural and anthropogenic factors. The research results indicate that: (1) From 1985 to 2019, the total area of Chongming Island expanded, while wetland vegetation decreased due to embankment construction and island connection projects. (2) The total area of wetland vegetation on Chongming Island dropped to its lowest point in 2002 (3812.76 ha), and then gradually recovered. (3) Human reclamation was the primary driver of vegetation changes from 1985 to 1995. (4) Vegetation distribution in Dongtan was influenced by both human and natural factors, whereas Beiliuyao affected by the invasion and expansion of the S. alterniflor. These findings provide valuable insights into the drivers of long-term vegetation distribution changes, offering essential data and theoretical support for sustainable development and management of Chongming Island's ecosystems.}, }
@article {pmid39937595, year = {2025}, author = {Royaux, C and Mihoub, JB and Jossé, M and Pelletier, D and Norvez, O and Reecht, Y and Fouilloux, A and Rasche, H and Hiltemann, S and Batut, B and Marc, E and Seguineau, P and Massé, G and Amossé, A and Bissery, C and Lorrilliere, R and Martin, A and Bas, Y and Virgoulay, T and Chambon, V and Arnaud, E and Michon, E and Urfer, C and Trigodet, E and Delannoy, M and Loïs, G and Julliard, R and Grüning, B and Le Bras, Y and , }, title = {Guidance framework to apply best practices in ecological data analysis: lessons learned from building Galaxy-Ecology.}, journal = {GigaScience}, volume = {14}, number = {}, pages = {}, pmid = {39937595}, issn = {2047-217X}, support = {2020-1-NL01-KA203-064717//European Union/ ; //Agence Nationale de la Recherche/ ; //Mus&#xe9;um National d'Histoire Naturelle/ ; //Ministry of Higher Education and Research/ ; }, mesh = {*Ecology/methods/standards ; *Software ; *Data Analysis ; Reproducibility of Results ; *Computational Biology/methods/standards ; }, abstract = {Numerous conceptual frameworks exist for best practices in research data and analysis (e.g., Open Science and FAIR principles). In practice, there is a need for further progress to improve transparency, reproducibility, and confidence in ecology. Here, we propose a practical and operational framework for researchers and experts in ecology to achieve best practices for building analytical procedures from individual research projects to production-level analytical pipelines. We introduce the concept of atomization to identify analytical steps that support generalization by allowing us to go beyond single analyses. The term atomization is employed to convey the idea of single analytical steps as "atoms" composing an analytical procedure. When generalized, "atoms" can be used in more than a single case analysis. These guidelines were established during the development of the Galaxy-Ecology initiative, a web platform dedicated to data analysis in ecology. Galaxy-Ecology allows us to demonstrate a way to reach higher levels of reproducibility in ecological sciences by increasing the accessibility and reusability of analytical workflows once atomized and generalized.}, }
@article {pmid39936843, year = {2025}, author = {Kim, KK and Backonja, U}, title = {Digital health equity frameworks and key concepts: a scoping review.}, journal = {Journal of the American Medical Informatics Association : JAMIA}, volume = {32}, number = {5}, pages = {932-944}, pmid = {39936843}, issn = {1527-974X}, support = {//The MITRE Innovation Program/ ; //MITRE Corporation/ ; //MITRE Innovation Program/ ; }, mesh = {*Health Equity ; Humans ; *Telemedicine ; Digital Health ; }, abstract = {OBJECTIVES: Digital health equity, the opportunity for all to engage with digital health tools to support good health outcomes, is an emerging priority across the world. The field of digital health equity would benefit from a comprehensive and systematic understanding of digital health, digital equity, and health equity, with a focus on real-world applications. We conducted a scoping review to identify and describe published frameworks and concepts relevant to digital health equity interventions.<br><br>MATERIALS AND METHODS: We conducted a scoping review of published peer-reviewed literature guided by the PRISMA Extension for Scoping Reviews. We searched 5 databases for frameworks related to or applied to digital health or equity interventions. Using deductive and inductive approaches, we analyzed frameworks and concepts based on the socio-ecological model.<br><br>RESULTS: Of the 910 publications initially identified, we included 44 (4.8%) publications in our review that described 42 frameworks that sought to explain the ecosystem of digital and/or health equity, but none were comprehensive. From the frameworks we identified 243 concepts grouped into 43 categories including characteristics of individuals, communities, and organizations; societal context; perceived value of the intervention by and impacts on individuals, community members, and the organization; partnerships; and access to digital health services, in-person services, digital services, and data and information, among others.<br><br>DISCUSSION: We suggest a consolidated definition of digital health equity, highlight illustrative frameworks, and suggest concepts that may be needed to enhance digital health equity intervention development and evaluation.<br><br>CONCLUSION: The expanded understanding of frameworks and relevant concepts resulting from this study may inform communities and stakeholders who seek to achieve digital inclusion and digital health equity.}, }
@article {pmid39936183, year = {2025}, author = {Brait, N and Hackl, T and Lequime, S}, title = {detectEVE: Fast, Sensitive and Precise Detection of Endogenous Viral Elements in Genomic Data.}, journal = {Molecular ecology resources}, volume = {25}, number = {4}, pages = {e14083}, pmid = {39936183}, issn = {1755-0998}, mesh = {*Computational Biology/methods ; *Genomics/methods ; *Software ; Genome, Viral ; *Viruses/genetics ; Sensitivity and Specificity ; }, abstract = {Endogenous viral elements (EVEs) are fragments of viral genomic material embedded within the host genome. Retroviruses contribute to the majority of EVEs because of their genomic integration during their life cycle; however, the latter can also arise from non-retroviral RNA or DNA viruses, then collectively known as non-retroviral (nr) EVEs. Detecting nrEVEs poses challenges because of their sequence and genomic structural diversity, contributing to the scarcity of specific tools designed for nrEVEs detection. Here, we introduce detectEVE, a user-friendly and open-source tool designed for the accurate identification of nrEVEs in genomic assemblies. detectEVE deviates from other nrEVE detection pipelines, which usually classify sequences in a more rigid manner as either virus-associated or not. Instead, we implemented a scaling system assigning confidence scores to hits in protein sequence similarity searches, using bit score distributions and search hints related to various viral characteristics, allowing for higher sensitivity and specificity. Our benchmarking shows that detectEVE is computationally efficient and accurate, as well as considerably faster than existing approaches, because of its resource-efficient parallel execution. Our tool can help to fill current gaps in both host-associated fields and virus-related studies. This includes (i) enhancing genome annotations with metadata for EVE loci, (ii) conducting large-scale paleo-virological studies to explore deep viral evolutionary histories, and (iii) aiding in the identification of actively expressed EVEs in transcriptomic data, reducing the risk of misinterpretations between exogenous viruses and EVEs.}, }
@article {pmid39934999, year = {2025}, author = {De Moor, D and Skelton, M and ,  and Amici, F and Arlet, ME and Balasubramaniam, KN and Ballesta, S and Berghänel, A and Berman, CM and Bernstein, SK and Bhattacharjee, D and Bliss-Moreau, E and Brotcorne, F and Butovskaya, M and Campbell, LAD and Carosi, M and Chatterjee, M and Cooper, MA and Cowl, VB and De la O, C and De Marco, A and Dettmer, AM and Dhawale, AK and Erinjery, JJ and Evans, CL and Fischer, J and García-Nisa, I and Giraud, G and Hammer, R and Hansen, MF and Holzner, A and Kaburu, S and Konečná, M and Kumara, HN and Larrivaz, M and Leca, JB and Legrand, M and Lehmann, J and Li, JH and Lezé, AS and MacIntosh, A and Majolo, B and Maréchal, L and Marty, PR and Massen, JJM and Maulany, RI and McCowan, B and McFarland, R and Merieau, P and Meunier, H and Micheletta, J and Mishra, PS and Sah, SAM and Molesti, S and Morrow, KS and Müller-Klein, N and Ngakan, PO and Palagi, E and Petit, O and Pflüger, LS and di Sorrentino, EP and Raghaven, R and Raimbault, G and Ram, S and Reichard, UH and Riley, EP and Rincon, AV and Ruppert, N and Sadoughi, B and Santhosh, K and Schino, G and Sheeran, LK and Silk, JB and Singh, M and Sinha, A and Sosa, S and Stribos, MS and Sueur, C and Tiddi, B and Tkaczynski, PJ and Trebouet, F and Widdig, A and Whitehouse, J and Wooddell, LJ and Xia, DP and von Fersen, L and Young, C and Schülke, O and Ostner, J and Neumann, C and Duboscq, J and Brent, LJN}, title = {MacaqueNet: Advancing comparative behavioural research through large-scale collaboration.}, journal = {The Journal of animal ecology}, volume = {94}, number = {4}, pages = {519-534}, pmid = {39934999}, issn = {1365-2656}, support = {864461//H2020 European Research Council/ ; LSC-AF2023_03//Leibniz ScienceCampus EEGA/ ; }, mesh = {Animals ; *Databases, Factual ; *Behavior, Animal ; *Social Behavior ; *Macaca ; *Behavioral Research ; Cooperative Behavior ; }, abstract = {There is a vast and ever-accumulating amount of behavioural data on individually recognised animals, an incredible resource to shed light on the ecological and evolutionary drivers of variation in animal behaviour. Yet, the full potential of such data lies in comparative research across taxa with distinct life histories and ecologies. Substantial challenges impede systematic comparisons, one of which is the lack of persistent, accessible and standardised databases. Big-team approaches to building standardised databases offer a solution to facilitating reliable cross-species comparisons. By sharing both data and expertise among researchers, these approaches ensure that valuable data, which might otherwise go unused, become easier to discover, repurpose and synthesise. Additionally, such large-scale collaborations promote a culture of sharing within the research community, incentivising researchers to contribute their data by ensuring their interests are considered through clear sharing guidelines. Active communication with the data contributors during the standardisation process also helps avoid misinterpretation of the data, ultimately improving the reliability of comparative databases. Here, we introduce MacaqueNet, a global collaboration of over 100 researchers (https://macaquenet.github.io/) aimed at unlocking the wealth of cross-species data for research on macaque social behaviour. The MacaqueNet database encompasses data from 1981 to the present on 61 populations across 14 species and is the first publicly searchable and standardised database on affiliative and agonistic animal social behaviour. We describe the establishment of MacaqueNet, from the steps we took to start a large-scale collective, to the creation of a cross-species collaborative database and the implementation of data entry and retrieval protocols. We share MacaqueNet's component resources: an R package for data standardisation, website code, the relational database structure, a glossary and data sharing terms of use. With all these components openly accessible, MacaqueNet can act as a fully replicable template for future endeavours establishing large-scale collaborative comparative databases.}, }
@article {pmid39934908, year = {2025}, author = {Wang, L and Simopoulos, CMA and Serrana, JM and Ning, Z and Li, Y and Sun, B and Yuan, J and Figeys, D and Li, L}, title = {PhyloFunc: phylogeny-informed functional distance as a new ecological metric for metaproteomic data analysis.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {50}, pmid = {39934908}, issn = {2049-2618}, support = {201906015034//China Scholarship Council/ ; TECHNOMISE Program//Natural Sciences and Engineering Research Council of Canada/ ; 32370050//National Natural Science Foundation of China/ ; }, mesh = {*Phylogeny ; *Gastrointestinal Microbiome/genetics ; Animals ; Mice ; *Proteomics/methods ; Humans ; *Bacteria/classification/genetics ; }, abstract = {BACKGROUND: Beta-diversity is a fundamental ecological metric for exploring dissimilarities between microbial communities. On the functional dimension, metaproteomics data can be used to quantify beta-diversity to understand how microbial community functional profiles vary under different environmental conditions. Conventional approaches to metaproteomic functional beta-diversity often treat protein functions as independent features, ignoring the evolutionary relationships among microbial taxa from which different proteins originate. A more informative functional distance metric that incorporates evolutionary relatedness is needed to better understand microbiome functional dissimilarities.<br><br>RESULTS: Here, we introduce PhyloFunc, a novel functional beta-diversity metric that incorporates microbiome phylogeny to inform on metaproteomic functional distance. Leveraging the phylogenetic framework of weighted UniFrac distance, PhyloFunc innovatively utilizes branch lengths to weigh between-sample functional distances for each taxon, rather than differences in taxonomic abundance as in weighted UniFrac. Proof of concept using a simulated toy dataset and a real dataset from mouse inoculated with a synthetic gut microbiome and fed different diets show that PhyloFunc successfully captured functional compensatory effects between phylogenetically related taxa. We further tested a third dataset of complex human gut microbiomes treated with five different drugs to compare PhyloFunc's performance with other traditional distance methods. PCoA and machine learning-based classification algorithms revealed higher sensitivity of PhyloFunc in microbiome responses to paracetamol. We provide PhyloFunc as an open-source Python package (available at https://pypi.org/project/phylofunc/), enabling efficient calculation of functional beta-diversity distances between a pair of samples or the generation of a distance matrix for all samples within a dataset.<br><br>CONCLUSIONS: Unlike traditional approaches that consider metaproteomics features as independent and unrelated, PhyloFunc acknowledges the role of phylogenetic context in shaping the functional landscape in metaproteomes. In particular, we report that PhyloFunc accounts for the functional compensatory effect of taxonomically related species. Its effectiveness, ecological relevance, and enhanced sensitivity in distinguishing group variations are demonstrated through the specific applications presented in this study. Video Abstract.}, }
@article {pmid39931107, year = {2024}, author = {Boyes, D and Murray, C and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Bird-cherry Ermine moth, Yponomeuta evonymella (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {618}, pmid = {39931107}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Yponomeuta evonymella (the Bird-cherry Ermine; Arthropoda; Insecta; Lepidoptera; Yponomeutidae). The genome sequence has a total length of 572.70 megabases. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the trivalent sex chromosomes Z 1, Z 2 and W. The mitochondrial genome has also been assembled and is 16.16 kilobases in length.}, }
@article {pmid39929026, year = {2025}, author = {Song, J and Zhou, S and Kwan, MP and Song, G and Long, J and Song, W}, title = {The time-lagged effect of noise exposure on noise annoyance: The role of temporal, spatial and social contexts.}, journal = {Social science &amp; medicine (1982)}, volume = {368}, number = {}, pages = {117817}, doi = {10.1016/j.socscimed.2025.117817}, pmid = {39929026}, issn = {1873-5347}, mesh = {Humans ; Male ; Female ; Ecological Momentary Assessment ; *Noise/adverse effects ; Adult ; *Environmental Exposure/adverse effects ; Time Factors ; Middle Aged ; }, abstract = {While some research has examined the time-lagged effect of restorative soundscape in specific contexts (e.g., parks), how the time-lagged effect of noise annoyance during people's daily activities may vary across different temporal, spatial, and social contexts remains largely unknown. To address this research gap, we utilized Ecological Momentary Assessment (EMA) data to measure people's real-time noise annoyance and activity diary data to assess their time-lagged noise annoyance. Real-time noise exposure was captured by portable noise sensors. We employed fixed effects ordered panel logistic regression to examine the effects of different thresholds of noise levels on people's time-lagged noise annoyance, and how it varied across different temporal, spatial, and social contexts. The results indicated that: (1) there were significant time-lagged effects between participants' real-time noise exposure and their time-lagged noise annoyance; (2) participants' time-lagged noise annoyance associated with an activity was influenced by its temporal, spatial, and social contexts, particularly on weekdays; (3) participants' time-lagged noise annoyance was significantly associated with measured noise levels, with the highest coefficient for 65 dB, followed by 70 dB; and (4) there were significant interaction effects between noise levels and temporal-spatial-social contexts on participants' time-lagged noise annoyance (particularly when noise levels exceeded 70 dB). These findings enhance our understanding and have crucial implications for the implementation of noise control policies, which should consider not only noise levels but also the time-lagged effects of noise, particularly on weekdays, at outdoor recreational activity sites, as well as the potential vulnerabilities of individuals experiencing noise exposure in isolation.}, }
@article {pmid39928107, year = {2025}, author = {Güneri, FD and Karaarslan, F and Özen, H and Odabaşi, E}, title = {Medical mud-pack treatment with different temperatures in patients with knee osteoarthritis.}, journal = {International journal of biometeorology}, volume = {69}, number = {9}, pages = {2071-2080}, pmid = {39928107}, issn = {1432-1254}, mesh = {Humans ; *Osteoarthritis, Knee/therapy ; Male ; Female ; Middle Aged ; Aged ; *Mud Therapy/methods ; Temperature ; Pain Measurement ; Treatment Outcome ; }, abstract = {To compare the effects of medical mud-pack (MMP) treatments applied at different temperatures on the pain and joint functions of patients with knee osteoarthritis (KOA). Kellgren Lawrence (KL) stage 3 or 4 KOA patients were included and randomized into three groups. Patients in groups 1, 2, and 3 took MMP treatment to both knees at 39 °C, 42 °C, and 45 °C, respectively. The treatment was performed for 12 days (only weekdays) and was 30 min long per day. The same blinded physician evaluated the patients at baseline and at the end of the treatment. The assessments were done before and after the intervention. The primary outcome was to achieve a minimal clinically important improvement (MCII) for KOA (decrease of at least 19 mm (-40.8%) on the VAS for pain, a decrease of 18.3 mm (-39%) on the patient's global assessment (PGA), and/or a decrease of at least 9.1 points (-26%) on the Western Ontario and McMaster Universities Osteoarthritis Index function subscale (WOMAC-FS). Secondary outcomes were pain (VAS), patient's global assessment (VAS), physician's global assessment (VAS), Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC), Patient's health state, Patient Acceptable Symptom State (PASS). 217 patients were analyzed. Groups 1, 2, and 3 had 68, 81,68 patients, respectively. The MCII measurement revealed that MMP treatment did not show a significant difference between groups 2 and 3 (p > 0.05). Also, it was observed that more patients in groups 2 and 3 reached the MCII compared to group 1 (p < 0.001). For the secondary outcomes, significant improvements were observed within-group evaluations for each of the three groups (p < 0.001). Between groups comparisons, the improvements at the end of the treatment were found to be superior for group 2 and group 3 compared to group 1 (p < 0.001). There was no statistically significant difference between groups 2 and 3 for any parameters (p > 0.05). The number of patients who achieved the PASS was statistically lower for group 1 compared to groups 2 and 3 (p < 0.001). We observed significant improvements in all groups after treatment. The main result, as measured by MCII, suggests that MMP treatments at 42-45 °C is more effective than at 39 °C in managing severe KOA patients' pain and functional status. We found no significant difference in pain and joint function improvement between 42 °C and 45 °C after MMP.}, }
@article {pmid39925235, year = {2025}, author = {Shi, T and Gao, Z and Zhang, Y and Rausher, MD and Chen, J}, title = {A Strategy of Assessing Gene Copy Number Differentiation Between Populations Using Ultra-Fast De Novo Assembly of Next-Generation Sequencing Data.}, journal = {Molecular ecology resources}, volume = {25}, number = {4}, pages = {e14080}, doi = {10.1111/1755-0998.14080}, pmid = {39925235}, issn = {1755-0998}, support = {31570220//National Natural Science Foundation of China/ ; 31870208//National Natural Science Foundation of China/ ; 32170240//National Natural Science Foundation of China/ ; KFJ-BRP-007-009//Biological Resources Program, CAS/ ; }, mesh = {*High-Throughput Nucleotide Sequencing/methods ; *DNA Copy Number Variations ; *Computational Biology/methods ; *Genetics, Population/methods ; *Gene Dosage ; Sequence Analysis, DNA/methods ; }, abstract = {Gene duplication and loss play pivotal roles in the evolutionary dynamics of genomes, contributing to species phenotypic diversity and adaptation. However, detecting copy number variations (CNVs) in homoploid populations and newly-diverged species using short reads from next-generation sequencing (NGS) with traditional methods can often be challenging due to uneven read coverage caused by variations in GC content and the presence of repetitive sequences. To address these challenges, we developed a novel pipeline, ST4gCNV, which leverages ultra-fast de novo assemblies of NGS data to detect gene-specific CNVs between populations. The pipeline effectively reduces the variance of read coverage due to technical factors such as GC bias, providing a reliable CNV detection with a minimum sequencing depth of 10. We successfully apply ST4gCNV to the resequencing analysis of homoploid species Nelumbo nucifera and Nelumbo lutea (lotus). We reveal significant CNV-driven differentiation between these species, particularly in genes related to petal colour diversity such as those involved in the anthocyanin pathway. By highlighting the extensive gene duplication and loss events in Nelumbo, our study demonstrates the utility of ST4gCNV in population genomics and underscores its potential of integrating genomic CNV analysis with traditional SNP-based resequencing analysis.}, }
@article {pmid39923474, year = {2025}, author = {Lucca, E and Kofinas, D and Avellán, T and Kleemann, J and Mooren, CE and Blicharska, M and Teutschbein, C and Sperotto, A and Sušnik, J and Milliken, S and Fader, M and Đorđević, D and Dašić, T and Vasilić, V and Taiwo, B and Baubekova, A and Pineda-Martos, R and Spyropoulou, A and Baganz, GFM and El Jeitany, J and Oral, HV and Merheb, M and Castelli, G and Pagano, A and Sambo, B and Suškevičs, M and Arnold, M and Rađenović, T and Psomas, A and Masia, S and La Jeunesse, I and Amorocho-Daza, H and Das, SS and Bresci, E and Munaretto, S and Brouwer, F and Laspidou, C}, title = {Integrating "nature" in the water-energy-food Nexus: Current perspectives and future directions.}, journal = {The Science of the total environment}, volume = {966}, number = {}, pages = {178600}, doi = {10.1016/j.scitotenv.2025.178600}, pmid = {39923474}, issn = {1879-1026}, abstract = {Integrated approaches for managing natural resources are said to meet increasing demand for water, energy, and food, while maintaining the integrity of ecosystems, and ensuring equitable access to resources. The Water-Energy-Food (WEF) Nexus has been proposed as a cross-sectoral approach to manage trade-offs and exploit synergies that arise among these sectors. Although not initially included as a component of the Nexus, the role of nature in sustaining the water, energy, and food sectors and in regulating their interrelationships is increasingly recognised by Nexus researchers and practitioners. To converge existing approaches that integrate nature into the WEF Nexus and suggest a common framework, we - an interdisciplinary group of natural resources management researchers and systems thinkers from the European research network NEXUSNET COST Action - followed a collaborative process of knowledge creation combining literature review, elicitation of expert opinion and collaborative writing. Our results reveal a multiplicity of concepts utilised in the literature to represent, partially or fully, "nature" in the Nexus, such as "environment", "ecosystems", "ecosystem services", "social-ecological systems", and "biodiversity". Disparity was also found in the role attributed to nature, represented by three key paradigms: (1) ecosystems as the fourth component of an expanded Nexus, i.e., the WEF-Ecosystems (WEFE) Nexus; (2) ecosystems as a foundational layer to the Nexus; and (3) the WEF Nexus as a central component of social-ecological systems (SES). By creating a hybrid approach that brings together the benefits of the respective paradigms, we present a forward-looking WEFE Nexus conceptualisation. This paradigm expands the mutual interlinkages among water, energy and food to the entirety of SES, thus acknowledging the social-ecological processes that are affected by and affect the WEF Nexus. The results of this collaborative research effort intend to provide researchers and stakeholders with means to better understand and ultimately manage Nexus issues towards a transformative change.}, }
@article {pmid39923291, year = {2025}, author = {de Melo, LRS and Dos Santos Pereira, J and Melo, MS and Andrade, LA and Bezerra-Santos, M and Lima, CA and Dos Santos, AD}, title = {Spatial and temporal dynamic of colorectal cancer mortality in Brazil: A nationwide population-based study of four decades (1980-2021).}, journal = {Cancer epidemiology}, volume = {95}, number = {}, pages = {102766}, doi = {10.1016/j.canep.2025.102766}, pmid = {39923291}, issn = {1877-783X}, mesh = {Humans ; Brazil/epidemiology ; *Colorectal Neoplasms/mortality ; Female ; Male ; Middle Aged ; Aged ; Adult ; Spatio-Temporal Analysis ; Mortality/trends ; Aged, 80 and over ; }, abstract = {BACKGROUND: Regardless of being preventable through screening strategies and prompt diagnosis, deaths from colorectal cancer (CRC) still represent a serious public health concern in Brazil, with more than 20 thousand deaths annually. Herein, we aimed to assess the temporal trends and spatiotemporal patterns of CRC mortality in all Brazilian states.<br><br>METHODS: An ecological study using temporal and spatial analysis techniques on deaths due to CRC as the underlying cause in Brazil from 1980 to 2021 was conducted. Death certificate and population data were provided by the Department of Informatics of the Unified Health System (DATASUS) and by the Brazilian Institute of Geography and Statistics (IBGE), respectively.<br><br>RESULTS: A total of 395,782 deaths from CRC were recorded in this period and most of them were in female (205,479; 51.92&#x202f;%), &#x2265;&#x202f;65 years old (233,059; 58.89&#x202f;%), diagnosed with malignant neoplasm of the colon (212,277; 53.63&#x202f;%), with 1-7 years of education (157.564; 39.81&#x202f;%), married (192.276; 48.58&#x202f;%), hospital as place of death (331.393; 83.73&#x202f;%) and white (212.666; 65.07&#x202f;%). Moreover, there was an increasing temporal trend in the Northeast region (APC: 2.6; p&#x202f;<&#x202f;0.05), men (APC: 1.5; p&#x202f;<&#x202f;0.05) and 45-64 years old (APC: 1.2; p&#x202f;<&#x202f;0.05). Also, the spatial analysis showed positive spatial autocorrelation in all periods, with the South and Southeast regions presenting the highest concentration of high-risk clusters CRC deaths. Nevertheless, high-risk clusters were also observed in capitals and municipalities in metropolitan regions in the Northeast region.<br><br>CONCLUSIONS: In general, a temporal and spatial expansion of CRC mortality has been observed in Brazil over the last few decades.}, }
@article {pmid39921816, year = {2025}, author = {Asuako, PAG and Stojan, R and Bock, O and Mack, M and Voelcker-Rehage, C}, title = {Multitasking: does task-switching add to the effect of dual-tasking on everyday-like driving behavior?.}, journal = {Cognitive research: principles and implications}, volume = {10}, number = {1}, pages = {5}, pmid = {39921816}, issn = {2365-7464}, support = {SPP 1772//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Humans ; Female ; Male ; Young Adult ; Adult ; Adolescent ; *Automobile Driving/psychology ; *Psychomotor Performance/physiology ; *Executive Function/physiology ; *Multitasking Behavior/physiology ; Reaction Time/physiology ; *Attention/physiology ; }, abstract = {It is well established that performing multiple tasks simultaneously (dual-tasking) or sequentially (task-switching) degrades performance on one or both tasks. However, it is unknown whether task-switching adds to the effects of dual-tasking in a single setup. We investigated this in a simulated everyday-like car driving scenario. We expected an additive effect of task-switching on dual-tasking, leading to a stronger deterioration of driving performance due to the increased cognitive load required to handle multiple task-sets. Forty-five young adults aged 18 to 30 years (age: 23.62 ± 2.51, 28 females) were instructed to follow a lead car driving at a constant speed of 70 km/h through a rural landscape while concurrently performing additional tasks. The additional tasks were typing and arguing, in response to stimuli presented visually or auditorily. The tasks were presented either in separate blocks or in intermixed order (conditions: repetitive vs. switching). Driving performance was assessed by use of the average velocity and the standard deviation of lateral position, and performance in the additional tasks was assessed by reaction time. Linear-mixed effect models revealed better performance in the repetitive, compared to the switch condition only for the standard deviation of the lateral lane position while performing the additional typing task. This provides limited evidence for the view that task-switching adds to the challenges of dual-tasking. We therefore posit that already dual-tasking alone involves processing demands that are not substantially increased by adding switching demands.}, }
@article {pmid39918865, year = {2025}, author = {Astill Wright, L and Moore, M and Reeves, S and Vallejos, EP and Morriss, R}, title = {Improving the Utility, Safety, and Ethical Use of a Passive Mood-Tracking App for People With Bipolar Disorder Using Coproduction: Qualitative Focus Group Study.}, journal = {JMIR formative research}, volume = {9}, number = {}, pages = {e65140}, pmid = {39918865}, issn = {2561-326X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Bipolar Disorder/psychology/therapy ; Male ; Female ; *Mobile Applications/ethics ; Focus Groups ; Adult ; Middle Aged ; Qualitative Research ; *Affect ; Telemedicine ; }, abstract = {BACKGROUND: Coproduction with users of new digital technology, such as passive mood monitoring, is likely to improve its utility, safety, and successful implementation via improved design and consideration of how such technology fits with their daily lives. Mood-monitoring interventions are commonly used by people with bipolar disorder (BD) and have promising potential for digitization using novel technological methods.<br><br>OBJECTIVE: This study aims to explore how a passive behavioral monitoring platform, Remote Assessment of Disease and Relapse, would meet the needs of people with BD by specifically considering purpose and function, diversity of need, personal preference, essential components and potential risks, and harms and mitigation strategies through an iterative coproduction process.<br><br>METHODS: A total of 17 people with BD were recruited via national charities. We conducted 3 web-based focus groups as a part of an iterative coproduction process in line with responsible research and innovation principles and with consideration of clinical challenges associated with BD. Data were analyzed thematically. Results were cross-checked by someone with lived experience of BD.<br><br>RESULTS: Focus groups were transcribed and analyzed using thematic analysis. Six themes were identified as follows: (1) the purpose of using the app, (2) desired features, (3) when to use the app, (4) risks of using the app, (5) sharing with family and friends, and (6) sharing with health care professionals.<br><br>CONCLUSIONS: People with BD who are interested in using passive technology to monitor their mood wish to do so for a wide variety of purposes, identifying several preferences and potential risks. Principally, people with BD wished to use this novel technology to aid them in self-managing their BD with greater insight and a better understanding of potential triggers. We discuss key features that may aid this functionality and purpose, including crisis plans and sharing with others. Future development of passive mood-monitoring technologies should not assume that the involvement of formal mental health services is desired.}, }
@article {pmid39917311, year = {2025}, author = {Lysholm, S and Chaters, GL and Di Bari, C and Hughes, EC and Huntington, B and Rushton, J and Thomas, L}, title = {A framework for quantifying the multisectoral burden of animal disease to support decision making.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1476505}, pmid = {39917311}, issn = {2297-1769}, abstract = {Animal diseases have wide-ranging impacts in multiple societal arenas, including agriculture, public health and the environment. These diseases cause significant economic losses for farmers, disrupt food security and present zoonotic risks to human populations. Additionally, they contribute to antimicrobial resistance and a range of environmental issues such as greenhouse gas emissions. The societal and ecological costs of livestock diseases are frequently underrepresented or unaddressed in policy decisions and resource allocations. Social cost-benefit analysis (SCBA) offers a comprehensive framework to evaluate the broad impacts of animal diseases across different sectors. This approach aligns with the One Health concept, which seeks to integrate and optimize the health of humans, animals and the environment. Traditional economic evaluations often focus narrowly on profit maximization within the livestock sector, neglecting wider externalities such as public health and environmental impacts. In contrast, SCBA takes a multi-sectoral whole-system view, considering multiple factors to guide public and private sector investments toward maximizing societal benefits. This paper discusses three separate sector specific (Animal health, Human health, Environmental health) methodologies for quantifying the burden of animal diseases. It then discusses how these estimates can be combined to generate multisectoral estimates of the impacts of animal diseases on human societies and the environment using monetary values. Finally this paper explores how this framework can support the evaluation of interventions from a One Health perspective though SCBA. This integrated assessment framework supports informed decision-making and resource allocation, ultimately contributing to improved public health outcomes, enhanced animal welfare, and greater environmental sustainability.}, }
@article {pmid39915771, year = {2025}, author = {Gould, E and Fraser, HS and Parker, TH and Nakagawa, S and Griffith, SC and Vesk, PA and Fidler, F and Hamilton, DG and Abbey-Lee, RN and Abbott, JK and Aguirre, LA and Alcaraz, C and Aloni, I and Altschul, D and Arekar, K and Atkins, JW and Atkinson, J and Baker, CM and Barrett, M and Bell, K and Bello, SK and Beltrán, I and Berauer, BJ and Bertram, MG and Billman, PD and Blake, CK and Blake, S and Bliard, L and Bonisoli-Alquati, A and Bonnet, T and Bordes, CNM and Bose, APH and Botterill-James, T and Boyd, MA and Boyle, SA and Bradfer-Lawrence, T and Bradham, J and Brand, JA and Brengdahl, MI and Bulla, M and Bussière, L and Camerlenghi, E and Campbell, SE and Campos, LLF and Caravaggi, A and Cardoso, P and Carroll, CJW and Catanach, TA and Chen, X and Chik, HYJ and Choy, ES and Christie, AP and Chuang, A and Chunco, AJ and Clark, BL and Contina, A and Covernton, GA and Cox, MP and Cressman, KA and Crotti, M and Crouch, CD and D'Amelio, PB and de Sousa, AA and Döbert, TF and Dobler, R and Dobson, AJ and Doherty, TS and Drobniak, SM and Duffy, AG and Duncan, AB and Dunn, RP and Dunning, J and Dutta, T and Eberhart-Hertel, L and Elmore, JA and Elsherif, MM and English, HM and Ensminger, DC and Ernst, UR and Ferguson, SM and Fernandez-Juricic, E and Ferreira-Arruda, T and Fieberg, J and Finch, EA and Fiorenza, EA and Fisher, DN and Fontaine, A and Forstmeier, W and Fourcade, Y and Frank, GS and Freund, CA and Fuentes-Lillo, E and Gandy, SL and Gannon, DG and García-Cervigón, AI and Garretson, AC and Ge, X and Geary, WL and Géron, C and Gilles, M and Girndt, A and Gliksman, D and Goldspiel, HB and Gomes, DGE and Good, MK and Goslee, SC and Gosnell, JS and Grames, EM and Gratton, P and Grebe, NM and Greenler, SM and Griffioen, M and Griffith, DM and Griffith, FJ and Grossman, JJ and Güncan, A and Haesen, S and Hagan, JG and Hager, HA and Harris, JP and Harrison, ND and Hasnain, SS and Havird, JC and Heaton, AJ and Herrera-Chaustre, ML and Howard, TJ and Hsu, BY and Iannarilli, F and Iranzo, EC and Iverson, ENK and Jimoh, SO and Johnson, DH and Johnsson, M and Jorna, J and Jucker, T and Jung, M and Kačergytė, I and Kaltz, O and Ke, A and Kelly, CD and Keogan, K and Keppeler, FW and Killion, AK and Kim, D and Kochan, DP and Korsten, P and Kothari, S and Kuppler, J and Kusch, JM and Lagisz, M and Lalla, KM and Larkin, DJ and Larson, CL and Lauck, KS and Lauterbur, ME and Law, A and Léandri-Breton, DJ and Lembrechts, JJ and L'Herpiniere, K and Lievens, EJP and de Lima, DO and Lindsay, S and Luquet, M and MacLeod, R and Macphie, KH and Magellan, K and Mair, MM and Malm, LE and Mammola, S and Mandeville, CP and Manhart, M and Manrique-Garzon, LM and Mäntylä, E and Marchand, P and Marshall, BM and Martin, CA and Martin, DA and Martin, JM and Martinig, AR and McCallum, ES and McCauley, M and McNew, SM and Meiners, SJ and Merkling, T and Michelangeli, M and Moiron, M and Moreira, B and Mortensen, J and Mos, B and Muraina, TO and Murphy, PW and Nelli, L and Niemelä, P and Nightingale, J and Nilsonne, G and Nolazco, S and Nooten, SS and Novotny, JL and Olin, AB and Organ, CL and Ostevik, KL and Palacio, FX and Paquet, M and Parker, DJ and Pascall, DJ and Pasquarella, VJ and Paterson, JH and Payo-Payo, A and Pedersen, KM and Perez, G and Perry, KI and Pottier, P and Proulx, MJ and Proulx, R and Pruett, JL and Ramananjato, V and Randimbiarison, FT and Razafindratsima, OH and Rennison, DJ and Riva, F and Riyahi, S and Roast, MJ and Rocha, FP and Roche, DG and Román-Palacios, C and Rosenberg, MS and Ross, J and Rowland, FE and Rugemalila, D and Russell, AL and Ruuskanen, S and Saccone, P and Sadeh, A and Salazar, SM and Sales, K and Salmón, P and Sánchez-Tójar, A and Santos, LP and Santostefano, F and Schilling, HT and Schmidt, M and Schmoll, T and Schneider, AC and Schrock, AE and Schroeder, J and Schtickzelle, N and Schultz, NL and Scott, DA and Scroggie, MP and Shapiro, JT and Sharma, N and Shearer, CL and Simón, D and Sitvarin, MI and Skupien, FL and Slinn, HL and Smith, GP and Smith, JA and Sollmann, R and Whitney, KS and Still, SM and Stuber, EF and Sutton, GF and Swallow, B and Taff, CC and Takola, E and Tanentzap, AJ and Tarjuelo, R and Telford, RJ and Thawley, CJ and Thierry, H and Thomson, J and Tidau, S and Tompkins, EM and Tortorelli, CM and Trlica, A and Turnell, BR and Urban, L and Van de Vondel, S and van der Wal, JEM and Van Eeckhoven, J and van Oordt, F and Vanderwel, KM and Vanderwel, MC and Vanderwolf, KJ and Vélez, J and Vergara-Florez, DC and Verrelli, BC and Vieira, MV and Villamil, N and Vitali, V and Vollering, J and Walker, J and Walker, XJ and Walter, JA and Waryszak, P and Weaver, RJ and Wedegärtner, REM and Weller, DL and Whelan, S and White, RL and Wolfson, DW and Wood, A and Yanco, SW and Yen, JDL and Youngflesh, C and Zilio, G and Zimmer, C and Zimmerman, GM and Zitomer, RA}, title = {Same data, different analysts: variation in effect sizes due to analytical decisions in ecology and evolutionary biology.}, journal = {BMC biology}, volume = {23}, number = {1}, pages = {35}, pmid = {39915771}, issn = {1741-7007}, mesh = {Animals ; *Ecology/methods ; *Biological Evolution ; Eucalyptus/growth &amp; development ; }, abstract = {Although variation in effect sizes and predicted values among studies of similar phenomena is inevitable, such variation far exceeds what might be produced by sampling error alone. One possible explanation for variation among results is differences among researchers in the decisions they make regarding statistical analyses. A growing array of studies has explored this analytical variability in different fields and has found substantial variability among results despite analysts having the same data and research question. Many of these studies have been in the social sciences, but one small "many analyst" study found similar variability in ecology. We expanded the scope of this prior work by implementing a large-scale empirical exploration of the variation in effect sizes and model predictions generated by the analytical decisions of different researchers in ecology and evolutionary biology. We used two unpublished datasets, one from evolutionary ecology (blue tit, Cyanistes caeruleus, to compare sibling number and nestling growth) and one from conservation ecology (Eucalyptus, to compare grass cover and tree seedling recruitment). The project leaders recruited 174 analyst teams, comprising 246 analysts, to investigate the answers to prespecified research questions. Analyses conducted by these teams yielded 141 usable effects (compatible with our meta-analyses and with all necessary information provided) for the blue tit dataset, and 85 usable effects for the Eucalyptus dataset. We found substantial heterogeneity among results for both datasets, although the patterns of variation differed between them. For the blue tit analyses, the average effect was convincingly negative, with less growth for nestlings living with more siblings, but there was near continuous variation in effect size from large negative effects to effects near zero, and even effects crossing the traditional threshold of statistical significance in the opposite direction. In contrast, the average relationship between grass cover and Eucalyptus seedling number was only slightly negative and not convincingly different from zero, and most effects ranged from weakly negative to weakly positive, with about a third of effects crossing the traditional threshold of significance in one direction or the other. However, there were also several striking outliers in the Eucalyptus dataset, with effects far from zero. For both datasets, we found substantial variation in the variable selection and random effects structures among analyses, as well as in the ratings of the analytical methods by peer reviewers, but we found no strong relationship between any of these and deviation from the meta-analytic mean. In other words, analyses with results that were far from the mean were no more or less likely to have dissimilar variable sets, use random effects in their models, or receive poor peer reviews than those analyses that found results that were close to the mean. The existence of substantial variability among analysis outcomes raises important questions about how ecologists and evolutionary biologists should interpret published results, and how they should conduct analyses in the future.}, }
@article {pmid39910401, year = {2025}, author = {Fatima, M and Butt, I and MohammadEbrahimi, S and Kiani, B and Gruebner, O}, title = {Spatiotemporal clusters of acute respiratory infections associated with socioeconomic, meteorological, and air pollution factors in South Punjab, Pakistan.}, journal = {BMC public health}, volume = {25}, number = {1}, pages = {469}, pmid = {39910401}, issn = {1471-2458}, mesh = {Pakistan/epidemiology ; Humans ; Socioeconomic Factors ; *Respiratory Tract Infections/epidemiology ; *Air Pollution/adverse effects/statistics &amp; numerical data ; Spatio-Temporal Analysis ; Incidence ; *Meteorological Concepts ; Acute Disease ; Weather ; Female ; Male ; Risk Factors ; }, abstract = {BACKGROUND: In Pakistan, acute respiratory infections (ARI) continue to be a major public health problem. However, there is still a lack of scholarly work regarding different environmental and socioeconomic influencing factors and how they interact with respiratory infections. Furthermore, we do not know much about geographic variation in this context. Therefore, our study examines the ecological-level spatial and temporal patterns of acute respiratory infection incidence (ARI) and their geographic relationship with selected socio-economic, meteorological, and air pollution factors in Pakistan.<br><br>METHODS: We applied the spatiotemporal scan statistics to examine the purely temporal, spatial, and spatiotemporal clusters of ARI in South Punjab, Pakistan for five years (2016-2020). Generalized Linear Model (GLM) and geographically weighted regression (GWR) were also applied to model the linear and non-linear spatial relationships between selected variables and ARI.<br><br>RESULTS: Our results indicate that in the central and northern regions of Pakistan, two spatial clusters of ARI were present, accounting for 28.5% of the total cases. A spatiotemporal cluster with a relative risk of 1.57 was discovered in the northeastern area. The results obtained from the season-based GLM highlighted the significance of climatic factors (temperature, fog, dust storms) and air pollutants (NO2) in influencing ARI incidence, while socio-economic variables (rural population, literacy) had limited impact. In addition, GWR revealed that the relationships between predictors and ARI incidence varied across locations, emphasizing the importance of considering local settings. Season-based non-stationary GLM revealed a multifaceted interaction among socio-economic, meteorological, and air pollution factors.<br><br>CONCLUSIONS: Our study provides evidence about environmental and socio-economic factors significantly associated with ARI incidence. In addition, this study provides the first baseline of ARI cases in Pakistan to plan for intervention and adaptation strategies and may be replicated in other regions of comparable settings worldwide.}, }
@article {pmid39909332, year = {2025}, author = {Cheng, Z and He, Y and Wang, N and Wu, L and Xu, J and Shi, J}, title = {Uncovering soil amendment-induced genomic and functional divergence in soybean rhizosphere microbiomes during cadmium-contaminated soil remediation: Novel insights from field multi-omics.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {368}, number = {}, pages = {125787}, doi = {10.1016/j.envpol.2025.125787}, pmid = {39909332}, issn = {1873-6424}, mesh = {*Cadmium/analysis ; *Rhizosphere ; *Soil Pollutants/analysis ; *Glycine max/microbiology ; *Soil Microbiology ; *Microbiota ; Soil/chemistry ; Biodegradation, Environmental ; *Environmental Restoration and Remediation/methods ; Multiomics ; }, abstract = {Soil amendments exhibit great potential in reducing cadmium (Cd) bioavailability and its accumulation in crop grains, but their practical implications on microbial characteristics (genomic traits and ecological functions) remain unclear. The objective of this study was to combine metagenomics and metatranscriptomics to track the dynamics of bacterial and viral communities in the soybean rhizosphere during the remediation of Cd-contaminated soil using a commercial Mg-Ca-Si conditioner (CMC), applied at low and high (975 kg ha[-1] and 1950 kg ha[-1]) rates under field conditions. Application of CMC increased the average size and decreased the guanine-cytosine (GC) content of microbial genomes, which were strongly shaped by soil pH and available Cd (ACd). Gene and transcript abundances analysis indicated that CMC promoted the enrichment of Alphaproteobacterial metagenome-assembled genomes (MAGs) carrying czcC gene encoding Cd efflux and dsbB gene encoding disulfide bond oxidoreductase. These genes are closely related to Cd resistance and exhibited notable (p < 0.05) increased expression in CMC-treated soils. Additionally, low and high CMC addition significantly increased viral alpha diversity by 5.7% and 9.6%, and viral activity by 3.3% and 7.8%, respectively, in comparison to the control. Temperate viruses were predicted as the major group (64%) and actively linked to the dominant host, and CMC amendment increased host metabolism and adaptability by enhancing (p < 0.05) the abundance and transcriptional activity of virus-encoded auxiliary metabolic genes (AMGs) involved in heavy metal resistance (ABC transport), sulfur cycling (cysH), and host metabolism (galE and queD) through "piggyback-the-winner" strategy. Structural equation modeling further revealed that CMC application influences Cd accumulation in soybean grains through its direct and indirect effects on soil properties and rhizosphere microbiomes, and highlighted the potential role of rhizosphere viruses in agricultural soil remediation.}, }
@article {pmid39907430, year = {2025}, author = {Hebert, JD and Tang, YJ and Szamecz, M and Andrejka, L and Lopez, SS and Petrov, DA and Boross, G and Winslow, MM}, title = {Combinatorial In Vivo Genome Editing Identifies Widespread Epistasis and an Accessible Fitness Landscape During Lung Tumorigenesis.}, journal = {Molecular biology and evolution}, volume = {42}, number = {2}, pages = {}, pmid = {39907430}, issn = {1537-1719}, support = {P30 CA124435/CA/NCI NIH HHS/United States ; R01 CA230025/CA/NCI NIH HHS/United States ; R01 CA231253/CA/NCI NIH HHS/United States ; R01 CA234349/CA/NCI NIH HHS/United States ; }, mesh = {*Epistasis, Genetic ; Animals ; Mice ; *Lung Neoplasms/genetics ; *Carcinogenesis/genetics ; *Gene Editing ; Genetic Fitness ; *Adenocarcinoma of Lung/genetics ; }, abstract = {Lung adenocarcinoma, the most common subtype of lung cancer, is genomically complex, with tumors containing tens to hundreds of non-synonymous mutations. However, little is understood about how genes interact with each other to enable the evolution of cancer in vivo, largely due to a lack of methods for investigating genetic interactions in a high-throughput and quantitative manner. Here, we employed a novel platform to generate tumors with inactivation of pairs of ten diverse tumor suppressor genes within an autochthonous mouse model of oncogenic KRAS-driven lung cancer. By quantifying the fitness of tumors with every single and double mutant genotype, we show that most tumor suppressor genetic interactions exhibited negative epistasis, with diminishing returns on tumor fitness. In contrast, Apc inactivation showed positive epistasis with the inactivation of several other genes, including synergistic effects on tumor fitness in combination with Lkb1 or Nf1 inactivation. Sign epistasis was extremely rare, suggesting a surprisingly accessible fitness landscape during lung tumorigenesis. These findings expand our understanding of the interactions that drive tumorigenesis in vivo.}, }
@article {pmid39906497, year = {2025}, author = {Palande, S and Arsenault, J and Basurto-Lozada, P and Bleich, A and Brown, BNI and Buysse, SF and Connors, NA and Das Adhikari, S and Dobson, KC and Guerra-Castillo, FX and Guerrero-Carrillo, MF and Harlow, S and Herrera-Orozco, H and Hightower, AT and Izquierdo, P and Jacobs, M and Johnson, NA and Leuenberger, W and Lopez-Hernandez, A and Luckie-Duque, A and Martínez-Avila, C and Mendoza-Galindo, EJ and Plancarte, DC and Schuster, JM and Shomer, H and Sitar, SC and Steensma, AK and Thomson, JE and Villaseñor-Amador, D and Waterman, R and Webster, BM and Whyte, M and Zorilla-Azcué, S and Montgomery, BL and Husbands, AY and Krishnan, A and Percival, S and Munch, E and VanBuren, R and Chitwood, DH and Rougon-Cardoso, A}, title = {Expression-based machine learning models for predicting plant tissue identity.}, journal = {Applications in plant sciences}, volume = {13}, number = {1}, pages = {e11621}, pmid = {39906497}, issn = {2168-0450}, abstract = {PREMISE: The selection of Arabidopsis as a model organism played a pivotal role in advancing genomic science. The competing frameworks to select an agricultural- or ecological-based model species were rejected, in favor of building knowledge in a species that would facilitate genome-enabled research.<br><br>METHODS: Here, we examine the ability of models based on Arabidopsis gene expression data to predict tissue identity in other flowering plants. Comparing different machine learning algorithms, models trained and tested on Arabidopsis data achieved near perfect precision and recall values, whereas when tissue identity is predicted across the flowering plants using models trained on Arabidopsis data, precision values range from 0.69 to 0.74 and recall from 0.54 to 0.64.<br><br>RESULTS: The identity of belowground tissue can be predicted more accurately than other tissue types, and the ability to predict tissue identity is not correlated with phylogenetic distance from Arabidopsis. k-nearest neighbors is the most successful algorithm, suggesting that gene expression signatures, rather than marker genes, are more valuable to create models for tissue and cell type prediction in plants.<br><br>DISCUSSION: Our data-driven results highlight that the assertion that knowledge from Arabidopsis is translatable to other plants is not always true. Considering the current landscape of abundant sequencing data, we should reevaluate the scientific emphasis on Arabidopsis and prioritize plant diversity.}, }
@article {pmid39904391, year = {2025}, author = {Mihaljevic, JR and Páez, DJ}, title = {Systematic shifts in the variation among host individuals must be considered in climate-disease theory.}, journal = {Proceedings. Biological sciences}, volume = {292}, number = {2040}, pages = {20242515}, pmid = {39904391}, issn = {1471-2954}, support = {//Exxon Valdez Oil Spill Trustee Council/ ; //Division of Environmental Biology/ ; }, mesh = {*Climate Change ; Temperature ; *Host-Pathogen Interactions ; Animals ; Population Dynamics ; Models, Biological ; Disease Susceptibility ; }, abstract = {To make more informed predictions of host-pathogen interactions under climate change, studies have incorporated the thermal performance of host, vector and pathogen traits into disease models to quantify effects on average transmission rates. However, this body of work has omitted the fact that variation in susceptibility among individual hosts affects disease spread and long-term patterns of host population dynamics. Furthermore, and especially for ectothermic host species, variation in susceptibility is likely to be plastic, influenced by variables such as environmental temperature. For example, as host individuals respond idiosyncratically to temperature, this could affect the population-level variation in susceptibility, such that there may be predictable functional relationships between variation in susceptibility and temperature. Quantifying the relationship between temperature and among-host trait variation will therefore be critical for predicting how climate change and disease will interact to influence host-pathogen population dynamics. Here, we use a model to demonstrate how short-term effects of temperature on the distribution of host susceptibility can drive epidemic characteristics, fluctuations in host population sizes and probabilities of host extinction. Our results emphasize that more research is needed in disease ecology and climate biology to understand the mechanisms that shape individual trait variation, not just trait averages.}, }
@article {pmid39903560, year = {2025}, author = {Thomas, GWC and Hughes, JJ and Kumon, T and Berv, JS and Nordgren, CE and Lampson, M and Levine, M and Searle, JB and Good, JM}, title = {The Genomic Landscape, Causes, and Consequences of Extensive Phylogenomic Discordance in Murine Rodents.}, journal = {Genome biology and evolution}, volume = {17}, number = {2}, pages = {}, pmid = {39903560}, issn = {1759-6653}, support = {RRID:SCR_021757//Cornell University Biotechnology Resource Center BioHPC/ ; //Cornell Center for Vertebrate Genomics/ ; //University of Michigan Museum of Zoology/ ; R35 GM124684/GM/NIGMS NIH HHS/United States ; DEB-1754096//National Science Foundation/ ; CC-2018112//University of Montana Griz Shared Computing Cluster/ ; MRI-2215705//University of California Riverside HPCC/ ; //Jean Wright Cohn Endowment Fund/ ; //University of Michigan Life Sciences Fellows Program/ ; S10 OD016290/OD/NIH HHS/United States ; R01 HD094787/HD/NICHD NIH HHS/United States ; //Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; R01-HD094787/NH/NIH HHS/United States ; }, mesh = {Animals ; *Phylogeny ; Mice/genetics ; *Genome ; Rats/genetics ; Evolution, Molecular ; Rodentia/genetics ; Genomics ; Conserved Sequence ; Selection, Genetic ; Recombination, Genetic ; }, abstract = {A species tree is a central concept in evolutionary biology whereby a single branching phylogeny reflects relationships among species. However, the phylogenies of different genomic regions often differ from the species tree. Although tree discordance is widespread in phylogenomic studies, we still lack a clear understanding of how variation in phylogenetic patterns is shaped by genome biology or the extent to which discordance may compromise comparative studies. We characterized patterns of phylogenomic discordance across the murine rodents-a large and ecologically diverse group that gave rise to the laboratory mouse and rat model systems. Combining recently published linked-read genome assemblies for seven murine species with other available rodent genomes, we first used ultraconserved elements (UCEs) to infer a robust time-calibrated species tree. We then used whole genomes to examine finer-scale patterns of discordance across ∼12 million years of divergence. We found that proximate chromosomal regions tended to have more similar phylogenetic histories. There was no clear relationship between local tree similarity and recombination rates in house mice, but we did observe a correlation between recombination rates and average similarity to the species tree. We also detected a strong influence of linked selection whereby purifying selection at UCEs led to appreciably less discordance. Finally, we show that assuming a single species tree can result in substantial deviation from the results with gene trees when testing for positive selection under different models. Collectively, our results highlight the complex relationship between phylogenetic inference and genome biology and underscore how failure to account for this complexity can mislead comparative genomic studies.}, }
@article {pmid39903189, year = {2025}, author = {Gallardo García Freire, P and Matías, E and Malizia, A and Monmany-Garzia, AC and Galindo-Cardona, A}, title = {Pollution risk assessment in sub-basins of an open dump using drones and geographic information systems.}, journal = {Waste management &amp; research : the journal of the International Solid Wastes and Public Cleansing Association, ISWA}, volume = {43}, number = {9}, pages = {1425-1433}, doi = {10.1177/0734242X251314180}, pmid = {39903189}, issn = {1096-3669}, mesh = {*Geographic Information Systems ; Risk Assessment ; Argentina ; *Environmental Monitoring/methods ; *Unmanned Aerial Devices ; *Refuse Disposal/methods ; Satellite Imagery ; *Solid Waste/analysis ; *Environmental Pollution/analysis ; }, abstract = {The sustainable management of municipal solid waste (MSW) presents a pressing global challenge. This study introduces an innovative methodology for analysing open dumps in Tucumán, Argentina, using unmanned aerial vehicles (UAVs) and DroneDeploy software for data collection, coupled with QGIS for estimating contamination risk at the sub-basin level. By integrating satellite imagery, ground surveys, high-resolution UAV imagery and a multi-criteria decision analysis within geographic information system, we provide a comprehensive overview of dumpsite conditions at one open dump. Commercial drone flights facilitate the rapid and cost-effective creation of digital elevation models and digital terrain models, along with orthomosaic imagery, from which waste footprints are delineated using artificial intelligence to enhance the understanding of geospatial issues. Approaching data layers, such as leachate pools, riverbanks and solar radiation, supports informed decision-making in MSW management through a replicable methodology. Field validation and the inclusion of subsurface and groundwater processes are recommended for future research to improve accuracy and maximize socio-ecological benefits.}, }
@article {pmid39900590, year = {2025}, author = {Chen, Y and Zheng, L and Ma, J and Zhu, H and Gan, Y}, title = {The Mediating Role of Meaning-Making in the Relationship Between Mental Time Travel and Positive Emotions in Stress-Related Blogs: Big Data Text Analysis Research.}, journal = {Journal of medical Internet research}, volume = {27}, number = {}, pages = {e63407}, pmid = {39900590}, issn = {1438-8871}, mesh = {Humans ; *Emotions ; *Stress, Psychological/psychology ; *Big Data ; *Blogging ; }, abstract = {BACKGROUND: Given the ubiquity of stress, a key focus of stress research is exploring how to better coexist with stress.<br><br>OBJECTIVE: This study conducted text analysis on stress-related Weibo posts using a web crawler to investigate whether these posts contained positive emotions, as well as elements of mental time travel and meaning-making. A mediation model of mental time travel, meaning-making, and positive emotions was constructed to examine whether meaning-making triggered by mental time travel can foster positive emotions under stress.<br><br>METHODS: Using Python 3.8, the original public data from active Weibo users were crawled, yielding 331,711 stress-related posts. To avoid false positives, these posts were randomly divided into two large samples for cross-validation (sample 1: n=165,374; sample 2: n=166,337). Google's natural language processing application programming interface was used for word segmentation, followed by text and mediation analysis using the Chinese psychological analysis system "Wenxin." A mini-meta-analysis of the mediation path coefficients was conducted. Text analysis identified mental time travel words, meaning-making words, and positive emotion words in stress-related posts.<br><br>RESULTS: The constructed mediation model of mental time travel words (time words), meaning-making words (causal and insightful words), and positive poststress emotions validated positive adaptation following stress. A mini-meta-analysis of two different mediation models constructed in the two subsamples indicated a stable mediation effect across the 2 random subsamples. The combined effect size (B) obtained was .013 (SE 0.003, 95% CI 0.007-0.018; P<.001), demonstrating that meaning-making triggered by mental time travel in stress-related blog posts can predict positive emotions under stress.<br><br>CONCLUSIONS: Individuals can adapt positively to stress by engaging in meaning-making processes that are triggered by mental time travel and reflected in their social media posts. The study's mediation model confirmed that mental time travel leads to meaning-making, which fosters positive emotional responses to stress. Mental time travel serves as a psychological strategy to facilitate positive adaptation to stressful situations.}, }
@article {pmid39899643, year = {2025}, author = {Hozé, N and Pons-Salort, M and Metcalf, CJE and White, M and Salje, H and Cauchemez, S}, title = {RSero: A user-friendly R package to reconstruct pathogen circulation history from seroprevalence studies.}, journal = {PLoS computational biology}, volume = {21}, number = {2}, pages = {e1012777}, pmid = {39899643}, issn = {1553-7358}, support = {/WT_/Wellcome Trust/United Kingdom ; R01 AI175941/AI/NIAID NIH HHS/United States ; U01 AI151758/AI/NIAID NIH HHS/United States ; }, mesh = {Seroepidemiologic Studies ; Humans ; Bayes Theorem ; *Software ; *Computational Biology/methods ; Computer Simulation ; Disease Outbreaks/statistics &amp; numerical data ; Epidemiological Models ; }, abstract = {Population-based serological surveys are a key tool in epidemiology to characterize the level of population immunity and reconstruct the past circulation of pathogens. A variety of serocatalytic models have been developed to estimate the force of infection (FOI) (i.e., the rate at which susceptible individuals become infected) from age-stratified seroprevalence data. However, few tool currently exists to easily implement, combine, and compare these models. Here, we introduce an R package, Rsero, that implements a series of serocatalytic models and estimates the FOI from age-stratified seroprevalence data using Bayesian methods. The package also contains a series of features to perform model comparison and visualise model fit. We introduce new serocatalytic models of successive outbreaks and extend existing models of seroreversion to any transmission model. The different features of the package are illustrated with simulated and real-life data. We show we can identify the correct epidemiological scenario and recover model parameters in different epidemiological settings. We also show how the package can support serosurvey study design in a variety of epidemic situations. This package provides a standard framework to epidemiologists and modellers to study the dynamics of past pathogen circulation from cross-sectional serological survey data.}, }
@article {pmid39899630, year = {2025}, author = {Sheen, JK and Kennedy-Shaffer, L and Levy, MZ and Metcalf, CJE}, title = {Design of field trials for the evaluation of transmissible vaccines in animal populations.}, journal = {PLoS computational biology}, volume = {21}, number = {2}, pages = {e1012779}, pmid = {39899630}, issn = {1553-7358}, mesh = {Animals ; *Vaccines/immunology ; *Vaccination/veterinary ; Computational Biology ; Research Design ; }, abstract = {Vaccines which can transmit from vaccinated to unvaccinated animals may be especially useful for increasing immunity in hard to reach populations or in populations where achieving high coverage is logistically infeasible. However, gauging the public health utility for future use of such transmissible vaccines and assessing their risk-benefit tradeoff, given their potential for unintended evolution, hinges on accurate estimates of their indirect protective effect. Here, we establish the conditions under which a two-stage randomized field trial can characterize the protective effects of a transmissible vaccine relative to a traditional vaccine. We contrast the sample sizes required to adequately power these trials when the vaccine is weakly and strongly transmissible. We also identify how required sample sizes change based on the characteristics of host ecology such as the overdispersion of the contact structure of the population, as well as the efficacy of the vaccine and timing of vaccination. Our results indicate the range of scenarios where two-stage randomized field trial designs are feasible and appropriate to capture the protective effects of transmissible vaccines. Our estimates identify the protective benefit of using transmissible vaccines compared to traditional vaccines, and thus can be used to weigh against evolutionary risks.}, }
@article {pmid39899595, year = {2025}, author = {McKenzie-Smith, GC and Wolf, SW and Ayroles, JF and Shaevitz, JW}, title = {Capturing continuous, long timescale behavioral changes in Drosophila melanogaster postural data.}, journal = {PLoS computational biology}, volume = {21}, number = {2}, pages = {e1012753}, pmid = {39899595}, issn = {1553-7358}, support = {R01 ES029929/ES/NIEHS NIH HHS/United States ; R35 GM124881/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Drosophila melanogaster/physiology ; *Behavior, Animal/physiology ; Locomotion/physiology ; Circadian Rhythm/physiology ; *Posture/physiology ; Computational Biology ; Female ; Grooming/physiology ; }, abstract = {Animal behavior spans many timescales, from short, seconds-scale actions to daily rhythms over many hours to life-long changes during aging. To access longer timescales of behavior, we continuously recorded individual Drosophila melanogaster at 100 frames per second for up to 7 days at a time in featureless arenas on sucrose-agarose media. We use the deep learning framework SLEAP to produce a full-body postural dataset for 47 individuals resulting in nearly 2 billion pose instances. We identify stereotyped behaviors such as grooming, proboscis extension, and locomotion and use the resulting ethograms to explore how the flies' behavior varies across time of day and days in the experiment. We find distinct daily patterns in all stereotyped behaviors, adding specific information about trends in different grooming modalities, proboscis extension duration, and locomotion speed to what is known about the D. melanogaster circadian cycle. Using our holistic measurements of behavior, we find that the hour after dawn is a unique time point in the flies' daily pattern of behavior, and that the behavioral composition of this hour tracks well with other indicators of health such as locomotion speed and the fraction of time spend moving vs. resting. The method, data, and analysis presented here give us a new and clearer picture of D. melanogaster behavior across timescales, revealing novel features that hint at unexplored underlying biological mechanisms.}, }
@article {pmid39897903, year = {2025}, author = {Doshi, P and Klas, M and Kyzek, S and Zahoranová, A and Šerá, B}, title = {Investigating the effect of plasma activated water on entomopathogenic nematodes under laboratory conditions.}, journal = {Heliyon}, volume = {11}, number = {2}, pages = {e42038}, pmid = {39897903}, issn = {2405-8440}, abstract = {Entomopathogenic nematodes are currently being tested for their efficiency in controlling several insect pests. In recent years, non-thermal plasma has been investigated as a state-of-the-art technology for its disinfection/decontamination properties on the seed surface. In addition, it is also used to induce seed germination. In this investigation, the effect of plasma activated water (PAW) was tested on three EPN species, namely Steinernema feltiae Filipjev (1934), S. carpocapsae Weiser (1955), and Heterorhabditis bacteriophora Poinar (1976). Seven different PAW prepared at different treatment times, that is, (1s, 3s, 5s, 10s, 20s, 60s, 90s) were tested directly on the three selected nematode species. Distilled water was used as a control treatment (0s). In the case of H. bacteriophora, significantly higher mortality was observed in PAW preparation times of 5, 10, 20, 60 and 90s compared to the control. In the case of S. feltiae, significantly high mortality was observed for PAW preparation times of 10, 20, 60 and 90s. However, S. carpocapsae was found to have the least sensitivity against all PAW treatments, with a maximum mortality of 14 % (<20 %), indicating the potential synergy between PAW and EPNs. The possibility of combined treatments in the context of integrated pest management is presented and discussed.}, }
@article {pmid39897842, year = {2025}, author = {Loukili, I and Laamrani, A and El Ghorfi, M and El Moutak, S and Ghafiri, A}, title = {Monitoring land changes at an open mine site using remote sensing and multi-spectral indices.}, journal = {Heliyon}, volume = {11}, number = {2}, pages = {e41845}, pmid = {39897842}, issn = {2405-8440}, abstract = {This study investigates the growth of mining activities in Benguerir, one of Morocco's largest and fastest-growing phosphate mines and a global leader in phosphate production, using remote sensing and ancillary data. The study examines spatio-temporal changes in land use and land cover (LULC) within this phosphate mining city to analyze the impacts of mining on agricultural areas, built-up lands, and water bodies over time. A series of images from 1984 to 2021 were processed in to assess patterns of change within the city. Five LULC maps were generated using supervised classification with the maximum likelihood method, providing detailed insights into both urban and non-urban transformations during the study period. Classification quality was evaluated using accuracy assessment and the Kappa index. Additionally, multi-spectral indices, including the Normalized Difference Vegetation Index (NDVI), Normalized Difference Water Index (NDWI), and Normalized Difference Built-up Index (NDBI), were simulated and analyzed across four intervals. The results reveal significant variations in LULC and ecological indices over time, which are associated with mining activities, water stress, urban sprawl, and socio-economic changes in the region.These results provide a valuable means for decision-makers and planners to effectively manage the spaces and lands in the future.}, }
@article {pmid39897809, year = {2025}, author = {Milling, M and Rampp, SDN and Triantafyllopoulos, A and Plaza, MP and Brunner, JO and Traidl-Hoffmann, C and Schuller, BW and Damialis, A}, title = {Automating airborne pollen classification: Identifying and interpreting hard samples for classifiers.}, journal = {Heliyon}, volume = {11}, number = {2}, pages = {e41656}, pmid = {39897809}, issn = {2405-8440}, abstract = {Deep-learning-based classification of pollen grains has been a major driver towards automatic monitoring of airborne pollen. Yet, despite an abundance of available datasets, little effort has been spent to investigate which aspects pose the biggest challenges to the (often black-box- resembling) pollen classification approaches. To shed some light on this issue, we conducted a sample-level difficulty analysis based on the likelihood for one of the largest automatically-generated datasets of pollen grains on microscopy images and investigated the reason for which certain airborne samples and specific pollen taxa pose particular problems to deep learning algorithms. It is here concluded that the main challenges lie in A) the (partly) co-occurring of multiple pollen grains in a single image, B) the occlusion of specific markers through the 2D capturing of microscopy images, and C) for some taxa, a general lack of salient, unique features. Our code is publicly available under https://github.com/millinma/SDPollen.}, }
@article {pmid39897501, year = {2025}, author = {Fuster-Calvo, A and Valentin, S and Tamayo, WC and Gravel, D}, title = {Evaluating the feasibility of automating dataset retrieval for biodiversity monitoring.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e18853}, pmid = {39897501}, issn = {2167-8359}, mesh = {*Biodiversity ; *Databases, Factual ; *Information Storage and Retrieval/methods ; Algorithms ; Feasibility Studies ; *Conservation of Natural Resources/methods ; Quebec ; }, abstract = {AIM: Effective management strategies for conserving biodiversity and mitigating the impacts of global change rely on access to comprehensive and up-to-date biodiversity data. However, manual search, retrieval, evaluation, and integration of this information into databases present a significant challenge to keeping pace with the rapid influx of large amounts of data, hindering its utility in contemporary decision-making processes. Automating these tasks through advanced algorithms holds immense potential to revolutionize biodiversity monitoring.<br><br>INNOVATION: In this study, we investigate the potential for automating the retrieval and evaluation of biodiversity data from Dryad and Zenodo repositories. We have designed an evaluation system based on various criteria, including the type of data provided and its spatio-temporal range, and applied it to manually assess the relevance for biodiversity monitoring of datasets retrieved through an application programming interface (API). We evaluated a supervised classification to identify potentially relevant datasets and investigate the feasibility of automatically ranking the relevance. Additionally, we applied the same appraoch on a scientific literature source, using data from Semantic Scholar for reference. Our evaluation centers on the database utilized by a national biodiversity monitoring system in Quebec, Canada.<br><br>MAIN CONCLUSIONS: We retrieved 89 (55%) relevant datasets for our database, showing the value of automated dataset search in repositories. Additionally, we find that scientific publication sources offer broader temporal coverage and can serve as conduits guiding researchers toward other valuable data sources. Our automated classification system showed moderate performance in detecting relevant datasets (with an F-score up to 0.68) and signs of overfitting, emphasizing the need for further refinement. A key challenge identified in our manual evaluation is the scarcity and uneven distribution of metadata in the texts, especially pertaining to spatial and temporal extents. Our evaluative framework, based on predefined criteria, can be adopted by automated algorithms for streamlined prioritization, and we make our manually evaluated data publicly available, serving as a benchmark for improving classification techniques.}, }
@article {pmid39892263, year = {2025}, author = {Yang, W and Liu, Y and Shao, H and Iravani, M and Yu, Z and Weber, M}, title = {Developing a cloud-based WebGIS tool for communicating integrated ecosystem services assessment modeling to conservation stakeholders.}, journal = {Journal of environmental management}, volume = {375}, number = {}, pages = {124372}, doi = {10.1016/j.jenvman.2025.124372}, pmid = {39892263}, issn = {1095-8630}, mesh = {*Cloud Computing ; *Geographic Information Systems ; Ecosystem ; *Agriculture/economics/methods/statistics &amp; numerical data ; *Conservation of Natural Resources/economics/methods/statistics &amp; numerical data ; Environmental Monitoring ; Models, Statistical ; Farms/economics/statistics &amp; numerical data ; Cost-Effectiveness Analysis ; Alberta ; Agroecology/economics/methods/statistics &amp; numerical data ; Stakeholder Participation ; Hydrology ; }, abstract = {Various modeling efforts have been conducted to evaluate ecosystem services (ES) of agricultural conservation practices but typically these models are too complex for conservation stakeholders to use. This research developed a cloud-based WebGIS tool for communicating integrated ES modeling to conservation stakeholders. The integrated ES modeling was developed by linking farm economic, watershed hydrologic, and soil carbon modeling within a spatial optimization framework for identifying conservation practices to minimize economic costs subject to multiple ES targets including water quality and soil carbon improvement benefits. The WebGIS tool, named "Ecosystem Services Assessment Tool" (ESAT), has a suite of functions to visualize watershed characteristics, summarize the effectiveness of existing agricultural conservation practices, examine the cost, effectiveness, and cost-effectiveness of future agricultural conservation practices, and further, identify optimal sets of conservation practices for achieving cost-effectiveness. The study area for the integrated ES modeling and WebGIS tool development was the 4,820-km[2] Modeste watershed in Alberta, Canada. The ESAT application demonstrated its functionalities to support decision making, particularly in identifying cost-effective conservation practices for achieving sediment, phosphorus or nitrogen reduction, or soil carbon increase target. In the research, conservation stakeholders including municipal and provincial governments, conservation management agencies, and NGOs were actively engaged in data collection, modeling development, WebGIS tool development, and training for the use of the WebGIS tool. Conservation stakeholders assessed that the ESAT is a very useful tool for supporting decision making in agri-environmental programs. However, the WebGIS tool can be further simplified and streamlined to improve the user-friendliness of the ESAT.}, }
@article {pmid39891349, year = {2025}, author = {Wang, Y and Li, J and Chiu, TP and Gompel, N and Rohs, R}, title = {DNAdesign: feature-aware in silico design of synthetic DNA through mutation.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {2}, pages = {}, pmid = {39891349}, issn = {1367-4811}, support = {R35 GM130376/GM/NIGMS NIH HHS/United States ; RGP0021/2018//Human Frontier Science Program/ ; }, mesh = {*DNA/chemistry/genetics ; *Software ; *Mutation ; Nucleic Acid Conformation ; Computer Simulation ; *Computational Biology/methods ; Binding Sites ; Sequence Analysis, DNA/methods ; Base Sequence ; Synthetic Biology/methods ; }, abstract = {MOTIVATION: DNA sequence and shape readout represent different modes of protein-DNA recognition. Current tools lack the functionality to simultaneously consider alterations in different readout modes caused by sequence mutations. DNAdesign is a web-based tool to compare and design mutations based on both DNA sequence and shape characteristics. Users input a wild-type sequence, select sites to introduce mutations and choose a set of DNA shape parameters for mutation design.<br><br>RESULTS: DNAdesign utilizes Deep DNAshape to provide ultra-fast predictions of DNA shape based on extended k-mers and offers multiple encoding methods for nucleotide sequences, including the physicochemical encoding of DNA through their functional groups in the major and minor groove. DNAdesign provides all mutation candidates along the sequence and shape dimensions, with interactive visualization comparing each candidate with the wild-type DNA molecule. DNAdesign provides an approach to studying gene regulation and applications in synthetic biology, such as the design of synthetic enhancers and transcription factor binding sites.<br><br>The DNAdesign webserver and documentation are freely accessible at https://dnadesign.usc.edu.}, }
@article {pmid39890763, year = {2025}, author = {Kuru, A and Yüzer, MA and Yüzer, A&#x15e; and Güney, BG and Yüzer, ME}, title = {Integrated site selection model for industrial areas: case study for İnegöl furniture industry.}, journal = {Environmental science and pollution research international}, volume = {32}, number = {8}, pages = {4771-4793}, pmid = {39890763}, issn = {1614-7499}, mesh = {*Interior Design and Furnishings ; *Industry ; Noise ; Odorants/analysis ; Environmental Monitoring ; Socioeconomic Factors ; Geographic Information Systems ; *Environment ; }, abstract = {Industrial activities in the central area have adverse effects such as noise, odor, and traffic congestion. Simultaneously, due to changing technological and economic advances, existing industrial areas cannot meet the needs, spatial inadequacies obstruct competition, and production capacity decreases. Decentralizing industrial activities from urban centers are ecologically and economically necessary. Various elements on a macro and micro scale need to be considered to select suitable sites for new industrial areas. Natural, socioeconomic, and built environment features must be examined to ensure sustainability. The objective of this study is to develop an integrated industrial site location model that considers the needs of authorities and industrial stakeholders, as well as economic and ecological sustainability for the İnegöl district, one of Turkey's leading settlements in the furniture industry. Thirty-seven criteria were evaluated using GIS based multi-criteria decision making methods. The criteria were defined through spatial analysis, expert opinions, and in-depth interviews with industry and local government representatives. Using weighted linear combination process the five sub-regions exhibiting the lowest economic costs and the least environmental degradation have been identified. Advantages and disadvantages were identified through the use of sketches and comparisons between the sub-regions. A decision support system was developed for local and central government institutions to be used in industrial site selection processes.}, }
@article {pmid39889433, year = {2025}, author = {Shukla, S and Khan, R and Chrzanowski, &#x141; and Vagliasindi, FGA and Roccaro, P}, title = {Advancing sustainable agriculture through multi-omics profiling of biosolids for safe application: A review.}, journal = {Journal of environmental management}, volume = {375}, number = {}, pages = {124292}, doi = {10.1016/j.jenvman.2025.124292}, pmid = {39889433}, issn = {1095-8630}, mesh = {*Agriculture/methods ; Soil ; Multiomics ; }, abstract = {Biosolids, derived from wastewater treatment processes, are valuable resources for soil amendment in agriculture due to their nutrient-rich composition. However, various contaminants of concern (CEC) such as pharmaceuticals, per-and poly-fluoroalkyl substances, endocrine disruptive chemicals, surfactants, pathogens, nanoplastics, and microplastics, are also reported in biosolids. The use of biosolids for agriculture may introduce these CEC into the soil, which raises concerns about their environmental and human health impacts. Moreover, the presence of pathogens (Escherichia coli, Salmonella sp., Shigella, Giardia, Rotavirus, etc.) even after treatment calls for microbial profiling of biosolids, especially in developing countries. Multi-omics approaches can be used as powerful tools for characterizing microbial communities and highlighting metabolic pathways. Moreover, these approaches also help in predicting the ecological and agronomic effects of biosolids application in agricultural soils. This review discusses the advantages and challenges of using biosolids in agriculture, considering the range of different CEC reported in biosolids. Moreover, the current legislation for the use of biosolids in agriculture is also presented, highlighting the limitations with respect to guidelines for emerging contaminants in biosolids. Furthermore, the role of the multi-omics approach in biosolids management, focusing on genomics, transcriptomics, proteomics, and metabolomics is also assessed. Multi-omics also allows for real-time monitoring, ensuring continuous optimization of biosolids towards changing environmental conditions. This dynamic approach not only enhances the safe use, but also enhances the sustainability of waste management practices, minimizing the negative effects. Finally, the future research directions for integrating the multi-omics approach into biosolid management practices are also suggested. The need for updating the legislative framework, continued innovation to promote sustainable and robust agricultural systems, bringing the process closer to the principles of a circular bioeconomy is also empahasized.}, }
@article {pmid39889380, year = {2025}, author = {Weeks, F and Myerson, R and Gangnon, R and Dykema, J and Cornelius, C and Green, T}, title = {Racial disparities in intrapartum care experiences and birth hospital characteristics.}, journal = {Social science &amp; medicine (1982)}, volume = {367}, number = {}, pages = {117720}, doi = {10.1016/j.socscimed.2025.117720}, pmid = {39889380}, issn = {1873-5347}, mesh = {Humans ; Female ; Adult ; Pregnancy ; *Healthcare Disparities/ethnology/statistics &amp; numerical data ; Wisconsin ; *Hospitals/statistics &amp; numerical data/standards ; Surveys and Questionnaires ; *Racial Groups/statistics &amp; numerical data/ethnology ; Black or African American/statistics &amp; numerical data ; Patient-Centered Care ; Logistic Models ; White ; }, abstract = {Policymakers and researchers have posited intrapartum care as a potential mediator of racial inequities in perinatal outcomes. However, few studies have measured patient-centered quality of intrapartum care or explored differences by race. To address this gap, we developed a survey supplement using cognitive interviewing and administered it to a probability-based race-stratified random sample of people who recently gave birth in Wisconsin in 2020, including oversamples of non-Hispanic Black and Indigenous birthing people. We estimate overall and race-specific prevalences of intrapartum care experiences and use survey-weighted mixed effects ordinal and logistic regression to estimate differences in intrapartum care experiences by race/ethnicity and hospital characteristics. We find significant racial differences in the population prevalence of negative experiences of intrapartum care providers, including disrespect, lack of responsiveness, inclusion in decision-making about care, and pressure to use epidural analgesia. In unadjusted models, both non-Hispanic Indigenous (American Indian/Alaska Native) and non-Hispanic Black respondents had higher odds (than non-Hispanic White birthing people) of reporting several negative intrapartum experiences, including feeling disrespected by providers and experiencing a lower level of care team responsiveness. In adjusted models, Indigenous respondents had significantly higher odds of reporting that intrapartum care providers withheld information, showed disrespect, and were less responsive. Giving birth at a low birth-volume hospital was associated with higher odds of reporting greater participation in decision-making. CONCLUSION: While all birthing people are entitled to respectful and person-centered care, in practice, Indigenous and Black birthing persons are more likely than their white counterparts to endure negative intrapartum experiences including disrespect and lack of responsiveness to their needs. Equitable implementation of person-centered care principles will require concerted efforts to institutionalize practices that preserve patient dignity and autonomy.}, }
@article {pmid39888239, year = {2025}, author = {Giles, EC and González, VL and Carimán, P and Leiva, C and Suescún, AV and Lemer, S and Guillemin, ML and Ortiz-Barrientos, D and Saenz-Agudelo, P}, title = {Comparative Genomics Points to Ecological Drivers of Genomic Divergence Among Intertidal Limpets.}, journal = {Molecular ecology resources}, volume = {25}, number = {4}, pages = {e14075}, doi = {10.1111/1755-0998.14075}, pmid = {39888239}, issn = {1755-0998}, support = {2190878//BECA CONICYT-PCHA/Doctorado Nacional Chile/2019/ ; 1190710//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; OIA-1946352//National Science Foundation NSF-EPSCoR/ ; }, mesh = {Animals ; *Gastropoda/genetics/classification ; *Genomics ; *Genetic Variation ; *Evolution, Molecular ; *Genome ; Transcriptome ; Ecosystem ; }, abstract = {Comparative genomic studies of closely related taxa are important for our understanding of the causes of divergence on a changing Earth. This being said, the genomic resources available for marine intertidal molluscs are limited and currently, there are few publicly available high-quality annotated genomes for intertidal species and for molluscs in general. Here we report transcriptome assemblies for six species of Patellogastropoda and genome assemblies and annotations for three of these species (Scurria scurra, Scurria viridula and Scurria zebrina). Comparative analysis using these genomic resources suggest that and recently diverging lineages (10-20 Mya) have experienced similar amounts of contractions and expansions but across different gene families. Furthermore, differences among recently diverged species are reflected in variation in the amount of coding and noncoding material in genomes, such as amount of repetitive elements and lengths of transcripts and introns and exons. Additionally, functional ontologies of species-specific and duplicated genes together with demographic inference support the finding that recent divergence among members of the genus Scurria aligns with their unique ecological characteristics. Overall, the resources presented here will be valuable for future studies of adaptation in molluscs and in intertidal habitats as a whole.}, }
@article {pmid39882857, year = {2025}, author = {Grettenberger, C and Gold, DA and Brown, CT}, title = {Distribution of early-branching Cyanobacteriia and the potential habitats that gave rise to the earliest oxygenic phototrophs.}, journal = {mSphere}, volume = {10}, number = {2}, pages = {e0101324}, pmid = {39882857}, issn = {2379-5042}, mesh = {*Cyanobacteria/genetics/classification/metabolism ; *Ecosystem ; Photosynthesis ; Phylogeny ; *Oxygen/metabolism ; *Phototrophic Processes ; Computational Biology ; Metagenome ; Biological Evolution ; }, abstract = {The evolution of oxygenic photosynthesis in the Cyanobacteria was one of the most transformative events in Earth history, eventually leading to the oxygenation of Earth's atmosphere. However, it is difficult to understand how the earliest Cyanobacteria functioned or evolved on early Earth in part because we do not understand their ecology, including the environments in which they lived. Here, we use a cutting-edge bioinformatics tool to survey nearly 500,000 metagenomes for relatives of the taxa that likely bookended the evolution of oxygenic photosynthesis to identify the modern environments in which these organisms live. Ancestral state reconstruction suggests that the common ancestors of these organisms lived in terrestrial (soil and/or freshwater) environments. This restricted distribution may have increased the lag between the evolution of oxygenic photosynthesis and the oxygenation of Earth's atmosphere.IMPORTANCECyanobacteria generate oxygen as part of their metabolism and are responsible for the rise of oxygen in Earth's atmosphere over two billion years ago. However, we do not know how long this process may have taken. To help constrain how long this process would have taken, it is necessary to understand where the earliest Cyanobacteria may have lived. Here, we use a cutting-edge bioinformatics tool called branch water to examine the environments where modern Cyanobacteria and their relatives live to constrain those inhabited by the earliest Cyanobacteria. We find that these species likely lived in non-marine environments. This indicates that the rise of oxygen may have taken longer than previously believed.}, }
@article {pmid39880083, year = {2025}, author = {Vande Moortele, T and Verschaffelt, P and Huang, Q and Doncheva, NT and Holstein, T and Jachmann, C and Dawyndt, P and Martens, L and Mesuere, B and Van Den Bossche, T}, title = {PathwayPilot: A User-Friendly Tool for Visualizing and Navigating Metabolic Pathways.}, journal = {Molecular &amp; cellular proteomics : MCP}, volume = {24}, number = {3}, pages = {100918}, pmid = {39880083}, issn = {1535-9484}, mesh = {*Software ; *Metabolic Networks and Pathways ; Humans ; *Proteomics/methods ; Gastrointestinal Microbiome ; User-Computer Interface ; Proteome/metabolism ; *Computational Biology/methods ; Caloric Restriction ; }, abstract = {Metaproteomics, the study of collective proteomes in environmental communities, plays a crucial role in understanding microbial functionalities affecting ecosystems and human health. Pathway analysis offers structured insights into the biochemical processes within these communities. However, no existing tool effectively combines pathway analysis with peptide- or protein-level data. We here introduce PathwayPilot, a web-based application designed to improve metaproteomic data analysis by integrating pathway analysis with peptide- and protein-level data, filling a critical gap in current metaproteomics bioinformatics tools. By allowing users to compare functional annotations across different samples or multiple organisms within a sample, PathwayPilot provides valuable insights into microbial functions. In the re-analysis of a study examining the effects of caloric restriction on gut microbiota, the tool successfully identified shifts in enzyme expressions linked to short-chain fatty acid biosynthesis, aligning with its original findings. PathwayPilot's user-friendly interface and robust capabilities make it a significant advancement in metaproteomics, with the potential for widespread application in microbial ecology and health sciences. All code is open source under the Apache2 license and is available at https://pathwaypilot.ugent.be.}, }
@article {pmid39874571, year = {2025}, author = {Sahandi Far, M and Fischer, JM and Senge, S and Rathmakers, R and Meissner, T and Schneble, D and Narava, M and Eickhoff, SB and Dukart, J}, title = {Cross-Platform Ecological Momentary Assessment App (JTrack-EMA+): Development and Usability Study.}, journal = {Journal of medical Internet research}, volume = {27}, number = {}, pages = {e51689}, pmid = {39874571}, issn = {1438-8871}, mesh = {*Mobile Applications/standards ; *Software/standards ; *Self Report ; Pilot Projects ; *Patient Compliance/statistics &amp; numerical data ; Humans ; Infant, Newborn ; Adult ; Parents ; *Clinical Studies as Topic/instrumentation ; }, abstract = {BACKGROUND: Traditional in-clinic methods of collecting self-reported information are costly, time-consuming, subjective, and often limited in the quality and quantity of observation. However, smartphone-based ecological momentary assessments (EMAs) provide complementary information to in-clinic visits by collecting real-time, frequent, and longitudinal data that are ecologically valid. While these methods are promising, they are often prone to various technical obstacles. However, despite the potential of smartphone-based EMAs, they face technical obstacles that impact adaptability, availability, and interoperability across devices and operating systems. Deficiencies in these areas can contribute to selection bias by excluding participants with unsupported devices or limited digital literacy, increase development and maintenance costs, and extend deployment timelines. Moreover, these limitations not only impede the configurability of existing solutions but also hinder their adoption for addressing diverse clinical challenges.<br><br>OBJECTIVE: The primary aim of this research was to develop a cross-platform EMA app that ensures a uniform user experience and core features across various operating systems. Emphasis was placed on maximizing the integration and adaptability to various study designs, all while maintaining strict adherence to security and privacy protocols. JTrack-EMA+ was designed and implemented per the FAIR (findable, accessible, interpretable, and reusable) principles in both its architecture and data management layers, thereby reducing the burden of integration for clinicians and researchers.<br><br>METHODS: JTrack-EMA+ was built using the Flutter framework, enabling it to run seamlessly across different platforms. This platform comprises two main components. JDash (Research Centre J&#xfc;lich, Institute of Neuroscience and Medicine, Brain and Behaviour [INM-7]) is an online management tool created using Python (Python Software Foundation) with the Django (Django Software Foundation) framework. This online dashboard offers comprehensive study management tools, including assessment design, user administration, data quality control, and a reminder casting center. The JTrack-EMA+ app supports a wide range of question types, allowing flexibility in assessment design. It also has configurable assessment logic and the ability to include supplementary materials for a richer user experience. It strongly commits to security and privacy and complies with the General Data Protection Regulations to safeguard user data and ensure confidentiality.<br><br>RESULTS: We investigated our platform in a pilot study with 480 days of follow-up to assess participants' compliance. The 6-month average compliance was 49.3%, significantly declining (P=.004) from 66.7% in the first month to 42% in the sixth month.<br><br>CONCLUSIONS: The JTrack-EMA+ platform prioritizes platform-independent architecture, providing an easy entry point for clinical researchers to deploy EMA in their respective clinical studies. Remote and home-based assessments of EMA using this platform can provide valuable insights into patients' daily lives, particularly in a population with limited mobility or inconsistent access to health care services.}, }
@article {pmid39871222, year = {2025}, author = {Diongue, FB and Faye, A and Loucoubar, C and Sougou, NM and Sy, I and Tall, A and Ndiaye, Y and Sarr, SC}, title = {Situational analysis of the quality of maternal, child, and adolescent health data in the health districts of Thiès, Mbour, Kédougou, and Saraya in Senegal.}, journal = {BMC public health}, volume = {25}, number = {1}, pages = {337}, pmid = {39871222}, issn = {1471-2458}, mesh = {Senegal ; Humans ; Adolescent ; Female ; *Data Accuracy ; Child ; *Health Information Systems/standards ; *Child Health/statistics &amp; numerical data ; *Adolescent Health/statistics &amp; numerical data ; Qualitative Research ; Lot Quality Assurance Sampling ; *Maternal Health ; }, abstract = {INTRODUCTION: In Senegal, the Routine Health Information System (RHIS) captures the majority of data from the Ministry of Health and Social Action (MHSA) public structures and very little health data from the private sector and other ministerial departments. Quality data strengthens the validity and reliability of research results. Common areas of data quality include accuracy, completeness, consistency, credibility, and timeliness. The work aims to assess the quality of routine maternal, child, and adolescent health data in Senegal.<br><br>MATERIALS AND METHODS: A mixed quantitative and qualitative design was chosen in four health districts, including Thi&#xe8;s, Mbour, K&#xe9;dougou, and Saraya. The study included functional health structures that produce maternal, child, and adolescent health data. For the quantitative part, a descriptive and analytical study was carried out. Lot Quality Assurance Sampling (LQAS) was used as the sampling method. Data were collected using Performance of Routine Information Systems Management (PRISM) data collection tools and the ODK application and analyzed (univariate and bivariate) using R and Stata with an alpha risk of 5%. The following data quality indicators (accuracy, completeness, and promptness) were estimated. An exploratory case study and purposive sampling supported the qualitative part by implementing individual interviews.<br><br>RESULTS: The study showed an accuracy ratio of 1 in the intervention districts, a difference in the control districts, and a disparity in the transmission of guidelines between districts (inter- and intra-region). The average level of completeness was 0.64 (+/- 0.44) for all regions combined, with no significant difference between districts. The promptness rate for K&#xe9;dougou, Saraya, Thi&#xe8;s, and Mbour districts was 81%, 75.9%, 72.2%, and 86.7%, respectively. Between 40% and 60% of facilities in each district carried out self-assessments. Data collection tools were considered to be numerous. A large number of tools were easy to use. The recording space was appreciated. On the other hand, the length of the forms was little or not appreciated by the providers. Few of the providers in the 4 districts had been trained to record data in DHIS2.<br><br>CONCLUSION: Assessment of data quality in the districts studied shows shortcomings in terms of completeness and timeliness. Many factors influence the SMEA data quality situation, including knowledge or application of RHIS policies, standards, and protocols, perception of the importance of RHIS, ease of use of data collection tools, training of providers, and diversity of data production sources.}, }
@article {pmid39871100, year = {2025}, author = {Terauds, A and Lee, JR and Wauchope, HS and Raymond, B and Bergstrom, DM and Convey, P and Mason, C and Patterson, CR and Robinson, SA and Van de Putte, A and Watts, D and Chown, SL}, title = {The biodiversity of ice-free Antarctica database.}, journal = {Ecology}, volume = {106}, number = {1}, pages = {e70000}, pmid = {39871100}, issn = {1939-9170}, support = {n&#xb0;FR/36/AN1/AntaBIS(EU-LifeWatch)//Belgian Science Policy Office/ ; n&#xb0;RT/23/ADVANCE//Belgian Science Policy Office/ ; //Royal Commission for the Exhibition of 1851 Research Fellowship/ ; SRIEAS-SR200100005//Australian Research Council/ ; //Securing Antarctica's Environmental Future/ ; AAS 4296//Australian Antarctic Division/ ; AAS 4297//Australian Antarctic Division/ ; }, mesh = {Antarctic Regions ; *Biodiversity ; *Databases, Factual ; Animals ; Conservation of Natural Resources ; }, abstract = {Antarctica is one of Earth's most untouched, inhospitable, and poorly known regions. Although knowledge of its biodiversity has increased over recent decades, a diverse, wide-ranging, and spatially explicit compilation of the biodiversity that inhabits Antarctica's permanently ice-free areas is unavailable. This absence hinders both Antarctic biodiversity research and the integration of Antarctica in global biodiversity-related studies. Fundamental and applied research on biodiversity patterns, ecological structure and function, and options for conservation are reliant on spatially resolved, taxonomically consistent observations. Such information is especially important for modern, data-driven biodiversity science, in both Antarctica and globally, and forms the backbone of biodiversity informatics, reflected, for example, in the Darwin Core Standard used by the Global Biodiversity Information Facility. Biodiversity data are also essential to fulfill the conservation requirements for Antarctica, as set out in the Protocol on Environmental Protection to the Antarctic Treaty and inform the design of systematic surveys to address biodiversity and ecological knowledge gaps, for both specific taxa and ecosystems. Such surveys are key requirements for understanding and mitigating the impacts of environmental change on the region's biodiversity. Here, we address these requirements through the public release of The Biodiversity of Ice-free Antarctica Database. In 2008, we extracted a subset of biodiversity records only from terrestrial ice-free areas from the Scientific Committee on Antarctic Research (SCAR) Antarctic Biodiversity Database. We have subsequently added thousands of records from a range of sources: checking, and where necessary (and possible), correcting the spatial location, clarifying, cross-referencing, and harmonizing taxonomy with globally recognized sources, and documenting the original source of records. The Biodiversity of Ice-free Antarctica Database spans the early 1800s to 2019 (with most records collected after 1950) and represents the most comprehensive consolidation of Antarctic ice-free biodiversity occurrence data yet compiled into a single database. The Biodiversity of Ice-free Antarctica Database contains 35,654 records of 1890 species in over 800 genera across six kingdoms and spans all Antarctic Conservation Biogeographic Regions. These data are released under a CC BY Attribution License (http://creativecommons.org/licenses/by/4.0/).}, }
@article {pmid39870942, year = {2025}, author = {Lazaro, A and Tiago, I and Mendes, J and Ribeiro, J and Bernardes, A and Oliveira, F and Regateiro, F and Caramelo, F and Silva, H}, title = {Sleeve Gastrectomy and Gastric Bypass Impact in Patient's Metabolic, Gut Microbiome, and Immuno-inflammatory Profiles-A Comparative Study.}, journal = {Obesity surgery}, volume = {35}, number = {3}, pages = {733-745}, pmid = {39870942}, issn = {1708-0428}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Gastric Bypass ; *Gastrectomy/methods ; Female ; *Obesity, Morbid/surgery/microbiology/immunology/metabolism ; Prospective Studies ; Male ; Adult ; Middle Aged ; Weight Loss ; *Metabolic Syndrome/metabolism ; Treatment Outcome ; }, abstract = {BACKGROUND: Bariatric surgery is the most long-term effective treatment option for severe obesity. The role of gut microbiome (GM) in either the development of obesity or in response to obesity management strategies has been a matter of debate. This study aims to compare the impact of two of the most popular procedures, sleeve gastrectomy (SG) and Roux-en-Y gastric bypass (GB), on metabolic syndrome parameters and gut bacterial microbiome and in systemic immuno-inflammatory response.<br><br>METHODS: A prospective observational study enrolled 24 patients with severe obesity, 14 underwent SG and 10&#xa0;GB. Evaluations before (0&#xa0;M) and 6&#xa0;months (6&#xa0;M) after surgical procedures included clinical and biochemical parameters, expression of 17 immuno-inflammatory genes in peripheral blood leukocytes, and assessment of gut microbiome profile using 16&#xa0;s rRNA next-generation sequencing approach. Statistical significance was set to a p value&#x2009;<&#x2009;0.05 with an FDR&#x2009;<&#x2009;0.1.<br><br>RESULTS: A significant and similar decrease in weight-associated parameters and for most metabolic markers was achieved with both surgeries. Considering the gut microbiome in the whole study population, there was an increase in alpha diversity at family-level taxa. Beta diversity between SG and GB at 6&#xa0;M showed near significant differences (p&#x2009;=&#x2009;0.042) at genus levels. Analysis of the relative abundance of individual taxonomic groups highlighted differences between pre- and post-surgical treatment and between both approaches, namely, a higher representation of family Enterobacteriaceae and genera Veillonella and Enterobacteriaceae_unclassified after GB. Increased expression of immune-inflammatory genes was observed mainly for SG patients.<br><br>CONCLUSIONS: We conclude that SG and GB have similar clinical and metabolic outcomes but different impacts in the gut bacterial microbiome. Results also suggest reactivation of immune response after bariatric surgery.}, }
@article {pmid39870652, year = {2025}, author = {Koizumi, T and Suzuki, K and Mizuki, I and Kumaishi, K and Ichihashi, Y}, title = {A quantitative prediction method utilizing whole omics data for biosensing.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {1928}, pmid = {39870652}, issn = {2045-2322}, support = {21J00762//Japan Society for the Promotion of Science/ ; Technologies for Smart Bio-industry and Agriculture//the Cabinet Office, Goverment of Japan/ ; }, mesh = {Transcriptome ; Biomarkers/analysis ; *Biosensing Techniques/methods ; Humans ; Metabolome ; *Computational Biology/methods ; Microbiota ; Gene Expression Profiling ; Algorithms ; *Genomics/methods ; }, abstract = {Omics data provide a plethora of quantifiable information that can potentially be used to identify biomarkers targeting the physiological processes and ecological phenomena of organisms. However, omics data have not been fully utilized because current prediction methods in biomarker construction are susceptible to data multidimensionality and noise. We developed OmicSense, a quantitative prediction method that uses a mixture of Gaussian distributions as the probability distribution, yielding the most likely objective variable predicted for each biomarker. Our benchmark test using a transcriptome dataset revealed that OmicSense achieves accurate and robust prediction against background noise without overfitting. Weighted gene co-expression network analysis revealed that OmicSense preferentially utilized hub nodes of the network, indicating the interpretability of the method. Application of OmicSense to single-cell transcriptome, metabolome, and microbiome datasets confirmed high prediction performance (r > 0.8), suggesting applicability to diverse scientific fields. Given the recent rapidly expanding availability of omics data, the developed prediction tool OmicSense, can accelerate the use of omics data as a "biosensor" based on an assemblage of potential biomarkers.}, }
@article {pmid39869900, year = {2025}, author = {Yeom, JW and Kim, H and Pack, SP and Lee, HJ and Cheong, T and Cho, CH}, title = {Exploring the Psychological and Physiological Insights Through Digital Phenotyping by Analyzing the Discrepancies Between Subjective Insomnia Severity and Activity-Based Objective Sleep Measures: Observational Cohort Study.}, journal = {JMIR mental health}, volume = {12}, number = {}, pages = {e67478}, pmid = {39869900}, issn = {2368-7959}, mesh = {Humans ; *Sleep Initiation and Maintenance Disorders/physiopathology/psychology/diagnosis ; Middle Aged ; Male ; Female ; Adult ; Severity of Illness Index ; Aged ; Young Adult ; Cohort Studies ; *Sleep/physiology ; Exercise/physiology ; Wearable Electronic Devices ; Surveys and Questionnaires ; Ecological Momentary Assessment ; }, abstract = {BACKGROUND: Insomnia is a prevalent sleep disorder affecting millions worldwide, with significant impacts on daily functioning and quality of life. While traditionally assessed through subjective measures such as the Insomnia Severity Index (ISI), the advent of wearable technology has enabled continuous, objective sleep monitoring in natural environments. However, the relationship between subjective insomnia severity and objective sleep parameters remains unclear.<br><br>OBJECTIVE: This study aims to (1) explore the relationship between subjective insomnia severity, as measured by ISI scores, and activity-based objective sleep parameters obtained through wearable devices; (2) determine whether subjective perceptions of insomnia align with objective measures of sleep; and (3) identify key psychological and physiological factors contributing to the severity of subjective insomnia complaints.<br><br>METHODS: A total of 250 participants, including both individuals with and without insomnia aged 19-70 years, were recruited from March 2023 to November 2023. Participants were grouped based on ISI scores: no insomnia, mild, moderate, and severe insomnia. Data collection involved subjective assessments through self-reported questionnaires and objective measurements using wearable devices (Fitbit Inspire 3) that monitored sleep parameters, physical activity, and heart rate. The participants also used a smartphone app for ecological momentary assessment, recording daily alcohol consumption, caffeine intake, exercise, and stress. Statistical analyses were used to compare groups on subjective and objective measures.<br><br>RESULTS: Results indicated no significant differences in general sleep structure (eg, total sleep time, rapid eye movement sleep time, and light sleep time) among the insomnia groups (mild, moderate, and severe) as classified by ISI scores (all P>.05). Interestingly, the no insomnia group had longer total awake times and lower sleep quality compared with the insomnia groups. Among the insomnia groups, no significant differences were observed regarding sleep structure (all P>.05), suggesting similar sleep patterns regardless of subjective insomnia severity. There were significant differences among the insomnia groups in stress levels, dysfunctional beliefs about sleep, and symptoms of restless leg syndrome (all P&#x2264;.001), with higher severity associated with higher scores in these factors. Contrary to expectations, no significant differences were observed in caffeine intake (P=.42) and alcohol consumption (P=.07) between the groups.<br><br>CONCLUSIONS: The findings demonstrate a discrepancy between subjective perceptions of insomnia severity and activity-based objective sleep parameters, suggesting that factors beyond sleep duration and quality may contribute to subjective sleep complaints. Psychological factors, such as stress, dysfunctional sleep beliefs, and symptoms of restless legs syndrome, appear to play significant roles in the perception of insomnia severity. These results highlight the importance of considering both subjective and objective assessments in the evaluation and treatment of insomnia and suggest potential avenues for personalized treatment strategies that address both psychological and physiological aspects of sleep disturbances.<br><br>TRIAL REGISTRATION: Clinical Research Information Service KCT0009175; https://cris.nih.go.kr/cris/search/detailSearch.do?seq=26133.}, }
@article {pmid39868965, year = {2025}, author = {Grikscheit, K and Berger, A and Rabenau, H and Kohmer, N and Appel, KS and Scherer, M and Bals, R and Blaschke, S and Hamprecht, A and Hopff, SM and Krefting, D and Meybohm, P and Nürnberger, C and Heuschmann, P and Pley, C and Nunes de Miranda, SM and Dahl, E and Jensen, B and Illig, T and Anton, G and Vehreschild, JJ and Ciesek, S}, title = {Occurrence and clinical correlates of SARS-CoV-2 viremia in two German patient cohorts.}, journal = {Emerging microbes &amp; infections}, volume = {14}, number = {1}, pages = {2459137}, pmid = {39868965}, issn = {2222-1751}, mesh = {Humans ; *COVID-19/epidemiology/virology/blood/diagnosis ; *Viremia/epidemiology/virology ; Germany/epidemiology ; Male ; Female ; Middle Aged ; *SARS-CoV-2/genetics/isolation &amp; purification/immunology ; Aged ; Cross-Sectional Studies ; Antibodies, Viral/blood ; Adult ; RNA, Viral/blood ; Cohort Studies ; Antibodies, Neutralizing/blood ; Severity of Illness Index ; Aged, 80 and over ; }, abstract = {Viremia defined as detectable SARS-CoV-2 RNA in the blood is a potential marker of disease severity and prognosis in COVID-19 patients. Here, we determined the frequency of viremia in serum of two independent COVID-19 patient cohorts within the German National Pandemic Cohort Network (German: Nationales Pandemie Kohorten Netzwerk, NAPKON) with diagnostic RT-PCR against SARS-CoV-2. A cross-sectional cohort with 1122 COVID-19 patients (German: Sektorenuebergreifende Platform, SUEP) and 299 patients recruited in a high-resolution platform with patients at high risk to develop severe courses (German: Hochaufloesende Plattform, HAP) were tested for viremia. Our study also involved a comprehensive analysis and association of serological, diagnostic, and clinical parameters of the NAPKON medical dataset. Prevalence of viremia at the recruitment visit was 12.8% (SUEP) and 13% (HAP), respectively. Serological analysis revealed that viremic patients had lower levels of SARS-CoV-2 specific antibodies as well as lower neutralizing antibodies compared to aviremic patients. Viremia was associated with severity (<0.0001 SUEP; 0.002 HAP) and mortality of COVID-19 (both cohorts <0.0001) compared to aviremic patients. While rare, viremia was also detected in patients with mild disease (0.7%). In patients of the SUEP cohort with acute kidney disease (p = 0.0099) and hematooncological conditions (p = 0.0091), viremia was detected more frequently. Compared to the aviremic group, treatment with immunomodulating drugs as well as elevated levels of inflammatory markers in the blood was more frequent in the viremic group. In conclusion, our analysis revealed that detectable viremia correlates with hyperinflammatory conditions and higher risk for severe COVID-19 disease.}, }
@article {pmid39865039, year = {2024}, author = {Alekseeva, AO and Zolotovskaia, MA and Sorokin, MI and Suntsova, MV and Zakharova, GS and Pugacheva, PA and Tinkov, AA and Korobeinikova, TV and Sekacheva, MI and Poddubskaya, EV and Skalny, AV and Kushlinskii, NE and Buzdin, AA}, title = {The First Multiomics Association Study of Trace Element and Mineral Concentration and RNA Sequencing Profiles in Human Cancers.}, journal = {Biochemistry. Biokhimiia}, volume = {89}, number = {12}, pages = {2274-2286}, doi = {10.1134/S0006297924120150}, pmid = {39865039}, issn = {1608-3040}, mesh = {Humans ; *Trace Elements/analysis/metabolism ; Sequence Analysis, RNA ; *Neoplasms/metabolism/genetics ; *Minerals/analysis/metabolism ; Gene Expression Profiling ; Female ; Multiomics ; }, abstract = {Integration of various types of omics data is an important trend in contemporary molecular oncology. In this regard, high-throughput analysis of trace and essential elements in cancer biosamples is an emerging field that has not yet been sufficiently addressed. For the first time, we simultaneously obtained gene expression profiles (RNA sequencing) and essential and trace element profiles (inductively coupled plasma mass spectrometry) for a set of human cancer samples. The biosamples were formalin-fixed, paraffin-embedded primary tumor tissue blocks: 67 for colorectal cancer patients and 18 for other solid cancer types (16 types). Mass spectrometry profiles were obtained for 45 chemical elements: Ag, Al, As, Au, B, Ba, Be, Bi, Ca, Cd, Co, Cr, Cu, Fe, Ga, Ge, Hg, I, K, La, Li, Mg, Mn, Mo, Na, Ni, P, Pb, Pd, Pt, Rb, Sb, Sc, Se, Si, Sn, Sr, Te, Ti, Tl, Zn, U, V, W, and Zr. The expression levels were profiled for 36,596 known human genes, and the activation levels were assessed for 10,520 human intracellular molecular pathways. For the concentrations of essential elements Ca, Cu, Fe, K, Mg, Na, P, and Zn we detected statistically significant correlations on both gene expression and pathway activation levels for both colorectal cancer samples and at the pan-cancer level. In total, 222/137, 122/220, 1/0, 239/186, 71/44, 1/0, 354/294, 69/82 gene/pathway biomarkers were detected for Ca, Cu, Fe, K, Mg, Na, P, and Zn, respectively. We believe that this first-in-class database provided here will be valuable for multiomics cancer research.}, }
@article {pmid39860723, year = {2025}, author = {Dewmini, H and Meedeniya, D and Perera, C}, title = {Elephant Sound Classification Using Deep Learning Optimization.}, journal = {Sensors (Basel, Switzerland)}, volume = {25}, number = {2}, pages = {}, pmid = {39860723}, issn = {1424-8220}, mesh = {*Deep Learning ; Animals ; *Elephants/physiology ; *Vocalization, Animal/physiology/classification ; Bayes Theorem ; Sound ; Sound Spectrography ; }, abstract = {Elephant sound identification is crucial in wildlife conservation and ecological research. The identification of elephant vocalizations provides insights into the behavior, social dynamics, and emotional expressions, leading to elephant conservation. This study addresses elephant sound classification utilizing raw audio processing. Our focus lies on exploring lightweight models suitable for deployment on resource-costrained edge devices, including MobileNet, YAMNET, and RawNet, alongside introducing a novel model termed ElephantCallerNet. Notably, our investigation reveals that the proposed ElephantCallerNet achieves an impressive accuracy of 89% in classifying raw audio directly without converting it to spectrograms. Leveraging Bayesian optimization techniques, we fine-tuned crucial parameters such as learning rate, dropout, and kernel size, thereby enhancing the model's performance. Moreover, we scrutinized the efficacy of spectrogram-based training, a prevalent approach in animal sound classification. Through comparative analysis, the raw audio processing outperforms spectrogram-based methods. In contrast to other models in the literature that primarily focus on a single caller type or binary classification that identifies whether a sound is an elephant voice or not, our solution is designed to classify three distinct caller-types namely roar, rumble, and trumpet.}, }
@article {pmid39856573, year = {2025}, author = {Sun, Z and Zhang, F and Zhong, N and Zhou, K and Tang, J}, title = {Genome sequence resources for three strains of the genus Clonostachys.}, journal = {BMC genomic data}, volume = {26}, number = {1}, pages = {8}, pmid = {39856573}, issn = {2730-6844}, support = {No. 2022AH051346 and No. KJ2021A0676//the Key Natural Science Research Projects in Anhui Universities/ ; No. KJTS2022002; No. KJTS2022003//Science and Technology Innovation Capability Enhancement Projects in Fuyang National Agricultural Sci-Tech Park/ ; No. 2022AH020081//Natural Science Foundation of Universities of Anhui Province for Distinguished Young Project/ ; No. 2020KYQD0023//The Fuyang Normal University Research Project/ ; [2023]13//Biological and Medical Sciences of Applied Summit Nurturing Disciplines in Anhui Province, Anhui Education Secretary Department/ ; }, mesh = {*Ascomycota/classification/genetics ; Datasets as Topic ; Genome, Fungal ; Molecular Sequence Annotation ; Biological Control Agents ; }, abstract = {OBJECTIVE: Clonostachys, a genus with rich morphological and ecological diversity in Bionectriaceae, has a wide distribution among diverse habitats. Several studies have reported Clonostachys fungi as effective biological agents against multiple fungal plant pathogens. To clarify the diversity and biocontrol mechanisms of the Clonostachys fungi, this study was undertaken to sequence and assemble the genomes of two C. chloroleuca and one C. rhizophaga.<br><br>DATA DESCRIPTION: Here, we performed genomic sequencing of three strains of genus Clonostachys collected from the China General Microbiological Culture Collection Center (CGMCC) using Illumina HiSeq 2500 sequencing technology. Whole genome analysis indicated that their genomes consist of 58,484,224&#xa0;bp with a GC content of 48.58%, 58,114,960&#xa0;bp with a GC content of 47.74% and 58,450,453&#xa0;bp with a GC content of 48.58%, respectively. BUSCO analysis of the genome assembly indicated that the completeness of these genomes was at least 98%. In summary, these datasets provide a valuable resource for ongoing studies that include further exploration of biological function, marker development, enhanced biological control ability of Clonostachys fungi, and population diversity.}, }
@article {pmid39856257, year = {2025}, author = {Gulakhmadov, A and Chen, X and Gulahmadov, N and Rizwan, M and Gulakhmadov, M and Nadeem, MU and Rakhimova, M and Liu, T}, title = {Modeling of historical and future changes in temperature and precipitation in the Panj River Basin in Central Asia under the CMIP5 RCP and CMIP6 SSP scenarios.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {3037}, pmid = {39856257}, issn = {2045-2322}, support = {42150410393//Research Fund for International Scientists of the National Natural Science Foundation of China/ ; 42150410393//Research Fund for International Scientists of the National Natural Science Foundation of China/ ; 42150410393//Research Fund for International Scientists of the National Natural Science Foundation of China/ ; 2023000137//Tianshan Talent Training Program of Xinjiang Uygur Autonomous region/ ; 2023000137//Tianshan Talent Training Program of Xinjiang Uygur Autonomous region/ ; 42230708/42361144887//National Natural Science Foundation of China/ ; 42230708/42361144887//National Natural Science Foundation of China/ ; GJTD-2020-14//K.C. Wong Education Foundation/ ; GJTD-2020-14//K.C. Wong Education Foundation/ ; HZXM20225001MI//Joint CAS-MPG Research Project/ ; HZXM20225001MI//Joint CAS-MPG Research Project/ ; }, abstract = {This study examines the complexities of climate modeling, specifically in the Panj River Basin (PRB) in Central Asia, to evaluate the transition from CMIP5 to CMIP6 models. The research aimed to identify differences in historical simulations and future predictions of rainfall and temperature, examining the accuracy of eight General Circulation Models (GCMs) used in both CMIP5 (RCP4.5 and 8.5) and CMIP6 (SSP2-4.5 and 5-8.5). The evaluation metrics demonstrated that the GCMs have a high level of accuracy in reproducing maximum temperature (Tmax) with a correlation coefficient of 0.96. The models also performed well in replicating minimum temperature (Tmin) with a correlation coefficient of 0.94. This suggests that the models have improved modeling capabilities in both CMIPs. The performance of Max Plank Institute (MPI) across all variables in CMIP6 models was exceptional. Within the CMIP5 domain, Geophysical Fluid Dynamics (GFDL) demonstrated outstanding skill in reproducing maximum temperature (Tmax) and precipitation (KGE 0.58 and 0.34, respectively), while (Institute for Numerical Mathematics) INMCM excelled in replicating minimum temperature (Tmin) (KGE 0.28). The uncertainty analysis revealed a significant improvement in the CMIP6 precipitation bias bands, resulting in a more precise depiction of diverse climate zones compared to CMIP5. Both CMIPs consistently tended to underestimate Tmax in the Csa zone and overestimate it in the Bwk zone throughout all months. Nevertheless, the CMIP6 models demonstrated a significant decrease in uncertainty, especially in ensemble simulations, suggesting improvements in forecasting PRB climate dynamics. The projections revealed a complex story, as the CMIP6 models predict a relatively small increase in temperature and a simultaneous drop in precipitation. This indicates a trend towards more uniform temperature patterns across different areas. Nevertheless, the precipitation forecasts exhibited increased variability, highlighting the intricate interaction of climate dynamics in the PRB area under the impact of global warming scenarios. Hydrological components in global climate models can be further improved and developed with the theoretical reference provided by this study.}, }
@article {pmid39854567, year = {2025}, author = {Moody, NM and Williams, CM and Ramachandran, S and Fuxjager, MJ}, title = {Social mates dynamically coordinate aggressive behavior to produce strategic territorial defense.}, journal = {PLoS computational biology}, volume = {21}, number = {1}, pages = {e1012740}, pmid = {39854567}, issn = {1553-7358}, support = {R35 GM139628/GM/NIGMS NIH HHS/United States ; T32 GM128596/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Female ; Male ; *Aggression/physiology ; *Territoriality ; *Birds/physiology ; Social Behavior ; Behavior, Animal/physiology ; Computational Biology ; Sexual Behavior, Animal/physiology ; }, abstract = {Negotiating social dynamics among allies and enemies is a complex problem that often requires individuals to tailor their behavioral approach to a specific situation based on environmental and/or social factors. One way to make these contextual adjustments is by arranging behavioral output into intentional patterns. Yet, few studies explore how behavioral patterns vary across a wide range of contexts, or how allies might interlace their behavior to produce a coordinated response. Here, we investigate the possibility that resident female and male downy woodpeckers guard their breeding territories from conspecific intruders by deploying defensive behavior in context-specific patterns. To study whether this is the case, we use correlation networks to reveal how suites of agonistic behavior are interrelated. We find that residents do organize their defense into definable patterns, with female and male social mates deploying their behaviors non-randomly in a correlated fashion. We then employ spectral clustering analyses to further distill these responses into distinct behavioral motifs. Our results show that this population of woodpeckers adjusts the defensive motifs deployed according to threat context. When we combine this approach with behavioral transition analyses, our results reveal that pair coordination is a common feature of territory defense in this species. However, if simulated intruders are less threatening, residents are more likely to defend solo, where only one bird deploys defensive behaviors. Overall, our study supports the hypothesis that nonhuman animals can pattern their behavior in a strategic and coordinated manner, while demonstrating the power of systems approaches for analyzing multiagent behavioral dynamics.}, }
@article {pmid39854555, year = {2025}, author = {Zhou, J and Johnson, VC and Shi, J and Tan, ML and Zhang, F}, title = {Multi-scenario land use change simulation and spatial-temporal evolution of carbon storage in the Yangtze River Delta region based on the PLUS-InVEST model.}, journal = {PloS one}, volume = {20}, number = {1}, pages = {e0316255}, pmid = {39854555}, issn = {1932-6203}, mesh = {*Rivers/chemistry ; China ; *Conservation of Natural Resources ; *Carbon Sequestration ; *Carbon/analysis ; *Models, Theoretical ; Spatio-Temporal Analysis ; Urbanization ; Computer Simulation ; Ecosystem ; Humans ; }, abstract = {Influenced by urban expansion, population growth, and various socio-economic activities, land use in the Yangtze River Delta (YRD) area has undergone prominent changes. Modifications in land use have resulted in adjustments to ecological structures, leading to subsequent fluctuations in carbon storage. This study focuses on YRD region and analyzes the characteristics of land use changes in the area using land use data from 2000 to 2020, with a 10-year interval. Utilizing InVEST Model's Carbon Storage module in combination with PLUS model (patch-generating land use simulation), we simulated and projected future land use patterns and carbon storage across YRD region under five scenarios including natural development (ND), urban development (UD), ecological protection (EP), cropland protection (CP), and balanced development (BD). Upon comparing carbon storage levels predicted for 2030 under the five scenarios with those in 2020, carbon stocks decrease in the initial four scenarios and then increase in the fifth scenario. In the initial four declining scenarios, CP scenario had the least reduction in carbon storage, followed by EP scenario. The implementation of policies aimed at safeguarding cropland and preserving ecological integrity can efficaciously curtail the expansion of developed land into woodland and cropland, enhance the structure of land use, and mitigate the loss of carbon storage.}, }
@article {pmid39854538, year = {2025}, author = {Katchali, M and Richard, E and Tonnang, HEZ and Tanga, CM and Beesigamukama, D and Senagi, K}, title = {Mathematical and computational modeling for organic and insect frass fertilizer production: A systematic review.}, journal = {PloS one}, volume = {20}, number = {1}, pages = {e0292418}, pmid = {39854538}, issn = {1932-6203}, support = {INV-032416/GATES/Gates Foundation/United States ; }, mesh = {*Fertilizers ; Animals ; *Computer Simulation ; *Models, Theoretical ; *Insecta ; Agriculture/methods ; }, abstract = {Organic fertilizers have been identified as a sustainable agricultural practice that can enhance productivity and reduce environmental impact. Recently, the European Union defined and accepted insect frass as an innovative and emerging organic fertilizer. In the wider domain of organic fertilizers, mathematical and computational models have been developed to optimize their production and application conditions. However, with the advancement in policies and regulations, modelling has shifted towards efficiencies in the deployment of these technologies. Therefore, this paper reviews and critically analyzes the recent developments in the mathematical and computation modeling that have promoted various organic fertilizer products including insect frass. We reviewed a total of 35 studies and discussed the methodologies, benefits, and challenges associated with the use of these models. The results show that mathematical and computational modeling can improve the efficiency and effectiveness of organic fertilizer production, leading to improved agricultural productivity and reduced environmental impact. Mathematical models such as simulation, regression, dynamics, and kinetics have been applied while computational data driven machine learning models such as random forest, support vector machines, gradient boosting, and artificial neural networks have also been applied as well. These models have been used in quantifying nutrients concentration/release, effects of nutrients in agro-production, and fertilizer treatment. This paper also discusses prospects for the use of these models, including the development of more comprehensive and accurate models and integration with emerging technologies such as Internet of Things.}, }
@article {pmid39853577, year = {2025}, author = {Pierrat, ZA and Magney, TS and Richardson, WP and Runkle, BRK and Diehl, JL and Yang, X and Woodgate, W and Smith, WK and Johnston, MR and Ginting, YRS and Koren, G and Albert, LP and Kibler, CL and Morgan, BE and Barnes, M and Uscanga, A and Devine, C and Javadian, M and Meza, K and Julitta, T and Tagliabue, G and Dannenberg, MP and Antala, M and Wong, CYS and Santos, ALD and Hufkens, K and Marrs, JK and Stovall, AEL and Liu, Y and Fisher, JB and Gamon, JA and Cawse-Nicholson, K}, title = {Proximal remote sensing: an essential tool for bridging the gap between high-resolution ecosystem monitoring and global ecology.}, journal = {The New phytologist}, volume = {246}, number = {2}, pages = {419-436}, pmid = {39853577}, issn = {1469-8137}, support = {//National Research Council Postdoctoral Research Associateship Program/ ; 2020/37/B/ST10/01213//National Science Centre of Poland/ ; //TVL E-13 work contract at the Climate Monitoring Group of the University of Bonn/ ; //The LEMONTREE project by E. Schmidt and W. Schmidt/ ; 1926090//National Science Foundation/ ; 2044818//National Science Foundation/ ; 2131853//National Science Foundation/ ; IOS-2005574 OPP-2023205//National Science Foundation/ ; 80NSSC20K1805/NASA/NASA/United States ; 80NSSC21K1002/NASA/NASA/United States ; 80NSSC21K1639/NASA/NASA/United States ; 80NSSC21K1707/NASA/NASA/United States ; 80NSSC23K0109/NASA/NASA/United States ; 80NSSC23K0309/NASA/NASA/United States ; 80NSSC24K0135/NASA/NASA/United States ; NNH20ZDA001N-BIODIV/NASA/NASA/United States ; DE190101182//Australian Research Council/ ; }, mesh = {*Remote Sensing Technology/methods ; *Ecosystem ; *Ecology/methods ; *Environmental Monitoring/methods ; *Internationality ; }, abstract = {A new proliferation of optical instruments that can be attached to towers over or within ecosystems, or 'proximal' remote sensing, enables a comprehensive characterization of terrestrial ecosystem structure, function, and fluxes of energy, water, and carbon. Proximal remote sensing can bridge the gap between individual plants, site-level eddy-covariance fluxes, and airborne and spaceborne remote sensing by providing continuous data at a high-spatiotemporal resolution. Here, we review recent advances in proximal remote sensing for improving our mechanistic understanding of plant and ecosystem processes, model development, and validation of current and upcoming satellite missions. We provide current best practices for data availability and metadata for proximal remote sensing: spectral reflectance, solar-induced fluorescence, thermal infrared radiation, microwave backscatter, and LiDAR. Our paper outlines the steps necessary for making these data streams more widespread, accessible, interoperable, and information-rich, enabling us to address key ecological questions unanswerable from space-based observations alone and, ultimately, to demonstrate the feasibility of these technologies to address critical questions in local and global ecology.}, }
@article {pmid39852552, year = {2025}, author = {Yang, H and Luo, X and Shang, Z and Li, K and Cai, J and Chen, Y and Xin, L and Ju, J}, title = {Metabolic Blockade-Based Genome Mining of Malbranchea circinata SDU050: Discovery of Diverse Secondary Metabolites.}, journal = {Marine drugs}, volume = {23}, number = {1}, pages = {}, pmid = {39852552}, issn = {1660-3397}, support = {U2106207//National Natural Science Foundation of China/ ; 2022YFC2804100//National Key Research and Development Program of China/ ; 22037006//National Natural Science Foundation of China/ ; SYS202205//Shandong Laboratory Program/ ; }, mesh = {*Anti-Bacterial Agents/pharmacology/isolation &amp; purification ; *Secondary Metabolism/genetics ; Multigene Family ; Polyketide Synthases/genetics/metabolism ; Biosynthetic Pathways/genetics ; Methicillin-Resistant Staphylococcus aureus/drug effects ; Genome, Fungal ; Microbial Sensitivity Tests ; Gram-Positive Bacteria/drug effects ; Staphylococcus aureus/drug effects ; Bacillus subtilis/drug effects ; *Ascomycota/genetics/metabolism ; Isocoumarins/pharmacology ; Computational Biology ; Geologic Sediments/microbiology ; }, abstract = {Malbranchea circinata SDU050, a fungus derived from deep-sea sediment, is a prolific producer of diverse secondary metabolites. Genome sequencing revealed the presence of at least 69 biosynthetic gene clusters (BGCs), including 30 encoding type I polyketide synthases (PKSs). This study reports the isolation and identification of four classes of secondary metabolites from wild-type M. circinata SDU050, alongside five additional metabolite classes, including three novel cytochalasins (7-9), obtained from a mutant strain through the metabolic blockade strategy. Furthermore, bioinformatic analysis of the BGC associated with the isocoumarin sclerin (1) enabled the deduction of its biosynthetic pathway based on gene function predictions. Bioactivity assays demonstrated that sclerin (1) and (-)-mycousnine (10) exhibited weak antibacterial activity against Gram-positive bacteria such as Staphylococcus aureus, methicillin-resistant Staphylococcus aureus (MRSA), and Bacillus subtilis. These findings underscore the chemical diversity and biosynthetic potential of M. circinata SDU050 and highlight an effective strategy for exploring marine fungal metabolites.}, }
@article {pmid39849009, year = {2025}, author = {Calderón-Osorno, M and Rojas-Villalta, D and Lejzerowicz, F and Cortés, J and Arias-Andres, M and Rojas-Jimenez, K}, title = {The influence of depth on the global deep-sea plasmidome.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {2959}, pmid = {39849009}, issn = {2045-2322}, support = {SIA 0483-21//Universidad Nacional de Costa Rica/ ; C1455//Vicerrector&#xed;a de Investigacion de la Universidad Costa Rica/ ; C2650//Vicerrector&#xed;a de Investigacion de la Universidad Costa Rica/ ; C3509//Vicerrector&#xed;a de Investigacion de la Universidad Costa Rica/ ; }, mesh = {*Plasmids/genetics ; *Metagenome ; *Seawater/microbiology ; Ecosystem ; Gammaproteobacteria/genetics ; Alphaproteobacteria/genetics ; Oceans and Seas ; Bacteria/genetics ; Computational Biology/methods ; Indian Ocean ; }, abstract = {Plasmids play a crucial role in facilitating genetic exchange and enhancing the adaptability of microbial communities. Despite their importance, environmental plasmids remain understudied, particularly those in fragile and underexplored ecosystems such as the deep-sea. In this paper we implemented a bioinformatics pipeline to study the composition, diversity, and functional attributes of plasmid communities (plasmidome) in 81 deep-sea metagenomes from the Tara and Malaspina expeditions, sampled from the Pacific, Atlantic, and Indian Oceans at depths ranging from 270 to 4005 m. We observed an association between depth and plasmid traits, with the 270-1000 m range (mesopelagic samples) exhibiting the highest number of plasmids and the largest plasmid sizes. Plasmids of Alphaproteobacteria and Gammaproteobacteria were predominant across the oceans, particularly in this depth range, which also showed the highest species diversity and abundance of metabolic pathways, including aromatic compound degradation. Surprisingly, relatively few antibiotic resistance genes were found in the deep-sea ecosystem, with most being found in the mesopelagic layer. These included classes such as beta-lactamase, biocide resistance, and aminoglycosides. Our study also identified the MOBP and MOBQ relaxase families as prevalent across various taxonomic classes. This research underscores the importance of studying the plasmidome independently from the chromosomal context. Our limited understanding of the deep-sea's microbial ecology, especially its plasmidome, necessitates caution in human activities like mining. Such activities could have unforeseen impacts on this largely unexplored ecosystem.}, }
@article {pmid39848196, year = {2025}, author = {Wang, S and Liping, Y and Arif, M}, title = {Evolutionary analysis of ecological-production-living space-carrying capacity in tourism-centric traditional villages in Guangxi, China.}, journal = {Journal of environmental management}, volume = {375}, number = {}, pages = {124182}, doi = {10.1016/j.jenvman.2025.124182}, pmid = {39848196}, issn = {1095-8630}, mesh = {China ; *Tourism ; Humans ; Geographic Information Systems ; *Conservation of Natural Resources ; }, abstract = {The carrying capacity of ecological-production-living space (EPLS) is pivotal to the development of traditional villages and the optimization of their tourism industries. However, research on tourism-centric traditional villages in China remains limited. This study addresses this gap by examining EPLS carrying capacity in tourism-focused villages in Guangxi, China. Using remote sensing imagery of Chengyang Bazhai (CYBZ) along with data on local tourism and socio-economic development, the study classifies different types of EPLS and establishes a comprehensive indicator system. Geographic information system spatial analysis, combined with grey correlation analysis, was employed to assess the evolution of EPLS carrying capacity and its influencing factors in CYBZ. The findings indicate that between 2006 and 2015, the overall carrying capacity of EPLS experienced a decline. While the carrying capacity of production spaces remained relatively stable, ecological and living spaces saw notable decreases. However, from 2015 to 2021, EPLS carrying capacity increased substantially. The most substantial growth was observed in Pingyan Village, followed by Chengyang Village, with Pingfu Village exhibiting the smallest improvement. The expansion of the tourism industry has significantly influenced the evolution of EPLS carrying capacity in CYBZ, creating a greater need for strategic future planning. Optimal EPLS and durable tourism development require continuous enhancements in EPLS capacity, reductions in negative interactions between carrying capacity and tourism growth, as well as ecological revitalization. This study contributes to the existing literature by enhancing EPLS carrying capacity understanding. It offers theoretical guidance for its optimization in Chengyang and practical insights into sustainable tourism development in similar regions.}, }
@article {pmid39843543, year = {2025}, author = {Gioiosa, S and Gasparini, S and Presutti, C and Rinaldi, A and Castrignanò, T and Mannironi, C}, title = {Integrated gene expression and alternative splicing analysis in human and mouse models of Rett syndrome.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {2778}, pmid = {39843543}, issn = {2045-2322}, support = {GJC22071//Cariplo Telethon Alliance/ ; }, mesh = {*Rett Syndrome/genetics ; Animals ; Humans ; *Alternative Splicing ; Mice ; Disease Models, Animal ; *Methyl-CpG-Binding Protein 2/genetics ; Gene Expression Profiling ; Computational Biology/methods ; Gene Expression Regulation ; Mutation ; Transcriptome ; }, abstract = {Mutations of the MECP2 gene lead to Rett syndrome (RTT), a rare developmental disease causing severe intellectual and physical disability. How the loss or defective function of MeCP2 mediates RTT is still poorly understood. MeCP2 is a global gene expression regulator, acting at transcriptional and post-transcriptional levels. Little attention has been given so far to the contribution of alternative splicing (AS) dysregulation to RTT pathophysiology. To perform a comparative analysis of publicly available RNA sequencing (RNA-seq) studies and generate novel data resources for AS, we explored 100 human datasets and 130 mouse datasets from Mecp2-mutant models, processing data for gene expression and alternative splicing. Our comparative analysis across studies indicates common species-specific differentially expressed genes (DEGs) and differentially alternatively spliced (DAS) genes. Human and mouse dysregulated genes are involved in two main functional categories: cell-extracellular matrix adhesion regulation and synaptic functions, the first category more significantly enriched in human datasets. Our extensive bioinformatics study indicates, for the first time, a significant dysregulation of AS in human RTT datasets, suggesting the crucial contribution of altered RNA processing to the pathophysiology of RTT.}, }
@article {pmid39842565, year = {2025}, author = {Zheng, JY and Jiang, G and Gao, FH and Ren, SN and Zhu, CY and Xie, J and Li, Z and Yin, W and Xia, X and Li, Y and Wang, HL}, title = {MCTASmRNA: A deep learning framework for alternative splicing events classification.}, journal = {International journal of biological macromolecules}, volume = {300}, number = {}, pages = {139941}, doi = {10.1016/j.ijbiomac.2025.139941}, pmid = {39842565}, issn = {1879-0003}, mesh = {*Deep Learning ; *Alternative Splicing/genetics ; Humans ; RNA, Messenger/genetics ; *Computational Biology/methods ; Animals ; }, abstract = {Alternative splicing (AS) plays crucial post-transcriptional gene function regulation roles in eukaryotic. Despite progress in studying AS at the RNA level, existing methods for AS event identification face challenges such as inefficiency, lengthy processing times, and limitations in capturing the complexity of RNA sequences. To overcome these challenges, we evaluated 10 AS detection tools and selected rMATS for dataset construction. We then developed a multi-scale convolutional and Transformer-based model (MCTASmRNA) to classify AS events in mRNA sequences without relying on a reference genome. To handle the problem of large intra-class and small inter-class difference in AS event sequences, we incorporated an efficient channel attention mechanism and designed a new joint loss function to optimize MCTASmRNA training. MCTASmRNA outperformed baseline models, with an accuracy improvement and exhibited enhanced cross-species generalizability. This model provides valuable support for AS research across different organisms. Future work will focus on optimizing and expanding the model to further explore the complex mechanisms underlying AS.}, }
@article {pmid39841777, year = {2025}, author = {Cardoso, ADRO and Ferreira, ACG and Rabahi, MF}, title = {Asthma-related deaths in Brazil: data from an ecological study.}, journal = {Jornal brasileiro de pneumologia : publicacao oficial da Sociedade Brasileira de Pneumologia e Tisilogia}, volume = {50}, number = {6}, pages = {e20240296}, pmid = {39841777}, issn = {1806-3756}, mesh = {Humans ; Brazil/epidemiology ; *Asthma/mortality ; Female ; Male ; Middle Aged ; Adult ; *Hospitalization/statistics &amp; numerical data/trends ; Aged ; Sex Distribution ; Young Adult ; Age Distribution ; Adolescent ; Child ; Child, Preschool ; Sex Factors ; Infant ; Age Factors ; }, abstract = {OBJECTIVE: The aim of this study was to present epidemiological data on hospitalizations and deaths related to asthma in Brazil over the past 11 years.<br><br>METHODS: An ecological study was conducted on asthma-related hospitalizations and mortality in Brazil from 2013 to 2023, using data extracted from the Department of Informatics of the Brazilian Unified Health System and the Mortality Information System.<br><br>RESULTS: Asthma-related deaths showed an increasing trend during the analyzed period. A surge in deaths was observed in 2022 compared to 2014 (difference between means = 56.08 &#xb1; 19.7; 95% CI = 15.2-96.9). The mean number of deaths was higher among females, with their rate remaining stable, while the rate for males increased. Individuals aged >60 years accounted for approximately 65% of all asthma-related deaths from 2013 to 2023, with a strong direct correlation observed between age and the number of deaths, regardless of sex. During the same period, the total number of asthma-related hospitalizations in Brazil showed a declining trend, decreasing from 134,322 in 2013 to 87,707 in 2023.<br><br>CONCLUSION: Over the past 11 years, asthma-related deaths have increased in Brazil, with the majority occurring among females. Older individuals accounted for most asthma-related deaths, and a positive correlation was observed between age and the number of deaths.}, }
@article {pmid39840283, year = {2024}, author = {Yan, B and Nam, Y and Li, L and Deek, RA and Li, H and Ma, S}, title = {Recent advances in deep learning and language models for studying the microbiome.}, journal = {Frontiers in genetics}, volume = {15}, number = {}, pages = {1494474}, pmid = {39840283}, issn = {1664-8021}, support = {R01 GM123056/GM/NIGMS NIH HHS/United States ; U24 OD035523/OD/NIH HHS/United States ; }, abstract = {Recent advancements in deep learning, particularly large language models (LLMs), made a significant impact on how researchers study microbiome and metagenomics data. Microbial protein and genomic sequences, like natural languages, form a language of life, enabling the adoption of LLMs to extract useful insights from complex microbial ecologies. In this paper, we review applications of deep learning and language models in analyzing microbiome and metagenomics data. We focus on problem formulations, necessary datasets, and the integration of language modeling techniques. We provide an extensive overview of protein/genomic language modeling and their contributions to microbiome studies. We also discuss applications such as novel viromics language modeling, biosynthetic gene cluster prediction, and knowledge integration for metagenomics studies.}, }
@article {pmid39838963, year = {2024}, author = {Guan, J and Ji, Y and Peng, C and Zou, W and Tang, X and Shang, J and Sun, Y}, title = {GOPhage: protein function annotation for bacteriophages by integrating the genomic context.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {1}, pages = {}, pmid = {39838963}, issn = {1477-4054}, support = {11209823//City University of Hong Kong/ ; }, mesh = {*Bacteriophages/genetics ; *Genome, Viral ; *Viral Proteins/genetics/metabolism/chemistry ; *Molecular Sequence Annotation/methods ; Genomics/methods ; Computational Biology/methods ; }, abstract = {Bacteriophages are viruses that target bacteria, playing a crucial role in microbial ecology. Phage proteins are important in understanding phage biology, such as virus infection, replication, and evolution. Although a large number of new phages have been identified via metagenomic sequencing, many of them have limited protein function annotation. Accurate function annotation of phage proteins presents several challenges, including their inherent diversity and the scarcity of annotated ones. Existing tools have yet to fully leverage the unique properties of phages in annotating protein functions. In this work, we propose a new protein function annotation tool for phages by leveraging the modular genomic structure of phage genomes. By employing embeddings from the latest protein foundation models and Transformer to capture contextual information between proteins in phage genomes, GOPhage surpasses state-of-the-art methods in annotating diverged proteins and proteins with uncommon functions by 6.78% and 13.05% improvement, respectively. GOPhage can annotate proteins lacking homology search results, which is critical for characterizing the rapidly accumulating phage genomes. We demonstrate the utility of GOPhage by identifying 688 potential holins in phages, which exhibit high structural conservation with known holins. The results show the potential of GOPhage to extend our understanding of newly discovered phages.}, }
@article {pmid39834325, year = {2025}, author = {Chen, L and Xu, Z and He, Y and Zhang, X and Li, L and Zhu, R and Zhang, Z and Lin, H and Hong, G}, title = {Multiomics Analysis Reveals Key Targeted Metabolic Pathways Underlying the Hormesis and Detrimental Effects of Enrofloxacin on Rice Plants.}, journal = {Journal of agricultural and food chemistry}, volume = {73}, number = {4}, pages = {2678-2695}, doi = {10.1021/acs.jafc.4c09001}, pmid = {39834325}, issn = {1520-5118}, mesh = {*Oryza/metabolism/drug effects/genetics/growth &amp; development ; Hormesis ; *Anti-Bacterial Agents/pharmacology/toxicity ; *Enrofloxacin/toxicity/pharmacology ; Metabolic Networks and Pathways/drug effects ; *Plant Proteins/metabolism/genetics ; Plant Growth Regulators/metabolism ; Gene Expression Regulation, Plant/drug effects ; Antioxidants/metabolism ; Metabolomics ; Reactive Oxygen Species/metabolism ; Multiomics ; }, abstract = {Fluoroquinolone antibiotic enrofloxacin (ENR) is frequently detected in agricultural environments. The hormesis and detrimental effects of ENR on crops have been extensively observed. However, the molecular mechanisms underlying these crops' responses to ENR remain limited. Here, integrated physiological, transcriptomic, and metabolomic analysis revealed the key metabolic pathway responses underlying the ENR-induced effects on rice. The results showed that ENR mainly affected three metabolic pathways: 'biosynthesis of amino acids', "tryptophan metabolism", and 'phenylpropanoid/flavonoid biosynthesis'. A low level of ENR treatment promoted root elongation and enhanced the antioxidant capacity by increasing the phytohormone gibberellin A3 and the flavonol quercetin-3-O-neohesperidoside, respectively. However, the high dose of ENR significantly stimulated ROS production, inhibited photosynthesis, and ultimately impaired plant growth. In response to high ENR toxicity, plants accumulated more quercetin derivatives as antioxidants and produced defense-related substances, such as N-hydroxytryptamine, indole-3-acetonitrile, and jasmonic acid, to combat biotic stress. In conclusion, this study provides new insights into the molecular mechanism accounting for the ecological effects of antibiotic pollution in farmland.}, }
@article {pmid39833495, year = {2025}, author = {Akar, SE and Nwachukwu, W and Adewuyi, OS and Ahumibe, AA and Akanimo, I and Okunromade, O and Babatunde, O and Ihekweazu, C and Hitachi, M and Kato, K and Takamatsu, Y and Hirayama, K and Kaneko, S}, title = {Epidemiology of Yellow Fever in Nigeria: Analysis of Climatic, Ecological, Socio-Demographic, and Clinical Factors Associated with Viral Positivity Among Suspected Cases Using National Surveillance Data, 2017-2023.}, journal = {Journal of epidemiology and global health}, volume = {15}, number = {1}, pages = {2}, pmid = {39833495}, issn = {2210-6014}, mesh = {Humans ; Nigeria/epidemiology ; *Yellow Fever/epidemiology/prevention &amp; control ; Female ; Male ; Retrospective Studies ; Adolescent ; Adult ; Middle Aged ; Child ; Young Adult ; Child, Preschool ; Infant ; Climate ; Population Surveillance ; Socioeconomic Factors ; Risk Factors ; Disease Outbreaks ; Aged ; Yellow fever virus/isolation &amp; purification ; }, abstract = {BACKGROUND: Since its resurgence in 2017, Yellow fever (YF) outbreaks have continued to occur in Nigeria despite routine immunization and the implementation of several reactive mass vaccinations. Nigeria, Africa's most populous endemic country, is considered a high-priority country for implementing the End Yellow fever Epidemics strategy.<br><br>METHODS: This retrospective analysis described the epidemiological profile, trends, and factors associated with Yellow fever viral positivity in Nigeria. We conducted a multivariable binary logistic regression analysis to identify factors associated with YF viral positivity.<br><br>RESULTS: Of 16,777 suspected cases, 8532(50.9%) had laboratory confirmation with an overall positivity rate of 6.9%(585). Predictors of YFV positivity were the Jos Plateau, Derived/Guinea Savanah, and the Freshwater/Lowland rainforest compared to the Sahel/Sudan Savannah; dry season compared to rainy season; the hot dry or humid compared to the temperate, dry cool/humid climatic zone; 2019, 2020, 2021, 2022, and 2023 epidemic years compared to compared to 2017; first, third, and fourth quarters compared to the second; male sex compared to female; age group&#x2009;>&#x2009;=&#x2009;15 years compared to <&#x2009;15 years; working in outdoor compared to indoor settings; having traveled within the last two weeks; being of unknown vaccination status compared to being vaccinated; and vomiting.<br><br>CONCLUSION: Ecological, climatic, and socio-demographic characteristics are drivers of YF outbreaks in Nigeria, and public health interventions need to target these factors to halt local epidemics and reduce the risk of international spread. Inadequate vaccination coverage alone may not account for the recurrent outbreaks of YF in Nigeria.}, }
@article {pmid39833389, year = {2025}, author = {Schroeder, MW and Frumkin, MR and Mace, RA}, title = {Proof-of-concept for integrating multimodal digital health assessments into lifestyle interventions for older adults with dementia risk factors.}, journal = {Journal of behavioral medicine}, volume = {48}, number = {2}, pages = {373-384}, pmid = {39833389}, issn = {1573-3521}, support = {1 K23 AG075257-01/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; Aged ; Female ; Male ; *Dementia/prevention &amp; control ; Actigraphy ; *Ecological Momentary Assessment ; Pilot Projects ; Mindfulness ; Middle Aged ; *Life Style ; Proof of Concept Study ; Risk Factors ; Sleep ; Cognitive Dysfunction ; Patient Compliance ; Aged, 80 and over ; Digital Health ; }, abstract = {Multimodal digital health assessments overcome the limitations of patient-reported outcomes by allowing for continuous and passive monitoring but remain underutilized in older adult lifestyle interventions for brain health. Therefore, we aim to (1) report ecological momentary assessment (EMA) and ActiGraph adherence among older adults during a lifestyle intervention; and (2) use dynamic data collected via EMA and ActiGraph to examine person-specific patterns of mindfulness, steps, and sleep throughout the intervention. We analyzed EMA and ActiGraph data from a pilot study of the 8-week My Healthy Brain program (N = 10) lifestyle group for older adults (60+) with subjective cognitive decline. EMA adherence metrics included proportion of EMA completed and the proportion of days with at least 10 mindfulness minutes. ActiGraph GT9X adherence metrics included the number of valid wear days (≥ 7 h) and the number of days participants achieved their step goal. We used linear mixed-effects models to examine person-specific patterns of step count, sleep efficiency, and mindfulness practice. On average, participants completed 39 of the 49 possible EMAs (80%) during the program. ActiGraph adherence was slightly higher than EMA (M = 61.40 days, 87.71%). Participants achieved the daily mindfulness goal (10 min/day) and step goal on 46.32% and 55.10% of days, respectively. Dynamic data revealed that on average, participant step counts increased by approximately 16.5 steps per day (b = 16.495, p = 0.002). However, some participants exhibited no changes while improvements made by other participants returned to baseline levels of activity. There was substantial heterogeneity in trajectories of mindfulness practice and sleep efficiency. EMA and ActiGraph are feasible for older adults enrolled in dementia risk reduction lifestyle interventions. Future studies are needed to better understand how mechanisms of lifestyle behaviors captured by EMA and ActiGraph are related to cognitive outcomes in older adults.}, }
@article {pmid39833104, year = {2024}, author = {Liu, F and Zhao, Z and Liu, Y}, title = {PHPGAT: predicting phage hosts based on multimodal heterogeneous knowledge graph with graph attention network.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {1}, pages = {}, pmid = {39833104}, issn = {1477-4054}, support = {62303193//National Natural Science Foundation of China/ ; 20230101064JC//Natural Science Foundation of Jilin Province, China/ ; }, mesh = {*Bacteriophages/physiology ; *Computational Biology/methods ; *Bacteria/virology ; }, abstract = {Antibiotic resistance poses a significant threat to global health, making the development of alternative strategies to combat bacterial pathogens increasingly urgent. One such promising approach is the strategic use of bacteriophages (or phages) to specifically target and eradicate antibiotic-resistant bacteria. Phages, being among the most prevalent life forms on Earth, play a critical role in maintaining ecological balance by regulating bacterial communities and driving genetic diversity. Accurate prediction of phage hosts is essential for successfully applying phage therapy. However, existing prediction models may not fully encapsulate the complex dynamics of phage-host interactions in diverse microbial environments, indicating a need for improved accuracy through more sophisticated modeling techniques. In response to this challenge, this study introduces a novel phage-host prediction model, PHPGAT, which leverages a multimodal heterogeneous knowledge graph with the advanced GATv2 (Graph Attention Network v2) framework. The model first constructs a multimodal heterogeneous knowledge graph by integrating phage-phage, host-host, and phage-host interactions to capture the intricate connections between biological entities. GATv2 is then employed to extract deep node features and learn dynamic interdependencies, generating context-aware embeddings. Finally, an inner product decoder is designed to compute the likelihood of interaction between a phage and host pair based on the embedding vectors produced by GATv2. Evaluation results using two datasets demonstrate that PHPGAT achieves precise phage host predictions and outperforms other models. PHPGAT is available at https://github.com/ZhaoZMer/PHPGAT.}, }
@article {pmid39832988, year = {2025}, author = {Shimels, T and Kantelhardt, EJ and Assefa, M and Fenta, TG}, title = {Spatiotemporal dynamics and prevention strategies of cervical cancer incidence in Addis Ababa, Ethiopia: an ecological study.}, journal = {BMJ open}, volume = {15}, number = {1}, pages = {e089521}, pmid = {39832988}, issn = {2044-6055}, mesh = {Humans ; Ethiopia/epidemiology ; Female ; *Uterine Cervical Neoplasms/epidemiology/prevention &amp; control ; Incidence ; Middle Aged ; Adult ; Spatio-Temporal Analysis ; Young Adult ; Aged ; Adolescent ; Bayes Theorem ; }, abstract = {OBJECTIVE: This study analysed the spatial and temporal patterns of cervical cancer incidence in Addis Ababa from 2012 to 2021.<br><br>DESIGN: An ecological study was conducted from 1 September to 30 November 2023 to examine the spatiotemporal trends of cervical cancer incidence.<br><br>SETTING: The research was conducted in Addis Ababa, the capital city of Ethiopia.<br><br>PARTICIPANTS: Included were all patients with clinically and/or histopathologically confirmed diagnoses of cervical cancer.<br><br>DATA ANALYSIS: The study employed advanced analytical tools including R programming, Quantum Geographic Information System V.3.36.0, GeoDa V.1.2.2 and System for Automated Geoscientific Analyses GIS V.9.3.2. Techniques such as Bayesian empirical testing with a block weighting matrix for hotspot identification, Global Moran's I for spatial autocorrelation, nearest neighbour imputation and universal Kriging interpolation were used to manage data gaps. Joinpoint trend analysis and direct age-standardised incidence rate (ASIR) using the Segi's World standard population was applied to compare trends across subcities. A statistical significance threshold was set at p<0.05.<br><br>RESULTS: Between 2012 and 2021, a total of 2435 new cervical cancer cases were recorded in the Addis Ababa City Population-based Cancer Registry, with significant spatial clustering observed in Nifas Silk Lafto, Bole, Kirkos as well as parts of Gulele and Yeka sub cities (z score>1.96) in 2018. The citywide age-standardised incidence rate varied from 19 to 26 cases per 100&#x2009;000&#x2009;women-years during 2013 and 2016, respectively. Subcity trends varied significantly, with increases and decreases noted in Akaki Kality and Kolfe Keraniyo over different periods while Bole subcity showed modest increase at 4.2% APC (95% CI: 0.6% to 7.9%; p=0.026).<br><br>CONCLUSION: The study highlights substantial fluctuations in ASIR and significant geographic disparities in cervical cancer throughout Addis Ababa. To address these challenges, the implementation of school-based human papillomavirus vaccination programmes, alongside targeted interventions, active campaigns and sustained surveillance, is critical. These strategies are essential to effectively reduce the cervical cancer burden and improve health outcomes in the community.}, }
@article {pmid39832144, year = {2024}, author = {Ištoňová, M and Dorko, E and Knap, V and Stehlíková, B and Murgová, A and Ondová, P and Rimárová, K}, title = {Assessment of depressive disorders and states of anxiety in patients following cerebrovascular accidents in connection with health care provision.}, journal = {Central European journal of public health}, volume = {32}, number = {Supplement}, pages = {18-24}, pmid = {39832144}, issn = {1210-7778}, mesh = {Humans ; Male ; Female ; Middle Aged ; Aged ; Aged, 80 and over ; *Stroke/psychology/complications ; Slovakia/epidemiology ; *Anxiety Disorders/epidemiology/etiology ; *Depressive Disorder/epidemiology/etiology ; *Anxiety/epidemiology ; Depression/epidemiology ; Surveys and Questionnaires ; }, abstract = {OBJECTIVE: Anxiety and depression in patients following cerebrovascular accidents are among frequently occurring complications of the medical condition. The consequences affect personal, family, professional, and social life. They cause severe functional and cognitive impairments, limit the ability to perform normal daily activities, which can result in complete disability. The aim of the study was to monitor the occurrence of anxiety and depression in patients following cerebrovascular accidents hospitalized in neurological departments in the region of eastern Slovakia.<br><br>METHODS: A total of 101 patients following cerebrovascular accidents, aged from 48-86 years, were included in the descriptive study. Demographic and clinical data were obtained from patients and from medical records. We determined the occurrence of anxiety disorders, depression and emotional distress in patients following cerebrovascular accidents using a standardized Hospital Anxiety and Depression Scale (HADS) questionnaire.<br><br>RESULTS: Data analysis confirms a high incidence of anxiety in the HADS-A subscale (9.23 &#xb1; 4.13) and depression in the HADS-D subscale (9.09 &#xb1; 4.43) during the hospitalization phase of the disease. It demonstrates the pathological occurrence of anxiety states in 37%, depression in 36%, emotional distress in 36%, and a serious degree of combination of pathological values of the anxiety subscale and the depression subscale in 27% of patients. The existence of a strong positive correlation between anxiety and depression indicators was confirmed.<br><br>CONCLUSION: The results confirm a high prevalence of anxiety and depression in the acute phase of the disease. The findings indicate that patients recovering from cerebrovascular accidents not only face physical difficulties and loss of independence but also struggle with anxiety and depression, which can negatively impact and slow their recovery. Given the high frequency of these psychological conditions, further research is needed to enhance the quality and effectiveness of care provided to patients with cerebrovascular accidents.}, }
@article {pmid39832137, year = {2025}, author = {Iobbi, V and Parisi, V and Giacomini, M and De Riccardis, F and Brun, P and Núñez-Pons, L and Drava, G and Giordani, P and Monti, MC and Poggi, R and Murgia, Y and De Tommasi, N and Bisio, A}, title = {Sesterterpenoids: sources, structural diversity, biological activity, and data management.}, journal = {Natural product reports}, volume = {42}, number = {3}, pages = {443-481}, doi = {10.1039/d4np00041b}, pmid = {39832137}, issn = {1460-4752}, mesh = {*Sesterterpenes/chemistry/pharmacology/isolation &amp; purification ; Molecular Structure ; Biological Products/chemistry/pharmacology ; Data Management ; Humans ; }, abstract = {Reviewing the literature published up to October 2024.Sesterterpenoids are one of the most chemically diverse and biologically promising subgroup of terpenoids, the largest family of secondary metabolites. The present review article summarizes more than seven decades of studies on isolation and characterization of more than 1600 structurally novel sesterterpenoids, supplemented by biological, pharmacological, ecological, and geographic distribution data. All the information have been implemented in eight tables available on the web and a relational database https://sesterterpenoids.unige.net/. The interface has two sections, one open to the public for reading only and the other, protected by an authentication mechanism, for timely updating of published results.}, }
@article {pmid39830898, year = {2025}, author = {Gartler, S and Scheer, J and Meyer, A and Abass, K and Bartsch, A and Doloisio, N and Falardeau, J and Hugelius, G and Irrgang, A and Haukur Ingimundarson, J and Jungsberg, L and Lantuit, H and Nymand Larsen, J and Lodi, R and Martin, VS and Mercer, L and Nielsen, D and Overduin, P and Povoroznyuk, O and Rautio, A and Schweitzer, P and Speetjens, NJ and Tomaškovičová, S and Timlin, U and Vanderlinden, JP and Vonk, J and Westerveld, L and Ingeman-Nielsen, T}, title = {A transdisciplinary, comparative analysis reveals key risks from Arctic permafrost thaw.}, journal = {Communications earth &amp; environment}, volume = {6}, number = {1}, pages = {21}, pmid = {39830898}, issn = {2662-4435}, abstract = {Permafrost thaw poses diverse risks to Arctic environments and livelihoods. Understanding the effects of permafrost thaw is vital for informed policymaking and adaptation efforts. Here, we present the consolidated findings of a risk analysis spanning four study regions: Longyearbyen (Svalbard, Norway), the Avannaata municipality (Greenland), the Beaufort Sea region and the Mackenzie River Delta (Canada) and the Bulunskiy District of the Sakha Republic (Russia). Local stakeholders' and scientists' perceptions shaped our understanding of the risks as dynamic, socionatural phenomena involving physical processes, key hazards, and societal consequences. Through an inter- and transdisciplinary risk analysis based on multidirectional knowledge exchanges and thematic network analysis, we identified five key hazards of permafrost thaw. These include infrastructure failure, disruption of mobility and supplies, decreased water quality, challenges for food security, and exposure to diseases and contaminants. The study's novelty resides in the comparative approach spanning different disciplines, environmental and societal contexts, and the transdisciplinary synthesis considering various risk perceptions.}, }
@article {pmid39830079, year = {2024}, author = {Couch, J and Arnaout, R and Arnaout, R}, title = {Beyond Size and Class Balance: Alpha as a New Dataset Quality Metric for Deep Learning.}, journal = {ArXiv}, volume = {}, number = {}, pages = {}, pmid = {39830079}, issn = {2331-8422}, support = {R01 AI148747/AI/NIAID NIH HHS/United States ; R01 HL150394/HL/NHLBI NIH HHS/United States ; }, abstract = {In deep learning, achieving high performance on image classification tasks requires diverse training sets. However, the current best practice-maximizing dataset size and class balance-does not guarantee dataset diversity. We hypothesized that, for a given model architecture, model performance can be improved by maximizing diversity more directly. To test this hypothesis, we introduce a comprehensive framework of diversity measures from ecology that generalizes familiar quantities like Shannon entropy by accounting for similarities among images. (Size and class balance emerge as special cases.) Analyzing thousands of subsets from seven medical datasets showed that the best correlates of performance were not size or class balance but A -"big alpha"-a set of generalized entropy measures interpreted as the effective number of image-class pairs in the dataset, after accounting for image similarities. One of these, A 0 , explained 67% of the variance in balanced accuracy, vs. 54% for class balance and just 39% for size. The best pair of measures was size-plus- A 1 (79%), which outperformed size-plus-class-balance (74%). Subsets with the largest A 0 performed up to 16% better than those with the largest size (median improvement, 8%). We propose maximizing A as a way to improve deep learning performance in medical imaging.}, }
@article {pmid39826720, year = {2025}, author = {Akhoon, BA and Qiao, Q and Stewart, A and Chen, J and Rodriguez Lopez, CM and Corbin, KR}, title = {Pangenomic analysis of the bacterial cellulose-producing genera Komagataeibacter and Novacetimonas.}, journal = {International journal of biological macromolecules}, volume = {298}, number = {}, pages = {139980}, doi = {10.1016/j.ijbiomac.2025.139980}, pmid = {39826720}, issn = {1879-0003}, mesh = {*Cellulose/biosynthesis ; Phylogeny ; *Genome, Bacterial ; *Genomics/methods ; *Acetobacteraceae/genetics/metabolism ; Multigene Family ; Genetic Variation ; }, abstract = {Bacterial cellulose holds significant commercial potential due to its unique structural and chemical properties, making it suitable for applications in electronics, medicine, and pharmaceuticals. However, large-scale BC production remains limited by challenges related to bacterial performance. In this study, we compared 79 microbial genomes from three genera-Komagataeibacter, Novacetimonas, and Gluconacetobacter-to investigate their pangenomes, genetic diversity, and evolutionary relationships. Through comparative genomic and phylogenetic analyses, we identified distinct genome compositions and evolutionary patterns that differ from previous reports. The role of horizontal gene transfer in shaping the genetic diversity and adaptability of these bacteria was also explored. Key determinants in BC production, such as variations in the bacterial cellulose biosynthesis (bcs) operon, carbohydrate uptake genes, and carbohydrate-active enzymes, were examined. Additionally, several biosynthetic gene clusters, including Linocin M18 and sactipeptides, which encode for antimicrobial peptides known as bacteriocins, were identified. These findings reveal new aspects of the genetic diversity in cellulose-producing bacteria and present a comprehensive genomic toolkit that will support future efforts to optimize BC production and improve microbial performance for commercial applications.}, }
@article {pmid39825388, year = {2025}, author = {Burthe, SJ and Kumbar, B and Schäfer, SM and Purse, BV and Vanak, AT and Balakrishnan, N and Hassall, R and Hoti, SL and Narayanaswamy, D and Potadar, S and Rahman, M and Chanda, MM}, title = {First evidence of transovarial transmission of Kyasanur Forest disease virus in Haemaphysalis and Rhipicephalus ticks in the wild.}, journal = {Parasites &amp; vectors}, volume = {18}, number = {1}, pages = {14}, pmid = {39825388}, issn = {1756-3305}, support = {MR/T029846/1//Global Challenges Research Fund/ ; MR/P024335/1//Global Challenges Research Fund/ ; }, mesh = {Animals ; *Encephalitis Viruses, Tick-Borne/isolation &amp; purification/genetics/physiology ; Female ; India/epidemiology ; *Rhipicephalus/virology ; *Kyasanur Forest Disease/transmission/virology ; Larva/virology ; *Ixodidae/virology ; Animals, Wild/virology ; *Arachnid Vectors/virology ; }, abstract = {BACKGROUND: Kyasanur forest disease virus (KFDV) is a tick-borne flavivirus causing debilitating and potentially fatal disease in people in the Western Ghats region of India. The transmission cycle is complex, involving multiple vector and host species, but there are significant gaps in ecological knowledge. Empirical data on pathogen-vector-host interactions and incrimination have not been updated since the last century, despite significant local changes in land use and the expansion of KFD to new areas. Mathematical models predict that transovarial transmission, whereby adult female ticks pass KFDV infections to their offspring, plays an important role in the persistence of KFD, but this has not been shown in the wild. Here we set out to establish whether transovarial transmission of KFDV was occurring under natural field conditions by assessing whether host-seeking larvae were positive for KFDV.<br><br>METHODS: Ticks were sampled by dragging and flagging across a broad range of habitats within the agro-forest matrix at 49 sites in two districts: Shivamogga, Karnataka and Wayanad, Kerala (September 2018-March 2019), and larvae were tested for KFDV by PCR.<br><br>RESULTS: In total, larval ticks from 7 of the 49 sites sampled tested positive for KFDV, indicating that transovarial transmission is occurring. Of the 13 KFDV-positive larval samples, 3 came from around houses and gardens, 5 from crops (3 from harvested rice paddy and 2 from areca plantation), 1 from teak plantation and 4 (2 from 1 transect) from forests. Five different tick species were found to have KFDV-positive larvae: Haemaphysalis spinigera, H. bispinosa, Rhipicephalus annulatus, R. microplus and an unidentifiable species of Haemaphysalis (no close match in GenBank).<br><br>CONCLUSIONS: Our empirical confirmation of transovarial transmission has important implications for understanding and predicting KFD dynamics, suggesting that ticks may act as a reservoir for KFDV. Moreover, small mammals and cattle may play crucial roles in transmission if small mammals are the main hosts for larvae infected via transovarial transmission, and cattle support large numbers of infected female adult ticks. This first report of transovarial transmission of KFDV, and within a hitherto undescribed range of vectors and habitats, will help disease managers improve KFD surveillance and mitigation strategies, ultimately leading to communities becoming more resilient to the risk of this tick-transmitted disease.}, }
@article {pmid39823836, year = {2025}, author = {Li, Z and Meng, C and Azad, MAK and Zhu, Q and Lin, W and Cui, Y and Lan, W and He, Q and Kong, X}, title = {Effects of the Salvia miltiorrhiza, Ligustrum lucidum, and Taraxacum mongolicum ultra-fine powder formula on meat quality of aged layers by multi-omics.}, journal = {Poultry science}, volume = {104}, number = {2}, pages = {104783}, pmid = {39823836}, issn = {1525-3171}, mesh = {Animals ; *Ligustrum/chemistry ; *Salvia miltiorrhiza/chemistry ; Dietary Supplements/analysis ; Animal Feed/analysis ; *Meat/analysis ; *Taraxacum/chemistry ; *Chickens/physiology ; Diet/veterinary ; *Drugs, Chinese Herbal/administration &amp; dosage/metabolism ; Female ; Powders ; Antioxidants/metabolism ; Random Allocation ; Multiomics ; }, abstract = {This study was aimed to identify the targets of 1% ultra-fine Chinese medicine formula (UCMF, 0.5% Salvia miltiorrhiza Bge. + 0.25% Ligustrum lucidum Ait. + 0.25% Taraxacum mongolicum Hand.-Mazz.) in delaying aging and explore its impacts on meat quality of aged layers. The effective components of the above three Chinese herbs were screened, and the network pharmacology analysis identified 91 common targets and enriched pathways between herbs and aging. The results showed that cellular response to chemical stimulus, response to oxidative stress, and response to oxygen-containing compound pathways were crucial for UCMF to resist aging. Further in vivo analyses confirmed that UCMF supplementation enhanced the antioxidant function in breast muscles of aged layers by upregulating (P < 0.05) the SOD2 gene expression. Meanwhile, UCMF supplementation reduced (P < 0.05) yellowness (b* value) and drip loss while enhancing (P < 0.05) cooked meat percentage of aged layers. For the health lipid indices in breast muscles, UCMF supplementation increased (P < 0.05) polyunsaturated fatty acids/saturated fatty acids and hypocholesterolemic/hypercholesterolemic ratios and decreased (P < 0.05) the thrombogenic index. The UCMF supplementation optimized the cecal microbiota of aged layers by enhancing the relative abundance of Firmicutes and reducing the relative abundances of Bacteroidetes and Spirochaetes (P < 0.05), which may be related to improving meat quality. In conclusion, dietary UCMF supplementation may be an effective strategy for improving antioxidant function and the meat quality of aged layers.}, }
@article {pmid39823671, year = {2025}, author = {Liu, T and Wang, M and Wang, M and Xiong, Q and Jia, L and Ma, W and Sui, S and Wu, W and Guo, X}, title = {Identification of the primary pollution sources and dominant influencing factors of soil heavy metals using a random forest model optimized by genetic algorithm coupled with geodetector.}, journal = {Ecotoxicology and environmental safety}, volume = {290}, number = {}, pages = {117731}, doi = {10.1016/j.ecoenv.2025.117731}, pmid = {39823671}, issn = {1090-2414}, mesh = {*Metals, Heavy/analysis ; *Soil Pollutants/analysis ; China ; *Environmental Monitoring/methods ; Soil/chemistry ; Algorithms ; Geographic Information Systems ; *Environmental Pollution/analysis/statistics &amp; numerical data ; Risk Assessment ; Monte Carlo Method ; Principal Component Analysis ; Genetic Algorithms ; Random Forest ; }, abstract = {Identifying and quantifying the dominant factors influencing heavy metal (HM) pollution sources are essential for maintaining soil ecological health and implementing effective pollution control measures. This study analyzed soil HM samples from 53 different land use types in Jiaozuo City, Henan Province, China. Pollution sources were identified using Absolute Principal Component Score (APCS), with 8 anthropogenic factors, 9 natural factors, and 4 soil physicochemical properties mapped using Geographic Information System (GIS) kernel density estimation. Geodetector and a genetic algorithm optimized random forest model (GA-RF) were employed to quantify the dominant factors and precisely identify pollution sources. A Monte Carlo model was further applied to assess source-oriented health risk probabilities across age groups in the study area. The results revealed three principal components representing pollution sources, with contribution rates of 47.2 %, 33.3 %, and 19.5 %, respectively. For pollution source 1, industrial activities were dominant, with factory density (27.7 %) and distance from the factory (36.3 %) identified as the main factors. Cr, Cu, Mn, and Ni had high loads in this source. Pollution source 2, a combination of natural and transportation influences, was primarily affected by the normalized difference vegetation index (NDVI, 37.8 %), road network density (16.8 %), and proximity to roads (15.3 %). Pollution source 3 was linked to agricultural activities, with cultivated land density (CLD) contributing 39.1 %. As exhibited a high load (91.1 %) in this source, with an exceedance rate of 93 % in cultivated soil, a moderate enrichment factor of 2.33, and a strong ecological risk index of 615.72, making it the most polluted metal in the area. The source-oriented Health Risk Assessment (HRA) showed that agricultural activities contributed 88.7 % to the carcinogenic risk from As in cultivated land. Overall, 99.3 % of the population faced an acceptable cancer risk level. Unlike traditional source apportionment methods, the GA-RF model effectively quantified the contributions of specific influencing factors (e.g., factory density) to pollution sources, rather than merely estimating the percentage contributions of the sources themselves. This approach provides a novel perspective for HM source apportionment under complex environmental conditions.}, }
@article {pmid39822595, year = {2024}, author = {Boyes, D and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Poplar Grey moth, Subacronicta megacephala (Denis &amp; Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {696}, pmid = {39822595}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Subacronicta megacephala (Poplar Grey moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 424.20 megabases. Most of the assembly (99.02%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.35 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,189 protein-coding genes.}, }
@article {pmid39822261, year = {2025}, author = {Proença Neto, MA and De Sousa, MPA}, title = {Pytaxon: A Python software for resolving and correcting taxonomic names in biodiversity data.}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e138257}, pmid = {39822261}, issn = {1314-2828}, abstract = {BACKGROUND: The standardisation and correction of taxonomic names in large biodiversity databases remain persistent challenges for researchers, as errors in species names can compromise ecological analyses, land-use planning and conservation efforts, particularly when inaccurate data are shared on global biodiversity portals.<br><br>NEW INFORMATION: We present pytaxon, a Python software designed to resolve and correct taxonomic names in biodiversity data by leveraging the Global Names Verifier (GNV) API and employing fuzzy matching techniques to suggest corrections for discrepancies and nomenclatural inconsistencies. The pytaxon offers both a Command Line Interface (CLI) and a Graphical User Interface (GUI), ensuring accessibility to users with different levels of computing expertise. Tests on spreadsheets derived from datasets published in the Global Biodiversity Information Facility (GBIF) demonstrated its effectiveness in identifying and resolving taxonomic errors. By mitigating the propagation of inaccuracies from researchers' datasets to global biodiversity databases, pytaxon supports more reliable conservation decisions and robust scientific investigations. Its contributions enhance data integrity and promote informed biodiversity management in a rapidly evolving global environment.}, }
@article {pmid39821365, year = {2025}, author = {Zhang, D and Cai, Y and Sun, Y and Zeng, P and Wang, W and Wang, W and Jiang, X and Lian, Y}, title = {A Real-World Disproportionality Analysis of Histamine H2-Receptors Antagonists (Famotidine): A Pharmacovigilance Study Based on Spontaneous Reports in the FDA Adverse Event Reporting System.}, journal = {Drug development research}, volume = {86}, number = {1}, pages = {e70045}, doi = {10.1002/ddr.70045}, pmid = {39821365}, issn = {1098-2299}, support = {//This study was funded by the National Natural Science Foundation of China (Grant No: 82303109), the Natural Science Foundation of Fujian Province, China (Grant No: 2022J05299), Cross-Strait Postdoctoral Exchange Funding Program of Fujian Province, China (Grant No: 2021B002)./ ; }, mesh = {Humans ; *Pharmacovigilance ; *Adverse Drug Reaction Reporting Systems/statistics &amp; numerical data ; *Histamine H2 Antagonists/adverse effects/administration &amp; dosage ; United States ; United States Food and Drug Administration ; *Famotidine/adverse effects/administration &amp; dosage ; Female ; Male ; Middle Aged ; Adult ; Aged ; Young Adult ; Adolescent ; Databases, Factual ; Child ; }, abstract = {Famotidine is an H2 receptor antagonist and is currently used on a large scale in gastroenterology. However, Famotidine may also cause severe toxicity to organ systems, including the blood system, digestive system, and urinary system. The objective of this study was to scientifically and systematically investigate the adverse events (AEs) of Famotidine in the real world through the FDA Adverse Event Reporting System (FAERS) database. A disproportionality analysis was used to quantify the signals of AEs associated with Famotidine in FAERS data from the first quarter of 2004 to the first quarter of 2023. The clinical features, onset time, oral and intravenous administration and severe consequences of Famotidine induced AEs were further analyzed. Among the four tests, we found several AEs that were not mentioned in the drug label. For example, abdominal pain upper, abdominal discomfort, dyspepsia, liver disorder, gastrooesophageal reflux disease, and rhabdomyolysis. These AEs are consistent with the drug instructions. Interestingly, we found several unreported AEs, such as: cerebral infarction, hypocalcaemia, hallucination, visual, hypomagnesaemia, hypoparathyroidism, diabetes insipidus, vulvovaginal candidiasis, retro-orbital neoplasm, neuroblastoma recurrent, and malignant cranial nerve neoplasm. Most of our findings are consistent with clinical observations and drug labels, and we also found possible new and unexpected AEs signals, which suggest the need for prospective clinical studies to confirm these results and explain their relationships. Our findings provide valuable evidence for further safety studies.}, }
@article {pmid39817434, year = {2025}, author = {Blum, J and Brüll, M and Hengstler, JG and Dietrich, DR and Gruber, AJ and Dipalo, M and Kraushaar, U and Mangas, I and Terron, A and Fritsche, E and Marx-Stoelting, P and Hardy, B and Schepky, A and Escher, S and Hartung, T and Landsiedel, R and Odermatt, A and Sachana, M and Koch, K and Dönmez, A and Masjosthusmann, S and Bothe, K and Schildknecht, S and Beilmann, M and Beltman, JB and Fitzpatrick, S and Mangerich, A and Rehm, M and Tangianu, S and Zickgraf, FM and Kamp, H and Burger, G and van de Water, B and Kleinstreuer, N and White, A and Leist, M}, title = {The long way from raw data to NAM-based information: Overview on data layers and processing steps.}, journal = {ALTEX}, volume = {42}, number = {1}, pages = {167-180}, doi = {10.14573/altex.2412171}, pmid = {39817434}, issn = {1868-8551}, mesh = {Animals ; Humans ; *Animal Testing Alternatives/methods ; Risk Assessment ; *Toxicity Tests/methods ; }, abstract = {Toxicological test methods generate raw data and provide instructions on how to use these to determine a final outcome such as a classification of test compounds as hits or non-hits. The data processing pipeline provided in the test method description is often highly complex. Usually, multiple layers of data, ranging from a machine-generated output to the final hit definition, are considered. Transition between each of these layers often requires several data processing steps. As changes in any of these processing steps can impact the final output of new approach methods (NAMs), the processing pipeline is an essential part of a NAM description and should be included in reporting templates such as the ToxTemp. The same raw data, processed in different ways, may result in different final outcomes that may affect the readiness status and regulatory acceptance of the NAM, as an altered output can affect robustness, performance, and relevance. Data management, pro­cessing, and interpretation are therefore important elements of a comprehensive NAM definition. We aim to give an overview of the most important data levels to be considered during the devel­opment and application of a NAM. In addition, we illustrate data processing and evaluation steps between these data levels. As NAMs are increasingly standard components of the spectrum of toxi­cological test methods used for risk assessment, awareness of the significance of data processing steps in NAMs is crucial for building trust, ensuring acceptance, and fostering the reproducibility of NAM outcomes.}, }
@article {pmid39814778, year = {2025}, author = {Gómez-Gras, D and Linares, C and Viladrich, N and Zentner, Y and Grinyó, J and Gori, A and McFadden, CS and Fabricius, KE and Madin, JS}, title = {The Octocoral Trait Database: a global database of trait information for octocoral species.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {82}, pmid = {39814778}, issn = {2052-4463}, mesh = {*Anthozoa ; Animals ; *Databases, Factual ; Coral Reefs ; Biodiversity ; Ecosystem ; }, abstract = {Trait-based approaches are revolutionizing our understanding of high-diversity ecosystems by providing insights into the principles underlying key ecological processes, such as community assembly, species distribution, resilience, and the relationship between biodiversity and ecosystem functioning. In 2016, the Coral Trait Database advanced coral reef science by centralizing trait information for stony corals (i.e., Subphylum Anthozoa, Class Hexacorallia, Order Scleractinia). However, the absence of trait data for soft corals, gorgonians, and sea pens (i.e., Class Octocorallia) limits our understanding of ecosystems where these organisms are significant members and play pivotal roles. To address this gap, we introduce the Octocoral Trait Database, a global, open-source database of curated trait data for octocorals. This database houses species- and individual-level data, complemented by contextual information that provides a relevant framework for analyses. The inaugural dataset, OctocoralTraits v2.2, contains over 97,500 global trait observations across 98 traits and over 3,500 species. The database aims to evolve into a steadily growing, community-led resource that advances future marine science, with a particular emphasis on coral reef research.}, }
@article {pmid39813953, year = {2025}, author = {Knight, ME and Farkas, K and Wade, M and Webster, G and Pass, DA and Perry, W and Kille, P and Singer, A and Jones, DL}, title = {Wastewater-based analysis of antimicrobial resistance at UK airports: Evaluating the potential opportunities and challenges.}, journal = {Environment international}, volume = {195}, number = {}, pages = {109260}, doi = {10.1016/j.envint.2025.109260}, pmid = {39813953}, issn = {1873-6750}, mesh = {*Wastewater/microbiology ; *Airports ; United Kingdom ; *Drug Resistance, Microbial/genetics ; Environmental Monitoring ; *Drug Resistance, Bacterial/genetics ; }, abstract = {With 40 million annual passenger flights, airports are key hubs for microbial communities from diverse geographic origins to converge, mix, and distribute. Wastewater derived from airports and aircraft represent both a potential route for the global dispersion of antimicrobial resistant (AMR) organisms and an under-utilised resource for strengthening global AMR surveillance. This study investigates the abundance and diversity of antimicrobial resistance genes (ARGs) in wastewater samples collected from airport terminals (n = 132), aircraft (n = 25), and a connected wastewater treatment plant (n = 11) at three international airports in the UK (London Heathrow, Edinburgh and Bristol). A total of 76 ARGs were quantified using high throughput qPCR (HT-qPCR) while a subset of samples (n = 30) was further analysed by metagenomic sequencing. Our findings reveal that aircraft wastewater resistomes were compositionally distinct from those observed at airport terminals, despite their similar diversity. Notably, flights originating from Asia and Africa carried a higher number of unique ARGs compared to those from Europe and North America. However, clustering of the ARG profile displayed no overall association with geography. Edinburgh terminal and pumping station wastewater had compositionally comparable resistomes to that of the connected urban wastewater treatment plant, though further research is needed to determine the relative contributions of the local population and international travellers. This study provides the first comprehensive investigation of AMR in wastewater from both aircraft and terminals across multiple international airports. Our results highlight aircraft wastewater as a potential route for cross-border AMR transmission and a valuable tool for global AMR surveillance. However, the findings also underscore the limitations and need for standardised approaches for AMR monitoring in airport environments, to effectively mitigate the global spread of AMR and enhance public health surveillance strategies.}, }
@article {pmid39813804, year = {2025}, author = {Ahmad, S and Peng, X and Ashraf, A and Yin, D and Chen, Z and Ahmed, R and Israr, M and Jia, H}, title = {Building resilient urban drainage systems by integrated flood risk index for evidence-based planning.}, journal = {Journal of environmental management}, volume = {374}, number = {}, pages = {124130}, doi = {10.1016/j.jenvman.2025.124130}, pmid = {39813804}, issn = {1095-8630}, mesh = {*Drainage, Sanitary/methods/statistics &amp; numerical data ; Cities/statistics &amp; numerical data ; *Floods/statistics &amp; numerical data ; *City Planning/methods ; Urbanization ; Climate Change ; *Risk Management/methods ; Geographic Information Systems ; Water Movements ; Risk Assessment ; Pakistan ; }, abstract = {Urban flooding poses a significant risk to cities worldwide, exacerbated by increasing urbanization and climate change. Effective flood risk management requires comprehensive assessments considering the complex interaction of social, economic, and environmental factors. This study developed an innovative Urban Flood Risk Index (FRI) to quantify and assess flood risk at the sub-catchment level, providing a tool for evidence-based planning and resilient infrastructure development. This study integrates Geographic Information System (GIS), Storm Water Management Model (SWMM), Analytic Hierarchy Process (AHP), and the Pressure-State-Response (PSR) framework. The FRI incorporates seven pressure and state indicators and three response indicators weighted by expert judgment. The FRI was calculated by combining the weighted sub-indices, classifying flood risk into five levels. Results showed that 51% of the study area experienced high pressure, with 26% facing very-high pressure. The state index indicated that 55% of the area falls under a moderate state, while 21% exhibits a high state. Importantly, the response index highlighted the effectiveness of Low Impact Development (LID) practices, with 20% of the area showing high to very-high response levels. The integrated FRI demonstrated an overall moderate flood risk level for maximum sub-catchments, emphasizing the positive impact of LID practices in mitigating flood risk despite existing pressures and system limitations. This evidence-based assessment provides a valuable tool for sub-catchment level flood risk assessment. It empowers decision-makers to prioritize investments, target interventions, and develop adaptive strategies to enhance urban resilience in a changing climate.}, }
@article {pmid39813347, year = {2025}, author = {Gu, S and Shao, Z and Qu, Z and Zhu, S and Shao, Y and Zhang, D and Allen, R and He, R and Shao, J and Xiong, G and Jousset, A and Friman, VP and Wei, Z and Kümmerli, R and Li, Z}, title = {Siderophore synthetase-receptor gene coevolution reveals habitat- and pathogen-specific bacterial iron interaction networks.}, journal = {Science advances}, volume = {11}, number = {3}, pages = {eadq5038}, pmid = {39813347}, issn = {2375-2548}, mesh = {*Siderophores/metabolism/genetics ; *Iron/metabolism ; *Ecosystem ; *Evolution, Molecular ; Microbial Interactions ; Humans ; *Pseudomonas/genetics/metabolism ; *Bacteria/metabolism/genetics ; Computational Biology/methods ; *Bacterial Proteins/genetics/metabolism ; }, abstract = {Bacterial social interactions play crucial roles in various ecological, medical, and biotechnological contexts. However, predicting these interactions from genome sequences is notoriously difficult. Here, we developed bioinformatic tools to predict whether secreted iron-scavenging siderophores stimulate or inhibit the growth of community members. Siderophores are chemically diverse and can be stimulatory or inhibitory depending on whether bacteria have or lack corresponding uptake receptors. We focused on 1928 representative Pseudomonas genomes and developed an experimentally validated coevolution algorithm to match encoded siderophore synthetases to corresponding receptor groups. We derived community-level iron interaction networks to show that siderophore-mediated interactions differ across habitats and lifestyles. Specifically, dense networks of siderophore sharing and competition were observed among environmental and nonpathogenic species, while small, fragmented networks occurred among human-associated and pathogenic species. Together, our sequence-to-ecology approach empowers the analyses of social interactions among thousands of bacterial strains and offers opportunities for targeted intervention to microbial communities.}, }
@article {pmid39810621, year = {2025}, author = {Gottlieb, E and Gupta, S and Gahan, L and Raymann, RJ and Watson, NF}, title = {Social jetlag decreases across the lifespan: A prospective big data analysis of objective sleep metrics.}, journal = {Journal of sleep research}, volume = {34}, number = {4}, pages = {e14433}, doi = {10.1111/jsr.14433}, pmid = {39810621}, issn = {1365-2869}, mesh = {Humans ; Female ; Male ; Middle Aged ; *Jet Lag Syndrome/physiopathology ; Adult ; *Sleep/physiology ; Prospective Studies ; Big Data ; Polysomnography ; Aged ; Longitudinal Studies ; Self Report ; Retirement ; Caffeine ; Age Factors ; Circadian Rhythm/physiology ; Cross-Sectional Studies ; }, abstract = {Changes in social zeitgebers across the lifespan affect the interaction between biological and social clocks, potentially contributing to social jetlag. Extant literature suggests a reduction in social jetlag given declining social obligations occurring after retirement, but is limited to self-reported methods and cross-sectional designs. Leveraging longitudinal and ecologically valid data from consumer sleep technology, we analysed objective sleep data from 2439 users of the polysomnography-validated SleepScore mobile application, encompassing 500,415 total nights recorded. We examined the relationship between age as a continuous variable, age as a proxy for retirement status, and social jetlag. Additional linear models were employed to assess the effect of self-reported chronotype, average reported daily caffeine, alcohol and stress on social jetlag. There was a significant negative association between overall age and social jetlag (β = -0.64, t = -9.90, p < 0.001, effect size = 0.040), such that every 1-year increase in age corresponded with a 0.64-min reduction in social jetlag. The inclusion of self-reported chronotype, stress, caffeine and alcohol increased the explanatory power of our models slightly, but the effect of age remained consistent (β = -0.642, t = -8.91, p < 0.001, effect size = 0.046). Retirement-aged individuals exhibited nearly 50% less reduction in social jetlag than pre-retirement (30.6 ± 48.2 min versus post-retirement: 15.8 ± 41.6 min, p < 0.0001). While social jetlag after retirement was most pronounced for strong evening chronotypes (β = -0.41, t = -2.876, p = 0.004, effect size = -0.4276), pairwise comparisons revealed no statistically significant differences in the slopes between chronotypes (p > 0.05). Thus, social jetlag decreases across the lifespan, and its reduction appears to be amplified post-retirement even after accounting for behavioural factors.}, }
@article {pmid39809974, year = {2025}, author = {Jia, W and Chan, JC and Wong, TY and Fisher, EB}, title = {Diabetes in China: epidemiology, pathophysiology and multi-omics.}, journal = {Nature metabolism}, volume = {7}, number = {1}, pages = {16-34}, pmid = {39809974}, issn = {2522-5812}, mesh = {Humans ; China/epidemiology ; *Diabetes Mellitus/epidemiology/physiopathology/genetics ; Metabolomics ; Risk Factors ; Prevalence ; Multiomics ; }, abstract = {Although diabetes is now a global epidemic, China has the highest number of affected people, presenting profound public health and socioeconomic challenges. In China, rapid ecological and lifestyle shifts have dramatically altered diabetes epidemiology and risk factors. In this Review, we summarize the epidemiological trends and the impact of traditional and emerging risk factors on Chinese diabetes prevalence. We also explore recent genetic, metagenomic and metabolomic studies of diabetes in Chinese, highlighting their role in pathogenesis and clinical management. Although heterogeneity across these multidimensional areas poses major analytic challenges in classifying patterns or features, they have also provided an opportunity to increase the accuracy and specificity of diagnosis for personalized treatment and prevention. National strategies and ongoing research are essential for improving diabetes detection, prevention and control, and for personalizing care to alleviate societal impacts and maintain quality of life.}, }
@article {pmid39809329, year = {2025}, author = {Amino, K and Hirakawa, T and Yago, M and Matsuo, T}, title = {Dorsoventral comparison of intraspecific variation in the butterfly wing pattern using a convolutional neural network.}, journal = {Biology letters}, volume = {21}, number = {1}, pages = {20240446}, pmid = {39809329}, issn = {1744-957X}, support = {//ACT-X/ ; //Japan Society for the Promotion of Science/ ; }, mesh = {Animals ; Female ; Male ; *Butterflies/anatomy &amp; histology ; *Convolutional Neural Networks ; Sex Characteristics ; Species Specificity ; *Wings, Animal/anatomy &amp; histology ; }, abstract = {Butterfly wing patterns exhibit notable differences between the dorsal and ventral surfaces, and morphological analyses of them have provided insights into the ecological and behavioural characteristics of wing patterns. Conventional methods for dorsoventral comparisons are constrained by the need for homologous patches or shared features between two surfaces, limiting their applicability across species. We used a convolutional neural network (CNN)-based analysis, which can compare images of the two surfaces without focusing on homologous patches or features, to detect dorsoventral bias in two types of intraspecific variation: sexual dimorphism and mimetic polymorphism. Using specimen images of 29 species, we first showed that the level of sexual dimorphism calculated by CNN-based analysis corresponded well with traditional assessments of sexual dissimilarity, demonstrating the validity of the method. Dorsal biases were widely detected in sexual dimorphism, suggesting that the conventional hypothesis of dorsally biased sexual selection can be supported in a broader range of species. In contrast, mimetic polymorphism showed no such bias, indicating the importance of both surfaces in mimicry. Our study demonstrates the potential versatility of CNN in comparing wing patterns between the two surfaces, while elucidating the relationship between dorsoventrally different selections and dorsoventral biases in intraspecific variations.}, }
@article {pmid39808665, year = {2025}, author = {Fonseca, LL and Böttcher, L and Mehrad, B and Laubenbacher, RC}, title = {Optimal control of agent-based models via surrogate modeling.}, journal = {PLoS computational biology}, volume = {21}, number = {1}, pages = {e1012138}, pmid = {39808665}, issn = {1553-7358}, support = {R01 AI135128/AI/NIAID NIH HHS/United States ; R01 GM127909/GM/NIGMS NIH HHS/United States ; R01 HL169974/HL/NHLBI NIH HHS/United States ; }, mesh = {*Algorithms ; Humans ; Computational Biology/methods ; Computer Simulation ; *Models, Biological ; }, abstract = {This paper describes and validates an algorithm to solve optimal control problems for agent-based models (ABMs). For a given ABM and a given optimal control problem, the algorithm derives a surrogate model, typically lower-dimensional, in the form of a system of ordinary differential equations (ODEs), solves the control problem for the surrogate model, and then transfers the solution back to the original ABM. It applies to quite general ABMs and offers several options for the ODE structure, depending on what information about the ABM is to be used. There is a broad range of applications for such an algorithm, since ABMs are used widely in the life sciences, such as ecology, epidemiology, and biomedicine and healthcare, areas where optimal control is an important purpose for modeling, such as for medical digital twin technology.}, }
@article {pmid39808116, year = {2024}, author = {Zárate, A and Díaz-González, L and Taboada, B}, title = {VirDetect-AI: a residual and convolutional neural network-based metagenomic tool for eukaryotic viral protein identification.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {1}, pages = {}, pmid = {39808116}, issn = {1477-4054}, mesh = {Humans ; Artificial Intelligence ; Computational Biology/methods ; *Convolutional Neural Networks ; *Eukaryota/virology ; Genome, Viral ; Metagenome ; *Metagenomics/methods ; *Viral Proteins/genetics ; *Viruses/genetics ; }, abstract = {This study addresses the challenging task of identifying viruses within metagenomic data, which encompasses a broad array of biological samples, including animal reservoirs, environmental sources, and the human body. Traditional methods for virus identification often face limitations due to the diversity and rapid evolution of viral genomes. In response, recent efforts have focused on leveraging artificial intelligence (AI) techniques to enhance accuracy and efficiency in virus detection. However, existing AI-based approaches are primarily binary classifiers, lacking specificity in identifying viral types and reliant on nucleotide sequences. To address these limitations, VirDetect-AI, a novel tool specifically designed for the identification of eukaryotic viruses within metagenomic datasets, is introduced. The VirDetect-AI model employs a combination of convolutional neural networks and residual neural networks to effectively extract hierarchical features and detailed patterns from complex amino acid genomic data. The results demonstrated that the model has outstanding results in all metrics, with a sensitivity of 0.97, a precision of 0.98, and an F1-score of 0.98. VirDetect-AI improves our comprehension of viral ecology and can accurately classify metagenomic sequences into 980 viral protein classes, hence enabling the identification of new viruses. These classes encompass an extensive array of viral genera and families, as well as protein functions and hosts.}, }
@article {pmid39807382, year = {2024}, author = {Smith, SD and Geraghty, EM and Rivas, AL and Fasina, FO and Kosoy, M and Malania, L and Hoogesteijn, AL and Fair, JM}, title = {Multidimensional perspectives of geo-epidemiology: from interdisciplinary learning and research to cost-benefit oriented decision-making.}, journal = {Frontiers in public health}, volume = {12}, number = {}, pages = {1492426}, pmid = {39807382}, issn = {2296-2565}, mesh = {Humans ; *Cost-Benefit Analysis ; *Decision Making ; *Epidemiology/education ; Geographic Information Systems ; Interdisciplinary Research ; }, abstract = {Research typically promotes two types of outcomes (inventions and discoveries), which induce a virtuous cycle: something suspected or desired (not previously demonstrated) may become known or feasible once a new tool or procedure is invented and, later, the use of this invention may discover new knowledge. Research also promotes the opposite sequence-from new knowledge to new inventions. This bidirectional process is observed in geo-referenced epidemiology-a field that relates to but may also differ from spatial epidemiology. Geo-epidemiology encompasses several theories and technologies that promote inter/transdisciplinary knowledge integration, education, and research in population health. Based on visual examples derived from geo-referenced studies on epidemics and epizootics, this report demonstrates that this field may extract more (geographically related) information than simple spatial analyses, which then supports more effective and/or less costly interventions. Actual (not simulated) bio-geo-temporal interactions (never captured before the emergence of technologies that analyze geo-referenced data, such as geographical information systems) can now address research questions that relate to several fields, such as Network Theory. Thus, a new opportunity arises before us, which exceeds research: it also demands knowledge integration across disciplines as well as novel educational programs which, to be biomedically and socially justified, should demonstrate cost-effectiveness. Grounded on many bio-temporal-georeferenced examples, this report reviews the literature that supports this hypothesis: novel educational programs that focus on geo-referenced epidemic data may help generate cost-effective policies that prevent or control disease dissemination.}, }
@article {pmid39806613, year = {2024}, author = {Shen, A and Ye, J and Zhao, H and Qiang, W and Zhao, H and Huang, Y and Zhou, Y and Wang, Y and Li, X and Zhang, Z and Bian, J and Zhang, L and Wu, P and Wang, Y and Lu, Q}, title = {Risk factors and prediction model of breast cancer-related lymphoedema in a Chinese cancer centre: a prospective cohort study protocol.}, journal = {BMJ open}, volume = {14}, number = {12}, pages = {e089769}, pmid = {39806613}, issn = {2044-6055}, mesh = {Adult ; Female ; Humans ; Middle Aged ; *Breast Cancer Lymphedema/epidemiology/etiology ; *Breast Neoplasms/surgery/complications ; China/epidemiology ; Incidence ; *Lymphedema/epidemiology/etiology ; Observational Studies as Topic ; Prospective Studies ; Risk Assessment ; Risk Factors ; East Asian People ; }, abstract = {INTRODUCTION: Lymphoedema is a distressing and long-term complication for breast cancer survivors. However, the reported incidence of lymphoedema varies, and its risk factors remain underexplored. Currently, a well-established risk prediction model is still lacking. This study aims to describe the rationale, objectives, protocol and baseline characteristics of a prospective cohort study focused on examining the incidence and risk factors of breast cancer-related lymphoedema (BCRL), as well as developing a risk prediction model.<br><br>METHODS AND ANALYSIS: This study is an ongoing single-centre prospective observational cohort study recruiting 1967 patients with breast cancer scheduled for surgery treatment in northern China between 15 February 2022 and 21 June 2023. Assessments will be conducted presurgery and at 1, 3, 6, 12, 18, 24, 30 and 36 months postsurgery. Bilateral limb circumferences will be measured by patients at home or by researchers at the outpatient clinics during follow-up visits. The diagnosis of lymphoedema is based on a relative limb volume increase of &#x2265;10% from the preoperative assessment. Self-reported symptoms will be assessed to assist in diagnosis. Potential risk factors are classified into innate personal traits, behavioural lifestyle, interpersonal networks, socioeconomic status and macroenvironmental factors, based on health ecology model. Data collection, storage and management were conducted using the online 'H6WORLD' data management platform. Survival analysis using the Kaplan-Meier estimate will determine the incidence of BCRL. Risk factors of BCRL will be analysed using log-rank test and COX-LASSO regression. Traditional COX regression analysis and seven common survival analysis machine learning algorithms (COX, CARST, RSF, GBSM, XGBS, SSVM and SANN) will be employed for model construction and validation.<br><br>ETHICS AND DISSEMINATION: The study protocol was approved by the Biomedical Ethics Committee of Peking University (IRB00001052-21124) and the Research Ethics Committee of Tianjin Medical University Cancer Institute and Hospital (bc2023013). The results of this study will be published in peer-reviewed journals and will be presented at several research conferences.<br><br>TRIAL REGISTRATION NUMBER: ChiCTR2200057083.}, }
@article {pmid39805953, year = {2025}, author = {Daruka, L and Czikkely, MS and Szili, P and Farkas, Z and Balogh, D and Grézal, G and Maharramov, E and Vu, TH and Sipos, L and Juhász, S and Dunai, A and Daraba, A and Számel, M and Sári, T and Stirling, T and Vásárhelyi, BM and Ari, E and Christodoulou, C and Manczinger, M and Enyedi, MZ and Jaksa, G and Kovács, K and van Houte, S and Pursey, E and Pintér, L and Haracska, L and Kintses, B and Papp, B and Pál, C}, title = {ESKAPE pathogens rapidly develop resistance against antibiotics in development in vitro.}, journal = {Nature microbiology}, volume = {10}, number = {2}, pages = {313-331}, pmid = {39805953}, issn = {2058-5276}, mesh = {*Anti-Bacterial Agents/pharmacology ; Humans ; Microbial Sensitivity Tests ; *Drug Resistance, Bacterial/genetics ; Klebsiella pneumoniae/drug effects/genetics ; Pseudomonas aeruginosa/drug effects/genetics ; Acinetobacter baumannii/drug effects/genetics ; Escherichia coli/drug effects/genetics ; *Bacteria/drug effects/genetics ; Mutation ; Gastrointestinal Microbiome/genetics ; Metagenomics ; *Gram-Negative Bacteria/drug effects/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; }, abstract = {Despite ongoing antibiotic development, evolution of resistance may render candidate antibiotics ineffective. Here we studied in vitro emergence of resistance to 13 antibiotics introduced after 2017 or currently in development, compared with in-use antibiotics. Laboratory evolution showed that clinically relevant resistance arises within 60 days of antibiotic exposure in Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa, priority Gram-negative ESKAPE pathogens. Resistance mutations are already present in natural populations of pathogens, indicating that resistance in nature can emerge through selection of pre-existing bacterial variants. Functional metagenomics showed that mobile resistance genes to antibiotic candidates are prevalent in clinical bacterial isolates, soil and human gut microbiomes. Overall, antibiotic candidates show similar susceptibility to resistance development as antibiotics currently in use, and the corresponding resistance mechanisms overlap. However, certain combinations of antibiotics and bacterial strains were less prone to developing resistance, revealing potential narrow-spectrum antibacterial therapies that could remain effective. Finally, we develop criteria to guide efforts in developing effective antibiotic candidates.}, }
@article {pmid39801085, year = {2025}, author = {Anderson, EC and Giglio, RM and DeSaix, MG and Smyser, TJ}, title = {gscramble: Simulation of Admixed Individuals Without Reuse of Genetic Material.}, journal = {Molecular ecology resources}, volume = {25}, number = {4}, pages = {e14069}, pmid = {39801085}, issn = {1755-0998}, support = {//National Wildlife Research Center/ ; //Southwest Fisheries Science Center/ ; }, mesh = {*Computer Simulation ; *Computational Biology/methods ; *Genetics, Population/methods ; Genotype ; *Software ; }, abstract = {While a best practice for evaluating the behaviour of genetic clustering algorithms on empirical data is to conduct parallel analyses on simulated data, these types of simulation techniques often involve sampling genetic data with replacement. In this paper we demonstrate that sampling with replacement, especially with large marker sets, inflates the perceived statistical power to correctly assign individuals (or the alleles that they carry) back to source populations-a phenomenon we refer to as resampling-induced, spurious power inflation (RISPI). To address this issue, we present gscramble, a simulation approach in R for creating biologically informed individual genotypes from empirical data that: (1) samples alleles from populations without replacement and (2) segregates alleles based on species-specific recombination rates. This framework makes it possible to simulate admixed individuals in a way that respects the physical linkage between markers on the same chromosome and which does not suffer from RISPI. This is achieved in gscramble by allowing users to specify pedigrees of varying complexity in order to simulate admixed genotypes, segregating and tracking haplotype blocks from different source populations through those pedigrees, and then sampling-using a variety of permutation schemes-alleles from empirical data into those haplotype blocks. We demonstrate the functionality of gscramble with both simulated and empirical data sets and highlight additional uses of the package that users may find valuable.}, }
@article {pmid39799926, year = {2025}, author = {Fridman, M and Krasko, O and Veyalkin, I}, title = {The incidence trends of papillary thyroid carcinoma in Belarus during the post-Chernobyl epoch.}, journal = {Cancer epidemiology}, volume = {95}, number = {}, pages = {102745}, doi = {10.1016/j.canep.2025.102745}, pmid = {39799926}, issn = {1877-783X}, mesh = {Humans ; Republic of Belarus/epidemiology ; *Chernobyl Nuclear Accident ; Incidence ; *Thyroid Neoplasms/epidemiology/etiology ; Adolescent ; Male ; *Thyroid Cancer, Papillary/epidemiology/etiology ; Female ; Adult ; Child ; Young Adult ; *Neoplasms, Radiation-Induced/epidemiology ; Registries/statistics &amp; numerical data ; Middle Aged ; Child, Preschool ; Infant ; Iodine Radioisotopes/adverse effects ; }, abstract = {BACKGROUND: The increase of papillary thyroid cancer (PTC) rate among children who were exposed to post-Chernobyl 131-I release was reported only four years after the accident, first in Belarus where the heaviest fallout happened. The evolution of the occurrence of thyroid carcinoma based on the age-period-cohort analysis and the effects of age, period, and birth cohort on time trends aimed to reveal if post-Chernobyl follicular cells irradiation still has been impacting on incidence rate of papillary thyroid carcinoma nowadays.<br><br>METHODS: The Belarusian Cancer Registry was used to identify patients with PTC diagnosed during the years 1980-2019. The incidence trends were analysed using Join-point regression software.<br><br>RESULTS: The highest peak of age-specific incidence curve was shown during the years 1980-2001 in the age group of 15-19 years old that was associated also with short-latency cases of post-Chernobyl PTC. This is the same age group that demonstrated significant growth of the incidence rate during the years 2006-2019, largely because of the increasing number of non-exposed patients with PTC (p&#x202f;<&#x202f;0.001). Influence of post-Chernobyl exposure also can be seen in the young adults age-groups of patients (for 20-24 years old during the years 1980-2003 and 2013-2019, p&#x202f;<&#x202f;0.001; for 25-29 years old during the years 1980-1999 and 1999-2011, p&#x202f;<&#x202f;0.001).<br><br>CONCLUSION: After the Chernobyl accident, epidemiological waves that reflect the age shift of the group of children exposed to 131-I have consistently emerged. Currently, the incidence rate continues to increase only in the cohort of patients aged 20-44 years.}, }
@article {pmid39798660, year = {2025}, author = {Li, J and Lu, Y and Chen, X and Wang, L and Cao, Z and Lei, H and Zhang, Z and Wang, P and Sun, B}, title = {Seasonal variation of microbial community and diversity in the Taiwan Strait sediments.}, journal = {Environmental research}, volume = {268}, number = {}, pages = {120809}, doi = {10.1016/j.envres.2025.120809}, pmid = {39798660}, issn = {1096-0953}, mesh = {*Seasons ; Taiwan ; *Geologic Sediments/microbiology ; *Bacteria/genetics/classification ; RNA, Ribosomal, 16S/genetics ; *Biodiversity ; *Microbiota ; Archaea/genetics ; }, abstract = {Human activities and ocean currents in the Taiwan Strait exhibit significant seasonal variation, yet the response of marine microbes to ocean changes under anthropogenic and climatic stress remains unclear. Using 16S rRNA gene amplicon sequencing, we investigated the spatiotemporal dynamics and functional variations of microbial communities in sediment samples. Our findings revealed distinct seasonal patterns in microbial diversity and composition. Proteobacteria, Desulfobacterota, and Crenarchaeota dominated at the phylum level, while Candidatus Nitrosopumilus, Woeseia, and Subgroup 10 were prevalent at the genus level. Iron concentrations, heavy metals and C/N ratio were primary factors influencing microbial communities during specific seasons, whereas sulfur content, temperature fluctuations, and heavy metals shaped the entire microbial structure and diversity. Core microbial groups, including Desulfobulbus, Subgroup 10, Unidentified Latescibacterota, and Sumerlaea, played essential roles in regulating community structure and functional transitions. Marker species, such as Aliidiomarina sanyensis, Spirulina platensis, Croceimarina litoralis and Sulfuriflexus mobilis, acted as seasonal indicators. Bacteria exhibited survival strategy akin to higher organisms, encompassing process of synthesis, growth, dormancy, and disease resistance throughout the seasonal cycle. Core microbial groups and marker species in specific seasons can serve as indicators for monitoring and assessing the health of the Taiwan Strait ecosystem.}, }
@article {pmid39794678, year = {2025}, author = {Sasia, I and Bueno, G and Etxano, I}, title = {Amalur EIS: a system for calculating the environmental impacts of industrial sites from E-PRTR records.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {2}, pages = {163}, pmid = {39794678}, issn = {1573-2959}, support = {IT 1567-22 Ekopol Research Group&#xa0;(UPV/EHU)//Department of Education of the Basque Government/ ; }, mesh = {*Environmental Monitoring/methods ; *Environmental Pollutants/analysis ; Europe ; *Industry/statistics &amp; numerical data ; *Environmental Pollution/statistics &amp; numerical data ; Databases, Factual ; Climate Change ; }, abstract = {This article presents Amalur EIS (https://www.amalur-eis.eus/), an Environmental Information System that estimates environmental impacts using data sourced from the European Pollutant Release and Transfer Register database (E-PRTR). The system uses data on the releases into land, air and water of 31,556 European industrial facilities for the period 2007-2021. Amalur EIS calculates environmental impacts of industrial releases using 31 life cycle impact assessment methods (LCIA) and covering 78 of the 91 pollutants regulated by the PRTR Protocol. The system has been constructed using a two-layer software infrastructure: (i) a data layer supported by a relational database built in Postgres and (ii) a presentation layer built in Tableau, so it provides user-friendly access to the information. For an illustrative analysis of the tool, the EF 3.0 LCIA method recommended by the European Commission was used, including normalisation and weighting steps for a better comparison. The analysis concludes that the climate change impact category contributes the most (68.6%) to the total impacts, while the largest contributor from an economic activity perspective is the energy sector (59.5%). Geographically, both elements coincide in the German regions of Düsseldorf, Köln and Brandenburg, resulting in the concentration of the largest impacts at the European regional level. In fact, Germany is the country with the highest impact (20.3% of total). Beyond this analysis, Amalur EIS is poised to be a valuable tool for tracking the transition towards sustainability, particularly in Europe.}, }
@article {pmid39794649, year = {2025}, author = {Mohammad, L and Bandyopadhyay, J and Mondal, I and Altuwaijri, HA and Khatun, S and Hossain, SKA and Juliev, M}, title = {Assessing cropping system dynamics over three decades: remote sensing and GIS insights in Murshidabad-Jiaganj Block.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {2}, pages = {164}, pmid = {39794649}, issn = {1573-2959}, mesh = {*Remote Sensing Technology ; *Agriculture/methods/statistics &amp; numerical data ; *Environmental Monitoring/methods ; *Geographic Information Systems ; China ; Crops, Agricultural/growth &amp; development ; }, abstract = {Agriculture is a significant contributor to the country's economic development. We used multiple Landsat images from 1990 to 2021 in the Murshidabad-Jiaganj Block to assess changes in the agricultural system and their underlying causes. The Rabi season saw a 10.99% growth in agrarian regions from 1990 to 2000 and an 8.86% increase in 2010, yet it declined by 28.12% in 2021. During the summer, the cultivated lands diminished by 26.63%, 19.43%, and 19.64%, while in the Kharif season, they declined by 21.78%, 15.68%, and 11.99% from 1990 in the years 2000, 2010, and 2021, respectively. The agricultural area had 36.82%, 34.16%, and 19.01% increases between 1990 and 2021, respectively. Regarding direction, farmland acreage decreased in all zones except the SSE, which had a 0.95% increase. Mono-, double-, and triple-cropping systems have decreased in area, while multi-cropping systems have experienced increases of 43.51%, 4.50%, and 18.49% in 1990-2021, respectively. The multi-cropping system has a good correlation with all agroclimatic factors. The reduction of irrigated lands post-2009 significantly affected the agriculture system. The fall in agricultural employment in recent decades is attributable to migration seeking higher-paying occupations. The advancement of accurate remote sensing-based modeling is crucial for mitigating food security risks, particularly those posed by climate change, and informing policy decisions.}, }
@article {pmid39793648, year = {2025}, author = {Ji, G and Wang, Y and Lu, Z and Long, G and Xu, C}, title = {Associations between ambient benzene and stroke, and the mediating role of accelerated biological aging: Findings from the UK biobank.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {367}, number = {}, pages = {125656}, doi = {10.1016/j.envpol.2025.125656}, pmid = {39793648}, issn = {1873-6424}, mesh = {*Benzene/analysis ; Humans ; United Kingdom/epidemiology ; *Stroke/epidemiology ; Male ; Female ; *Environmental Exposure/statistics &amp; numerical data ; Middle Aged ; Aged ; *Air Pollutants ; *Aging ; Biological Specimen Banks ; Cohort Studies ; UK Biobank ; }, abstract = {Benzene can cause respiratory diseases. However, the associations between benzene and stroke are unclear. A total of 13,116 patients with stroke and 377,120 controls from the UK Biobank were included. The benzene exposure concentrations were matched on the basis of the address information of each participant via a data form from the UK Department for Environment, Food and Rural Affairs. Weighted Cox regression was used to investigate the association between benzene and stroke risk. The polygenic risk score (PRS) was used to observe the joint effects of benzene exposure and genetic factors on stroke risk. We conducted a mediation analysis to investigate the mediating role of accelerated biological aging in this cohort study. After adjusting for covariates, every 1 μg/m[3] increase in benzene exposure increased the risk of stroke by 70%, which may be mediated by accelerated biological aging. The population with high benzene exposure concentrations and high PRSs had a 44% greater risk of stroke than did those with low benzene exposure concentrations and low PRSs. Benzene exposure and the PRS have joint effects on the risk of stroke. Benzene exposure was associated with stroke risk, possibly through increased biological aging, and the PRS modified this association.}, }
@article {pmid39793033, year = {2025}, author = {Clauss, M and Roller, M and Bertelsen, MF and Rudolf von Rohr, C and Müller, DWH and Schiffmann, C and Kummrow, M and Encke, D and Ferreira, S and Duvall, ES and Maré, C and Abraham, AJ}, title = {Zoos must embrace animal death for education and conservation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {1}, pages = {e2414565121}, pmid = {39793033}, issn = {1091-6490}, support = {101062339//EC | Horizon Europe | Excellent Science | HORIZON EUROPE Marie Sklodowska-Curie Actions (MSCA)/ ; }, }
@article {pmid39792995, year = {2025}, author = {Soeishi, T and Nakata, A and Nagata, T and Akutsu, S and Tondokoro, T and Inoue, Y and Katsumura, F and Kikunaga, K}, title = {Predicting Depressive Symptoms and Psychological Distress by Circulating Inflammatory Mediators: A 16-Month Prospective Study in Japanese White-Collar Employees.}, journal = {Journal of occupational and environmental medicine}, volume = {67}, number = {4}, pages = {235-244}, doi = {10.1097/JOM.0000000000003307}, pmid = {39792995}, issn = {1536-5948}, mesh = {Humans ; Female ; Male ; Prospective Studies ; *Depression/blood/diagnosis ; Adult ; Middle Aged ; *Psychological Distress ; Japan ; Sex Factors ; *Inflammation Mediators/blood ; Tumor Necrosis Factor-alpha/blood ; Interferon-gamma/blood ; *Stress, Psychological/blood ; Psychiatric Status Rating Scales ; East Asian People ; }, abstract = {OBJECTIVE: Although increasing evidence suggests that depression/distress involves inflammatory processes, its potential sex differences and the temporal directions for this association remain elusive.<br><br>METHODS: We examined the temporal association between serum inflammatory mediators and depression/distress as measured by the Center for Epidemiologic Studies Depression Scale (CES-D) and the Kessler Psychological Distress Scale (K6), in nondepressed working men and women (n = 61 and 43, respectively) by a 16-month prospective design.<br><br>RESULTS: Fully adjusted partial correlation analyses revealed that, in men, a lower IFN-&#x3b3; predicted subsequent increases in CES-D and K6 scores, whereas a higher TNF-&#x3b1; predicted increased K6 scores. In women, a higher IFN-&#x3b3; predicted a subsequent increase in the CES-D score. CES-D and K6 scores did not predict inflammatory mediators at follow-up.<br><br>CONCLUSIONS: The finding suggests that inflammatory activation precedes depression/distress with distinct sex differences.}, }
@article {pmid39792790, year = {2025}, author = {Kherroubi Garcia, I and Erdmann, C and Gesing, S and Barton, M and Cadwallader, L and Hengeveld, G and Kirkpatrick, CR and Knight, K and Lemmen, C and Ringuette, R and Zhan, Q and Harrison, M and Mac Gabhann, F and Meyers, N and Osborne, C and Till, C and Brenner, P and Buys, M and Chen, M and Lee, A and Papin, J and Rao, Y}, title = {Ten simple rules for good model-sharing practices.}, journal = {PLoS computational biology}, volume = {21}, number = {1}, pages = {e1012702}, pmid = {39792790}, issn = {1553-7358}, mesh = {*Information Dissemination/methods ; Humans ; *Computational Biology ; Computer Simulation ; }, abstract = {Computational models are complex scientific constructs that have become essential for us to better understand the world. Many models are valuable for peers within and beyond disciplinary boundaries. However, there are no widely agreed-upon standards for sharing models. This paper suggests 10 simple rules for you to both (i) ensure you share models in a way that is at least "good enough," and (ii) enable others to lead the change towards better model-sharing practices.}, }
@article {pmid39789290, year = {2025}, author = {Sağlam, S and Özdemir, E and Özden, &#xd6; and Makineci, E and Özkan, UY and Bingöl, D and Güzelçimen, F}, title = {The effects of some chemical compounds on the sound absorbing ability of tree bark.}, journal = {Biologia futura}, volume = {76}, number = {1}, pages = {49-57}, pmid = {39789290}, issn = {2676-8607}, mesh = {*Plant Bark/chemistry ; *Trees/chemistry ; *Sound ; Pinus/chemistry ; }, abstract = {Tree bark is an important natural polymer for sound absorption. The main components in the bark of different tree species are polymers with high molecular weight such as cellulose, hemicellulose, and lignin. The aim of this study is to determine the noise reduction coefficient (NRC), lignin, alcohol-benzene solubility (ABS), carbon (C), and nitrogen (N) contents in samples taken from the bark of different tree species-black locust (Robinia pseudoacacia), narrow-leaved ash (Fraxinus angustifolia), stone pine (Pinus pinea), silver lime (Tilia tomentosa), sweet chestnut (Castanea sativa), sessile oak (Quercus petraea), and maritime pine (Pinus pinaster) and to investigate the relationship between these chemical properties and sound absorption measurements. Tree species showed a statistically significant difference in terms of all measured variables. In the correlation matrix obtained as a result of the analysis, only ABS showed a significant and the highest positive correlation with the NRC, with a correlation coefficient of r = 0.812. ABS in bark is seen as the most important chemical factor regarding sound retention, indicating the abundance of extractives in barks of different tree species. An investigation into the relationship between sound retention and different extractive substance and contents of different extractive substances in bark is recommended for further studies.}, }
@article {pmid39789035, year = {2025}, author = {Li, F and Xia, H and Miao, J and Yang, J}, title = {Changes of the ecological environment status in villages under the background of traditional village preservation: a case study in Enshi Tujia and Miao Autonomous Prefecture.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {1504}, pmid = {39789035}, issn = {2045-2322}, support = {42271318//National Natural Science Foundation of China/ ; }, mesh = {*Conservation of Natural Resources/methods ; *Ecosystem ; China ; Humans ; Rural Population ; Geographic Information Systems ; }, abstract = {The preservation of Chinese traditional villages plays a crucial role in promoting the sustainable development of rural natural, cultural, and ecological environments. It is also a key strategy for achieving rural revitalization. Current research on traditional villages predominantly focuses on the realm of cultural landscapes, with an emphasis on preserving the cultural ecological value of these communities. In comparison, discussions on the quality of the ecological environment of villages from the perspectives of natural environment, economic environment, and the social organizational environment within regional development are relatively scarce. Our study employed GIS and RS technology and refers to the Technical Criterion for Ecosystem Status Evaluation. Several sub-indices of the ecological environment status, including the biological richness index, vegetation coverage index, water network density index, and land stress index, were selected to construct an ecological environment assessment model. This model was used to analyze the spatial-temporal changes in the ecological environment status of each county, county-level city, and traditional village within the jurisdiction of Enshi Tujia and Miao Autonomous Prefecture and its surrounding areas from 2010 to 2020. The study quantitatively evaluated the ecological environment status of each county, county-level city, and village in Enshi before and after the implementation of traditional village preservation policies. Through comparative analysis, the study revealed the impact of these policies on the natural ecological environment of the study area. The results indicated the following: (1) From 2010 to 2020, the ecological index (EI) values in the villages of Enshi Prefecture exhibited a similar trend to the EI values in the respective counties and county-level cities they are located in, although significant differences in magnitude of change were observed. (2) The EI values in the counties, county-level cities, and villages demonstrated greater variation in the latter five years of the decade (2015-2020) compared to the previous five years (2010-2015). (3) In 2020, the EI value of the villages experienced more significant changes compared to 2010, whereas the overall EI value of the counties and county-level cities showed less pronounced changes. The findings of this study suggest that the traditional village preservation policies implemented in Enshi Prefecture have both positive and negative impacts on the ecological environment of the surrounding areas of protected villages, and these impacts become increasingly evident over time. By comparing and analyzing the ecological changes in the surrounding areas of traditional villages in Enshi Prefecture with the overall ecological changes in the respective counties and county-level cities, our study employs quantitative analytical methods to delve into the impact of traditional village conservation policies on the natural ecological environment. It assesses the effects of policy implementation on the natural ecological environment of traditional villages, analyzing both the positive and negative impacts brought about by the execution of these policies, with the aim of effectively guiding the natural ecological conditions of traditional villages towards a more healthy trajectory of development.}, }
@article {pmid39788970, year = {2025}, author = {Sánchez-Jardón, L and Hernández de Diego, A and Mackenzie, R and Villodre, M and Arnaiz-Schmitz, C and Schmitz, MF and Acosta-Gallo, B}, title = {Bryophyte literature records database of Aysén, Chilean sub-Antarctic ecoregion.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {36}, pmid = {39788970}, issn = {2052-4463}, mesh = {*Bryophyta ; Chile ; *Biodiversity ; Antarctic Regions ; Ecosystem ; Databases, Factual ; }, abstract = {The Chilean sub-Antarctic ecoregion hosts the largest expanse of temperate forests, wetlands and peatlands, as well as the largest proportion of protected areas in the southern hemisphere. Bryophytes are highly diverse and ecologically essential in sub-Antarctic ecosystems and are considered as biodiversity loss indicators caused by the current socio-ecological crisis. However, knowledge about their biodiversity is rather limited. Integrating the available information on bryophyte diversity in regional platforms such as SIB-Aysén can be useful to acknowledge their ecological importance and remarkable biodiversity. This article integrates 345 records of 273 bryophyte taxa known in the region of Aysén and emphasizes the need to include citizen science as a tool to increase observations in lesser-known taxonomic groups.}, }
@article {pmid39787642, year = {2025}, author = {Aanes, H and Vigeland, MD and Star, B and Gilfillan, GD and Mattingsdal, M and Trøan, S and Strand, M and Eide, LM and Hanssen, EN}, title = {Heating up three cold cases in Norway using investigative genetic genealogy.}, journal = {Forensic science international. Genetics}, volume = {76}, number = {}, pages = {103217}, doi = {10.1016/j.fsigen.2024.103217}, pmid = {39787642}, issn = {1878-0326}, mesh = {Humans ; Databases, Nucleic Acid ; DNA/genetics/isolation &amp; purification ; *DNA Fingerprinting/methods ; Forensic Genetics/methods ; Microsatellite Repeats ; Norway ; *Pedigree ; }, abstract = {With the advent of commercial DNA databases, investigative genetic genealogy (IGG) has emerged as a powerful forensic tool, rivalling the impact of STR analyses, introduced four decades ago. IGG has been frequently applied in the US and tested in other countries, but never in Norway. Here, we apply IGG to three cold criminal cases and successfully identify the donor of the DNA in two of these cases. Our findings suggest that when combined with phenotypic prediction and case information, IGG holds substantial potential for resolving both active and cold cases in Norway. This potential is amplified by the digitalization of archives and the transparent and structured nature of society in Norway. Additionally, the databases exhibit sufficient representation to yield matches with distant relatives. Moreover, this work has uncovered a series of lingering research questions spanning the entire workflow from DNA extraction to genealogy research. Finally, we highlight the possibility that more insights can be gleaned from genetic profiles, for instance using an accurate age prediction method. The results show that IGG can be successfully applied in Norway, having reached a level of maturity that enables identification of unknown individuals in cases where DNA is accessible.}, }
@article {pmid39787194, year = {2025}, author = {Bantie, GM and Tadege, M and Nigussie, TZ and Woya, AA and Tekile, AK and Melese, AA and Ayalew, S and Beyene, BB and Wubetu, GY}, title = {Regional disparities of full pentavalent vaccine uptake and the determinants in Ethiopia: Mapping and spatial analysis using the EDHS data.}, journal = {PloS one}, volume = {20}, number = {1}, pages = {e0312514}, pmid = {39787194}, issn = {1932-6203}, mesh = {Humans ; Ethiopia ; Infant ; Female ; Adult ; *Spatial Analysis ; Male ; *Vaccination/statistics &amp; numerical data ; Diphtheria-Tetanus-Pertussis Vaccine/administration &amp; dosage ; Hepatitis B Vaccines/administration &amp; dosage ; Young Adult ; Immunization Programs/statistics &amp; numerical data ; Middle Aged ; Haemophilus Vaccines ; Adolescent ; Vaccination Coverage/statistics &amp; numerical data ; Vaccines, Combined ; }, abstract = {BACKGROUND: The full pentavalent (DPT-HepB-Hib) vaccination is the main strategy to prevent five communicable diseases in early childhood, especially in countries with huge communicable disease burdens like Ethiopia. Exploring spatial distributions and determinants of full pentavalent vaccination status in minor ecological areas in Ethiopia is crucial for creating targeted immunization campaigns and monitoring the advancement of accomplishing sustainable development goals. This study aimed to investigate the spatial disparities and determinants of full pentavalent vaccination among 12-23-month-old children in Ethiopia.<br><br>METHOD: The data on pentavalent vaccine uptake was found in the Ethiopian Health and Demographic Survey (EDHS, 2019). A two-stage cluster sampling method was applied to collect the EDHS data. The enumeration area was the primary sample unit while the household served as the secondary sampling unit. The geographical variations of full pentavalent vaccine uptake were explored using Quantum Geographic Information System (QGIS) software. The significant predictors of full pentavalent vaccination were identified using a simple logistic regression model through R version 4.1 software.<br><br>RESULT: The national full pentavalent vaccine uptake was 59.2%. The spatial distribution of full pentavalent vaccine uptake was not uniform in Ethiopia. Spatial cluster analysis revealed that most of low coverage regions for full pentavalent vaccine uptake were Afar, Somali, and Harari. The regions with the highest and lowest rates of vaccine uptake were Tigray and Harari region, respectively. Maternal age of 35-49 years (AOR = 3.42; 95% CI: 1.99, 5.87), and 25-34 years (AOR = 1.55; 95% CI: 1.17, 2.19), primary education attended (AOR = 1.51; 95%CI: 1.07, 2.11), richness wealth index (AOR = 1.96; 95% CI: 1.40, 2.75), birth order of 1-3 (AOR = 1.88; 95% CI: 1.19, 2.96), and delivery in the health facility (AOR = 3.41: 95% CI: 2.52, 4.61) were the determinants of full pentavalent vaccine uptake in Ethiopia.<br><br>CONCLUSION: Ethiopia's full pentavalent vaccine uptake was far lower than the global target. Older maternal age, maternal education, wealth index, birth order, and giving birth in a health facility were the determinants of full pentavalent vaccine uptake. Special attention should be given to Afar, Somali, and Harari regions, to strengthen the vaccine uptake. Moreover, improved socioeconomic status and getting maternal health services during delivery are necessary to enhance vaccine uptake.}, }
@article {pmid39778451, year = {2025}, author = {Lausch, A and Selsam, P and Heege, T and von Trentini, F and Almeroth, A and Borg, E and Klenke, R and Bumberger, J}, title = {Monitoring and modelling landscape structure, land use intensity and landscape change as drivers of water quality using remote sensing.}, journal = {The Science of the total environment}, volume = {960}, number = {}, pages = {178347}, doi = {10.1016/j.scitotenv.2024.178347}, pmid = {39778451}, issn = {1879-1026}, abstract = {The interactions between landscape structure, land use intensity (LUI), climate change, and ecological processes significantly impact hydrological processes, affecting water quality. Monitoring these factors is crucial for understanding their influence on water quality. Remote sensing (RS) provides a continuous, standardized approach to capture landscape structures, LUI, and landscape changes over long-term time series. In this study, RS-based indicators from Landsat data (2018-2021) were used to assess landscape structure, LUI, and land use change for a study area in northern Germany, applying the ESIS/Imalys tool. These indicators were then used to model and predict water quality (Chla) in 119 standing waters. Various machine learning methods, including Generalised Linear Models, Support Vector Machines, Deep Learning, Decision Trees, Random Forest, and Gradient Boosted Trees, were tested. The Random Forest model performed best, with a correlation of 0.744 ± 0.11. Indicators related to landscape structure, such as diversity_mean (0.376) and relation_mean (0.292), had the highest global correlation weights, while LUI and land use change indicators like NirV2_mean (0.369) and NirV_regme (0.284) were also significant. All indicators and their effects on water quality (Chla) are discussed in detail. The study highlights the potential of the ESIS/Imalys tool for quantifying landscape structure, LUI, and land use change with RS to model and predict water quality and suggests directions for future model improvements by incorporating additional influencing factors.}, }
@article {pmid39777935, year = {2025}, author = {Mond, L and Geyer, S and Tetzlaff, J and Weißenborn, K and Schneider, J and Epping, J}, title = {More Drugs and Fewer Strokes? Time Trends in CVD Medication and Incidence of Stroke With German Health Insurance Data.}, journal = {Pharmacoepidemiology and drug safety}, volume = {34}, number = {1}, pages = {e70077}, pmid = {39777935}, issn = {1099-1557}, support = {//Allgemeine Ortskrankenkasse Niedersachsen/ ; GE 1167/15-1//Deutsche Forschungsgemeinschaft/ ; GE 1167/19-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Humans ; Germany/epidemiology ; Female ; Male ; Incidence ; Middle Aged ; Aged ; *Stroke/epidemiology/prevention &amp; control ; Adult ; Aged, 80 and over ; *Cardiovascular Diseases/epidemiology/prevention &amp; control ; Young Adult ; Adolescent ; *Insurance, Health/statistics &amp; numerical data ; Prevalence ; Cardiovascular Agents/therapeutic use/adverse effects ; Age Factors ; Time Factors ; Databases, Factual ; }, abstract = {BACKGROUND: Successful prevention of cardiovascular diseases (CVD) may reduce the burden of diseases. Preventive medication is an important measure to decrease the risks of cardiovascular events, in particular myocardial infarction and stroke. The aim of this study is to analyze the prevalence of CVD preventive medication in Germany over time with respect to sex and age and to compare it with the temporal development of strokes.<br><br>METHODS: The study is based on statutory health insurance claims data from the AOK Niedersachsen (AOKN) covering the years 2005-2018. The study population comprises all AOKN insured persons aged 18&#x2009;years and older (N&#x2009;=&#x2009;2&#x2009;088&#x2009;495). Age-standardized time trends of the prevalence of CVD preventive medication and incidence of stroke were calculated for men and women in different age groups. After that, the relationship of both measures was examined in an ecological correlation.<br><br>RESULTS: We found a clear increase in medication prevalence over time. In 2018, about 35% of the total population and about 85% of those over 85&#x2009;years of age received CVD preventive medication. At the same time, age-standardized incidence rates of ischemic stroke were decreasing slightly. The ecological correlation showed a negative association between medication prevalence and stroke incidence especially in the higher age groups.<br><br>CONCLUSION: High correlation coefficients indicate that higher medication prevalence could be linked to better population health. Further research is needed to draw conclusions about the effects of increasing medicalization, including adverse risks and side effects at the population level.}, }
@article {pmid39776539, year = {2024}, author = {Chandel, N and Maile, A and Shrivastava, S and Verma, AK and Thakur, V}, title = {Establishment and perturbation of human gut microbiome: common trends and variations between Indian and global populations.}, journal = {Gut microbiome (Cambridge, England)}, volume = {5}, number = {}, pages = {e8}, pmid = {39776539}, issn = {2632-2897}, abstract = {Human gut microbial species are crucial for dietary metabolism and biosynthesis of micronutrients. Digested products are utilised by the host as well as several gut bacterial species. These species are influenced by various factors such as diet, age, geographical location, and ethnicity. India is home to the largest human population in the world. It is spread across diverse ecological and geographical locations. With variable dietary habits and lifestyles, Indians have unique gut microbial composition. This review captures contrasting and common trends of gut bacterial community establishment in infants (born through different modes of delivery), and how that bacterial community manifests itself along infancy, through old age between Indian and global populations. Because dysbiosis of the gut community structure is associated with various diseases, this review also highlights the common and unique bacterial species associated with various communicable as well as noncommunicable diseases such as diarrhoea, amoebiasis, malnutrition, type 2 diabetes, obesity, colorectal cancer, inflammatory bowel disease, and gut inflammation and damage to the brain in the global and Indian population.}, }
@article {pmid39776261, year = {2025}, author = {Nolasco, M and Balzarini, M}, title = {Assessment of temporal aggregation of Sentinel-2 images on seasonal land cover mapping and its impact on landscape metrics.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {2}, pages = {142}, pmid = {39776261}, issn = {1573-2959}, mesh = {*Environmental Monitoring/methods ; *Ecosystem ; *Seasons ; Satellite Imagery ; Geographic Information Systems ; }, abstract = {Landscape metrics (LM) play a crucial role in fields such as urban planning, ecology, and environmental research, providing insights into the ecological and functional dynamics of ecosystems. However, in dynamic systems, generating thematic maps for LM analysis poses challenges due to the substantial data volume required and issues such as cloud cover interruptions. The aim of this study was to compare the accuracy of land cover maps produced by three temporal aggregation methods: median reflectance, maximum normalised difference vegetation index (NDVI), and a two-date image stack using Sentinel-2 (S2) and then to analyse their implications for LM calculation. The Google Earth Engine platform facilitated data filtering, image selection, and aggregation. A random forest algorithm was employed to classify five land cover classes across ten sites, with classification accuracy assessed using global measurements and the Kappa index. LM were then quantified. The analysis revealed that S2 data provided a high-quality, cloud-free dataset suitable for analysis, ensuring a minimum of 25 cloud-free pixels over the study period. The two-date and median methods exhibited superior land cover classification accuracy compared to the max NDVI method. In particular, the two-date method resulted in lower fragmentation-heterogeneity and complexity metrics in the resulting maps compared to the median and max NDVI methods. Nevertheless, the median method holds promise for integration into operational land cover mapping programmes, particularly for larger study areas exceeding the width of S2 swath coverage. We find patch density combined with conditional entropy to be particularly useful metrics for assessing fragmentation and configuration complexity.}, }
@article {pmid39771200, year = {2024}, author = {Sedmáková, D and Jaloviar, P and Mišíková, O and Šumichrast, L and Slováčková, B and Kucbel, S and Vencurik, J and Bosela, M and Sedmák, R}, title = {Small Gap Dynamics in High Mountain Central European Spruce Forests-The Role of Standing Dead Trees in Gap Formation.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {24}, pages = {}, pmid = {39771200}, issn = {2223-7747}, support = {APVV-21-0199//Slovak Research and Development Agency/ ; APVV-19-0183//Slovak Research and Development Agency/ ; APVV-20-0408//Slovak Research and Development Agency/ ; 1/0515/23//The Ministry of Education, Science, Research and Sport of the Slovak Republic/ ; }, abstract = {Gap dynamics are driving many important processes in the development of temperate forest ecosystems. What remains largely unknown is how often the regeneration processes initialized by endogenous mortality of dominant and co-dominant canopy trees take place. We conducted a study in the high mountain forests of the Central Western Carpathians, naturally dominated by the Norway spruce. Based on the repeated forest inventories in two localities, we quantified the structure and amount of deadwood, as well as the associated mortality of standing dead canopy trees. We determined the basic specific gravity of wood and anatomical changes in the initial phase of wood decomposition. The approach for estimating the rate of gap formation and the number of canopy trees per unit area needed for intentional gap formation was formulated based on residence time analysis of three localities. The initial phase of gap formation (standing dead tree in the first decay class) had a narrow range of residence values, with a 90-95% probability that gap age was less than 10 or 13 years. Correspondingly, a relatively constant absolute number of 12 and 13 canopy spruce trees per hectare died standing in 10 years, with a mean diameter reaching 50-58 cm. Maximum diameters trees (70-80 cm) were represented by 1-4 stems per hectare. The values of the wood-specific gravity of standing trees were around 0.370-0.380 g.cm[-3], and varied from 0.302 to 0.523 g.cm[-3]. Microscopically, our results point out that gap formation is a continuous long-lasting process, starting while canopy trees are living. We observed early signs of wood degradation and bacteria, possibly associated with bark beetles, that induce a strong effect when attacking living trees with vigorous defenses. New information about the initial phase of gap formation has provided a basis for the objective proposal of intervals and intensities of interventions, designed to promote a diversified structure and the long-term ecological stability of the mountain spruce stands in changing climate conditions.}, }
@article {pmid39763978, year = {2024}, author = {Palma-Martínez, MJ and Posadas-García, YS and López-Ángeles, BE and Quiroz-López, C and Lewis, ACF and Bird, KA and Lasisi, T and Zaidi, AA and Sohail, M}, title = {The multi-scale complexity of human genetic variation beyond continental groups.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39763978}, issn = {2692-8205}, support = {K99 HG012809/HG/NHGRI NIH HHS/United States ; R00 GM137076/GM/NIGMS NIH HHS/United States ; }, abstract = {Traditional clustering and visualization approaches in human genetics often operate under frameworks that assume inherent, discrete groupings[1,2]. These methods can inadvertently simplify multifaceted relationships, functioning to entrench the idea of typological groups[3]. We introduce a network-based pipeline and visualization tool grounded in relational thinking[4], which constructs networks from a variety of genetic similarity metrics. We identify communities at multiple resolutions, departing from typological models of analysis and interpretation that categorize individuals into a (predefined) number of sets. We applied our pipeline to a dataset merged from the 1000 Genomes and Human Genome Diversity Project[5], revealing the limitations of traditional groupings and capturing the complexities introduced by demographic events and evolutionary processes. This method embraces the context-specificity of genetic similarities that are salient depending on the question, markers of interest, and study individuals. Different numbers of communities are revealed depending on the resolution chosen and metric used, underscoring a fluid spectrum of genetic relationships and challenging the notion of universal categorization. We provide a web application (https://sohail-lab.shinyapps.io/GG-NC/) for interactive visualization and engagement with these intricate genetic landscapes.}, }
@article {pmid39761773, year = {2025}, author = {Banakar, SN and Karan, R and Prasannakumar, MK and Venkateshbabu, G and Harish, J and Patil, SS and Chandrashekar, BS and Mahesh, HB and Devanna, P and Manjunatha, C and Vamsidharreddy, N and Pallavi, KN and Sarangi, AN and Vaidya, K and Guru Murthy, DS}, title = {Unveiling Fusarium falciforme: Genome sequencing of a Novel wilt causing pathogen in subabul (Leucaena leucocephala L.) in India.}, journal = {Microbial pathogenesis}, volume = {200}, number = {}, pages = {107281}, doi = {10.1016/j.micpath.2025.107281}, pmid = {39761773}, issn = {1096-1208}, mesh = {*Fusarium/genetics/isolation &amp; purification/pathogenicity/classification ; *Plant Diseases/microbiology ; Phylogeny ; India ; *Genome, Fungal ; *Fabaceae/microbiology ; Virulence Factors/genetics ; Whole Genome Sequencing ; Sequence Analysis, DNA ; Host Specificity ; Cicer/microbiology ; DNA, Fungal/genetics ; Glycine max/microbiology ; Fungal Proteins/genetics ; }, abstract = {Subabul (Leucaena leucocephala L.) is a leguminous species often referred to as the "miracle tree," it provides numerous ecosystem services and exhibits robust ecological characteristics. However, the infection caused by phytopathogenic fungi is poorly understood in Subabul. Therefore, this study provides comprehensive insights into the molecular and genomic characteristics of Fusarium falciforme, the causal agent of wilt disease in Subabul (Leucaena leucocephala). Pathogen isolation from infected samples, followed by morpho-molecular characterization through DNA sequencing of key markers (ITS, LSU, TEF1α) and phylogenetic analysis, confirmed the identity of F. falciforme. Host range analysis demonstrated the pathogen's ability to infect additional leguminous crops, including chickpea (Cicer arietinum) and soybean (Glycine max). A complete genome assembly revealed a genome size of 59.19 Mb, comprising 18,853 protein-coding genes. Comparative genomic analysis elucidated evolutionary relationships with other Fusarium species, while functional annotation identified critical virulence factors, such as polyketide synthases, ABC transporters, and secretory proteins, which facilitate host tissue invasion. These findings enhance the understanding of F. falciforme pathogenicity, enabling improved diagnostic tools and management strategies for controlling wilt disease in Subabul and related legumes.}, }
@article {pmid39761073, year = {2025}, author = {Sangeetha, S and Sajeev, S and Hamza, MK and Shome, BR and Raisen, C and Holmes, MA and Sivaraman, GK}, title = {Whole-Genome Sequencing of Antimicrobial Resistant Klebsiella quasipneumoniae, a Novel Sequence Type 5655 from Retail Fish Market, Assam, India.}, journal = {Foodborne pathogens and disease}, volume = {}, number = {}, pages = {}, doi = {10.1089/fpd.2023.0017}, pmid = {39761073}, issn = {1556-7125}, abstract = {Klebsiella quasipneumoniae is a recently described species that can be differentiated from Klebsiella pneumoniae. However, in clinical settings, they are frequently misidentified as K. pneumoniae. In this study, our objective was to conduct genomic characterization and bioinformatics analysis of K. quasipneumoniae subsp. quasipneumoniae (KpII-A) isolated from a sample obtained from a retail fish market in Assam, India. Notably, this particular isolate was identified as K. pneumoniae when identified using BD Pheonix™ M50 (BD Difco, USA). This represents a serious pitfall of conventional microbiological methods for distinguishing between K. pneumoniae and K. quasipneumoniae. In this connection, identifying differences in nuclear gene content is key to avoid misidentification. The isolate was confirmed to be KpII-A using species identification by Mash Screen and whole-genome sequencing by the Illumina platform. We report the draft genome sequence of this strain, comprising of 53 contigs with an average GC content of 58.11%. The annotation revealed 5,095 protein coding sequences, 69 tRNA genes, and 4 rRNA genes. The isolated strain acknowledges the presence of oqxA, oqxB, fosA, and blaOKP-A-3 antimicrobial resistance genes (ARGs). Additionally two phage genomes were detected in contigs 3 and 19 of the bacterial genome. Based on the multilocus sequence typing and genome sequencing, the isolate was identified as a novel sequence type, ST5655, within the species K. quasipneumoniae under the phylogroup KpII-A. The presence of antimicrobial resistance genes in KpII-A, isolated from retail fish samples, raises concerns regarding transmission across barriers in ecological niches and possible transmission to consumers. Given that fish may serve as a potential vehicle for ARG transmission, our findings are highly relevant and paramount to human health. Moreover, our study supports the robustness of the sequence-based microbial identification.}, }
@article {pmid39760247, year = {2025}, author = {Lee, CE and Messer, LF and Wattiez, R and Matallana-Surget, S}, title = {Decoding Microbial Plastic Colonisation: Multi-Omic Insights Into the Fast-Evolving Dynamics of Early-Stage Biofilms.}, journal = {Proteomics}, volume = {25}, number = {7}, pages = {e202400208}, pmid = {39760247}, issn = {1615-9861}, support = {//Joint UKRI Natural Environment Research Council (NERC) and National Research Foundation (NRF) Singapore/ ; NE/V009621/1//UKRI NERC/NRF/ ; NRF-SEAP-2020-0001//UKRI NERC/NRF/ ; NE/S007342/1//NERC Scottish Universities Partnership for Environmental Research (SUPER) Doctoral Training Partnership (DTP)/ ; }, mesh = {*Biofilms/growth &amp; development ; *Proteomics/methods ; *Plastics ; *Bacterial Proteins/metabolism/genetics ; Pseudomonas/genetics/metabolism ; Metagenomics/methods ; *Proteome/metabolism ; *Bacteria/metabolism/genetics ; Metagenome ; Multiomics ; }, abstract = {Marine plastispheres represent dynamic microhabitats where microorganisms colonise plastic debris and interact. Metaproteomics has provided novel insights into the metabolic processes within these communities; however, the early metabolic interactions driving the plastisphere formation remain unclear. This study utilised metaproteomic and metagenomic approaches to explore early plastisphere formation on low-density polyethylene (LDPE) over 3 (D3) and 7 (D7) days, focusing on microbial diversity, activity and biofilm development. In total, 2948 proteins were analysed, revealing dominant proteomes from Pseudomonas and Marinomonas, with near-complete metagenome-assembled genomes (MAGs). Pseudomonas dominated at D3, whilst at D7, Marinomonas, along with Acinetobacter, Vibrio and other genera became more prevalent. Pseudomonas and Marinomonas showed high expression of reactive oxygen species (ROS) suppression proteins, associated with oxidative stress regulation, whilst granule formation, and alternative carbon utilisation enzymes, also indicated nutrient limitations. Interestingly, 13 alkanes and other xenobiotic degradation enzymes were expressed by five genera. The expression of toxins, several type VI secretion system (TVISS) proteins, and biofilm formation proteins by Pseudomonas indicated their competitive advantage against other taxa. Upregulated metabolic pathways relating to substrate transport also suggested enhanced nutrient cross-feeding within the more diverse biofilm community. These insights enhance our understanding of plastisphere ecology and its potential for biotechnological applications.}, }
@article {pmid39753915, year = {2025}, author = {Davidson, SC and Cagnacci, F and Newman, P and Dettki, H and Urbano, F and Desmet, P and Bajona, L and Bryant, E and Carneiro, APB and Dias, MP and Fujioka, E and Gambin, D and Hoenner, X and Hunter, C and Kato, A and Kot, CY and Kranstauber, B and Lam, CH and Lepage, D and Naik, H and Pye, JD and Sequeira, AMM and Tsontos, VM and van Loon, E and Vo, D and Rutz, C}, title = {Establishing bio-logging data collections as dynamic archives of animal life on Earth.}, journal = {Nature ecology &amp; evolution}, volume = {9}, number = {2}, pages = {204-213}, pmid = {39753915}, issn = {2397-334X}, support = {80NSSC21K1182//National Aeronautics and Space Administration (NASA)/ ; Fellowship at Fondation Im&#xe9;RA//Institut de Recherche pour le D&#xe9;veloppement (French Research Institute for Development)/ ; CN00000033//Ministero dell'Istruzione, dell'Universit&#xe0; e della Ricerca (Ministry of Education, University and Research)/ ; LifeWatch//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; DP210103091//Department of Education and Training | Australian Research Council (ARC)/ ; GBMF9881//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; NGS-82515R-20//National Geographic Society/ ; }, mesh = {Animals ; *Data Collection/methods ; *Natural History/methods ; *Biodiversity ; *Conservation of Natural Resources/methods ; Archives ; }, abstract = {Rapid growth in bio-logging-the use of animal-borne electronic tags to document the movements, behaviour, physiology and environments of wildlife-offers opportunities to mitigate biodiversity threats and expand digital natural history archives. Here we present a vision to achieve such benefits by accounting for the heterogeneity inherent to bio-logging data and the concerns of those who collect and use them. First, we can enable data integration through standard vocabularies, transfer protocols and aggregation protocols, and drive their wide adoption. Second, we need to develop integrated data collections on standardized data platforms that support data preservation through public archiving and strategies that ensure long-term access. We outline pathways to reach these goals, highlighting the need for resources to govern community data standards and guide data mobilization efforts. We propose the launch of a community-led coordinating body and provide recommendations for how stakeholders-including government data centres, museums and those who fund, permit and publish bio-logging work-can support these efforts.}, }
@article {pmid39753746, year = {2025}, author = {Allegretti, E and D'Innocenzo, G and Coco, MI}, title = {The Visual Integration of Semantic and Spatial Information of Objects in Naturalistic Scenes (VISIONS) database: attentional, conceptual, and perceptual norms.}, journal = {Behavior research methods}, volume = {57}, number = {1}, pages = {42}, pmid = {39753746}, issn = {1554-3528}, support = {PTDC/PSI-ESP/30958/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; LISBOA-01-0145-FEDER-0309//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, mesh = {Humans ; *Semantics ; *Attention/physiology ; Female ; Adult ; Male ; Young Adult ; *Space Perception/physiology ; *Visual Perception/physiology ; Databases, Factual ; Eye-Tracking Technology ; Adolescent ; }, abstract = {The complex interplay between low- and high-level mechanisms governing our visual system can only be fully understood within ecologically valid naturalistic contexts. For this reason, in recent years, substantial efforts have been devoted to equipping the scientific community with datasets of realistic images normed on semantic or spatial features. Here, we introduce VISIONS, an extensive database of 1136 naturalistic scenes normed on a wide range of perceptual and conceptual norms by 185 English speakers across three levels of granularity: isolated object, whole scene, and object-in-scene. Each naturalistic scene contains a critical object systematically manipulated and normed regarding its semantic consistency (e.g., a toothbrush vs. a flashlight in a bathroom) and spatial position (i.e., left, right). Normative data are also available for low- (i.e., clarity, visual complexity) and high-level (i.e., name agreement, confidence, familiarity, prototypicality, manipulability) features of the critical object and its embedding scene context. Eye-tracking data during a free-viewing task further confirms the experimental validity of our manipulations while theoretically demonstrating that object semantics is acquired in extra-foveal vision and used to guide early overt attention. To our knowledge, VISIONS is the first database exhaustively covering norms about integrating objects in scenes and providing several perceptual and conceptual norms of the two as independently taken. We expect VISIONS to become an invaluable image dataset to examine and answer timely questions above and beyond vision science, where a diversity of perceptual, attentive, mnemonic, or linguistic processes could be explored as they develop, age, or become neuropathological.}, }
@article {pmid39753264, year = {2025}, author = {Aguirre Vergara, F and Pinker, I and Fischer, A and Seuring, T and Tichomirowa, MA and de Beaufort, C and Kamp, SM and Fagherazzi, G and Aguayo, GA}, title = {Readiness of adults with type 1 diabetes and diabetes caregivers for diabetes distress monitoring using a voice-based digital health solution: insights from the PsyVoice mixed methods study.}, journal = {BMJ open}, volume = {15}, number = {1}, pages = {e088424}, pmid = {39753264}, issn = {2044-6055}, mesh = {Humans ; *Diabetes Mellitus, Type 1/therapy/psychology ; Female ; Male ; Adult ; *Caregivers/psychology ; Middle Aged ; *Qualitative Research ; Telemedicine ; Young Adult ; Surveys and Questionnaires ; Interviews as Topic ; Stress, Psychological/etiology ; Digital Health ; }, abstract = {OBJECTIVES: Diabetes distress can negatively affect the well-being of individuals with type 1 diabetes (T1D). Voice-based (VB) technology can be used to develop inexpensive and ecological tools for managing diabetes distress. This study explored the competencies to engage with digital health services, needs and preferences of individuals with T1D or caring for a child with this condition regarding VB technology to inform the tailoring of a co-designed tool for supporting diabetes distress management.<br><br>DESIGN: We used a mixed methods design. We performed a qualitative reflexive thematic analysis of semistructured interviews of people living with T1D or caring for a child with T1D, complemented by quantitative analysis (descriptive statistics).<br><br>SETTING: 12 adults living with T1D who attended diabetes centres or cared for a child with this condition participated in semistructured interviews to collect opinions about voice technology. They also responded to three questionnaires on sociodemographics and diabetes management, diabetes distress and e-health literacy.<br><br>OUTCOME MEASURES: Main: Patient experiences and perceptions derived from the coded transcriptions of interview data. Secondary: Quantitative data generated from Socio-Demographic and Diabetes Management questionnaire; Problem Areas in Diabetes Scale and e-Health Literacy Questionnaire.<br><br>RESULTS: Five major themes were generated from the participants' interview responses: (1) Experience of T1D, (2) Barriers to VB technology use, (3) Facilitators of VB technology, (4) Expectations of VB technology management in T1D, (5) Role of healthcare professionals in implementing VB technology for T1D. Most participants expressed a favourable view of voice technology for diabetes distress management. Trust in technology and healthcare professionals emerged as the predominant sentiment, with participants' current device type impacting anticipated barriers to adopting new technologies.<br><br>CONCLUSION: The results highlighted positive participant views towards VB technology. Device use, previous experience and health professional endorsement were influential facilitators of novel VB digital health solutions. Further research involving younger people with T1D could further contribute to the successful development of these tools.<br><br>TRIAL REGISTRATION NUMBER: ClinicalTrials.gov, NCT05517772.}, }
@article {pmid39752826, year = {2025}, author = {Zhao, X and Jiang, WY and Liu, JJ and Yan, WJ and Zhang, YH and Zhang, Z and Zhang, PD}, title = {Unraveling the impact of PFOA toxicity on Zostera marina using a multi-omics approach: Insights from growth, physiological, transcriptomic, and metabolomic signatures.}, journal = {Journal of hazardous materials}, volume = {486}, number = {}, pages = {137024}, doi = {10.1016/j.jhazmat.2024.137024}, pmid = {39752826}, issn = {1873-3336}, mesh = {*Fluorocarbons/toxicity ; Transcriptome/drug effects ; *Water Pollutants, Chemical/toxicity ; *Zosteraceae/drug effects/growth &amp; development/metabolism/genetics ; *Caprylates/toxicity ; Metabolomics ; Gene Expression Profiling ; Metabolome/drug effects ; Multiomics ; }, abstract = {Perfluorooctanoic acid (PFOA), an anthropogenic organic pollutant known for its persistence, resistance to degradation, and toxicity, has raised significant concerns about its potential ecological impacts. Zostera marina, a common submerged seagrass species in temperate offshore areas, is highly vulnerable to pollutant stressors. However, the impact of PFOA on Z. marina remains unclear. In this study, Z. marina was exposed to different concentrations of PFOA (0, 0.5, 1, 5, 10, and 20 μg/L) for 14 days. We subsequently assessed survival rates, growth patterns, physiological indices, transcriptomic profiles, and metabolomic characteristics. The results revealed dose-dependent PFOA accumulation in Z. marina tissues and significant growth inhibition. Furthermore, exposure to PFOA resulted in a significant reduction in photosynthetic pigment content (IBRv2 indices: 2.78-10.29) and elevated enzyme activity (IBRv2 indices: 2.90-8.96). Transcriptomic analysis identified 1511 differentially expressed genes associated with 11 KEGG pathways predominantly affected by PFOA exposure. Weighted gene co-expression network analysis highlighted the crucial role of the hydroxyphenylpyruvate reductase (hppr) gene in antioxidant defense mechanisms and detoxification processes against PFOA-induced stress. Metabolomics identified 412 differentially expressed metabolites, mainly consisting of flavonoids, organic acids, and lipids. In summary, PFOA exposure resulted in the down-regulation of gene expression related to photosynthesis and energy metabolism while also affecting metabolite synthesis. The response of Z. marina to PFOA stress involves modulation of the cytoskeletal dynamics and signal transduction pathways, as well as activation of a suite of genes and metabolites to initiate defense mechanisms.}, }
@article {pmid39750058, year = {2024}, author = {Jain, S and Srinivasan, R and Helton, TJ and Karthikeyan, R}, title = {TXSELECT: a web-based decision support system for regional assessment of potential E. coli loads using a spatially explicit approach.}, journal = {Journal of environmental science and health. Part A, Toxic/hazardous substances &amp; environmental engineering}, volume = {59}, number = {10}, pages = {550-561}, doi = {10.1080/10934529.2024.2445953}, pmid = {39750058}, issn = {1532-4117}, mesh = {*Escherichia coli/isolation &amp; purification ; Texas ; *Internet ; Environmental Monitoring/methods ; Water Microbiology ; Decision Support Techniques ; }, abstract = {Bacterial source characterization and allocation are imperative to watershed planning and identifying best management practices. The Spatially Explicit Load Enrichment Calculation Tool (SELECT) has been extensively utilized in watershed protection plans to evaluate the potential bacteria loads and sources in impaired watersheds. However, collecting data, compiling inputs, and spatially mapping sources can be arduous, time-intensive, expensive, and iterative until potential bacteria loads are appropriately allocated to sources based on stakeholder recommendations. We developed a web-based decision support system (DSS), TXSELECT (https://tx.select.tamu.edu), providing a user-friendly interface to run the SELECT model on Texas watersheds. The DSS includes pre-determined watershed-specific inputs that can be readily adjusted within the interface based on user preference and stakeholder recommendations, obviating the necessity for expensive GIS tools and data extraction. To illustrate the applications of TXSELECT, we implemented it in the entire coverage area to identify the potential hotspots and source contributions for Escherichia coli at a regional scale. Median potential E. coli loads were significantly higher in subwatersheds not supporting recreation use. Overall, the large-scale application of SELECT has the potential to aid in prioritizing management measures in watersheds that are less frequently monitored but could have an elevated risk of impairment.}, }
@article {pmid39749768, year = {2025}, author = {Fifield, K and Veerakanjana, K and Hodsoll, J and Kuntsi, J and Tye, C and Simblett, S}, title = {Completion Rates of Smart Technology Ecological Momentary Assessment (EMA) in Populations With a Higher Likelihood of Cognitive Impairment: A Systematic Review and Meta-Analysis.}, journal = {Assessment}, volume = {32}, number = {8}, pages = {1175-1194}, pmid = {39749768}, issn = {1552-3489}, mesh = {Humans ; *Ecological Momentary Assessment ; *Cognitive Dysfunction/diagnosis/psychology ; *Smartphone ; }, abstract = {Ecological Momentary Assessment using smartphone technology (smart EMA) has grown substantially over the last decade. However, little is known about the factors associated with completion rates in populations who have a higher likelihood of cognitive impairment. A systematic review of Smart EMA studies in populations who have a higher likelihood of cognitive impairment was carried out (PROSPERO; ref no CRD42022375829). Smartphone EMA studies in neurological, neurodevelopmental and neurogenetic conditions were included. Six databases were searched, and bias was assessed using Egger's test. Completion rates and moderators were analyzed using meta-regression. Fifty-five cohorts were included with 18 cohorts reporting confirmed cognitive impairment. In the overall cohort, the completion rate was 74.4% and EMA protocol characteristics moderated completion rates. Participants with cognitive impairment had significantly lower completion rates compared with those without (p = .021). There were no significant moderators in the cognitive impairment group. Limitations included significant methodological issues in reporting of completion rates, sample characteristics, and associations with completion and dropout rates. These findings conclude that smart EMA is feasible for people with cognitive impairment. Future research should focus on the efficacy of using smart EMA within populations with cognitive impairment to develop an appropriate methodological evidence base.}, }
@article {pmid39749403, year = {2025}, author = {Bougiouri, K}, title = {Mind the Gap: A Neural Network Framework for Imputing Genotypes in Non-Model Species.}, journal = {Molecular ecology resources}, volume = {25}, number = {3}, pages = {e14066}, doi = {10.1111/1755-0998.14066}, pmid = {39749403}, issn = {1755-0998}, mesh = {*Genotype ; *Neural Networks, Computer ; Haplotypes ; *Computational Biology/methods ; Machine Learning ; }, abstract = {Reduced representation sequencing (RRS) has proven to be a cost-effective solution for sequencing subsets of the genome in non-model species for large-scale studies. However, the targeted nature of RRS approaches commonly introduces large amounts of missing data, leading to reduced statistical power and biased estimates in downstream analyses. Genotype imputation, the statistical inference of missing sites across the genome, is a powerful alternative to overcome the caveats associated with missing sites. Typically, genotype imputation requires the presence of a reference panel of haplotypes, however, this is not always feasible for non-model species. In this issue of Molecular Ecology Resources, Mora-Márquez et al. (2024) develop gtImputation, an unsupervised machine learning imputation tool with an interactive GUI, which leverages information from the underlying data structure itself, without the need for a reference panel. They showcase that their method performs equally well and even surpasses existing haplotype-clustering and unsupervised machine learning algorithms, particularly for sites with low minor allele frequency (MAF) and for data sets with strong underlying population structure. This innovative framework adds to the ongoing efforts to expand the applicability of imputation to non-model species, offering the opportunity to apply varied types of analyses requiring dense sets of markers, while also maintaining lower sequencing costs.}, }
@article {pmid39747897, year = {2025}, author = {Petrovic, M and Salovic, B and Tomic, A and Jesic-Petrovic, T and Matejic, A and Radovic, I and Babic, S and Korugic, A and Jelovac, D and Mikovic, N and Jakovljevic, S and Pelemis, S and Dimitrijevic, M and Milovanovic, J and Jotic, A and Trivic, A and Dimitrijevic, A and Bulatovic, S and Dudvarski, Z and Soldatovic, I and Ilic-Zivojinovic, J}, title = {Functional assessment of cancer therapy - head &amp; neck (FACT-HN) translation and validation in Serbian.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {298}, pmid = {39747897}, issn = {2045-2322}, mesh = {Humans ; *Head and Neck Neoplasms/therapy/psychology ; Male ; Serbia ; Female ; *Quality of Life ; Middle Aged ; *Psychometrics/methods ; Surveys and Questionnaires ; Aged ; Reproducibility of Results ; Adult ; Translations ; }, abstract = {This study aimed to translate and validate the Functional Assessment of Cancer Therapy - Head &amp; Neck (FACT-HN) in a Serbian-speaking population, assessing its psychometric properties and utility in evaluating the quality of life in head and neck cancer patients. The research focuses on determining the translated questionnaire's reliability, validity, and cultural relevance. A total of 106 Serbian-speaking head and neck cancer patients completed the translated FACT-HN, along with other validated instruments, including the EORTC QLQ-C30, EORTC QLQ-HN43, CES-D, and GAD-7. The translation followed a standard internationally accepted procedure. Psychometric analyses were conducted using confirmatory and exploratory factor analysis, Pearson correlations, and reliability measures such as Cronbach's alpha and intraclass correlation coefficients. The Serbian version of the FACT-HN showed excellent internal consistency across all subscales, with Cronbach's alpha ranging from 0.70 to 0.89. Confirmatory factor analysis confirmed the five-factor structure. Strong correlations were observed between the FACT-HN and other validated QoL measures, particularly with the EORTC QLQ-C30 and EORTC QLQ-HN43. Convergent validity was satisfactory for all components except the Social Well-Being component. The Serbian version of the FACT-HN is a valid and reliable tool for assessing the quality of life in head and neck cancer patients. It provides a comprehensive assessment of physical, social, emotional, and functional well-being, making it valuable for clinical and research applications in Serbian-speaking populations. Further research is needed to assess its sensitivity to longitudinal treatment-related changes.}, }
@article {pmid39747514, year = {2025}, author = {Liu, X and Tan, Y and Dong, J and Wu, J and Wang, X and Sun, Z}, title = {Assessing habitat selection parameters of Arabica coffee using BWM and BCM methods based on GIS.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {8}, pmid = {39747514}, issn = {2045-2322}, support = {51979133//National Natural Science Foundation of China/ ; 202301AS070030//Yunnan Fundamental Research Projects/ ; 202302AE090024//Yunnan Major Science and Technology Special Plan/ ; }, mesh = {*Ecosystem ; *Geographic Information Systems ; *Coffea/growth &amp; development ; China ; Coffee ; Climate ; Decision Making ; Conservation of Natural Resources/methods ; Soil/chemistry ; }, abstract = {Arabica coffee, as one of the world's three native coffee species, requires rational planning for its growing areas to ensure ecological and sustainable agricultural development. This study aims to establish a decision-making framework using Geographic Information Systems (GIS) and Multi-Criteria Decision-Making (MCDM), with a focus on assessing the habitat suitability of Arabica coffee in Yunnan Province, China. The impacts of climate, topography, soil, and socio-economic factors were considered by selecting 13 criteria through correlation analysis. Indicator weights were determined using the Best-Worst Method (BWM), while weighted processing was conducted using the Base-Criterion Method (BCM). Sensitivity analysis was performed to verify the accuracy and stability of the model. Additionally, several decision models were evaluated to investigate regionalizing Arabica coffee habitats in Yunnan. The results highlighted that minimum temperature during the coldest month is crucial for evaluation purposes. The BWM-GIS model identified suitable areas comprising 13.55% of the total area as most suitable, 27.46% as suitable, and 59.00% as unsuitable, whereas corresponding values for the BCM-GIS model were 9.97%, 30.43%, and 59.59%. Despite employing different decision-making methods, both models yielded similar and consistent results. The suitable areas mainly encompass Dehong, Pu'er, Lincang, Xishuangbanna, Baoshan, southern Chuxiong, eastern Honghe, southern Yuxi, and parts of Wenshan. BWM-GIS achieved an area under curve (AUC) value of 0.891, while BCM-GIS obtained an AUC value of 0.890, indicating the stability and reliability of the models. Among them, the evaluation process of BCM-GIS was simpler and more realistic. Therefore, it has high feasibility and practical value in practical application. The findings from this study provide a significant scientific foundation for optimizing Yunnan Province.}, }
@article {pmid39746011, year = {2025}, author = {Wohltjen, S and Colón, YI and Zhu, Z and Miller, K and Huang, WC and Mutlu, B and Li, Y and Niedenthal, PM}, title = {Uniting theory and data: the promise and challenge of creating an honest model of facial expression.}, journal = {Cognition &amp; emotion}, volume = {}, number = {}, pages = {1-15}, doi = {10.1080/02699931.2024.2446945}, pmid = {39746011}, issn = {1464-0600}, abstract = {People routinely use facial expressions to communicate successfully and to regulate other's behaviour, yet modelling the form and meaning of these facial behaviours has proven surprisingly complex. One reason for this difficulty may lie in an over-reliance on the assumptions inherent in existing theories of facial expression - specifically that (1) there is a putative set of facial expressions that signal an internal state of emotion, (2) patterns of facial movement have been empirically linked to the prototypical emotions in this set, and (3) static, non-social, posed images from convenience samples are adequate to validate the first two assumptions. These assumptions have guided the creation of datasets, which are then used to train unrepresentative computational models of facial expression. In this article, we discuss existing theories of facial expression and review how they have shaped current facial expression recognition tools. We then discuss the resources that are available to help researchers build a more ecologically valid model of facial expressions.}, }
@article {pmid39745426, year = {2025}, author = {Gulyaeva, A and Liu, L and Garmaeva, S and Kruk, M and Weersma, RK and Harmsen, HJM and Zhernakova, A}, title = {Identification and characterization of Faecalibacterium prophages rich in diversity-generating retroelements.}, journal = {Microbiology spectrum}, volume = {13}, number = {2}, pages = {e0106624}, pmid = {39745426}, issn = {2165-0497}, mesh = {*Prophages/genetics/isolation &amp; purification/classification ; *Retroelements/genetics ; Humans ; Genome, Viral ; Gastrointestinal Microbiome/genetics ; Metagenomics ; Host Specificity ; Computational Biology/methods ; Virome ; Feces/microbiology ; }, abstract = {Metagenomics has revealed the incredible diversity of phages within the human gut. However, very few of these phages have been subjected to in-depth experimental characterization. One promising method of obtaining novel phages for experimental characterization is through induction of the prophages integrated into the genomes of cultured gut bacteria. Here, we developed a bioinformatic approach to prophage identification that builds on prophage genomic properties, existing prophage-detecting software, and publicly available virome sequencing data. We applied our approach to 22 strains of bacteria belonging to the genus Faecalibacterium, resulting in identification of 15 candidate prophages, and validated the approach by demonstrating the activity of five prophages from four of the strains. The genomes of three active phages were identical or similar to those of known phages, while the other two active phages were not represented in the Viral RefSeq database. Four of the active phages possessed a diversity-generating retroelement (DGR), and one retroelement had two variable regions. DGRs of two phages were active at the time of the induction experiments, as evidenced by nucleotide variation in sequencing reads. We also predicted that the host range of two active phages may include multiple bacterial species. Finally, we noted that four phages were less prevalent in the metagenomes of inflammatory bowel disease patients compared to a general population cohort, a difference mainly explained by differences in the abundance of the host bacteria. Our study highlights the utility of prophage identification and induction for unraveling phage molecular mechanisms and ecological interactions.IMPORTANCEWhile hundreds of thousands of phage genomes have been discovered in metagenomics studies, only a few of these phages have been characterized experimentally. Here, we explore phage characterization through bioinformatic identification of prophages in genomes of cultured bacteria, followed by prophage induction. Using this approach, we detect the activity of five prophages in four strains of commensal gut bacteria Faecalibacterium. We further note that four of the prophages possess diversity-generating retroelements implicated in rapid mutation of phage genome loci associated with phage-host and phage-environment interactions and analyze the intricate patterns of retroelement activity. Our study highlights the potential of prophage characterization for elucidating complex molecular mechanisms employed by the phages.}, }
@article {pmid39742992, year = {2025}, author = {Kim, DH and Kim, Y}, title = {Factors Associated With Habitual Drug Use Among Adolescents: A Secondary Data Analysis.}, journal = {Asian nursing research}, volume = {19}, number = {1}, pages = {78-85}, doi = {10.1016/j.anr.2024.12.006}, pmid = {39742992}, issn = {2093-7482}, mesh = {Humans ; Adolescent ; Male ; Female ; *Substance-Related Disorders/epidemiology/psychology ; Republic of Korea/epidemiology ; *Adolescent Behavior/psychology ; Risk Factors ; Prevalence ; Risk-Taking ; Students/psychology/statistics &amp; numerical data ; Cross-Sectional Studies ; Surveys and Questionnaires ; Secondary Data Analysis ; }, abstract = {PURPOSE: Drug use during adolescence can have lasting health consequences, and understanding the factors that contribute to drug use is essential for effective prevention. This study aimed to identify the factors influencing habitual drug use among South Korean adolescents. It employed Bronfenbrenner's ecological model to examine personal, familial, school-related, and social factors.<br><br>METHODS: The study analyzed data from the 19th Korea Youth Risk Behavior Survey for 41,928 students from 1st grade of middle school to 3rd grade of high school. Data analysis involved cross-tabulation and logistic regression for complex samples.<br><br>RESULTS: The prevalence of habitual drug use was 1.4%. Significant personal factors included smoking [adjusted odds ratio (aOR)&#xa0;=&#xa0;2.61], alcohol consumption (aOR&#xa0;=&#xa0;1.55), sexual intercourse (aOR&#xa0;=&#xa0;1.45), smartphone overdependence (high-risk group aOR&#xa0;=&#xa0;2.04, potential risk group aOR&#xa0;=&#xa0;1.31), suicidal ideation (aOR&#xa0;=&#xa0;2.66), depressed mood (aOR&#xa0;=&#xa0;1.87), and loneliness (aOR&#xa0;=&#xa0;1.88). Significant family factors included non-cohabitation with family (aOR&#xa0;=&#xa0;1.86) and both parents being foreign-born (aOR&#xa0;=&#xa0;3.36). Experience of violence (aOR&#xa0;=&#xa0;2.95) was also a significant factor.<br><br>CONCLUSION: This study highlights the need for an integrated approach to prevent adolescent drug use by addressing adolescents' personal behaviors, family dynamics, and school environments. Prevention programs should account for the influence of multiple systems on habitual drug use. School and community nurses should adopt a comprehensive, multi-dimensional strategy that involves families, schools, and communities to prevent adolescent drug use. Additionally, there is a need to develop family-centered and culturally sensitive drug prevention programs for adolescents.}, }
@article {pmid39742640, year = {2025}, author = {Zhang, H and Dong, S and Shan, H and Yang, C and Wang, F}, title = {Application of the DEB-TKTD model with multi-omics data: Prediction of life history traits of Chinese mitten crab (Eriocheir sinensis) under different salinities.}, journal = {Ecotoxicology and environmental safety}, volume = {290}, number = {}, pages = {117635}, doi = {10.1016/j.ecoenv.2024.117635}, pmid = {39742640}, issn = {1090-2414}, mesh = {Animals ; *Brachyura/physiology/growth &amp; development ; *Salinity ; *Life History Traits ; Aquaculture ; Female ; Water Pollutants, Chemical/toxicity ; Metabolomics ; Multiomics ; }, abstract = {Saline-alkaline aquaculture plays a crucial role in the ecological restoration of saline soils, yet high water salinity can significantly restrict the growth of cultured organisms. The Chinese mitten crab (Eriocheir sinensis) is typically farmed in freshwater, to evaluate the effects of salinity stress on these crabs, this study conducted laboratory aquaculture experiments at salinities of ≤ 0.5 (freshwater), 6, 12, and 18 ‰. Regular data on crab survival and growth were collected over 35 days. Subsequently, tissues including the eyestalk, posterior gill, hepatopancreas, and ovary were sampled from crabs in both the freshwater control group and the 18 ‰ salinity treatment group for transcriptional and metabolomic analysis. The omics data were used to ascertain the physiological mode of action (pMoA) affected by salinity in the crabs. A dynamic energy budget toxicokinetic-toxicodynamic (DEB-TKTD) model was built based on these pMoAs to predict the life history traits of crabs across different salinities, including survival, growth, and reproduction. The omics results indicated that at 18 ‰, the osmoregulatory capacity and oxidative stress resistance were enhanced, and vitellogenin synthesis was stimulated. This suggests that the two pMoAs involved increasing maintenance costs and reallocating energy between soma and reproduction. DEB-TKTD model predictions fit well with the observed data, with high R[2] values (0.9704 for survival, 0.9842 for carapace width, and 0.9283 for reproduction) and low NRMSE (0.0093, 0.1175, and 0.0778, respectively). The predictions indicate that after 60 days, survival rates under salinities of 6, 12, and 18 ‰ decreased by 35.7 %, 56.7 %, and 66.2 %, respectively, compared to freshwater conditions. Growth in carapace width was similarly affected, with reductions of 21.5 %, 42.3 %, and 62.5 %, respectively. The maturation process was accelerated for crabs in saline conditions, with puberty achieved at 45, 36, and 31 days, compared to the freshwater group that had not matured. Furthermore, the LC50 for salinity decreased from 9.07 ‰ (95 % CI: 7.33-10.15 ‰) at 35 days to 4.59 ‰ (95 % CI: 3.12-5.83 ‰) at 60 days. The findings of this study indicate the significant impact of salinity on the survival, growth, and maturation of Chinese mitten crabs by altering maintenance costs and energy allocation. The DEB-TKTD model, informed by omics data, accurately predicts the life history traits of crabs under saline stress. This approach provides an innovative tool for ecological toxicological research in the aquaculture environment.}, }
@article {pmid39739202, year = {2025}, author = {Bard, NW and Davies, TJ and Cronk, QCB}, title = {Teknonaturalist: A Snakemake Pipeline for Assessing Fungal Diversity From Plant Genome Bycatch.}, journal = {Molecular ecology resources}, volume = {25}, number = {3}, pages = {e14056}, pmid = {39739202}, issn = {1755-0998}, support = {RGPIN-2019-04041//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2020-04439//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {*Fungi/classification/genetics/isolation &amp; purification ; *Plants/microbiology ; DNA, Ribosomal Spacer/genetics/chemistry ; *Computational Biology/methods ; DNA, Fungal/genetics/chemistry ; *DNA Barcoding, Taxonomic/methods ; *Genome, Plant ; Endophytes/classification/genetics ; *Biodiversity ; Sequence Analysis, DNA ; }, abstract = {Relatively little is known of the host associations and compatibility of fungal plant pathogens and endophytes. Publicly available plant genomic DNA can be mined to detect incidental fungal DNA, but taxonomic assignment can be challenging due to short lengths and variable discriminative power among different genomic regions and taxa. Here, we introduce a computationally lightweight and accessible Snakemake pipeline for rapid detection and classification (identification and assignment to taxonomic rank) of pathogenic and endophytic fungi (and other fungi associated with plants) that targets the internal transcribed spacer (ITS) region, a fungal barcode standard. We include methods for maximising query sequence length, which gives higher support for ITS1 and ITS2 taxonomic classifications by extending to other fragments of the ITS region and providing taxon-specific local cut-off and confidence scores. We demonstrate our pipeline with a case study using public genomic sequence data for six diverse plant species, including four species within Betula, an ecologically and economically important broadleaved forest tree genus, a shrub and a grass. Our pipeline classified fungi within minutes to a few hours per host individual, with 204 different fungal genera identified at high confidence (≥ 70%). Our pipeline detected and classified pathogenic and endophytic genera known to associate with Betula, and many others with no prior record of association. Our pipeline, leveraging existing sequence data, has several potential applications, including detecting cryptic fungal pathogens and helping characterise the endophytic fungal microbiome, bioprospecting commercially useful fungal species, and determining the plant host range of fungi.}, }
@article {pmid39736019, year = {2024}, author = {Kobzeva, K and Ivenkov, M and Gromov, R and Bushueva, O}, title = {HSP90 Family Members, Their Regulators and Ischemic Stroke Risk: A Comprehensive Molecular-Genetics and Bioinformatics Analysis.}, journal = {Frontiers in bioscience (Scholar edition)}, volume = {16}, number = {4}, pages = {19}, doi = {10.31083/j.fbs1604019}, pmid = {39736019}, issn = {1945-0524}, support = {22-15-00288//Russian Science Foundation/ ; }, mesh = {Humans ; *Polymorphism, Single Nucleotide ; *HSP90 Heat-Shock Proteins/genetics/metabolism ; *Ischemic Stroke/genetics ; Male ; Female ; Middle Aged ; *Computational Biology ; Aged ; *Genetic Predisposition to Disease ; Russia/epidemiology ; Risk Factors ; Case-Control Studies ; Heat Shock Transcription Factors/genetics/metabolism ; }, abstract = {BACKGROUND: Disruptions in proteostasis are recognized as key drivers in cerebro- and cardiovascular disease progression. Heat shock proteins (HSPs), essential for maintaining protein stability and cellular homeostasis, are pivotal in neuroperotection. Consequently, deepening the understanding the role of HSPs in ischemic stroke (IS) risk is crucial for identifying novel therapeutic targets and advancing neuroprotective strategies.<br><br>AIM: Our objective was to examine the potential correlation between single nucleotide polymorphisms (SNPs) in genes that encode members of the Heat shock protein 90 (HSP90), small heat shock proteins (HSPB), and heat shock factors (HSF) families, and the risk and clinical characteristics of IS.<br><br>METHODS: 953 IS patients and 1265 controls from Central Russia were genotyped for nine SNPs in genes encoding HSP90AA1, HSFs, and HSPBs using the MassArray-4 system and probe-based polymerase chain reaction (PCR).<br><br>RESULTS: In smokers, SNP rs1133026 HSPB8 increased the risk of IS (risk allele A, odds ratio (OR) = 1.43, 95% Confidence Interval (CI) 1.02-2.02, p = 0.035), and rs556439 HSF2 increased the brain infarct size (risk allele A, p = 0.02). In non-smokers, SNPs rs4279640 HSF1 (protective allele T, OR = 0.58, 95% CI 0.37-0.92, p = 0.02) and rs4264324 HSP90AA1 (protective allele C, OR = 0.11, 95% CI 0.01-0.78, p = 0.001) lowered the risk of recurrent stroke; SNP rs7303637 HSPB8 increased the age of onset of IS (protective allele T, p = 0.04). In patients with body mass index (BMI) &#x2265;25, SNPs rs556439 HSF2 (risk allele A, OR = 1.33, 95% CI 1.04-1.69, p = 0.02) and rs549302 HSF2 (risk allele G, OR = 1.34, 95% CI 1.02-1.75, p = 0.03) were linked to a higher risk of IS.<br><br>CONCLUSIONS: The primary molecular mechanisms through which the studied SNPs contribute to IS pathogenesis were found to be the regulation of cell death, inflammatory and oxidative stress responses.}, }
@article {pmid39730727, year = {2024}, author = {Kato, H}, title = {Daily walking time effects of the opening of a multifunctional facility "ONIKURU" using propensity score matching and GPS tracking techniques.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {31047}, pmid = {39730727}, issn = {2045-2322}, support = {24K17421//Japan Society for the Promotion of Science/ ; }, mesh = {Humans ; Female ; *Walking/physiology ; Male ; Adult ; *Geographic Information Systems ; *Propensity Score ; Middle Aged ; Young Adult ; Exercise/physiology ; Adolescent ; Environment Design ; Time Factors ; Smartphone ; }, abstract = {Urban design focused on improving walkability has received attention as a method of increasing physical activity among the population. However, only a few studies have examined the effect of walking time of opening multifunctional facilities as an architecture-scale intervention. This study aimed to clarify the effect of opening a multifunctional facility on residents' daily walking time. In addition, this study analyzed the gender and age subgroups. The natural experiment was conducted using the case of the Ibaraki City Cultural and Childcare Complex "ONIKURU," a public multifunctional facility. This study used GPS-trajectory data based on GPS tracking techniques, which is anonymized location data for smartphone users. The causal relationship was analyzed using propensity score matching and difference-in-differences analysis. The results showed that the opening of ONIKURU significantly increased the average walking time of visitors to 3.165 [- 1.697, 8.027] min/day compared with that of non-visitors. Specifically, visitors' average daily walking time improved to a level comparable to that of non-visitors after the opening of ONIKURU. In addition, opening ONIKURU significantly increased female young adults' average walking time to 3.385 [- 4.906, 11.676] min/day. Therefore, this study provides theoretical contributions to a health-promoting built environment significantly affecting walking at an architecture-scale intervention.}, }
@article {pmid39730187, year = {2025}, author = {Yan, M and Andersen, TO and Pope, PB and Yu, Z}, title = {Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases.}, journal = {Genome research}, volume = {35}, number = {2}, pages = {368-378}, pmid = {39730187}, issn = {1549-5469}, mesh = {Animals ; *Ruminants/microbiology/parasitology/genetics ; *Metagenomics/methods ; Metagenome ; *Deep Learning ; *Databases, Protein ; Rumen/microbiology ; Fungi/genetics/classification ; Computational Biology/methods ; *Eukaryota/genetics/classification ; *Gastrointestinal Microbiome/genetics ; }, abstract = {Metagenomics, particularly genome-resolved metagenomics, have significantly deepened our understanding of microbes, illuminating their taxonomic and functional diversity and roles in ecology, physiology, and evolution. However, eukaryotic populations within various microbiomes, including those in the mammalian gastrointestinal (GI) tract, remain relatively underexplored in metagenomic studies owing to the lack of comprehensive reference genome databases and robust bioinformatic tools. The GI tract of ruminants, particularly the rumen, contains a high eukaryotic biomass but a relatively low diversity of ciliates and fungi, which significantly impacts feed digestion, methane emissions, and rumen microbial ecology. In the present study, we developed GutEuk, a bioinformatics tool that improves upon the currently available Tiara and EukRep in accurately identifying eukaryotic sequences from metagenomes. GutEuk is optimized for high precision across different sequence lengths. It can also distinguish fungal and protozoal sequences, further elucidating their unique ecological, physiological, and nutritional impacts. GutEuk was shown to facilitate comprehensive analyses of protozoa and fungi within more than 1000 rumen metagenomes, revealing a greater genomic diversity among protozoa than previously documented. We further curated several ruminant eukaryotic protein databases, significantly enhancing our ability to distinguish the functional roles of ruminant fungi and protozoa from those of prokaryotes. Overall, the newly developed package GutEuk and its associated databases create new opportunities for the in-depth study of GI tract eukaryotes.}, }
@article {pmid39729740, year = {2025}, author = {Gupta, AK and Ravikumar, K and Gopal, V and Begum, N and Tabassum,  and Sangeetha, S and Narendran, P and Shankar, D}, title = {A trans-disciplinary agro-ecology strategy to grow medicinal plants.}, journal = {Journal of Ayurveda and integrative medicine}, volume = {16}, number = {1}, pages = {100985}, pmid = {39729740}, issn = {0975-9476}, abstract = {The scope of the emerging field of Ayurvedic-biology visualized thus far is confined to studies on dimensions pertaining to clinical and experimental pharmacology, basic trans-disciplinary science and drug design. However, given the multiple facets of classical Ayurveda knowledge system, its application in the field of organic agriculture perhaps also needs to be urgently explored. The urgency is due to the growing public acceptance of Ayurveda as a preferred clinical choice for well-being and disease management. The turnover of the sector across manufacturing and health services is estimated to be around Rs.1,00,000 crores per annum. Medicinal plants today and in the coming decade will therefore be required in large volumes and given that their applications are solely for enhancing health of humans, livestock (Pashu Ayurveda) and crops (Vriksh Ayurveda), it is imperative that they be cultivated in an organic manner employing the fusion of best available inter-cultural knowledge. The Ayurvedic subjects relevant for organic agriculture are Desh vichar, Dravya guna Shastra and Vriksh Ayurveda. From the perspective of modern biology subjects like soil micro biome, genetics, plant physiology and the natural geographical distribution of species are relevant. It must be stated at the very outset that this article is largely theoretical. While experiments in Vriksh Ayurveda have been attempted on a small scale, the fusion of Ayurveda and biology for improving organic agriculture of medicinal plants has thus far not been systematically explored.}, }
@article {pmid39727132, year = {2024}, author = {Xin, PY and Tian, T and Zhang, ML and Han, WZ and Song, YT}, title = {[Assessment of habitat quality changes and driving factors in Jilin Province based on InVEST model and geodetector].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {35}, number = {10}, pages = {2853-2860}, doi = {10.13287/j.1001-9332.202410.026}, pmid = {39727132}, issn = {1001-9332}, mesh = {China ; *Ecosystem ; *Conservation of Natural Resources ; *Models, Theoretical ; Environmental Monitoring ; Forests ; Trees/growth &amp; development ; Geographic Information Systems ; }, abstract = {Jilin Province is an important ecological security barrier in Northeast China as it is located at the junction of the Northeast forest belts and the northern sand prevention belts. In recent years, Jilin Province has actively carried out ecological protection and restoration projects, resulting in a continuous improvement trend for the overall ecological environment. However, the evolution patterns and mechanisms of habitat quality are largely unkown. We applied the InVEST model and geographic detector method to analyze the changes in habitat quality and evaluate the main driving factors from 2000 to 2020. The results showed that the average habitat quality in Jilin Province showed a slight downward trend, and that the spatial heterogeneity characteristics of habitat quality in east and west gradually increased. The degree of habitat degradation presented a single nuclear radiation pattern centered on Changchun City. Vegetation factors and terrain factors were the first and secondary causes of spatial heterogeneity of habitat quality, respectively. The average habitat quality within the eco-redline of Jilin Province was showing an increasing trend year by year, which was consistent with the overall distribution of regions with extremely high habitat quality levels. There was a local spatial dislocation (the phenomenon of extremely high habitat quality levels not within the eco-redline) in the eastern part of Jilin Province. Our results could provide reference basis for ecosystem protection and the spatial pattern optimization.}, }
@article {pmid39727130, year = {2024}, author = {Jia, J and Su, X and Zhang, J and Lu, CL and Zhang, MY and Li, X and Dong, YG and Ren, HC}, title = {[Land use changes and driving forces of landslide area in Tongwei County, Gansu Province, Northwest China from 1985 to 2020.].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {35}, number = {10}, pages = {2833-2841}, doi = {10.13287/j.1001-9332.202410.020}, pmid = {39727130}, issn = {1001-9332}, mesh = {China ; *Landslides ; *Conservation of Natural Resources ; *Crops, Agricultural/growth &amp; development ; Ecosystem ; Trees/growth &amp; development ; Forests ; Grassland ; Environmental Monitoring/methods ; Disasters ; Geographic Information Systems ; Poaceae/growth &amp; development ; }, abstract = {Accurately analyzing the type of land use and change characteristics of disaster damage in landslide areas is of great significance to scientifically promote the optimization of regional land use pattern and disaster prevention and mitigation. We analyzed the characteristic parameters of landslides as well as the characteristics and driving factors of land use change from 1985 to 2020 in Tongwei County, Gansu Province, using ALOS DEM data and 1985-2020 land use data, GIS spatial analysis, land-use dynamic attitude, transfer matrix, and Geodetector. The results showed that a total of 1012 landslide samples were identified, characterized by medium elevation, gentle gradient, low elevation difference, short length, and small size. During 1985-2020, landslide area land use types were cropland, woodland, grassland, bare land and impervious surface, dominated by grassland and cropland. During 2015-2020, each category of single land use dynamic attitude reached the largest, with the value of cropland, grassland, woodland, bare land, and the combined land use being 3.1%, 3.0%, 10.9%, 20.0%, 1.5%, respectively. During the study period, land use change was dominated by cropland and grassland, with a total reduction of 4.39 km[2] in cultivated land area, which was converted into grassland and forest. There was no change in bare land and impervious surfaces. We investigated the driving factors of land use change across 2000-2005 and 2015-2020. Slope and normalized difference vegetation index had a stronger explanatory power for land use change during 2000-2005, while slope, population density and total population had a stronger explanatory power during 2015-2020. The land use mode of regional individual landslide tended to be unified, and the increase of grassland enhanced the vegetation cover of the region. The findings would provide a scientific basis for the development and reuse of disaster damaged land and ecological restoration.}, }
@article {pmid39724715, year = {2025}, author = {Zhang, L and Du, Y and Li, Y and Wang, T and Pan, Y and Xue, X and Mu, X and Qiu, J and Qian, Y}, title = {Mitochondrial mechanism of florfenicol-induced nonalcoholic fatty liver disease in zebrafish using multi-omics technology.}, journal = {Journal of hazardous materials}, volume = {486}, number = {}, pages = {136958}, doi = {10.1016/j.jhazmat.2024.136958}, pmid = {39724715}, issn = {1873-3336}, mesh = {Animals ; Zebrafish ; *Thiamphenicol/analogs &amp; derivatives/toxicity ; *Non-alcoholic Fatty Liver Disease/chemically induced/metabolism/pathology ; *Anti-Bacterial Agents/toxicity ; *Mitochondria/drug effects/metabolism ; *Water Pollutants, Chemical/toxicity ; Oxidative Stress/drug effects ; Liver/drug effects/metabolism/pathology ; Metabolomics ; Multiomics ; }, abstract = {Florfenicol (FF), a third-generation chloramphenicol antibiotic widely used in food-producing animals, has become a "pseudopersistent" environmental contaminant, raising concerns about its potential ecological and human health impacts. However, its bioaccumulation behavior and hepatotoxic mechanisms remain poorly understood. This study aims to address these gaps with a 28-day exposure experiment in adult zebrafish at 0.05 and 0.5 mg/L FF. Multiomic analyses (metabolomics, lipidomics, and transcriptomics), combined with histological and mitochondrial function assessments, were employed. Higher bioaccumulation was observed at 0.05 mg/L, potentially due to metabolic saturation at higher concentrations. Histological analysis revealed significant hepatic steatosis (>5 % steatosis area), indicative of moderate nonalcoholic fatty liver disease (NAFLD). Multiomic data demonstrated global dysregulation in energy metabolism, including marked alterations in lipids (accumulation of toxic sphingolipids, excessive fatty acids, and acylglycerol), amino acids, tricarboxylic acid cycle intermediates, and nucleotides. Crucially, mitochondrial dysfunction was identified as a central mechanism, with impaired respiratory chain activities, adenosine triphosphate depletion, elevated reactive oxygen species, and oxidative stress promoting NAFLD progression. These findings highlight mitochondrial impairment and oxidative stress as key drivers of FF-induced hepatotoxicity, providing novel insights into its toxicological mechanisms and emphasizing the ecological risks posed by antibiotic pollution in aquatic systems.}, }
@article {pmid39724139, year = {2024}, author = {Stephens, JL and Fraga, LAO and Ferreira, JA and De Mondesert, L and Kitron, U and Clennon, JA and Fairley, JK}, title = {Spatial associations of Hansen's disease and schistosomiasis in endemic regions of Minas Gerais, Brazil.}, journal = {PLoS neglected tropical diseases}, volume = {18}, number = {12}, pages = {e0012682}, pmid = {39724139}, issn = {1935-2735}, mesh = {Humans ; Brazil/epidemiology ; *Leprosy/epidemiology ; *Endemic Diseases ; Female ; Male ; Spatial Analysis ; Adult ; Incidence ; Adolescent ; Middle Aged ; Young Adult ; Child ; Geographic Information Systems ; Animals ; *Schistosomiasis mansoni/epidemiology ; *Schistosomiasis/epidemiology ; Child, Preschool ; Aged ; }, abstract = {BACKGROUND: Brazil has the second highest case count of Hansen's disease (leprosy, HD), but factors contributing to transmission in highly endemic areas of the country remain unclear. Recent studies have shown associations of helminth infection and leprosy, supporting a biological plausibility for increased leprosy transmission in areas with helminths. However, spatial analyses of the overlap of these infections are limited. Therefore, we aimed to spatially analyze these two diseases in a co-endemic area of Minas Gerais, Brazil, in order to identify potential epidemiologic associations.<br><br>METHODS: An ecological study using public health surveillance records and census data was conducted to investigate whether the occurrence of HD -and specifically multibacillary (MB) disease- was associated with the presence of schistosomiasis in a community of 41 municipalities in eastern Minas Gerais, Brazil from 2011 to 2015. Multivariate logistic regression and spatial cluster analyses using geographic information systems (GIS) were performed.<br><br>RESULTS: The average annual incidence of HD in the study area was 35.3 per 100,000 while Schistosoma mansoni average annual incidence was 26 per 100,000. Both HD and schistosomiasis were spatially distributed showing significant clustering across the study area. Schistosomiasis was present in 10.4% of the tracts with HD and thirteen high-high clusters of local bivariate autocorrelation for HD and schistosomiasis cases were identified. A multivariate non-spatial analysis found that census tracts with MB disease were more likely to have schistosomiasis when adjusted for population density, household density, and household income (aOR = 1.7, 95% CI 1.0, 2.7). This remained significant when accounting for spatial correlation (aOR = 1.1, 95% CI (1.0, 1.2)).<br><br>CONCLUSION: We found clustering of both HD and schistosomiasis in this area with some statistically significant overlap of multibacillary HD with S. mansoni infection. Not only did we provide an effective approach to study the epidemiology of two endemic neglected tropical diseases with geographic spatial analyses, we highlight the need for further clinical and translational studies to study the potential epidemiologic associations uncovered.}, }
@article {pmid39720717, year = {2024}, author = {Luo, Z and Zhou, F and Jiang, S and Huang, J and Yang, L and Yang, Q and Shi, J and Li, E and Ma, Z and Li, Y}, title = {Immune and physiological responses in Penaeus monodon to ammonia-N stress: a multi-omics approach.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1510887}, pmid = {39720717}, issn = {1664-3224}, mesh = {Animals ; *Penaeidae/immunology ; *Ammonia/metabolism ; *Stress, Physiological/immunology ; *Oxidative Stress ; Transcriptome ; Metabolomics ; Immunity, Innate ; Gene Expression Profiling ; Nitrogen/metabolism ; Aquaculture ; Biomarkers ; Hepatopancreas/immunology/metabolism ; Multiomics ; }, abstract = {Ammonia-N stress is a significant environmental factor that adversely affects the health and productivity of aquaculture species. This study investigates the effects of ammonia-N stress on the shrimp Penaeus monodon through a combination of biochemical, histological, transcriptomic, and metabolomic analyses. Shrimp were exposed to ammonia-N stress for 12 and 96 hours, and key markers of oxidative stress, nitrogen metabolism, immune response, and overall health were assessed. The results showed that prolonged ammonia-N exposure causes significant hepatopancreatic damage, including atrophy and deformation. Transcriptomic analysis revealed significant changes in gene expression related to apoptosis, immune response, and key metabolic pathways, with particular emphasis on the disruption of innate immune signaling and defense mechanisms. Metabolomic analysis identified disruptions in nucleotide turnover, antioxidant defenses, and fundamental metabolic processes. These findings suggest that ammonia-N stress induces a multifaceted stress response in shrimp, involving oxidative stress, immune activation, and metabolic disturbances. Understanding these immune-related and metabolic mechanisms provides valuable insights into the molecular responses of crustaceans to environmental stress, laying the foundation for assessing the ecological risk of ammonia-N and identifying potential immunological biomarkers for monitoring and mitigating its adverse effects in aquaculture systems.}, }
@article {pmid39719706, year = {2025}, author = {Zhang, AN and Gaston, JM and Cárdenas, P and Zhao, S and Gu, X and Alm, EJ}, title = {CRISPR-Cas spacer acquisition is a rare event in human gut microbiome.}, journal = {Cell genomics}, volume = {5}, number = {1}, pages = {100725}, pmid = {39719706}, issn = {2666-979X}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *CRISPR-Cas Systems/genetics ; Gene Transfer, Horizontal/genetics ; Bacteriophages/genetics ; Bifidobacterium longum/genetics ; Metagenome/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Genome, Bacterial/genetics ; }, abstract = {Host-parasite relationships drive the evolution of both parties. In microbe-phage dynamics, CRISPR functions as an adaptive defense mechanism, updating immunity via spacer acquisition. Here, we investigated these interactions within the human gut microbiome, uncovering low frequencies of spacer acquisition at an average rate of one spacer every ∼2.9 point mutations using isolates' whole genomes and ∼2.7 years using metagenome time series. We identified a highly prevalent CRISPR array in Bifidobacterium longum spreading via horizontal gene transfer (HGT), with six spacers found in various genomic regions in 15 persons from the United States and Europe. These spacers, targeting two prominent Bifidobacterium phages, comprised 76% of spacer occurrence of all spacers targeting these phages in all B. longum populations. This result suggests that HGT of an entire CRISPR-Cas system introduced three times more spacers than local CRISPR-Cas acquisition in B. longum. Overall, our findings identified key ecological and evolutionary factors in prokaryote adaptive immunity.}, }
@article {pmid39718830, year = {2024}, author = {Kicsiny, R and Hufnagel, L and Lóczi, L and Székely, L and Varga, Z}, title = {Modeling the Mutation and Competition of Certain Nutrient-Producing Protocells by Means of Specific Turing Machines.}, journal = {Artificial life}, volume = {31}, number = {1}, pages = {2-30}, doi = {10.1162/artl_a_00463}, pmid = {39718830}, issn = {1530-9185}, mesh = {*Mutation ; *Artificial Cells/metabolism ; *Models, Biological ; *Nutrients/metabolism ; }, abstract = {It is very important to model the behavior of protocells as basic lifelike artificial organisms more and more accurately from the level of genomes to the level of populations. A better understanding of basic protocell communities may help us in describing more complex ecological systems accurately. In this article, we propose a new comprehensive, bilevel mathematical model of a community of three protocell species (one generalist and two specialists). The aim is to achieve a model that is as basic/fundamental as possible while already displaying mutation, selection, and complex population dynamics phenomena (like competitive exclusion and keystone species). At the microlevel of genetic codes, the protocells and their mutations are modeled with Turing machines (TMs). The specialists arise from the generalist by means of mutation. Then the species are put into a common habitat, where, at the macrolevel of populations, they have to compete for the available nutrients, a part of which they themselves can produce. Because of different kinds of mutations, the running times of the species as TMs (algorithms) are different. This feature is passed on to the macrolevel as different reproduction times. At the macrolevel, a discrete-time dynamic model describes the competition. The model displays complex lifelike behavior known from population ecology, including the so-called competitive exclusion principle and the effect of keystone species. In future works, the bilevel model will have a good chance of serving as a simple and useful tool for studying more lifelike phenomena (like evolution) in their pure/abstract form.}, }
@article {pmid39717656, year = {2024}, author = {Nguyen, TTT and de A Santiago, ALCM and Hallsworth, JE and Cordeiro, TRL and Voigt, K and Kirk, PM and Crous, PW and Júnior, MAM and Elsztein, C and Lee, HB}, title = {New Mucorales from opposite ends of the world.}, journal = {Studies in mycology}, volume = {109}, number = {}, pages = {273-321}, pmid = {39717656}, issn = {0166-0616}, abstract = {The Mucorales is a group of ancient fungi with global distribution. In the current study we accessed mucoralean fungi isolated from two countries on opposite sides of the Earth and in different hemispheres: South Korea and Brazil. Mucorales isolates were obtained from freshwater, soil, invertebrates, and fruit seeds and identified using phenotypic techniques combined with the DNA sequence data. These analyses revealed 15 new species including one that we affiliated to a newly proposed genus, Neofennellomyces. Names proposed for these 15 new species are Absidia cheongyangensis, A. fluvii, A. kunryangriensis, A. paracylindrospora, A. tarda, A. variiprojecta, A. variispora, Backusella varians, Mucor albicolonia, M. aurantiacus, M. cryophilus, M. glutinatus, M. paraorantomantidis, M. timomeni, and Neofennellomyces jeongsukae. Of these new species, 12 were isolated from South Korea: A. cheongyangensis, A. fluvii, A. kunryangriensis, A. paracylindrospora, B. varians, M. albicolonia, M. aurantiacus, M. cryophilus, M. glutinatus, M. paraorantomantidis, M. timomeni, and N. jeongsukae, and three from Brazil: A. tarda, A. variiprojecta, and A. variispora. Niche specificity of these fungi is discussed including newly recorded invertebrate hosts and a new geographic distribution for species of Backusella, Circinella, Cunninghamella, and Mucor. Given these findings, we provide an inventory of Mucorales. Taxonomic novelties: New genus: Neofennellomyces Hyang B. Lee &amp; T.T.T. Nguyen. New species: Absidia cheongyangensis Hyang B. Lee &amp; T.T.T. Nguyen, Absidia fluvii Hyang B. Lee, A.L. Santiago, P.M. Kirk, K. Voigt &amp; T.T.T. Nguyen, Absidia kunryangriensis Hyang B. Lee &amp; T.T.T. Nguyen, Absidia paracylindrospora Hyang B. Lee &amp; T.T.T. Nguyen, Absidia tarda T.R.L. Cordeiro, Hyang B. Lee &amp; A.L. Santiago, Absidia variiprojecta T.R.L. Cordeiro &amp; A.L. Santiago, Absidia variispora T.R.L. Cordeiro &amp; A.L. Santiago, Backusella varians Hyang B. Lee &amp; T.T.T. Nguyen, Mucor aurantiacus Hyang B. Lee &amp; T.T.T. Nguyen, Mucor cryophilus Hyang B. Lee &amp; T.T.T. Nguyen, Mucor albicolonia Hyang B. Lee &amp; T.T.T. Nguyen, Mucor glutinatus Hyang B. Lee &amp; T.T.T. Nguyen, Mucor paraorantomantidis Hyang B. Lee &amp; T.T.T. Nguyen, Mucor timomeni Hyang B. Lee &amp; T.T.T. Nguyen, Neofennellomyces jeongsukae Hyang B. Lee &amp; T.T.T. Nguyen. Citation: Nguyen TTT, de A. Santiago ALCM, Hallsworth JE, Cordeiro TRL, Voigt K, Kirk PM, Crous PW, Júnior MAM, Elsztein C, Lee HB (2024). New Mucorales from opposite ends of the world. Studies in Mycology 109: 273-321. doi: 10.3114/sim.2024.109.04.}, }
@article {pmid39717508, year = {2025}, author = {Wang, T and Campbell, C and Stockdale, AJ and Todd, S and McIntyre, K and Frankland, A and Jaworski, J and Glampson, B and Papadimitriou, D and Mercuri, L and Mayer, E and Jones, CR and Salih, H and Roadknight, G and Little, S and Noble, T and Várnai, KA and Davis, C and Heinson, AI and George, M and Borca, F and English, L and Romão, L and Ramlakhan, D and ,  and Woods, K and Davies, J and Nastouli, E and Khakoo, SI and Gelson, W and Cooke, GS and Barnes, E and Matthews, PC}, title = {Distinct virologic trajectories in chronic hepatitis B identify heterogeneity in response to nucleos(t)ide analogue therapy.}, journal = {JHEP reports : innovation in hepatology}, volume = {7}, number = {1}, pages = {101229}, pmid = {39717508}, issn = {2589-5559}, abstract = {BACKGROUND &amp; AIMS: The dynamics of HBV viral load (VL) in patients with chronic hepatitis B (CHB) on nucleos(t)ide analogue (NA) treatment and its relationship with liver disease are poorly understood. We aimed to study longitudinal VL patterns and their associations with CHB clinical outcomes.<br><br>METHODS: Utilising large scale, routinely collected electronic health records from six centres in England, collated by the National Institute for Health and Care Research Health Informatics Collaborative (NIHR HIC), we applied latent class mixed models to investigate VL trajectory patterns in adults receiving NA treatment. We assessed associations of VL trajectory with alanine transaminase, and with liver fibrosis/cirrhosis.<br><br>RESULTS: We retrieved data from 1,885 adults on NA treatment (median follow-up 6.2 years, IQR 3.7-9.3 years), with 21,691 VL measurements (median 10 per patient, IQR 5-17). Five VL classes were identified from the derivation cohort (n&#xa0;= 1,367, discrimination: 0.93, entropy: 0.90): class 1 'long term suppression' (n&#xa0;= 827, 60.5%), class 2 'timely virological suppression' (n&#xa0;= 254, 18.6%), class 3 'persistent moderate viraemia' (n&#xa0;= 140, 10.2%), class 4 'persistent high-level viraemia' (n&#xa0;= 44, 3.2%), and class 5 'slow virological suppression' (n&#xa0;= 102, 7.5%). The model demonstrated a discrimination of 0.93 and entropy of 0.88 for the validation cohort (n&#xa0;= 518). Alanine transaminase decreased variably over time in VL-suppressed groups (classes 1, 2, 5; all p <0.001), but did not significantly improve in those with persistent viraemia (classes 3, 4). Patients in class 5 had twofold increased hazards of fibrosis/cirrhosis compared with class 1 (adjusted hazard ratio, 2.00; 95% CI, 1.33-3.02).<br><br>CONCLUSIONS: Heterogeneity exists in virological response to NA therapy in CHB patients, with over 20% showing potentially suboptimal responses. Slow virological suppression is associated with liver disease progression.<br><br>IMPACT AND IMPLICATIONS: Treatment recommendations for people living with chronic hepatitis B virus (HBV) infection are becoming less stringent, meaning that more of the population will be eligible to receive therapy with nucleos(t)ide analogue agents. We explored outcomes of HBV treatment in a large UK dataset, describing different responses to treatment, and showing that the viral load is not completely suppressed after 1 year in about one in five cases, associated with an increased risk of liver complications. As treatment is rolled out more widely, patients and clinicians need to be aware of the potential for incomplete virologic responses. The findings can support the identification of high-risk individuals, improve early fibrosis and cirrhosis prediction, guide monitoring and preventive interventions, and support public health elimination goals.}, }
@article {pmid39716198, year = {2024}, author = {Mendoza, JN and Prūse, B and Ciriaco, A and Mendoza, A and Ciriaco, H and Buen, C and Pua, JJ and Primavera, F and Mattalia, G and Sõukand, R}, title = {Fishery and ecology-related knowledge about plants among fishing communities along Laguna Lake, Philippines.}, journal = {Journal of ethnobiology and ethnomedicine}, volume = {20}, number = {1}, pages = {108}, pmid = {39716198}, issn = {1746-4269}, mesh = {*Fisheries ; Philippines ; *Ethnobotany ; Humans ; *Knowledge ; *Conservation of Natural Resources ; *Lakes ; Ecosystem ; Fishes ; Animals ; Ecology ; Female ; Male ; Middle Aged ; Adult ; Plants ; }, abstract = {BACKGROUND: Ethnobotanical knowledge about plant roles in fisheries is crucial for sustainable resource management. Local ecological knowledge helps understand dynamics of the lake ecosystem. Fishers use plants based on availability and characteristics while adapting to the changes in the environment. Studying fishery related uses of plants and algae and the challenges interconnected with them from local perspectives can provide insights into their beneficial uses and impacts to the ecosystem.<br><br>METHODS: The study investigates the botanical knowledge of three fishing villages in Laguna Lake or Laguna de Bay (LB), Philippines, including Buhangin, Sampiruhan, and Mabato-Azufre, each with varying degrees of industrialization. The ethnobotanical study, which gathered 27 interviews between June 2022 and July 2024, included plant collection with the help of local collaborators, including local fishers as research guides.<br><br>RESULTS: Fishers in LB highlighted positive and negative plant-fishing interactions. The most frequently mentioned plant applications were fish habitat and fish hiding places. Fish food, spawning sites, conservation, and a number of challenges such as navigational concerns and aquaculture fish deaths had been previously reported in local use reports. The remaining observations provide new insights into plant-fishing interactions, including indicators of food quality and food sources for fish, the decrease in the action of waves, and how plants help in improving the quality of the water.<br><br>CONCLUSION: These results highlight that the knowledge of fishers regarding the ecosystem in which they conduct their fishing activities provides baseline information about the positive and negative relationships between plants and fishing activities in the region, which is vital for further understanding its biodiversity and ecosystem interactions. It is crucial to consider fisher knowledge and involve them as equal partners in conservation efforts of LB.}, }
@article {pmid39716000, year = {2025}, author = {Chunduri, JR and Sagar, SP}, title = {Insect Brain Proteomics: A Case Study of Periplaneta americana.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2884}, number = {}, pages = {99-118}, pmid = {39716000}, issn = {1940-6029}, mesh = {Animals ; *Periplaneta/metabolism ; *Proteomics/methods ; *Brain/metabolism ; *Insect Proteins/metabolism/analysis ; *Proteome ; Chromatography, Liquid/methods ; Mass Spectrometry/methods ; Computational Biology/methods ; }, abstract = {Insects are known invertebrate species with economic, ecological, pathological, and medicinal value, as well as closely associated with human populations. Entomophagy and entomotherapy are future promising prospects largely attributable to the abundant availability, high protein content, and climatic sustainability of insects. In particular, the insect brain is an important system with a secluded, compact, and protective exoskeleton. It is immunologically privileged and capable of producing a robust immune response against pathogens. It is also a source of materials that initiate key activity throughout the body. Proteomic interrogation of Periplaneta americana enables understanding the role of this insect in the fields of food and pharmacology. Proximate analyses of P. americana highlights its richness in proteins. Here we perform a simple proteomic analysis to study the brain proteome of P. americana. The processes applied during the study include gel-based isolation and separation of proteins, followed by NanoLC-MS (Orbitrap) analyses and bioinformatic interrogation of the data. The results demonstrated that this insect proteome comprises antimicrobial proteins, allergens, and proteins required for metabolic processes.}, }
@article {pmid39713561, year = {2024}, author = {Blair, ME and Noguera-Urbano, EA and Ochoa-Quintero, JM and Paz, A and Lopez-Gallego, C and Echeverry-Galvis, M&#xc1; and Zuloaga, J and Rodríguez, P and Lemus-Mejia, L and Ersts, P and López-Lozano, DF and Aiello-Lammens, ME and Arango, HM and Buitrago, L and Chang Triguero, S and Cruz-Rodríguez, CA and Díaz-Nieto, JF and Escobar, D and Grisales-Betancur, V and Johnson, BA and Kass, JM and Londoño-Murcia, MC and Merow, C and Muñoz-Rodríguez, CJ and Olaya-Rodríguez, MH and Parra, JL and Pinilla-Buitrago, GE and Roach, NS and Rojas-Soto, O and Roncancio-Duque, N and Suárez-Valencia, E and Urbina-Cardona, JN and Velásquez-Tibatá, J and Zapata-Martinez, CA and Anderson, RP}, title = {Software codesign between end users and developers to enhance utility for biodiversity conservation.}, journal = {Bioscience}, volume = {74}, number = {12}, pages = {867-873}, pmid = {39713561}, issn = {0006-3568}, abstract = {Creating software tools that address the needs of a wide range of decision-makers requires the inclusion of differing perspectives throughout the development process. Software tools for biodiversity conservation often fall short in this regard, partly because broad decision-maker needs may exceed the toolkits of single research groups or even institutions. We show that participatory, collaborative codesign enhances the utility of software tools for better decision-making in biodiversity conservation planning, as demonstrated by our experiences developing a set of integrated tools in Colombia. Specifically, we undertook an interdisciplinary, multi-institutional collaboration of ecological modelers, software engineers, and a diverse profile of potential end users, including decision-makers, conservation practitioners, and biodiversity experts. We leveraged and modified common paradigms of software production, including codesign and agile development, to facilitate collaboration through all stages (including conceptualization, development, testing, and feedback) to ensure the accessibility and applicability of the new tools to inform decision-making for biodiversity conservation planning.}, }
@article {pmid39710433, year = {2024}, author = {Yuan, H and Hicks, P and Ahmadian, M and Johnson, KA and Valtadoros, L and Krishnan, A}, title = {Annotating publicly-available samples and studies using interpretable modeling of unstructured metadata.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {1}, pages = {}, pmid = {39710433}, issn = {1477-4054}, support = {2328140//National Science Foundation/ ; }, mesh = {*Metadata ; *Natural Language Processing ; *Machine Learning ; Humans ; Computational Biology/methods ; Proteomics/methods ; Vocabulary, Controlled ; }, abstract = {Reusing massive collections of publicly available biomedical data can significantly impact knowledge discovery. However, these public samples and studies are typically described using unstructured plain text, hindering the findability and further reuse of the data. To combat this problem, we propose txt2onto 2.0, a general-purpose method based on natural language processing and machine learning for annotating biomedical unstructured metadata to controlled vocabularies of diseases and tissues. Compared to the previous version (txt2onto 1.0), which uses numerical embeddings as features, this new version uses words as features, resulting in improved interpretability and performance, especially when few positive training instances are available. Txt2onto 2.0 uses embeddings from a large language model during prediction to deal with unseen-yet-relevant words related to each disease and tissue term being predicted from the input text, thereby explaining the basis of every annotation. We demonstrate the generalizability of txt2onto 2.0 by accurately predicting disease annotations for studies from independent datasets, using proteomics and clinical trials as examples. Overall, our approach can annotate biomedical text regardless of experimental types or sources. Code, data, and trained models are available at https://github.com/krishnanlab/txt2onto2.0.}, }
@article {pmid39709508, year = {2024}, author = {De Wint, FC and Nicholson, S and Koid, QQ and Zahra, S and Chestney-Claassen, G and Seelan, JSS and Xie, J and Xing, S and Fayle, TM and Haelewaters, D}, title = {Introducing a global database of entomopathogenic fungi and their host associations.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1418}, pmid = {39709508}, issn = {2052-4463}, support = {2023 Student Mobility Grant to F.C.D.W.//EC | Erasmus+/ ; Senior Postdoctoral Fellowship 1206024N to D.H.//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; }, mesh = {Animals ; Biodiversity ; *Databases, Factual ; Host Specificity ; *Hypocreales ; *Insecta/microbiology ; *Internationality ; *Host Microbial Interactions ; }, abstract = {Pathogens significantly influence natural and agricultural ecosystems, playing a crucial role in the regulation of species populations and maintaining biodiversity. Entomopathogenic fungi (EF), particularly within the Hypocreales order, exemplify understudied pathogens that infect insects and other arthropods globally. Despite their ecological importance, comprehensive data on EF host specificity and geographical distribution are lacking. To address this, we present EntomoFun 1.0, an open-access database centralizing global records of EF-insect associations in Hypocreales. This database includes 1,791 records detailing EF species, insect host taxa, countries of occurrence, life stages of hosts, and information sources. EntomoFun 1.0 is constructed based on 600 literature sources, as well as herbarium specimens of the Royal Botanical Gardens, Kew. This database is intended to test hypotheses, identify knowledge gaps, and stimulate future research. Contents of the EntomoFun 1.0 database are visualized with a global map, taxonomic chart, bipartite community network, and graphs.}, }
@article {pmid39709502, year = {2024}, author = {Jakobsson, M and Mohammad, R and Karlsson, M and Salas-Romero, S and Vacek, F and Heinze, F and Bringensparr, C and Castro, CF and Johnson, P and Kinney, J and Cardigos, S and Bogonko, M and Accettella, D and Amblas, D and An, L and Bohan, A and Brandt, A and Bünz, S and Canals, M and Casamor, JL and Coakley, B and Cornish, N and Danielson, S and Demarte, M and Di Franco, D and Dickson, ML and Dorschel, B and Dowdeswell, JA and Dreutter, S and Fremand, AC and Hall, JK and Hally, B and Holland, D and Hong, JK and Ivaldi, R and Knutz, PC and Krawczyk, DW and Kristofferson, Y and Lastras, G and Leck, C and Lucchi, RG and Masetti, G and Morlighem, M and Muchowski, J and Nielsen, T and Noormets, R and Plaza-Faverola, A and Prescott, MM and Purser, A and Rasmussen, TL and Rebesco, M and Rignot, E and Rysgaard, S and Silyakova, A and Snoeijs-Leijonmalm, P and Sørensen, A and Straneo, F and Sutherland, DA and Tate, AJ and Travaglini, P and Trenholm, N and van Wijk, E and Wallace, L and Willis, JK and Wood, M and Zimmermann, M and Zinglersen, KB and Mayer, L}, title = {The International Bathymetric Chart of the Arctic Ocean Version 5.0.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1420}, pmid = {39709502}, issn = {2052-4463}, abstract = {Knowledge about seafloor depth, or bathymetry, is crucial for various marine activities, including scientific research, offshore industry, safety of navigation, and ocean exploration. Mapping the central Arctic Ocean is challenging due to the presence of perennial sea ice, which limits data collection to icebreakers, submarines, and drifting ice stations. The International Bathymetric Chart of the Arctic Ocean (IBCAO) was initiated in 1997 with the goal of updating the Arctic Ocean bathymetric portrayal. The project team has since released four versions, each improving resolution and accuracy. Here, we present IBCAO Version 5.0, which offers a resolution four times as high as Version 4.0, with 100 × 100 m grid cells compared to 200 × 200 m. Over 25% of the Arctic Ocean is now mapped with individual depth soundings, based on a criterion that considers water depth. Version 5.0 also represents significant advancements in data compilation and computing techniques. Despite these improvements, challenges such as sea-ice cover and political dynamics still hinder comprehensive mapping.}, }
@article {pmid39707199, year = {2024}, author = {Zhang, M and Sun, Y and Lan, Y and Cheng, L and Lv, Z and Han, M and Yang, L}, title = {Multiomics joint analysis reveals the potential mechanism of differences in the taproot thickening between cultivated ginseng and mountain-cultivated ginseng.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1228}, pmid = {39707199}, issn = {1471-2164}, support = {20230204001YY//the Key Research and Development Projects of Jilin Province Science and Technology Development Plan/ ; 20200504002YY//the Major Projects of Jilin Province Science and Technology Development Plan/ ; CARS-21//the National Modern Agricultural Industrial Technology System Fund Project/ ; }, mesh = {*Panax/genetics/growth &amp; development/metabolism ; *Plant Roots/genetics/growth &amp; development/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Transcriptome ; Metabolomics ; Starch/metabolism ; Sucrose/metabolism ; Phenotype ; Genomics ; Multiomics ; }, abstract = {Panax ginseng is an important medicinal plant in China and is classified into two types: cultivated ginseng (CFCG) and mountain-cultivated ginseng (MCG). The two types of genetic varieties are the same, but the growth environments and management practices are different, resulting in substantial differences in their taproot morphology. Currently, there is a paucity of research on the internal mechanisms that regulate the phenotypic differences between cultivated ginseng and mountain-cultivated ginseng. In this study, we explored the potential mechanisms underlying their phenotypic differences using transcriptomic and metabolomic techniques. The results indicate that the taproot thickening of CFCG was significantly greater than that of MCG. Compared with MCG-4, MCG-10, and MCG-18, the diameters of the taproots of CFCG-4 increased by 158.96, 81.57, and 43.21%, respectively. Additionally, the contents of sucrose and starch in the taproot, as well as TRA and DHZR, were markedly elevated. Transcriptome analysis revealed that compared with MCG of different age groups, genes associated with starch and sucrose metabolism pathways (PgSUS1, PgSPS1, PgSPS3, and PgglgC1) were significantly upregulated in CFCG-4, whereas genes involved in the phenylpropanoid biosynthesis pathway (PgPER3, PgPER51, and PgPER12) were significantly downregulated in CFCG-4. This imbalance in the metabolic pathways suggests that these genes play crucial roles in ginseng taproot thickening. PgbHLH130 and PgARF18 may be key regulators of transcriptional changes in these pathways. These findings elucidate the molecular mechanisms governing ginseng taproot thickening, and have important implications for enhancing the overall quality and value of ginseng.}, }
@article {pmid39705088, year = {2025}, author = {Deuker, A and Wittkugel, J and Dublin, Y and Braunstein, B and Rein, R and Davids, K and Vogt, T}, title = {Beyond the Pitch: Unveiling the Concave Hull as Soccer's Ecological Niche in Practice Design.}, journal = {Research quarterly for exercise and sport}, volume = {96}, number = {3}, pages = {463-474}, doi = {10.1080/02701367.2024.2434155}, pmid = {39705088}, issn = {2168-3824}, mesh = {*Soccer/physiology/psychology ; Humans ; *Athletic Performance/physiology/psychology ; Cross-Over Studies ; Geographic Information Systems ; Male ; Young Adult ; *Environment Design ; Adult ; }, abstract = {An ecological niche is a field in a landscape of affordances, rich in information inviting its inhabitants to develop functionality and effectiveness of their behavior. This idea means that, in sports like soccer, the playing area encapsulates an ecological niche, replete with affordances inviting collective and individual technical-tactical actions, contextualized with associated psychological and physical demands. To examine the co-adaptive relationships framing players' actions in their ecological niche, the present study employed a crossover design with repeated measures to compare the players' transactions within 11 vs. 11 training games across four different field dimensions (from official size to a small-sided game). Player transactions with the performance environment were analyzed across 40 game sequences, using 10Hz GPS positional data. Metrics such as convex hull dimensions, field occupancy, and proximity to opponents were derived. Repeated-measures ANOVA revealed significant differences between tendencies for forming synergies constrained by field dimensions scaling. When field size was reduced, the convex hull dimension significantly decreased. Additionally, relative field occupancy and distance to nearest opponent exhibited significant changes, especially when contrasted with performance transactions emerging on the official size field. These observations underline the essential functional relationship between the playing field dimension and emergent player actions. Such findings underscore the need for soccer coaches and training designers to integrate the specificity of field dimension scaling in training designs to represent competitive performance contexts. Data analytics deriving spatial constraint values from competitive matches may help researchers and practitioners improve task representativeness in practice and performance preparation, supporting the optimality of training niches in soccer.}, }
@article {pmid39703500, year = {2024}, author = {Townsend, HA and Rosenberger, KJ and Vanderlinden, LA and Inamo, J and Zhang, F}, title = {Evaluating methods for integrating single-cell data and genetics to understand inflammatory disease complexity.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1454263}, pmid = {39703500}, issn = {1664-3224}, support = {T15 LM009451/LM/NLM NIH HHS/United States ; }, mesh = {*Single-Cell Analysis/methods ; Humans ; *Genome-Wide Association Study ; Inflammation/genetics ; Arthritis, Rheumatoid/genetics/immunology ; Polymorphism, Single Nucleotide ; Genetic Predisposition to Disease ; Colitis, Ulcerative/genetics/immunology ; Algorithms ; Sequence Analysis, RNA/methods ; }, abstract = {BACKGROUND: Understanding genetic underpinnings of immune-mediated inflammatory diseases is crucial to improve treatments. Single-cell RNA sequencing (scRNA-seq) identifies cell states expanded in disease, but often overlooks genetic causality due to cost and small genotyping cohorts. Conversely, large genome-wide association studies (GWAS) are commonly accessible.<br><br>METHODS: We present a 3-step robust benchmarking analysis of integrating GWAS and scRNA-seq to identify genetically relevant cell states and genes in inflammatory diseases. First, we applied and compared the results of three recent algorithms, based on pathways (scGWAS), single-cell disease scores (scDRS), or both (scPagwas), according to accuracy/sensitivity and interpretability. While previous studies focused on coarse cell types, we used disease-specific, fine-grained single-cell atlases (183,742 and 228,211 cells) and GWAS data (Ns of 97,173 and 45,975) for rheumatoid arthritis (RA) and ulcerative colitis (UC). Second, given the lack of scRNA-seq for many diseases with GWAS, we further tested the tools' resolution limits by differentiating between similar diseases with only one fine-grained scRNA-seq atlas. Lastly, we provide a novel evaluation of noncoding SNP incorporation methods by testing which enabled the highest sensitivity/accuracy of known cell-state calls.<br><br>RESULTS: We first found that single-cell based tools scDRS and scPagwas called superior numbers of supported cell states that were overlooked by scGWAS. While scGWAS and scPagwas were advantageous for gene exploration, scDRS effectively accounted for batch effect and captured cellular heterogeneity of disease-relevance without single-cell genotyping. For noncoding SNP integration, we found a key trade-off between statistical power and confidence with positional (e.g. MAGMA) and non-positional approaches (e.g. chromatin-interaction, eQTL). Even when directly incorporating noncoding SNPs through 5' scRNA-seq measures of regulatory elements, non disease-specific atlases gave misleading results by not containing disease-tissue specific transcriptomic patterns. Despite this criticality of tissue-specific scRNA-seq, we showed that scDRS enabled deconvolution of two similar diseases with a single fine-grained scRNA-seq atlas and separate GWAS. Indeed, we identified supported and novel genetic-phenotype linkages separating RA and ankylosing spondylitis, and UC and crohn's disease. Overall, while noting evolving single-cell technologies, our study provides key findings for integrating expanding fine-grained scRNA-seq, GWAS, and noncoding SNP resources to unravel the complexities of inflammatory diseases.}, }
@article {pmid39701966, year = {2024}, author = {Oskolkov, N and Sandionigi, A and Götherström, A and Canini, F and Turchetti, B and Zucconi, L and Mimmo, T and Buzzini, P and Borruso, L}, title = {Unraveling the ancient fungal DNA from the Iceman gut.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1225}, pmid = {39701966}, issn = {1471-2164}, mesh = {*DNA, Ancient/analysis ; Humans ; *DNA, Fungal/genetics ; Metagenomics/methods ; Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract/microbiology ; Mummies/microbiology ; Computational Biology/methods ; Fungi/genetics/classification ; }, abstract = {BACKGROUND: Fungal DNA is rarely reported in metagenomic studies of ancient samples. Although fungi are essential for their interactions with all kingdoms of life, limited information is available about ancient fungi. Here, we explore the possibility of the presence of ancient fungal species in the gut of Ötzi, the Iceman, a naturally mummified human found in the Tyrolean Alps (border between Italy and Austria).<br><br>METHODS: A robust bioinformatic pipeline has been developed to detect and authenticate fungal ancient DNA (aDNA) from muscle, stomach, small intestine, and large intestine samples.<br><br>RESULTS: We revealed the presence of ancient DNA associated with Pseudogymnoascus genus, with P. destructans and P. verrucosus as possible species, which were abundant in the stomach and small intestine and absent in the large intestine and muscle samples.<br><br>CONCLUSION: We suggest that &#xd6;tzi may have consumed these fungi accidentally, likely in association with other elements of his diet, and they persisted in his gut after his death due to their adaptability to harsh and cold environments. This suggests the potential co-occurrence of ancient humans with opportunistic fungal species and proposes and validates a conservative bioinformatic approach for detecting and authenticating fungal aDNA in historical metagenomic samples.}, }
@article {pmid39700981, year = {2025}, author = {Wong, SY and Machado-de-Lima, NM and Wilkins, D and Zhang, E and Ferrari, BC}, title = {Fine-scale landscape heterogeneity drives microbial community structure at Robinson Ridge, East Antarctica.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {177964}, doi = {10.1016/j.scitotenv.2024.177964}, pmid = {39700981}, issn = {1879-1026}, mesh = {Antarctic Regions ; *Soil Microbiology ; *Microbiota ; *Environmental Monitoring ; Soil/chemistry ; Biodiversity ; Ecosystem ; }, abstract = {Life at Robinson Ridge, located in the Windmill Islands region of East Antarctica, is susceptible to a changing climate. At this site, responses of the vegetation communities and moss-beds have been well researched, but corresponding information for microbial counterparts is still lacking. To bridge this knowledge gap, we established baseline data for monitoring the environmental drivers shaping the soil microbial community on the local 'hillslope' scale. Using triplicate 300-m long transects encompassing a hillslope with wind-exposed arid soils near the top, and snowmelt-sustained-moss beds at the bottom, we assessed the fine-scale heterogeneity of the soil environmental and microbial properties. Moist, low-lying, and vegetated soils exhibited higher soil fertility and unique biodiversity, with taxa adapted to thrive in moist conditions (i.e., Tardigrada, Phragmoplastophyta, Chloroflexi) and those that have previously demonstrated strong specificity for moss species (i.e., Fibrobacterota, Mucoromycota and Cyanobacteria) dominating. In contrast, elevated soils with limited moisture and nutrients were dominated by metabolically diverse phyla like Actinobacteriota and Ascomycota. Significant differences in microbial communities were observed at both hillslope (50-300 m) and fine spatial scales, as small as 0.1 m. Vertical heterogeneity was observed with higher abundances of Cyanobacteria and micro-algae in surfaces compared to subsoil, potentially indicating early biocrust formation. Stochastic and deterministic processes governing phylogenetic assembly were linked to soil positional groups and microbial domains rather than soil depth. Gradient Forest modeling identified critical environmental thresholds, such as ammonia, manganese, and sulphur, responsible for drastic community changes following level alterations. This reinforces the existence of strong niche preferences and distinct distribution patterns within the local microbial communities. This study highlights the need for finer-scale investigations considering site topography to better understand the relationship between environmental drivers and local microbiota. Ultimately, these insights enable us to understand environmental drivers and predict Antarctic ecosystem responses, helping safeguard this fragile environment.}, }
@article {pmid39700412, year = {2024}, author = {Duan, HN and Hearne, G and Polikar, R and Rosen, GL}, title = {The Naïve Bayes classifier++ for metagenomic taxonomic classification-query evaluation.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {1}, pages = {}, pmid = {39700412}, issn = {1367-4811}, support = {1936791//National Science Foundation/ ; }, mesh = {*Metagenomics/methods ; Bayes Theorem ; *Software ; Algorithms ; Databases, Genetic ; }, abstract = {MOTIVATION: This study examines the query performance of the NBC++ (Incremental Naive Bayes Classifier) program for variations in canonicality, k-mer size, databases, and input sample data size. We demonstrate that both NBC++ and Kraken2 are influenced by database depth, with macro measures improving as depth increases. However, fully capturing the diversity of life, especially viruses, remains a challenge.<br><br>RESULTS: NBC++ can competitively profile the superkingdom content of metagenomic samples using a small training database. NBC++ spends less time training and can use a fraction of the memory than Kraken2 but at the cost of long querying time. Major NBC++ enhancements include accommodating canonical k-mer storage (leading to significant storage savings) and adaptable and optimized memory allocation that accelerates query analysis and enables the software to be run on nearly any system. Additionally, the output now includes log-likelihood values for each training genome, providing users with valuable confidence information.<br><br>Source code and Dockerfile are available at http://github.com/EESI/Naive_Bayes.}, }
@article {pmid39695923, year = {2024}, author = {Zhang, Z and Li, Q and Li, H and Wei, S and Yu, W and Peng, Z and Wei, F and Zhou, W}, title = {Integrative multi-omics analysis reveals the contribution of neoVTX genes to venom diversity of Synanceia verrucosa.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1210}, pmid = {39695923}, issn = {1471-2164}, support = {2023YFF1304900//Ministry of Science and Technology of the People's Republic of China/ ; 2024A1515013196//Science and Technology Department of Guangdong Province/ ; SLYJ2023B4004//Guangdong Forestry Administration/ ; GML2020GD0804//PI Project of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; GML2022GD0804//PI Project of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; 32222014//National Natural Science Foundation of China/ ; 2021YFF0502804//Ministry of Science and Technology of China/ ; }, mesh = {Animals ; *Transcriptome ; Fish Venoms/genetics/chemistry ; Genomics/methods ; Proteomics ; Proteome ; Alternative Splicing ; Fishes/genetics ; Phylogeny ; Gene Expression Profiling ; Multiomics ; }, abstract = {BACKGROUND: Animal venom systems are considered as valuable model for investigating the molecular mechanisms underlying phenotypic evolution. Stonefish are the most venomous and dangerous fish because of severe human envenomation and occasionally fatalities, whereas the genomic background of their venom has not been fully explored compared with that in other venomous animals.<br><br>RESULTS: In this study, we followed modern venomic pipelines to decode the Synanceia verrucosa venom components. A catalog of 478 toxin genes was annotated based on our assembled chromosome-level genome. Integrative analysis of the high-quality genome, the transcriptome of the venom gland, and the proteome of crude venom revealed mechanisms underlying the venom complexity in S. verrucosa. Six tandem-duplicated neoVTX subunit genes were identified as the major source for the neoVTX protein production. Further isoform sequencing revealed massive alternative splicing events with a total of 411 isoforms demonstrated by the six genes, which further contributed to the venom diversity. We then characterized 12 dominantly expressed toxin genes in the venom gland, and 11 of which were evidenced to produce the venom protein components, with the neoVTX proteins as the most abundant. Other major venom proteins included a presumed CRVP, Kuntiz-type serine protease inhibitor, calglandulin protein, and hyaluronidase. Besides, a few of highly abundant non-toxin proteins were also characterized and they were hypothesized to function in housekeeping or hemostasis maintaining roles in the venom gland. Notably, gastrotropin like non-toxin proteins were the second highest abundant proteins in the venom, which have not been reported in other venomous animals and contribute to the unique venom properties of S. verrucosa.<br><br>CONCLUSIONS: The results identified the major venom composition of S. verrucosa, and highlighted the contribution of neoVTX genes to the diversity of venom composition through tandem-duplication and alternative splicing. The diverse neoVTX proteins in the venom as lethal particles are important for understanding the adaptive evolution of S. verrucosa. Further functional studies are encouraged to exploit the venom components of S. verrucosa for pharmaceutical innovation.}, }
@article {pmid39695260, year = {2024}, author = {Ma, X and Zheng, G and Xu, C and Moskal, LM and Gong, P and Guo, Q and Huang, H and Li, X and Liang, X and Pang, Y and Wang, C and Xie, H and Yu, B and Zhao, B and Zhou, Y}, title = {A global product of 150-m urban building height based on spaceborne lidar.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1387}, pmid = {39695260}, issn = {2052-4463}, support = {42171340//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Urban building height, as a fundamental 3D urban structural feature, has far-reaching applications. However, creating readily available datasets of recent urban building heights with fine spatial resolutions and global coverage remains a challenging task. Here, we provide a 150-m global urban building heights dataset around 2020 by combining the spaceborne lidar (Global Ecosystem Dynamics Investigation, GEDI), multi-sourced data (Landsat-8, Sentinel-2, and Sentinel-1), and topographic data. The validation results revealed that the GEDI-estimated building height samples were effective compared to the reference data (Pearson's r = 0.81, RMSE = 3.58 m). The mapping product also demonstrated good performance, as indicated by its strong correlation with the reference data (Pearson's r = 0.71, RMSE = 4.73 m). Compared with the currently existing datasets, it holds the ability to provide a spatial resolution (150 m) with a great level of inherent details about the spatial heterogeneity and flexibility of updating using the GEDI samples as inputs. This product will boost future urban studies across many fields, including environmental, ecological, and social sciences.}, }
@article {pmid39694720, year = {2025}, author = {Reynolds, SA and Beery, S and Burgess, N and Burgman, M and Butchart, SHM and Cooke, SJ and Coomes, D and Danielsen, F and Di Minin, E and Durán, AP and Gassert, F and Hinsley, A and Jaffer, S and Jones, JPG and Li, BV and Mac Aodha, O and Madhavapeddy, A and O'Donnell, SAL and Oxbury, WM and Peck, L and Pettorelli, N and Rodríguez, JP and Shuckburgh, E and Strassburg, B and Yamashita, H and Miao, Z and Sutherland, WJ}, title = {The potential for AI to revolutionize conservation: a horizon scan.}, journal = {Trends in ecology &amp; evolution}, volume = {40}, number = {2}, pages = {191-207}, doi = {10.1016/j.tree.2024.11.013}, pmid = {39694720}, issn = {1872-8383}, mesh = {*Conservation of Natural Resources/methods ; *Biodiversity ; *Artificial Intelligence ; Animals ; }, abstract = {Artificial Intelligence (AI) is an emerging tool that could be leveraged to identify the effective conservation solutions demanded by the urgent biodiversity crisis. We present the results of our horizon scan of AI applications likely to significantly benefit biological conservation. An international panel of conservation scientists and AI experts identified 21 key ideas. These included species recognition to uncover 'dark diversity', multimodal models to improve biodiversity loss predictions, monitoring wildlife trade, and addressing human-wildlife conflict. We consider the potential negative impacts of AI adoption, such as AI colonialism and loss of essential conservation skills, and suggest how the conservation field might adapt to harness the benefits of AI while mitigating its risks.}, }
@article {pmid39692459, year = {2024}, author = {Shitindo, M}, title = {Interactions between wild pigs and the spread of disease.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {39692459}, issn = {2050-084X}, mesh = {Animals ; *Animals, Wild ; Swine ; Swine Diseases ; Geographic Information Systems ; Humans ; }, abstract = {Tracking wild pigs with GPS devices reveals how their social interactions could influence the spread of disease, offering new strategies for protecting agriculture, wildlife, and human health.}, }
@article {pmid39691468, year = {2024}, author = {Winders, S and Yoo, L and Heitkemper, M and Kamp, K}, title = {Multilevel Factors and Sleep in Adults With Inflammatory Bowel Disease: A Qualitative Study.}, journal = {Crohn's &amp; colitis 360}, volume = {6}, number = {4}, pages = {otae075}, pmid = {39691468}, issn = {2631-827X}, abstract = {BACKGROUND: This study aimed to describe the patient-reported factors that impact sleep among individuals with inflammatory bowel disease (IBD), aligning with the Social Ecological Model of Sleep. This addresses the gap in IBD sleep research, which predominantly focuses on individual-level factors and their impact on sleep.<br><br>METHODS: Adults (ages 18-65) with IBD were recruited online through ResearchMatch in June 2023. Participants filled out survey questions on their demographic characteristics, health history, sleep, and IBD-related symptoms. Content analysis was conducted on 2 open-ended questions about factors that impacted their sleep.<br><br>RESULTS: This analysis included 163 adults with IBD (M&#x2005;=&#x2005;39 years of age, 76.7% White, 91.4% non-Hispanic or Latino, 66.9% female, and 83.4% active IBD) who answered open-ended questions with comments about their sleep. Most participants indicated an individual-level factor impacted their sleep quality (85.3%, n&#x2005;=&#x2005;139), categorized into 5 subthemes: Mental health, health, behavior and choices, physiology, and attitudes. Additionally, participants (43.6%, n&#x2005;=&#x2005;71) mentioned social-level factors divided into 7 subthemes: Family, work, home, neighborhood, social network, and school. A smaller group of participants (17.2%, n&#x2005;=&#x2005;28) mentioned societal-level factors designated into 4 subthemes: Natural environment and geography, technology, 24/7 society, and economics.<br><br>CONCLUSIONS: This study highlights the need for tailored sleep interventions for those with IBD that consider not only disease activity but also mental health, family, work, and the natural environment. IBD clinics should prioritize sleep health using an interdisciplinary approach to holistically address the unique needs of those with IBD.}, }
@article {pmid39689860, year = {2025}, author = {Wu, Z and Huang, Z and Tang, N and Wang, K and Bian, C and Li, D and Kuraki, V and Schmid, F}, title = {Research on Sports Injury Rehabilitation Detection Based on IoT Models for Digital Health Care.}, journal = {Big data}, volume = {13}, number = {2}, pages = {144-160}, doi = {10.1089/big.2023.0134}, pmid = {39689860}, issn = {2167-647X}, mesh = {Humans ; *Internet of Things ; *Athletic Injuries/rehabilitation/diagnosis ; Delivery of Health Care ; Telemedicine ; Digital Health ; }, abstract = {Physical therapists specializing in sports rehabilitation detection help injured athletes recover from their wounds and avoid further harm. Sports rehabilitators treat not just commonplace sports injuries but also work-related musculoskeletal injuries, discomfort, and disorders. Sensor-equipped Internet of Things (IoT) monitors the real-time location of medical equipment such as scooters, cardioverters, nebulizer treatments, oxygenation pumps, or other monitor gear. Analysis of medicine deployment across sites is possible in real time. Health care delivery based on digital technology to improve access, affordability, and sustainability of medical treatment is known as digital health care. The challenging characteristics of such sports injury rehabilitation for digital health care are playing position, game strategies, and cybersecurity. Hence, in this research, health care IoT-enabled body area networks (HIoT-BAN) have been designed to improve sports injury rehabilitation detection for digital health care. The health care sector may benefit significantly from IoT adoption since it allows for enhanced patient safety; health care investment management includes controlling the hospital's pharmaceutical stock and monitoring the heat and humidity levels. Digital health describes a group of programmers made to aid health care delivery, whether by assisting with clinical decision-making or streamlining back-end operations in health care institutions. A HIoT-BAN effectively predicts the rise in sports injury rehabilitation detection with faster digital health care based on IoT. The research concludes that the HIoT-BAN effectively indicates sports injury rehabilitation detection for digital health care. The experimental analysis of HIoT-BAN outperforms the IoT method in terms of performance, accuracy, prediction ratio, and mean square error rate.}, }
@article {pmid39689854, year = {2024}, author = {Radice, VZ and Hernández-Agreda, A and Pérez-Rosales, G and Booker, R and Bellworthy, J and Broadribb, M and Carpenter, GE and Diaz, C and Eckert, RJ and Foster, NL and Gijsbers, JC and Gress, E and Laverick, JH and Micaroni, V and Pierotti, M and Rouzé, H and Stevenson, A and Sturm, AB and Bongaerts, P}, title = {Recent trends and biases in mesophotic ecosystem research.}, journal = {Biology letters}, volume = {20}, number = {12}, pages = {20240465}, pmid = {39689854}, issn = {1744-957X}, mesh = {*Ecosystem ; Animals ; Oceans and Seas ; Research/trends ; Anthozoa/physiology ; Bias ; Databases, Factual ; }, abstract = {Mesophotic ecosystems (approx. 30-150 m) represent a significant proportion of the world's oceans yet have long remained understudied due to challenges in accessing these deeper depths. Owing to advances in underwater technologies and a growing scientific and management interest, there has been a major expansion in research of both (sub)tropical mesophotic coral ecosystems and temperate mesophotic ecosystems. Here, we characterize the recent global trends in mesophotic research through an updated release of the 'mesophotic.org' database (www.mesophotic.org) where we reviewed and catalogued 1500 scientific publications. In doing so, we shed light on four major research biases: a gross imbalance in (a) the geographical spread of research efforts, differences in (b) the focal depth range and (c) research fields associated with study organisms and research platforms, and (d) the lack of temporal studies. Overall, we are optimistic about the future of mesophotic research and hope that by highlighting current trends and imbalances, we can raise awareness and stimulate discussion on the future directions of this emerging field.}, }
@article {pmid39689059, year = {2024}, author = {Bernadou, A and Jeanson, R}, title = {Randomness as a driver of inactivity in social groups.}, journal = {PLoS computational biology}, volume = {20}, number = {12}, pages = {e1012668}, pmid = {39689059}, issn = {1553-7358}, mesh = {Animals ; *Ants/physiology ; Bees/physiology ; Behavior, Animal/physiology ; Computational Biology ; Computer Simulation ; Models, Biological ; *Social Behavior ; }, abstract = {Social insects, such as ants and bees, are known for their highly efficient and structured colonies. Division of labour, in which each member of the colony has a specific role, is considered to be one major driver of their ecological success. However, empirical evidence has accumulated showing that many workers, sometimes more than half, remain idle in insect societies. Several hypotheses have been put forward to explain these patterns, but none provides a consensual explanation. Task specialisation exploits inter-individual variations, which are mainly influenced by genetic factors beyond the control of the colony. As a result, individuals may also differ in the efficiency with which they perform tasks. In this context, we aimed to test the hypothesis that colonies generate a large number of individuals in order to recruit only the most efficient to perform tasks, at the cost of producing and maintaining a fraction of workers that remain inactive. We developed a model to explore the conditions under which variations in the scaling of workers' production and maintenance costs, along with activity costs, allow colonies to sustain a fraction of inactive workers. We sampled individual performances according to different random distributions in order to simulate the variability associated with worker efficiency. Our results show that the inactivity of part of the workforce can be beneficial for a wide range of parameters if it allows colonies to select the most efficient workers. In decentralised systems such as insect societies, we suggest that inactivity is a by-product of the random processes associated with the generation of individuals whose performance levels cannot be controlled.}, }
@article {pmid39688289, year = {2025}, author = {Bao, Y and Jia, F and Geng, Y and Song, G and Xu, R and Wang, H and Mu, Y and Tong, HHY and Zhang, F and Guo, J}, title = {Uncovering the Differed Susceptibility of Fusarium oxysporum (Fo32931 and FocII5) to Fungicide Phenamacril: From Computational and Experimental Perspectives.}, journal = {Journal of agricultural and food chemistry}, volume = {73}, number = {1}, pages = {189-201}, doi = {10.1021/acs.jafc.4c07865}, pmid = {39688289}, issn = {1520-5118}, mesh = {*Fusarium/drug effects/genetics/metabolism ; *Fungicides, Industrial/pharmacology/chemistry ; *Fungal Proteins/genetics/metabolism/chemistry ; *Drug Resistance, Fungal/genetics ; Plant Diseases/microbiology ; }, abstract = {Fo32931 and FoCII5 are two subtypes of Fusarium oxysporum (Fo), a pathogenic filamentous fungus. Phenamacril (PHA), a Fusarium-specific fungicide that targets myosin I, exhibits significant hyphal growth inhibition in Fo32931 but shows weak resistance in FocII5, despite only two amino acid differences in the PHA-binding pocket of myosin I. In this study, we aim to elucidate the molecular basis for the differential sensitivity ofF. oxysporum myosin I variants (FoMyoI[32931] and FoMyoI[cII5]) to phenamacril through computational methods and biochemical validation. The results suggest that phenamacril functions as an allosteric inhibitor for FoMyoI[32931], inhibiting the large oscillation of the converter lever domain (CLD) upon ATP binding and promoting the opening of the outer cleft, further impairing protein function. PHA significantly reduced the coupling between the CLD, especially the converter, and the catalytic center, diminishing the response of the CLD to the motor domain in FoMyoI[32931]. From the residue mutation experiment, we found that the S418T substitution in FoMyoI[cII5] is the key to the reduced phenamacril sensitivity of FocII5. According to the microscale thermophoresis (MST) assay and pocket conformation analysis, the S418T mutation disturbs the orientation of pocket residues, especially Lys537, leading to a looser pocket and reduced interaction between Lys537 and phenamacril, which lowers the binding affinity of FoMyoI[cII5] for phenamacril. These findings provide deeper insights into the reasons for the lower sensitivity of FoCII5 to phenamacril from both molecular and structural perspectives and will also guide the design of novel inhibitors against resistant Fusarium spp., like FoCII5.}, }
@article {pmid39684926, year = {2024}, author = {Liu, R and Zhang, P and Bai, J and Zhong, Z and Shan, Y and Cheng, Z and Zhang, Q and Guo, Q and Zhang, H and Zhang, B}, title = {Integrated Transcriptomic and Proteomic Analyses of Antler Growth and Ossification Mechanisms.}, journal = {International journal of molecular sciences}, volume = {25}, number = {23}, pages = {}, pmid = {39684926}, issn = {1422-0067}, support = {23CB063 and 24CE-BGS-09//Beijing Academy of Science and Technology Financial Support Projects/ ; }, mesh = {*Antlers/growth &amp; development/metabolism ; Animals ; *Osteogenesis/genetics ; *Deer/genetics/growth &amp; development ; *Transcriptome ; *Proteomics/methods ; Proteome/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Computational Biology/methods ; }, abstract = {Antlers are the sole mammalian organs capable of continuous regeneration. This distinctive feature has evolved into various biomedical models. Research on mechanisms of antler growth, development, and ossification provides valuable insights for limb regeneration, cartilage-related diseases, and cancer mechanisms. Here, ribonucleic acid sequencing (RNA-seq) and four-dimensional data-independent acquisition (4D DIA) technologies were employed to examine gene and protein expression differences among four tissue layers of the Chinese milu deer antler: reserve mesenchyme (RM), precartilage (PC), transition zone (TZ), cartilage (CA). Overall, 4611 differentially expressed genes (DEGs) and 2388 differentially expressed proteins (DEPs) were identified in the transcriptome and proteome, respectively. Among the 828 DEGs common to both omics approaches, genes from the collagen, integrin, and solute carrier families, and signaling molecules were emphasized for their roles in the regulation of antler growth, development, and ossification. Bioinformatics analysis revealed that in addition to being regulated by vascular and nerve regeneration pathways, antler growth and development are significantly influenced by numerous cancer-related signaling pathways. This indicates that antler growth mechanisms may be similar to those of cancer cell proliferation and development. This study lays a foundation for future research on the mechanisms underlying the rapid growth and ossification of antlers.}, }
@article {pmid39684378, year = {2024}, author = {Zhang, KL and Leng, YN and Hao, RR and Zhang, WY and Li, HF and Chen, MX and Zhu, FY}, title = {Adaptation of High-Altitude Plants to Harsh Environments: Application of Phenotypic-Variation-Related Methods and Multi-Omics Techniques.}, journal = {International journal of molecular sciences}, volume = {25}, number = {23}, pages = {}, pmid = {39684378}, issn = {1422-0067}, support = {KYCX24_1376//Postgraduate Research &amp; Practice Innovation Program of Jiangsu Province/ ; 2023ZD0405602//STI 2030&#xff0d;Major Projects/ ; CX (21)2023//Jiangsu Agricultural Science and Technology Innovation Fund/ ; BK20240668//Basic Research Program of Jiangsu Province/ ; }, mesh = {*Altitude ; *Metabolomics/methods ; *Plants/metabolism/genetics ; *Proteomics/methods ; *Adaptation, Physiological ; *Genomics/methods ; *Phenotype ; Plant Physiological Phenomena ; Acclimatization ; Transcriptome ; Multiomics ; }, abstract = {High-altitude plants face extreme environments such as low temperature, low oxygen, low nutrient levels, and strong ultraviolet radiation, causing them to adopt complex adaptation mechanisms. Phenotypic variation is the core manifestation of ecological adaptation and evolution. Many plants have developed a series of adaptive strategies through long-term natural selection and evolution, enabling them to survive and reproduce under such harsh conditions. This article reviews the techniques and methods used in recent years to study the adaptive evolution of high-altitude plants, including transplantation techniques, genomics, transcriptomics, proteomics, and metabolomics techniques, and their applications in high-altitude plant adaptive evolution. Transplantation technology focuses on phenotypic variation, which refers to natural variations in morphological, physiological, and biochemical characteristics, exploring their key roles in nutrient utilization, photosynthesis optimization, and stress-resistance protection. Multiple omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, have revealed genes, regulatory pathways, and metabolic networks associated with phenotypic variations at the genetic and molecular levels. At the same time, the limitations and deficiencies of current technologies used to study plant adaptation to high-altitude environments were discussed. In addition, we propose future improvements to existing technologies and advocate for the integration of different technologies at multiple levels to study the molecular mechanisms of plant adaptation to high-altitude environments, thus providing insights for future research in this field.}, }
@article {pmid39683090, year = {2024}, author = {Chaligava, O and Zinicovscaia, I and Peshkova, A and Yushin, N and Frontasyeva, M and Vergel, K and Nurkassimova, M and Cepoi, L}, title = {Major and Trace Airborne Elements and Ecological Risk Assessment: Georgia Moss Survey 2019-2023.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {23}, pages = {}, pmid = {39683090}, issn = {2223-7747}, abstract = {The study, carried out as part of the International Cooperative Program on Effects of Air Pollution on Natural Vegetation and Crops, involved collecting 95 moss samples across the territory of Georgia during the period from 2019 to 2023. Primarily samples of Hypnum cupressiforme were selected, with supplementary samples of Abietinella abietina, Pleurozium schreberi, and Hylocomium splendens in cases of the former's absence. The content of 14 elements (Al, Ba, Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb, S, Sr, V, and Zn) was detected using Inductively Coupled Plasma Atomic Emission Spectroscopy (ICP-AES), while the Hg content was determined using a Direct Mercury Analyzer. To identify any relationships between chemical elements and to depict their sources, multivariate statistics was applied. Principal component analysis identified three main components: PC1 (geogenic, 43.4%), PC2 (anthropogenic, 13.3%), and PC3 (local anomalies, 8.5%). The results were compared with the first moss survey conducted in Georgia in the period from 2014 to 2017, offering insights into temporal trends of air quality. Utilizing GIS, a spatial map illustrating pollution levels across Georgia, based on the Pollution Load Index, was generated. The Potential Environmental Risk Index emphasized significant risks associated with mercury and cadmium at several locations. The study highlights the utility of moss biomonitoring in assessing air pollution and identifying hotspots of contamination. The findings from this study could be beneficial for future biomonitoring research in areas with varying physical and geographical conditions.}, }
@article {pmid39679384, year = {2024}, author = {Khosravi, M and Mojtabaeian, SM and Sarvestani, MA}, title = {A Systematic Review on the Outcomes of Climate Change in the Middle-Eastern Countries: The Catastrophes of Yemen and Syria.}, journal = {Environmental health insights}, volume = {18}, number = {}, pages = {11786302241302270}, pmid = {39679384}, issn = {1178-6302}, abstract = {The Middle East is facing serious climate change challenges, rendering it as one of the most affected regions worldwide. This paper aimed to investigate the outcomes of climate change in the Middle East. In 2024, a qualitative study was conducted employing a methodology that integrated systematic review for data collection and thematic analysis for data analysis. Such integration of the approaches provided valuable insights into the findings within the literature in a comprehensive and categorized format. PubMed, Scopus, ProQuest, and the Cochrane Database of Systematic Reviews were searched for relevant studies published between 2000 and 2024. The quality of these studies was assessed using the AACODS (Accuracy, Coverage, Objectivity, Date, Significance) checklist. The data extracted from the included studies underwent a thematic analysis utilizing Braun and Clarke's methodology. After completing the screening process, a total of 93 papers were deemed suitable for inclusion in the study. The quality assessment of these selected studies demonstrated a notably high standard, particularly in terms of authority, accuracy, coverage, objectivity, and significance. Moreover, minimal levels of bias were observed within the included studies. Subsequent thematic analysis of the findings from the systematic review identified 6 overarching themes: "Human Health Outcomes," "Animal Health Outcomes," "Plant Health Outcomes," "Ecological Outcomes," "Economic Outcomes," and "Political Outcomes." The study revealed ecological outcomes as the most prevalent consequences of climate change in the Middle East, including alterations in habitat distribution, temperature increase, water scarcity, and more. The outcomes seemed to be interconnected, exacerbating each other. Yemen and Syria had faced severe consequences, leading to political unrest and humanitarian crises in which Yemen ranking among the most water-stressed nations globally, while Syria contending with millions of displaced individuals living in dire conditions.}, }
@article {pmid39675288, year = {2025}, author = {Mu, X and Chen, C and Fan, Q and Zhang, W and Liu, F and Guo, J and Qi, W and Liu, H}, title = {Removal and ecological impact of sulfamethoxazole and N-acetyl sulfamethoxazole in mesocosmic wetlands dominated by submerged plants: Plant tolerance, microbial response, and nitrogen transformation.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {178034}, doi = {10.1016/j.scitotenv.2024.178034}, pmid = {39675288}, issn = {1879-1026}, mesh = {*Wetlands ; *Sulfamethoxazole/metabolism/analysis ; *Water Pollutants, Chemical/metabolism/analysis ; Nitrogen/metabolism ; Biodegradation, Environmental ; *Waste Disposal, Fluid/methods ; }, abstract = {Sulfamethoxazole (SMX) and its human metabolite N-acetylsulfamethoxazole (N-SMX) are frequently detected in aquatic environments, posing potential threats to freshwater ecosystem health. Constructed wetlands are pivotal for wastewater treatment, with plant species serving as key determinants of pollutant removal efficiency. In this study, wetlands dominated by three submerged plants (Myriophyllum verticillatum, Vallisneria spiralis, Hydrilla verticillata) were respectively constructed to investigate the removal of SMX and N-SMX, and the impact on wetland ecology regarding plant tolerance, microbial response, and nitrogen transformation. Results showed that wetlands removed N-SMX (82.3-99.8 %) more effectively than SMX (54.3-80.2 %), with the wetland dominated by Myriophyllum verticillatum showing the highest removal efficiency. However, high concentrations (5 mg/L) of SMX and N-SMX significantly reduced NH4[+]-N and TN removal (p < 0.05), accompanied by shifts in microbial communities, especially a decreased abundance of Proteobacteria and key nitrogen-transforming genes. A total of 22 different ARGs (antibiotic resistance genes) were detected. SMX significantly increased the relative abundance of sulfonamide resistance genes (sul1, sul2) (p < 0.05), while major denitrifying genera, such as Thiobacillus, which were not the primary hosts of these genes, showed a significant negative correlation with sul1 and sul2 (p < 0.05). This study provides a reference for ecological remediation of wetlands in response to antibiotic contamination.}, }
@article {pmid39656924, year = {2025}, author = {Bastian, FB and Cammarata, AB and Carsanaro, S and Detering, H and Huang, WT and Joye, S and Niknejad, A and Nyamari, M and Mendes de Farias, T and Moretti, S and Tzivanopoulou, M and Wollbrett, J and Robinson-Rechavi, M}, title = {Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools.}, journal = {Nucleic acids research}, volume = {53}, number = {D1}, pages = {D878-D885}, pmid = {39656924}, issn = {1362-4962}, support = {//University of Lausanne/ ; U01CA215010/GF/NIH HHS/United States ; //Service de la Sant&#xe9; Publique, Canton de Vaud/ ; U01 CA215010/CA/NCI NIH HHS/United States ; 31003A_173048/SNSF_/Swiss National Science Foundation/Switzerland ; 863410//Horizon 2020 - Research and Innovation Framework Programme/ ; //swissuniversities Programme Open Science/ ; //SIB Swiss Institute of Bioinformatics/ ; }, mesh = {Animals ; *Single-Cell Analysis/methods ; *RNA-Seq/methods ; *Software ; *Databases, Genetic ; Humans ; Internet ; Molecular Sequence Annotation ; Gene Expression Profiling/methods ; Data Curation ; Single-Cell Gene Expression Analysis ; }, abstract = {Bgee (https://www.bgee.org/) is a database to retrieve and compare gene expression patterns in multiple animal species. Expression data are integrated and made comparable between species thanks to consistent data annotation and processing. In the past years, we have integrated single-cell RNA-sequencing expression data into Bgee through careful curation of public datasets in multiple species. We have fully integrated this new technology along with the wealth of other data existing in Bgee. As a result, Bgee can now provide one definitive answer all the way to the cell resolution about a gene's expression pattern, comparable between species. We have updated our programmatic access tools to adapt to these changes accordingly. We have introduced a new web interface, providing detailed access to our annotations and expression data. It enables users to retrieve data, e.g. for specific organs, cell types or developmental stages, and leverages ontology reasoning to build powerful queries. Finally, we have expanded our species count from 29 to 52, emphasizing fish species critical for vertebrate genome studies, species of agronomic and veterinary importance and nonhuman primates.}, }
@article {pmid39656857, year = {2024}, author = {Alvarado, M and Gómez-Navajas, JA and Blázquez-Muñoz, MT and Gómez-Molero, E and Fernández-Sánchez, S and Eraso, E and Munro, CA and Valentín, E and Mateo, E and de Groot, PWJ}, title = {The good, the bad, and the hazardous: comparative genomic analysis unveils cell wall features in the pathogen Candidozyma auris typical for both baker's yeast and Candida.}, journal = {FEMS yeast research}, volume = {24}, number = {}, pages = {}, pmid = {39656857}, issn = {1567-1364}, support = {PID2020-117983RB-I00//Agencia Estatal de Investigaci&#xf3;n/ ; SBPLY/23/180225/000029//UCLM/ ; //European Regional Development Fund/ ; JDC2023-051226-I//European Social Fund Plus/ ; }, mesh = {*Cell Wall/metabolism ; *Saccharomyces cerevisiae/genetics/metabolism ; Computational Biology ; Genomics ; Candida auris/genetics/metabolism/drug effects ; beta-Glucans/metabolism ; Genome, Fungal ; Fungal Proteins/genetics/metabolism ; Glycosylphosphatidylinositols/metabolism/genetics ; Candida albicans/genetics/pathogenicity ; Candida/genetics/metabolism/pathogenicity ; }, abstract = {The drug-resistant pathogenic yeast Candidozyma auris (formerly named Candida auris) is considered a critical health problem of global importance. As the cell wall plays a crucial role in pathobiology, here we performed a detailed bioinformatic analysis of its biosynthesis in C. auris and related Candidozyma haemuli complex species using Candida albicans and Saccharomyces cerevisiae as references. Our data indicate that the cell wall architecture described for these reference yeasts is largely conserved in Candidozyma spp.; however, expansions or reductions in gene families point to subtle alterations, particularly with respect to β--1,3--glucan synthesis and remodeling, phosphomannosylation, β-mannosylation, and glycosylphosphatidylinositol (GPI) proteins. In several aspects, C. auris holds a position in between C. albicans and S. cerevisiae, consistent with being classified in a separate genus. Strikingly, among the identified putative GPI proteins in C. auris are adhesins typical for both Candida (Als and Hyr/Iff) and Saccharomyces (Flo11 and Flo5-like flocculins). Further, 26 putative C. auris GPI proteins lack homologs in Candida genus species. Phenotypic analysis of one such gene, QG37_05701, showed mild phenotypes implicating a role associated with cell wall β-1,3-glucan. Altogether, our study uncovered a wealth of information relevant for the pathogenicity of C. auris as well as targets for follow-up studies.}, }
@article {pmid39671935, year = {2025}, author = {Paulukonis, EA and Purucker, ST}, title = {Spatiotemporally derived agricultural field delineations for species effects assessments and environmental decision support.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {177967}, doi = {10.1016/j.scitotenv.2024.177967}, pmid = {39671935}, issn = {1879-1026}, mesh = {*Agriculture/methods ; *Environmental Monitoring/methods ; Pesticides ; Risk Assessment/methods ; *Decision Support Techniques ; Crops, Agricultural ; United States ; Geographic Information Systems ; Endangered Species ; }, abstract = {Rural landscapes are strongly defined by the spatial distribution of agricultural fields. GIS layers that capture this information have much utility in many decision support contexts, particularly with regards to the intersection of agricultural pesticide use and endangered species habitat. The United States Department of Agriculture's Cropland Data Layer (CDL) is a georeferenced, annual resource that often serves a crucial role in pesticide risk-related decision support applications. However, CDL agriculture timeseries data are not mapped to explicit field boundaries, contributing to increased uncertainty regarding differentiated crop type spatial homogeneity and geographic extent, inherently adding complexity to multi-temporal crop monitoring and analyses efforts. We describe the development and testing of an approach for field delineation based on timeseries information from the 2008-2021 CDL at spatial scales relevant for endangered species risk assessment. We validate and test the approach against quantitative crop information and contextualize the outputs as part of a case study reconstructing past agricultural pesticide exposures to non-target species to demonstrate the utility of the method for ecological risk assessment decision support. The approach resulted in delineated field unit boundaries that effectively incorporated the unmodified CDL crop type generalized spatial distribution patterns; derived metrics closely corresponded with reported crop metrics for landscapes with proportionally significant agriculture use. When modified to reflect areas of mixed/small crop acreages, the method can provide a useful framework for large-scale field delineation of the CDL, which can complement ongoing environmental risk assessment and conservation efforts in agricultural landscapes.}, }
@article {pmid39671449, year = {2024}, author = {Celiker, E and Woodrow, C and Guadayol, &#xd2; and Davranoglou, LR and Schlepütz, CM and Mortimer, B and Taylor, GK and Humphries, S and Montealegre-Z, F}, title = {Mechanical network equivalence between the katydid and mammalian inner ears.}, journal = {PLoS computational biology}, volume = {20}, number = {12}, pages = {e1012641}, pmid = {39671449}, issn = {1553-7358}, mesh = {Animals ; *Ear, Inner/anatomy &amp; histology/physiology ; *Mammals/physiology ; *Hearing/physiology ; Computer Simulation ; Insecta/physiology ; Computational Biology ; Models, Biological ; Cochlea/physiology/anatomy &amp; histology ; X-Ray Microtomography ; }, abstract = {Mammalian hearing operates on three basic steps: 1) sound capturing, 2) impedance conversion, and 3) frequency analysis. While these canonical steps are vital for acoustic communication and survival in mammals, they are not unique to them. An equivalent mechanism has been described for katydids (Insecta), and it is unique to this group among invertebrates. The katydid inner ear resembles an uncoiled cochlea, and has a length less than 1 mm. Their inner ears contain the crista acustica, which holds tonotopically arranged sensory cells for frequency mapping via travelling waves. The crista acustica is located on a curved triangular surface formed by the dorsal wall of the ear canal. While empirical recordings show tonotopic vibrations in the katydid inner ear for frequency analysis, the biophysical mechanism leading to tonotopy remains elusive due to the small size and complexity of the hearing organ. In this study, robust numerical simulations are developed for an in silico investigation of this process. Simulations are based on the precise katydid inner ear geometry obtained by synchrotron-based micro-computed tomography, and empirically determined inner ear fluid properties for an accurate representation of the underlying mechanism. We demonstrate that the triangular structure below the hearing organ drives the tonotopy and travelling waves in the inner ear, and thus has an equivalent role to the mammalian basilar membrane. This reveals a stronger analogy between the inner ear basic mechanical networks of two organisms with ancient evolutionary differences and independent phylogenetic histories.}, }
@article {pmid39671336, year = {2024}, author = {Karim, AAJ and Mahmud, MZ and Khan, R}, title = {Advanced vision transformers and open-set learning for robust mosquito classification: A novel approach to entomological studies.}, journal = {PLoS computational biology}, volume = {20}, number = {12}, pages = {e1012654}, pmid = {39671336}, issn = {1553-7358}, mesh = {Animals ; *Culicidae/classification ; *Deep Learning ; *Computational Biology/methods ; Entomology/methods ; Mosquito Vectors/classification ; Humans ; Algorithms ; Neural Networks, Computer ; }, abstract = {Mosquito-related diseases pose a significant threat to global public health, necessitating efficient and accurate mosquito classification for effective surveillance and control. This work presents an innovative approach to mosquito classification by leveraging state-of-the-art vision transformers and open-set learning techniques. A novel framework has been introduced that integrates Transformer-based deep learning models with comprehensive data augmentation and preprocessing methods, enabling robust and precise identification of ten mosquito species. The Swin Transformer model achieves the best performance for traditional closed-set learning with 99.60% accuracy and 0.996 F1 score. The lightweight MobileViT technique attains an almost equivalent accuracy of 98.90% with significantly reduced parameters and model complexities. Next, the applied deep learning models' adaptability and generalizability in a static environment have been enhanced by using new classes of data samples during the inference stage that have not been included in the training set. The proposed framework's ability to handle unseen classes like insects similar to mosquitoes, even humans, through open-set learning further enhances its practical applicability employing the OpenMax technique and Weibull distribution. The traditional CNN model, Xception, outperforms the latest transformer with higher accuracy and F1 score for open-set learning. The study's findings highlight the transformative potential of advanced deep-learning architectures in entomology, providing a strong groundwork for future research and development in mosquito surveillance and vector control. The implications of this work extend beyond mosquito classification, offering valuable insights for broader ecological and environmental monitoring applications.}, }
@article {pmid39670410, year = {2025}, author = {Alipio, K and García-Colón, J and Boscarino, N and Fox, K}, title = {Indigenous Data Sovereignty, Circular Systems, and Solarpunk Solutions for a Sustainable Future.}, journal = {Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing}, volume = {30}, number = {}, pages = {717-733}, doi = {10.1142/9789819807024_0054}, pmid = {39670410}, issn = {2335-6936}, mesh = {*Artificial Intelligence ; *Computational Biology ; Humans ; Cloud Computing/statistics &amp; numerical data ; Sustainable Development ; Indigenous Peoples/statistics &amp; numerical data ; Conservation of Natural Resources ; }, abstract = {Recent advancements in Artificial Intelligence (AI) and data center infrastructure have brought the global cloud computing market to the forefront of conversations about sustainability and energy use. Current policy and infrastructure for data centers prioritize economic gain and resource extraction, inherently unsustainable models which generate massive amounts of energy and heat waste. Our team proposes the formation of policy around earth-friendly computation practices rooted in Indigenous models of circular systems of sustainability. By looking to alternative systems of sustainability rooted in Indigenous values of aloha 'āina, or love for the land, we find examples of traditional ecological knowledge (TEK) that can be imagined alongside Solarpunk visions for a more sustainable future. One in which technology works with the environment, reusing electronic waste (e-waste) and improving data life cycles.}, }
@article {pmid39664868, year = {2024}, author = {Boyes, D and Zilli, A and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Grey Shoulder-knot, Lithophane ornitopus (Hufnagel, 1766).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {214}, pmid = {39664868}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Lithophane ornitopus (the Grey Shoulder-knot; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 508.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.33 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,397 protein coding genes.}, }
@article {pmid39664717, year = {2024}, author = {Baker, KS and Millerand, F}, title = {The Incremental Growth of Data Infrastructure in Ecology (1980-2020).}, journal = {Ecology and evolution}, volume = {14}, number = {12}, pages = {e70444}, pmid = {39664717}, issn = {2045-7758}, abstract = {After decades of growth, a research community's network information system and data repository were transformed to become a national data management office and a major element of data infrastructure for ecology and the environmental sciences. Developing functional data infrastructures is key to the support of ongoing Open Science and Open Data efforts. This example of data infrastructure growth contrasts with the top-down development typical of many digital initiatives. The trajectory of this network information system evolved within a collaborative, long-term ecological research community. This particular community is funded to conduct ecological research while collective data management is also carried out across its geographically dispersed study sites. From this longitudinal ethnography, we describe an Incremental Growth Model that includes a sequence of six relatively stable phases where each phase is initiated by a rapid response to a major pivotal event. Exploring these phases and the roles of data workers provides insight into major characteristics of digital growth. Further, a transformation in assumptions about data management is reported for each phase. Investigating the growth of a community information system over four decades as it becomes data infrastructure reveals details of its social, technical, and institutional dynamics. In addition to addressing how digital data infrastructure characteristics change, this study also considers when the growth of data infrastructure begins.}, }
@article {pmid39663400, year = {2025}, author = {Carter, KR and Cavaleri, MA and Atkin, OK and Bahar, NHA and Cheesman, AW and Choury, Z and Crous, KY and Doughty, CE and Dusenge, ME and Ely, KS and Evans, JR and Fonseca da Silva, J and Mau, AC and Medlyn, BE and Meir, P and Norby, RJ and Read, J and Reed, SC and Reich, PB and Rogers, A and Serbin, SP and Slot, M and Schwartz, EC and Tribuzy, ES and Uddling, J and Vårhammar, A and Walker, AP and Winter, K and Wood, TE and Wu, J}, title = {Photosynthetic responses to temperature across the tropics: a meta-analytic approach.}, journal = {Annals of botany}, volume = {135}, number = {7}, pages = {1293-1310}, pmid = {39663400}, issn = {1095-8290}, support = {DE-SC-0012000, DE-SC-0011806, DE-SC-0018942, 89243018S-SC-000014 and 89243018S-SC-000017//United States Department of Energy Office of Science/ ; 31922090//National Natural Science Foundation of China/ ; }, mesh = {*Photosynthesis/physiology ; Tropical Climate ; Temperature ; Climate Change ; Plant Leaves/physiology ; Carbon Dioxide/metabolism ; }, abstract = {BACKGROUND AND AIMS: Tropical forests exchange more carbon dioxide (CO2) with the atmosphere than any other terrestrial biome. Yet, uncertainty in the projected carbon balance over the next century is roughly three times greater for the tropics than other for ecosystems. Our limited knowledge of tropical plant physiological responses, including photosynthetic, to climate change is a substantial source of uncertainty in our ability to forecast the global terrestrial carbon sink.<br><br>METHODS: We used a meta-analytic approach, focusing on tropical photosynthetic temperature responses, to address this knowledge gap. Our dataset, gleaned from 18 independent studies, included leaf-level light-saturated photosynthetic (Asat) temperature responses from 108 woody species, with additional temperature parameters (35 species) and rates (250 species) of both maximum rates of electron transport (Jmax) and Rubisco carboxylation (Vcmax). We investigated how these parameters responded to mean annual temperature (MAT), temperature variability, aridity and elevation, as well as also how responses differed among successional strategy, leaf habit and light environment.<br><br>KEY RESULTS: Optimum temperatures for Asat (ToptA) and Jmax (ToptJ) increased with MAT but not for Vcmax (ToptV). Although photosynthetic rates were higher for 'light' than 'shaded' leaves, light conditions did not generate differences in temperature response parameters. ToptA did not differ with successional strategy, but early successional species had ~4 &#xb0;C wider thermal niches than mid/late species. Semi-deciduous species had ~1 &#xb0;C higher ToptA than broadleaf evergreen species. Most global modelling efforts consider all tropical forests as a single 'broadleaf evergreen' functional type, but our data show that tropical species with different leaf habits display distinct temperature responses that should be included in modelling efforts.<br><br>CONCLUSIONS: This novel research will inform modelling efforts to quantify tropical ecosystem carbon cycling and provide more accurate representations of how these key ecosystems will respond to altered temperature patterns in the face of climate warming.}, }
@article {pmid39660842, year = {2025}, author = {Xu, C and Song, LY and Li, J and Zhang, LD and Guo, ZJ and Ma, DN and Dai, MJ and Li, QH and Liu, JY and Zheng, HL}, title = {MangroveDB: A Comprehensive Online Database for Mangroves Based on Multi-Omics Data.}, journal = {Plant, cell &amp; environment}, volume = {48}, number = {5}, pages = {2950-2962}, doi = {10.1111/pce.15318}, pmid = {39660842}, issn = {1365-3040}, support = {//This work was supported by the Natural Science Foundation of China (NSFC) (32171740, 31870581); the National Key Research and Development Program of China (2017YFC0506102)/ ; }, mesh = {*Databases, Genetic ; Transcriptome/genetics ; Genomics ; *Wetlands ; Computational Biology/methods ; Gene Expression Profiling ; Internet ; *Avicennia/genetics ; Genome, Plant/genetics ; *Rhizophoraceae/genetics ; Multiomics ; }, abstract = {Mangroves are dominant flora of intertidal zones along tropical and subtropical coastline around the world that offer important ecological and economic value. Recently, the genomes of mangroves have been decoded, and massive omics data were generated and deposited in the public databases. Reanalysis of multi-omics data can provide new biological insights excluded in the original studies. However, the requirements for computational resource and lack of bioinformatics skill for experimental researchers limit the effective use of the original data. To fill this gap, we uniformly processed 942 transcriptome data, 386 whole-genome sequencing data, and provided 13 reference genomes and 40 reference transcriptomes for 53 mangroves. Finally, we built an interactive web-based database platform MangroveDB (https://github.com/Jasonxu0109/MangroveDB), which was designed to provide comprehensive gene expression datasets to facilitate their exploration and equipped with several online analysis tools, including principal components analysis, differential gene expression analysis, tissue-specific gene expression analysis, GO and KEGG enrichment analysis. MangroveDB not only provides query functions about genes annotation, but also supports some useful visualization functions for analysis results, such as volcano plot, heatmap, dotplot, PCA plot, bubble plot, population structure, and so on. In conclusion, MangroveDB is a valuable resource for the mangroves research community to efficiently use the massive public omics datasets.}, }
@article {pmid39660611, year = {2024}, author = {Mortzfeld, BM and Bhattarai, SK and Bucci, V}, title = {Novel class IIb microcins show activity against Gram-negative ESKAPE and plant pathogens.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {39660611}, issn = {2050-084X}, support = {R01 AG075283/AG/NIA NIH HHS/United States ; 457837076//Deutsche Forschungsgemeinschaft/ ; W81XWH2020013//Congressionally Directed Medical Research Programs/ ; 1R01AG075283-01A1/NH/NIH HHS/United States ; }, mesh = {*Bacteriocins/pharmacology/genetics/metabolism ; *Enterobacteriaceae/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology ; Gram-Negative Bacteria/drug effects/genetics ; Plant Diseases/microbiology ; Microbial Sensitivity Tests ; }, abstract = {Interspecies interactions involving direct competition via bacteriocin production play a vital role in shaping ecological dynamics within microbial ecosystems. For instance, the ribosomally produced siderophore bacteriocins, known as class IIb microcins, affect the colonization of host-associated pathogenic Enterobacteriaceae species. Notably, to date, only five of these antimicrobials have been identified, all derived from specific Escherichia coli and Klebsiella pneumoniae strains. We hypothesized that class IIb microcin production extends beyond these specific compounds and organisms. With a customized informatics-driven approach, screening bacterial genomes in public databases with BLAST and manual curation, we have discovered 12 previously unknown class IIb microcins in seven additional Enterobacteriaceae species, encompassing phytopathogens and environmental isolates. We introduce three novel clades of microcins (MccW, MccX, and MccZ), while also identifying eight new variants of the five known class IIb microcins. To validate their antimicrobial potential, we heterologously expressed these microcins in E. coli and demonstrated efficacy against a variety of bacterial isolates, including plant pathogens from the genera Brenneria, Gibbsiella, and Rahnella. Two newly discovered microcins exhibit activity against Gram-negative ESKAPE pathogens, i.e., Acinetobacter baumannii or Pseudomonas aeruginosa, providing the first evidence that class IIb microcins can target bacteria outside of the Enterobacteriaceae family. This study underscores that class IIb microcin genes are more prevalent in the microbial world than previously recognized and that synthetic hybrid microcins can be a viable tool to target clinically relevant drug-resistant pathogens. Our findings hold significant promise for the development of innovative engineered live biotherapeutic products tailored to combat these resilient bacteria.}, }
@article {pmid39657789, year = {2025}, author = {Zdouc, MM and Blin, K and Louwen, NLL and Navarro, J and Loureiro, C and Bader, CD and Bailey, CB and Barra, L and Booth, TJ and Bozhüyük, KAJ and Cediel-Becerra, JDD and Charlop-Powers, Z and Chevrette, MG and Chooi, YH and D'Agostino, PM and de Rond, T and Del Pup, E and Duncan, KR and Gu, W and Hanif, N and Helfrich, EJN and Jenner, M and Katsuyama, Y and Korenskaia, A and Krug, D and Libis, V and Lund, GA and Mantri, S and Morgan, KD and Owen, C and Phan, CS and Philmus, B and Reitz, ZL and Robinson, SL and Singh, KS and Teufel, R and Tong, Y and Tugizimana, F and Ulanova, D and Winter, JM and Aguilar, C and Akiyama, DY and Al-Salihi, SAA and Alanjary, M and Alberti, F and Aleti, G and Alharthi, SA and Rojo, MYA and Arishi, AA and Augustijn, HE and Avalon, NE and Avelar-Rivas, JA and Axt, KK and Barbieri, HB and Barbosa, JCJ and Barboza Segato, LG and Barrett, SE and Baunach, M and Beemelmanns, C and Beqaj, D and Berger, T and Bernaldo-Agüero, J and Bettenbühl, SM and Bielinski, VA and Biermann, F and Borges, RM and Borriss, R and Breitenbach, M and Bretscher, KM and Brigham, MW and Buedenbender, L and Bulcock, BW and Cano-Prieto, C and Capela, J and Carrion, VJ and Carter, RS and Castelo-Branco, R and Castro-Falcón, G and Chagas, FO and Charria-Girón, E and Chaudhri, AA and Chaudhry, V and Choi, H and Choi, Y and Choupannejad, R and Chromy, J and Donahey, MSC and Collemare, J and Connolly, JA and Creamer, KE and Crüsemann, M and Cruz, AA and Cumsille, A and Dallery, JF and Damas-Ramos, LC and Damiani, T and de Kruijff, M and Martín, BD and Sala, GD and Dillen, J and Doering, DT and Dommaraju, SR and Durusu, S and Egbert, S and Ellerhorst, M and Faussurier, B and Fetter, A and Feuermann, M and Fewer, DP and Foldi, J and Frediansyah, A and Garza, EA and Gavriilidou, A and Gentile, A and Gerke, J and Gerstmans, H and Gomez-Escribano, JP and González-Salazar, LA and Grayson, NE and Greco, C and Gomez, JEG and Guerra, S and Flores, SG and Gurevich, A and Gutiérrez-García, K and Hart, L and Haslinger, K and He, B and Hebra, T and Hemmann, JL and Hindra, H and Höing, L and Holland, DC and Holme, JE and Horch, T and Hrab, P and Hu, J and Huynh, TH and Hwang, JY and Iacovelli, R and Iftime, D and Iorio, M and Jayachandran, S and Jeong, E and Jing, J and Jung, JJ and Kakumu, Y and Kalkreuter, E and Kang, KB and Kang, S and Kim, W and Kim, GJ and Kim, H and Kim, HU and Klapper, M and Koetsier, RA and Kollten, C and Kovács, &#xc1;T and Kriukova, Y and Kubach, N and Kunjapur, AM and Kushnareva, AK and Kust, A and Lamber, J and Larralde, M and Larsen, NJ and Launay, AP and Le, NT and Lebeer, S and Lee, BT and Lee, K and Lev, KL and Li, SM and Li, YX and Licona-Cassani, C and Lien, A and Liu, J and Lopez, JAV and Machushynets, NV and Macias, MI and Mahmud, T and Maleckis, M and Martinez-Martinez, AM and Mast, Y and Maximo, MF and McBride, CM and McLellan, RM and Bhatt, KM and Melkonian, C and Merrild, A and Metsä-Ketelä, M and Mitchell, DA and Müller, AV and Nguyen, GS and Nguyen, HT and Niedermeyer, THJ and O'Hare, JH and Ossowicki, A and Ostash, BO and Otani, H and Padva, L and Paliyal, S and Pan, X and Panghal, M and Parade, DS and Park, J and Parra, J and Rubio, MP and Pham, HT and Pidot, SJ and Piel, J and Pourmohsenin, B and Rakhmanov, M and Ramesh, S and Rasmussen, MH and Rego, A and Reher, R and Rice, AJ and Rigolet, A and Romero-Otero, A and Rosas-Becerra, LR and Rosiles, PY and Rutz, A and Ryu, B and Sahadeo, LA and Saldanha, M and Salvi, L and Sánchez-Carvajal, E and Santos-Medellin, C and Sbaraini, N and Schoellhorn, SM and Schumm, C and Sehnal, L and Selem, N and Shah, AD and Shishido, TK and Sieber, S and Silviani, V and Singh, G and Singh, H and Sokolova, N and Sonnenschein, EC and Sosio, M and Sowa, ST and Steffen, K and Stegmann, E and Streiff, AB and Strüder, A and Surup, F and Svenningsen, T and Sweeney, D and Szenei, J and Tagirdzhanov, A and Tan, B and Tarnowski, MJ and Terlouw, BR and Rey, T and Thome, NU and Torres Ortega, LR and Tørring, T and Trindade, M and Truman, AW and Tvilum, M and Udwary, DW and Ulbricht, C and Vader, L and van Wezel, GP and Walmsley, M and Warnasinghe, R and Weddeling, HG and Weir, ANM and Williams, K and Williams, SE and Witte, TE and Rocca, SMW and Yamada, K and Yang, D and Yang, D and Yu, J and Zhou, Z and Ziemert, N and Zimmer, L and Zimmermann, A and Zimmermann, C and van der Hooft, JJJ and Linington, RG and Weber, T and Medema, MH}, title = {MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration.}, journal = {Nucleic acids research}, volume = {53}, number = {D1}, pages = {D678-D690}, pmid = {39657789}, issn = {1362-4962}, support = {//Conahcyt Mexico International PhD Studentship/ ; 32170080//National Natural Science Foundation of China/ ; 547394769//German Research Foundation/ ; 101066127//European Union/ ; NNF19SA0059360//Novo Nordisk Foundation INTERACT/ ; //Swedish Pharmaceutical Society PostDoc/ ; F32AT011475/AT/NCCIH NIH HHS/United States ; //Werner Siemens Foundation/ ; 027/E5/PG.02.00.PL/2024//Ministry of Education/ ; ANR-17-EUR-0007//EUR Saclay Plant Sciences-SPS/ ; PROYEXCEL_00012//Spanish "Junta de Andaluc&#xed;a"/ ; 1347411//CONAHCYT/ ; IM230100154//Australian Research Council Industry Fellowship/ ; 1229222N//Research Foundation-Flanders (FWO)/ ; R01 GM146224/GM/NIGMS NIH HHS/United States ; //Swiss Federal Government/ ; OSF.23.1.044//NWO Open Science Project 'BiG-CODEC'/ ; //NWO Merian/ ; R01 GM097142/GM/NIGMS NIH HHS/United States ; 024.004.014//MiCRop Consortium/ ; CZIF2022-007203//Chan Zuckerberg Initiative Foundation/ ; BB/T007222/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; DP230102668//Australian Research Council Discovery Project/ ; 57/0009//Ministry of Education and Science of Ukraine/ ; //Delta Stewardship Council Delta Science Program/ ; T32 GM136629/GM/NIGMS NIH HHS/United States ; //Basic Science Research Program/ ; R01-GM146224/GM/NIGMS NIH HHS/United States ; K12 GM068524/GM/NIGMS NIH HHS/United States ; AUFF-E-2022-9-42//AUFF/ ; 10062709//UK Innovation Funding Agency (UKRI)/ ; CBET-2032243//U.S. National Science Foundation/ ; //University of Illinois/ ; //HZI POF IV Cooperativity and Creativity Project Call/ ; //Horizon Europe Marie Sk&#x142;odowska-Curie Actions Postdoctoral Fellowship/ ; NE/T010959/1//Signals in the Soil/ ; ANR-24-CE20-7299-01//Agence Nationale de la Recherche/ ; DNRF137//Danish National Research Foundation/ ; OCENW.GROOT.2019.063//NWO-XL/ ; BB/V005723/2//BBSRC/ ; 101087181//EU/ ; 101000392//Horizon 2020/ ; 101072485//European Union's Horizon/ ; 10.55776/P 34036//Austrian Science Fund/ ; EP/X03142X/1//United Kingdom Research and Innovation/ ; 23/01956-2//S&#xe3;o Paulo Research Foundation/ ; //Department of Biotechnology/ ; 222676//USDA Evans-Allen Research/ ; //Saarland University/ ; 102022750//SINTEF/ ; //Hans Fischer Society/ ; 21K06336//KAKENHI/ ; CF22-1239//Carlsberg Foundation/ ; ANR-22-CE44-0011-01 UMISYN//Agence Nationale de la Recherche/ ; 495740318//German Research Foundation/ ; 802736//European Union Horizon 2020/ ; //Strathclyde University Global Research Scholarship/ ; NNF22OC0079021//Novo Nordisk Foundation Postdoctoral Fellowship/ ; 101055020-COMMUNITY//ERC Advanced/ ; 101099528//European Innovation Council/ ; GNT2021638//National Health and Medical Research Council/ ; 757173//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; NA22NOS4200050//NERRS/ ; 865738/ERC_/European Research Council/International ; DGE 2241144//NSF GRFP/ ; //National Research Fund of Ukraine/ ; RYC2020-029240-I//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; MR/V022334/1//UKRI Future Leaders Fellowship/ ; 102029187//SEP AGREE/ ; NNF22OC0078997//Novo Nodisk Foundation/ ; F31 ES036421/ES/NIEHS NIH HHS/United States ; KICH1.LWV04.21.013//NWO/ ; DM60066//Italian Ministry of Research/ ; 101117891-MeDiSyn//ERC Starting/ ; //European Union's Horizon 2020 Research/ ; R01 GM123998/GM/NIGMS NIH HHS/United States ; NRF 2018R1A5A2023127//Korea Government (MSIT)/ ; PS00349981//Fulbright/ ; NRF-2020R1A6A1A03044512//Korean Government (MSIT)/ ; 735867//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; 3141-00013A//Innovation Fund Denmark/ ; CFB 2.0//Novo Nordisk Foundation/ ; 21/07038-0//S&#xe3;o Paulo Research Foundation/ ; 2021YFA0909500//National Key Research and Development Program of China/ ; 101072485//European Union's Horizon Europe/ ; OCENW.XL21.XL21.088//NWO-XL/ ; //University Grants Commission/ ; //Natural Science and Research Council of Canada/ ; TTU 09.826//German Center for Infection Research/ ; //European Regional Development Fund/ ; 101072485//Horizon Europe Marie Sk&#x142;odowska-Curie/ ; DNRF137//Danish National Research Foundation CeMiSt/ ; BB/X010953/1//Growing Health Institute Strategic Programme/ ; BB/X01097X/1//BBSRC Institute Strategic Program/ ; 802736//European Union's Horizon 2020/ ; //Alexander von Humboldt-Stiftung/ ; //UK Government Department for Environment, Food &amp; Rural Affairs (DEFRA) Global Centre on Biodiversity for the Climate/ ; //Shanghai Pilot Program for Basic Research - Shanghai Jiao Tong University/ ; 102024676-14//POS BIOINFO 2024/ ; MR/W011247/1//UKRI Future Leaders Fellowship/ ; DGE 21-46756//National Science Foundation Graduate Research Fellowship/ ; 101106349//Marie Sklodowska-Curie/ ; T32-GM136629//Chemical-Biology Interface Training/ ; //University of Sydney/ ; 101000794//SECRETed EU Project Horizon 2020/ ; 2022R1C1C2004118//National Research Foundation of Korea/ ; //Indonesia Endowment Fund for Education Agency (LPDP)/ ; 101130799//European Union's Horizon/ ; 852600//Innovation Program ERC St/ ; //National Agri-Food Biotechnology Institute/ ; //German Academic Scholarship Foundation/ ; 205320_219638/SNSF_/Swiss National Science Foundation/Switzerland ; EXC-2124/1-09.029_0//Cluster of Excellence: Controlling Microbes to Fight Infection/ ; F32 AT011475/AT/NCCIH NIH HHS/United States ; 398967434-TRR 261//Deutsche Forschungsgemeinschaft/ ; 212747/SNSF_/Swiss National Science Foundation/Switzerland ; K445/2022//Leibniz Association/ ; NRF-RS-2024-00352229//Ministry of Science and ICT/ ; //Natural Sciences and Engineering Research Council of Canada Discovery/ ; VI.Veni.202.130//NWO Talent/ ; 106/IV/KS/11/2023//National Research and Innovation Agency/ ; T32GM136583/NH/NIH HHS/United States ; DE-AC02-05CH11231//U.S. Department of Energy/ ; }, mesh = {*Multigene Family ; *Databases, Genetic ; Biosynthetic Pathways/genetics ; Molecular Sequence Annotation ; Biological Products/metabolism/chemistry ; Data Curation ; }, abstract = {Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.}, }
@article {pmid39653494, year = {2024}, author = {Lee, HB and Nguyen, TTT and Noh, SJ and Kim, DH and Kang, KH and Kim, SJ and Kirk, PM and Avery, SV and Medina, A and Hallsworth, JE}, title = {Aspergillus ullungdoensis sp. nov., Penicillium jeongsukae sp. nov., and other fungi from Korea.}, journal = {Fungal biology}, volume = {128}, number = {8 Pt B}, pages = {2479-2492}, doi = {10.1016/j.funbio.2024.05.014}, pmid = {39653494}, issn = {1878-6146}, mesh = {Republic of Korea ; *Phylogeny ; *Penicillium/isolation &amp; purification/classification/genetics ; DNA, Fungal/genetics ; Soil Microbiology ; Aspergillus/isolation &amp; purification/classification/genetics ; Sequence Analysis, DNA ; Cluster Analysis ; DNA, Ribosomal Spacer/genetics/chemistry ; }, abstract = {Eurotiales fungi are thought to be distributed worldwide but there is a paucity of information about their occurrence on diverse substrates or hosts and at specific localities. Some of the Eurotiales, including Aspergillus and Penicillium species, produce an array of secondary metabolites of use for agricultural, medicinal, and pharmaceutical applications. Here, we carried out a survey of the Eurotiales in South Korea, focusing on soil, freshwater, and plants (dried persimmon fruits and seeds of Perilla frutescens, known commonly as shiso). We obtained 11 species that-based on morphology, physiology, and multi-locus (ITS, BenA, CaM, and RPB2) phylogenetic analyses-include two new species, Aspergillus ullungdoensis sp. nov. and Penicillium jeongsukae sp. nov., and nine species that were known, but previously not described in South Korea, Aspergillus aculeatinus, Aspergillus aurantiacoflavus, Aspergillus croceiaffinis, Aspergillus pseudoviridinutans, Aspergillus uvarum, Penicillium ferraniaense, Penicillium glaucoroseum, Penicillium sajarovii, and one, Penicillium charlesii, that was isolated from previously unknown host, woodlouse (Porcellio scaber). We believe that biodiversity survey and identifying new species can contribute to set a baseline for future changes in the context of humanitarian crises such as climate change.}, }
@article {pmid39652873, year = {2025}, author = {Naderian, M and Norland, K and Schaid, DJ and Kullo, IJ}, title = {Development and Evaluation of a Comprehensive Prediction Model for Incident Coronary Heart Disease Using Genetic, Social, and Lifestyle-Psychological Factors: A Prospective Analysis of the UK Biobank.}, journal = {Annals of internal medicine}, volume = {178}, number = {1}, pages = {1-10}, pmid = {39652873}, issn = {1539-3704}, support = {R35 GM140487/GM/NIGMS NIH HHS/United States ; U01 HG006379/HG/NHGRI NIH HHS/United States ; U01 HG011710/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; Male ; Female ; *Coronary Disease/genetics/epidemiology/psychology ; Middle Aged ; United Kingdom/epidemiology ; Prospective Studies ; Risk Assessment/methods ; *Life Style ; Incidence ; Machine Learning ; Aged ; Biological Specimen Banks ; Multifactorial Inheritance ; Adult ; UK Biobank ; }, abstract = {BACKGROUND: Clinical risk calculators for coronary heart disease (CHD) do not include genetic, social, and lifestyle-psychological risk factors.<br><br>OBJECTIVE: To improve CHD risk prediction by developing and evaluating a prediction model that incorporated a polygenic risk score (PRS) and a polysocial score (PSS), the latter including social determinants of health and lifestyle-psychological factors.<br><br>DESIGN: Cohort study.<br><br>SETTING: United Kingdom.<br><br>PARTICIPANTS: UK Biobank participants recruited between 2006 and 2010.<br><br>MEASUREMENTS: Incident CHD (myocardial infarction and/or coronary revascularization); 10-year clinical risk based on pooled cohort equations (PCE), Predicting Risk of cardiovascular disease EVENTs (PREVENT), and QRISK3; PRS (Polygenic Score Catalog identification: PGS000018) for CHD (PRSCHD); and PSSCHD from 100 related covariates. Machine-learning and time-to-event analyses and model performance indices.<br><br>RESULTS: In 388&#x2009;224 participants (age, 55.5 [SD, 8.1] years; 42.5% men; 94.9% White), the hazard ratio for 1 SD increase in PSSCHD for incident CHD was 1.43 (95% CI, 1.38 to 1.49; P&#x2009;<&#x2009;0.001) and for 1 SD increase in PRSCHD was 1.59 (CI, 1.53 to 1.66, P&#x2009;<&#x2009;0.001). Non-White persons had higher PSSCHD than White persons. The effects of PSSCHD and PRSCHD on CHD were independent and additive. At a 10-year CHD risk threshold of 7.5%, adding PSSCHD and PRSCHD to PCE reclassified 12% of participants, with 1.86 times higher CHD risk in the up- versus down-reclassified persons and showed superior performance compared with PCE as reflected by improved net benefit while maintaining good calibration relative to the clinical risk calculators. Similar results were seen when incorporating PSSCHD and PRSCHD into PREVENT and QRISK3.<br><br>LIMITATION: A predominantly White cohort; possible healthy participant effect and ecological fallacy.<br><br>CONCLUSION: A PSSCHD was associated with incident CHD and its joint modeling with PRSCHD improved the performance of clinical risk calculators.<br><br>PRIMARY FUNDING SOURCE: National Human Genome Research Institute.}, }
@article {pmid39652754, year = {2024}, author = {Pillay, R and Watson, JEM and Hansen, AJ and Burns, P and Virnig, ALS and Supples, C and Armenteras, D and González-Del-Pliego, P and Aragon-Osejo, J and A Jantz, P and Ervin, J and Goetz, SJ and Venter, O}, title = {Global rarity of high-integrity tropical rainforests for threatened and declining terrestrial vertebrates.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {51}, pages = {e2413325121}, pmid = {39652754}, issn = {1091-6490}, support = {NNX17AG51G/NASA/NASA/United States ; NNL15AA03/NASA/NASA/United States ; 80NSSC18K0338/NASA/NASA/United States ; }, mesh = {*Rainforest ; Animals ; *Biodiversity ; *Vertebrates/physiology ; *Conservation of Natural Resources/methods ; Tropical Climate ; Endangered Species ; Ecosystem ; }, abstract = {Structurally intact native forests free from major human pressures are vitally important habitats for the persistence of forest biodiversity. However, the extent of such high-integrity forest habitats remaining for biodiversity is unknown. Here, we quantify the amount of high-integrity tropical rainforests, as a fraction of total forest cover, within the geographic ranges of 16,396 species of terrestrial vertebrates worldwide. We found up to 90% of the humid tropical ranges of forest-dependent vertebrates was encompassed by forest cover. Concerningly, however, merely 25% of these remaining rainforests are of high integrity. Forest-dependent species that are threatened and declining and species with small geographic ranges have disproportionately low proportions of high-integrity forest habitat left. Our work brings much needed attention to the poor quality of much of the forest estate remaining for biodiversity across the humid tropics. The targeted preservation of the world's remaining high-integrity tropical rainforests that are currently unprotected is a critical conservation priority that may help alleviate the biodiversity crisis in these hyperdiverse and irreplaceable ecosystems. Enhanced efforts worldwide to preserve tropical rainforest integrity are essential to meet the targets of the Convention on Biological Diversity's 2022 Kunming-Montreal Global Biodiversity Framework which aims to achieve near zero loss of high biodiversity importance areas (including ecosystems of high integrity) by 2030.}, }
@article {pmid39649625, year = {2024}, author = {Boyes, D and Crowley, LC and Hutchinson, F and Wawman, DC and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Broad-barred Knot-horn, Acrobasis consociella (Hübner, 1813).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {429}, pmid = {39649625}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from one female Acrobasis consociella (the Broad-barred Knot-horn; Arthropoda; Insecta; Lepidoptera; Pyralidae). The genome sequence is 598.4 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.22 kilobases in length.}, }
@article {pmid39648557, year = {2025}, author = {Huang, Y and Wang, T and Li, Y and Wang, Z and Cai, X and Chen, J and Li, R and Li, X}, title = {In Vitro-to-In Vivo Extrapolation on Lung Toxicity Induced by Metal Oxide Nanoparticles via Data-Mining.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {3}, pages = {1673-1682}, doi = {10.1021/acs.est.4c06186}, pmid = {39648557}, issn = {1520-5851}, mesh = {Animals ; *Lung/drug effects ; Mice ; *Metal Nanoparticles/toxicity ; Data Mining ; Humans ; Oxides/toxicity ; }, abstract = {While in silico analyses are commonly employed for chemical risk assessments, predicting chronic lung toxicity induced by engineered nanoparticles (ENMs) in vivo still faces many challenges due to complex interactions at multiple nanobio interfaces. In this study, we developed a rigorous method to compile published evidence on the in vivo lung toxicity of metal oxide nanoparticles (MeONPs) and revealed previously overlooked in vitro-to-in vivo extrapolation (IVIVE) relationships. A comprehensive multidimensional data set containing 1102 in vivo data points, 75 pulmonary toxicological biomarkers, and 20 features (covering in vitro effects, physicochemical properties, and exposure conditions) was constructed. An IVIVE approach that related effects at the cellular level to in vivo lung toxicity in rodent model was established with prediction accuracy reaching 89 and 80% in training and test sets. Experimental validation was conducted by testing chronic lung fibrosis of 8 new MeONPs in 32 independent mice, with prediction accuracy reaching 88%. The IVIVE model indicated that the proinflammatory cytokine IL-1β in THP-1 cells could serve as an in vitro marker to predict lung toxicity. The IVIVE model showed great promise for minimizing unnecessary animal tests and understanding toxicological mechanisms.}, }
@article {pmid39647412, year = {2024}, author = {He, T and Xie, J and Jin, L and Zhao, J and Zhang, X and Liu, H and Li, XD}, title = {Seasonal dynamics of the phage-bacterium linkage and associated antibiotic resistome in airborne PM2.5 of urban areas.}, journal = {Environment international}, volume = {194}, number = {}, pages = {109155}, doi = {10.1016/j.envint.2024.109155}, pmid = {39647412}, issn = {1873-6750}, mesh = {*Bacteriophages/genetics ; *Particulate Matter ; China ; *Bacteria/genetics/drug effects ; *Seasons ; Humans ; Air Microbiology ; Cities ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Air Pollutants/analysis ; Metagenomics ; Drug Resistance, Bacterial/genetics ; Microbiota ; }, abstract = {Inhalable microorganisms in airborne fine particulate matter (PM2.5), including bacteria and phages, are major carriers of antibiotic resistance genes (ARGs) with strong ecological linkages and potential health implications for urban populations. A full-spectrum study on ARG carriers and phage-bacterium linkages will shed light on the environmental processes of antibiotic resistance from airborne dissemination to the human lung microbiome. Our metagenomic study reveals the seasonal dynamics of phage communities in PM2.5, their impacts on clinically important ARGs, and potential implications for the human respiratory microbiome in selected cities of China. Gene-sharing network comparisons show that air harbours a distinct phage community connected to human- and water-associated viromes, with 57 % of the predicted hosts being potential bacterial pathogens. The ARGs of common antibiotics, e.g., peptide and tetracycline, dominate both the antibiotic resistome associated with bacteria and phages in PM2.5. Over 60 % of the predicted hosts of vARG-carrying phages are potential bacterial pathogens, and about 67 % of these hosts have not been discovered as direct carriers of the same ARGs. The profiles of ARG-carrying phages are distinct among urban sites, but show a significant enrichment in abundance, diversity, temperate lifestyle, and matches of CRISPR (short for 'clustered regularly interspaced short palindromic repeats') to identified bacterial genomes in winter and spring. Moreover, phages putatively carry 52 % of the total mobile genetic element (MGE)-ARG pairs with a unique 'flu season' pattern in urban areas. This study highlights the role that phages play in the airborne dissemination of ARGs and their delivery of ARGs to specific opportunistic pathogens in human lungs, independent of other pathways of horizontal gene transfer. Natural and anthropogenic stressors, particularly wind speed, UV index, and level of ozone, potentially explained over 80 % of the seasonal dynamics of phage-bacterial pathogen linkages on antibiotic resistance. Therefore, understanding the phage-host linkages in airborne PM2.5, the full-spectrum of antibiotic resistomes, and the potential human pathogens involved, will be of benefit to protect human health in urban areas.}, }
@article {pmid39644634, year = {2025}, author = {Xie, Y and Guo, J and Fan, Q and Huang, S and Qi, W and Cao, X and Peng, J and Chen, Y and Chen, M}, title = {High-density sampling reveals the occurrence, levels and transport flux of 15 polycyclic aromatic hydrocarbons derivatives (PAHs-d) along the Yangtze River.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {177907}, doi = {10.1016/j.scitotenv.2024.177907}, pmid = {39644634}, issn = {1879-1026}, abstract = {Polycyclic aromatic hydrocarbons derivatives (PAHs-d) have higher toxicity levels compared to its parent polycyclic aromatic hydrocarbons (PPAHs). Their partitioning in different media and large-scale transport patterns in rivers remain largely unknown. This study investigated the occurrence of 15 PAHs-d and 19 PPAHs in water and suspended particulate matter (SPM) of the Yangtze River between 2019 and 2020. The range of Σ15PAHs-d concentrations was 20.54 to 2010.03 ng·L[-1] in water and 0.62 to 29.80 μg·g[-1] in SPM. The primary PAHs-d components were 2,6-dimethylnaphthalene, 2-methylnaphthalene, and anthraquinone. The range of Σ19PPAHs concentrations in water and SPM was 34.89 to 739.53 ng·L[-1] and 0.37 to 204.62 μg·g[-1], respectively. And low-ring PAHs-d and PPAHs were more prevalent in water than SPM. Partitioning behaviors indicated that PAHs-d and PPAHs were more readily partitioned into water and SPM during normal and dry periods, respectively. The concentrations of PAHs-d saw significant changes in their spatial distribution, which rose in water and reduced in SPM in downstream of the Three Gorges Dam. This is due to the dam's blocking effect on sediment transport. Positive matrix factorization source analysis revealed biomass combustion upstream and vehicle emissions downstream as primary sources, shaped by the evolving energy consumption patterns of urban areas situated around the Yangtze River. The annual fluxes of PAHs-d in water and SPM of the Yangtze River were 90.40 t·yr[-1] and 11.95 t·yr[-1], representing 88.3 % and 11.7 % of the overall PAHs-d fluxes, respectively. The total fluxes of PAHs-d and PPAHs in water and SPM tended to increase spatially along the river, with growth rates exceeding 76 and 24 times, respectively. Interception within the Three Gorges Reservoir area has resulted in the differences in the concentration and transport distribution of PAHs-d and PPAHs upstream and downstream, which play important roles in reducing PAHs-d and PPAHs entry into the sea. Future studies on PAHs-d in Yangtze River basin tributaries and estuaries are essential.}, }
@article {pmid39643871, year = {2024}, author = {Zhang, W and Jin, Z and Huang, R and Huang, W and Li, L and He, Y and Zhou, J and Tian, C and Xiao, L and Li, P and Quan, M and Zhang, D and Du, Q}, title = {Multi-omics analysis reveals genetic architecture and local adaptation of coumarins metabolites in Populus.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {1170}, pmid = {39643871}, issn = {1471-2229}, support = {No. 2021ZD0008//Major Science and Technology project of Inner Mongolia Autonomous Region/ ; No. 2021ZD0008//Major Science and Technology project of Inner Mongolia Autonomous Region/ ; No. 6212021//Project of the Natural Science Foundation of Beijing Municipality/ ; QNTD202305//Fundamental Research Funds for Central Universities of the Central South University/ ; }, mesh = {*Populus/genetics/metabolism ; *Coumarins/metabolism ; *Polymorphism, Single Nucleotide ; *Quantitative Trait Loci ; Adaptation, Physiological/genetics ; Gene Expression Regulation, Plant ; Genes, Plant ; Multiomics ; }, abstract = {BACKGROUND: Accumulation of coumarins plays key roles in response to immune and abiotic stress in plants, but the genetic adaptation basis of controlling coumarins in perennial woody plants remain unclear.<br><br>RESULTS: We detected 792 SNPs within 334 genes that were significantly associated with the phenotypic variations of 15 single-metabolic traits and multiple comprehensive index, such as principal components (PCs) of coumarins metabolites. Expression quantitative trait locus mapping uncovered that 337 eQTLs associated with the expression levels of 132 associated genes. Selective sweep revealed 55 candidate genes have potential selective signature among three geographical populations, highlighting that the coumarins biosynthesis have been encountered forceful local adaptation. Furthermore, we constructed a genetic network of seven candidate genes that coordinately regulate coumarins biosynthesis, revealing the multiple regulatory patterns affecting coumarins accumulation in Populus tomentosa. Validation of candidate gene variations in a drought-tolerated population and DUF538 heterologous transformation experiments verified the function of candidate genes and their roles in adapting to the different geographical conditions in poplar.<br><br>CONCLUSIONS: Our study uncovered the genetic regulation of the coumarins metabolic biosynthesis of Populus, and offered potential clues for drought-tolerance evaluation and regional improvement in woody plants.}, }
@article {pmid39642727, year = {2025}, author = {Mendrik, F and Hackney, CR and Cumming, VM and Waller, C and Hak, D and Dorrell, R and Hung, NN and Parsons, DR}, title = {The transport and vertical distribution of microplastics in the Mekong River, SE Asia.}, journal = {Journal of hazardous materials}, volume = {484}, number = {}, pages = {136762}, doi = {10.1016/j.jhazmat.2024.136762}, pmid = {39642727}, issn = {1873-3336}, abstract = {Rivers are primary vectors of plastic debris to oceans, but sources, transport mechanisms, and fate of fluvial microplastics (<5 mm) remain poorly understood, impeding accurate predictions of microplastic flux, ecological risk and socio-economic impacts. We report on microplastic concentrations, characteristics and dynamics in the Mekong River, one of the world's largest and polluting rivers, in Cambodia and Vietnam. Sampling throughout the water column at multiple localities detected an average of 24 microplastics m[-3] (0.073 mg l[-1]). Concentrations increased downstream from rural Kampi, Cambodia (344 km from river mouth; 2 microplastics m[-3,] 0.006 mg l[-1]), to Can Tho, Vietnam (83 km from river mouth; 64 microplastics m[-3], 0.182 mg l[-1]) with most microplastics being fibres (53 %), followed by fragments (44 %) and the most common polymer being polyethylene terephthalate (PET) or polyester. Pathways of microplastic pollution are expected to be from urban wastewater highlighting the need for improved wastewater treatment in this region. On average, 86 % of microplastics are transported within the water column and consequently we identified an optimum sampling depth capturing a representative flux value, highlighting that sampling only the water surface substantially biases microplastic concentration predictions. Additionally, microplastic abundance does not linearly follow discharge changes during annual monsoonal floods or mirror siliciclastic sediment transport, as microplastic concentrations decrease rapidly during higher monsoon flows. The findings reveal complex microplastic transport in large rivers and call for improved sampling methods and predictive models to better assess environmental risk and guide policy.}, }
@article {pmid39642364, year = {2024}, author = {Lee, TY and Chen, CH and Chen, IM and Chen, HC and Liu, CM and Wu, SI and Hsiao, CK and Kuo, PH}, title = {Dynamic Bidirectional Associations Between Global Positioning System Mobility and Ecological Momentary Assessment of Mood Symptoms in Mood Disorders: Prospective Cohort Study.}, journal = {Journal of medical Internet research}, volume = {26}, number = {}, pages = {e55635}, pmid = {39642364}, issn = {1438-8871}, mesh = {Humans ; *Geographic Information Systems ; *Ecological Momentary Assessment ; Prospective Studies ; Male ; Adult ; Female ; Middle Aged ; *Mood Disorders/psychology ; Smartphone/statistics &amp; numerical data ; Affect ; Mobile Applications ; }, abstract = {BACKGROUND: Although significant research has explored the digital phenotype in mood disorders, the time-lagged and bidirectional relationship between mood and global positioning system (GPS) mobility remains relatively unexplored. Leveraging the widespread use of smartphones, we examined correlations between mood and behavioral changes, which could inform future scalable interventions and personalized mental health monitoring.<br><br>OBJECTIVE: This study aims to investigate the bidirectional time lag relationships between passive GPS data and active ecological momentary assessment (EMA) data collected via smartphone app technology.<br><br>METHODS: Between March 2020 and May 2022, we recruited 45 participants (mean age 42.3 years, SD 12.1 years) who were followed up for 6 months: 35 individuals diagnosed with mood disorders referred by psychiatrists and 10 healthy control participants. This resulted in a total of 5248 person-days of data. Over 6 months, we collected 2 types of smartphone data: passive data on movement patterns with nearly 100,000 GPS data points per individual and active data through EMA capturing daily mood levels, including fatigue, irritability, depressed, and manic mood. Our study is limited to Android users due to operating system constraints.<br><br>RESULTS: Our findings revealed a significant negative correlation between normalized entropy (r=-0.353; P=.04) and weekly depressed mood as well as between location variance (r=-0.364; P=.03) and depressed mood. In participants with mood disorders, we observed bidirectional time-lagged associations. Specifically, changes in homestay were positively associated with fatigue (&#x3b2;=0.256; P=.03), depressed mood (&#x3b2;=0.235; P=.01), and irritability (&#x3b2;=0.149; P=.03). A decrease in location variance was significantly associated with higher depressed mood the following day (&#x3b2;=-0.015; P=.009). Conversely, an increase in depressed mood was significantly associated with reduced location variance the next day (&#x3b2;=-0.869; P<.001). These findings suggest a dynamic interplay between mood symptoms and mobility patterns.<br><br>CONCLUSIONS: This study demonstrates the potential of utilizing active EMA data to assess mood levels and passive GPS data to analyze mobility behaviors, with implications for managing disease progression in patients. Monitoring location variance and homestay can provide valuable insights into this process. The daily use of smartphones has proven to be a convenient method for monitoring patients' conditions. Interventions should prioritize promoting physical movement while discouraging prolonged periods of staying at home.}, }
@article {pmid39642189, year = {2024}, author = {Graham, AL and Regoes, RR}, title = {Dose-dependent interaction of parasites with tiers of host defense predicts "wormholes" that prolong infection at intermediate inoculum sizes.}, journal = {PLoS computational biology}, volume = {20}, number = {12}, pages = {e1012652}, pmid = {39642189}, issn = {1553-7358}, mesh = {*Host-Parasite Interactions/immunology ; Animals ; Computational Biology ; Parasites/physiology/immunology ; Immunity, Innate ; Models, Biological ; }, abstract = {Immune responses are induced by parasite exposure and can in turn reduce parasite burden. Despite such apparently simple rules of engagement, key drivers of within-host dynamics, including dose-dependence of defense and infection duration, have proven difficult to predict. Here, we model how varied inoculating doses interact with multi-tiered host defenses at a site of inoculation, by confronting barrier, innate, and adaptive tiers with replicating and non-replicating parasites across multiple orders of magnitude of dose. We find that, in general, intermediate parasite doses generate infections of longest duration because they are sufficient in number to breach barrier defenses, but insufficient to strongly induce subsequent tiers of defense. These doses reveal "wormholes" in defense from which parasites might profit: Deviation from the hypothesis of independent action, which postulates that each parasite has an independent probability of establishing infection, may therefore be widespread. Interestingly, our model predicts local maxima of duration at two doses-one for each tier transition. While some empirical evidence is consistent with nonlinear dose-dependencies, testing the predicted dynamics will require finer-scale dose variation than experiments usually incorporate. Our results help explain varied infection establishment and duration among differentially-exposed hosts and elucidate evolutionary pressures that shape both virulence and defense.}, }
@article {pmid39642168, year = {2024}, author = {Champion, C and Momal, R and Le Chatelier, E and Sola, M and Mariadassou, M and Berland, M}, title = {OneNet-One network to rule them all: Consensus network inference from microbiome data.}, journal = {PLoS computational biology}, volume = {20}, number = {12}, pages = {e1012627}, pmid = {39642168}, issn = {1553-7358}, mesh = {*Computational Biology/methods ; Humans ; *Microbiota/physiology ; *Algorithms ; *Gastrointestinal Microbiome/physiology ; Microbial Interactions/physiology ; }, abstract = {Modeling microbial interactions as sparse and reproducible networks is a major challenge in microbial ecology. Direct interactions between the microbial species of a biome can help to understand the mechanisms through which microbial communities influence the system. Most state-of-the art methods reconstruct networks from abundance data using Gaussian Graphical Models, for which several statistically grounded and computationnally efficient inference approaches are available. However, the multiplicity of existing methods, when applied to the same dataset, generates very different networks. In this article, we present OneNet, a consensus network inference method that combines seven methods based on stability selection. This resampling procedure is used to tune a regularization parameter by computing how often edges are selected in the networks. We modified the stability selection framework to use edge selection frequencies directly and combine them in the inferred network to ensure that only reproducible edges are included in the consensus. We demonstrated on synthetic data that our method generally led to slightly sparser networks while achieving much higher precision than any single method. We further applied the method to gut microbiome data from liver-cirrothic patients and demonstrated that the resulting network exhibited a microbial guild that was meaningful in terms of human health.}, }
@article {pmid39638881, year = {2024}, author = {Vojteková, J and Janizadeh, S and Vojtek, M and Tirpáková, A and Ruttkay, M and Petrovič, F}, title = {Prediction of potential occurrence of historical objects with defensive function in Slovakia using machine learning approach.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {30350}, pmid = {39638881}, issn = {2045-2322}, support = {033UKF-4/2023//Kult&#xfa;rna a Edukacn&#xe1; Grantov&#xe1; Agent&#xfa;ra M&#x160;VVa&#x160; SR/ ; }, abstract = {In this article, we aim at the prediction of possible locations of already defunct historical objects with a defensive function (HODFs) in Slovakia, which have not been found and documented so far, using three machine learning methods. Specifically, we used the support vector machine, k-nearest neighbors, and random forest algorithms, which were trained based on the following five factors influencing the possible occurrence of HODFs: elevation, distance from a river, distance from a settlement, lithological rock type, and type of representative geoecosystems. Training and testing datasets were based on a database of already documented 605 HODFs, which were divided into 70% of training samples and 30% of testing samples. All of the three models reached the AUC-ROC value over 0.74 based on the testing dataset. The best performance was recorded by the random forest predictive model with the AUC-ROC value equal to 0.79. The results of the random forest model were also validated with the recently documented HODFs via the archeological research.}, }
@article {pmid39636475, year = {2024}, author = {Ganie, PA and Posti, R and Bharti, VS and Sehgal, VK and Sarma, D and Pandey, PK}, title = {Erosion landscape characterization in the Himalayan basin: insights from geospatial data and multi-criteria evaluation.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {1}, pages = {29}, pmid = {39636475}, issn = {1573-2959}, mesh = {India ; *Environmental Monitoring ; *Rivers/chemistry ; *Geographic Information Systems ; Soil Erosion ; Conservation of Natural Resources ; Hydrology ; }, abstract = {In regions characterized by mountainous landscapes, such as watersheds with high elevations, steep inclines, and rugged terrains, there exists an inherent susceptibility to water-induced soil erosion. This susceptibility underscores the importance of identifying areas prone to erosion to mitigate the loss of valuable natural resources and ensure their preservation over time. In response to this need, the current research employed a combination of four multi-criteria decision-making (MCDM) models, namely TOPSIS-AHP, VIKOR-AHP, ARAS-AHP, and CODAS-AHP, for the identification of areas susceptible to soil erosion within the Himalayan River basin of Nandakini, Uttarakhand, India. This identification was facilitated through the utilization of remote sensing and geospatial technologies. The study considered a total of 19 prioritization parameters that included morphological, topo-hydrological, climatic, and environmental factors specific to the Nandakini catchment for the purpose of prioritization modeling. The adoption of morphometric parameters in depicting the geological structures and hydrodynamic behavior of the river basin proves to be a crucial approach in locales where hydrological data may be scarce. The investigation delineated twenty watersheds within the catchment by employing SRTM DEM, SOI toposheets, and Geographic Information Systems (GIS), calculating the catchment's total area to be approximately 540.98 km[2]. The analysis determined that the catchment is classified as a 6th-order catchment, exhibiting mainly a sub-dendritic to dendritic drainage pattern. It was identified that the catchment is vulnerable to flooding and subsequent gully erosion due to the slow movement of surface runoff. Furthermore, the catchment's elongated shape and the compactness coefficient suggest a delayed peak runoff. The drainage texture ranged from very coarse to coarse, and the relief characteristics highlighted that the watersheds within the catchment possess a high relief ratio, thereby increasing their erosion vulnerability. Topo-hydrological indices revealed significant topographic variability and spatial differences in water availability and erosion potential across the basin. The efficacy of the MCDM models was evaluated through the Spearman's correlation coefficient test, alongside indices of intensity and percentage of change, to validate the findings. The ARAS-AHP and CODAS-AHP models were found to exhibit superior efficiency and higher accuracy relative to the other methods assessed. The insights gained from the ARAS-AHP and CODAS-AHP models are instrumental in the development of strategies for sustainable catchment management plans and inform decision-making processes regarding water resources management within the catchment.}, }
@article {pmid39635120, year = {2024}, author = {Qiu, Y and He, Z and Yu, X and Jia, G and Wang, Y}, title = {Analysis of factors influencing groundwater drought in the Loess zone of China.}, journal = {iScience}, volume = {27}, number = {10}, pages = {110929}, pmid = {39635120}, issn = {2589-0042}, abstract = {Understanding the characteristics and factors influencing groundwater resources is important for regional water resources management. The Gravity Recovery and Climate Experiment (GRACE)-based groundwater conditions were used to analyze the spatiotemporal characteristics of and the factors influencing groundwater storage (GWS) distribution in the Loess zone of the Yellow River Basin. The results revealed that the spatiotemporal distribution of GWS anomalies in the Loess zone of China was best explained by the first three components of the empirical orthogonal function (EOF), representing 85.6% of the total variance. The normalized difference vegetation index (NDVI) was significantly correlated with groundwater drought (p < 0.05). In addition, NDVI and evapotranspiration (ET) were the dominant factors influencing groundwater drought. NDVI was the dominant influencing factor in 67% and 80% of the total study area between 2002-2014 and 2015-2021, respectively. This study provides important guidance for a future ecological restoration plan in the Loess zone.}, }
@article {pmid39631859, year = {2025}, author = {Suzuki, T and Nagasu, H and Ebara, T and Kagiyama, N and Kishi, T and Yano, Y and Kario, K and Nishiyama, A and Arima, H and Kawai, F and Shibata, S and Node, K and Mizuno, A}, title = {Unraveling the Implications of Digit Bias in Digital Health - A Literature Review.}, journal = {Internal medicine (Tokyo, Japan)}, volume = {64}, number = {14}, pages = {2090-2099}, pmid = {39631859}, issn = {1349-7235}, mesh = {Humans ; Bias ; *Digital Technology ; Digital Health ; }, abstract = {Digital health, which encompasses digital medicine and therapy, integrates advanced technologies across healthcare. Central to this transformation is 'digitization,' which converts continuous analog data into a discrete digital form. However, this process is challenging. First, digitization inherently has the potential to introduce information loss, thereby diminishing the richness and complexity of data. Second, "digit bias," a cognitive distortion, emerges in the interpretation phase, where individuals' perceptions of and reactions to digital data are intrinsically skewed. There exist two major cognitive biases during digitization process: "digit preferences," where healthcare providers prioritize specific numbers, and "left digit bias" where continuous variables are disproportionately estimated by focusing on the leftmost digit. Although information loss and cognitive biases can cause significant distortions in healthcare, the effects of this "digitization" process have not been adequately quantified, and the accumulation of further evidence in this field is anticipated.}, }
@article {pmid39627996, year = {2025}, author = {Rodman, KC and Bradford, JB and Formanack, AM and Fulé, PZ and Huffman, DW and Kolb, TE and Miller-Ter Kuile, AT and Normandin, DP and Ogle, K and Pedersen, RJ and Schlaepfer, DR and Stoddard, MT and Waltz, AEM}, title = {Restoration treatments enhance tree growth and alter climatic constraints during extreme drought.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {35}, number = {1}, pages = {e3072}, pmid = {39627996}, issn = {1939-5582}, support = {22-DG-11030000-012//U.S. Forest Service/ ; }, mesh = {*Droughts ; *Pinus ponderosa/growth &amp; development/physiology ; *Trees/growth &amp; development ; *Climate Change ; *Forestry/methods ; Forests ; *Pinus/growth &amp; development ; *Environmental Restoration and Remediation/methods ; }, abstract = {The frequency and severity of drought events are predicted to increase due to anthropogenic climate change, with cascading effects across forested ecosystems. Management activities such as forest thinning and prescribed burning, which are often intended to mitigate fire hazard and restore ecosystem processes, may also help promote tree resistance to drought. However, it is unclear whether these treatments remain effective during the most severe drought conditions or whether their impacts differ across environmental gradients. We used tree-ring data from a system of replicated, long-term (>20 years) experiments in the southwestern United States to evaluate the effects of forest restoration treatments (i.e., evidence-based thinning and burning) on annual growth rates (i.e., basal area increment; BAI) of ponderosa pine (Pinus ponderosa), a broadly distributed and heavily managed species in western North America. The study sites were established at the onset of the most extreme drought event in at least 1200 years and span much of the climatic niche of Rocky Mountain ponderosa pine. Across sites, tree-level BAI increased due to treatment, where trees in treated units grew 133.1% faster than trees in paired, untreated units. Likewise, trees in treated units grew an average of 85.6% faster than their pre-treatment baseline levels (1985 to ca. 2000), despite warm, dry conditions in the post-treatment period (ca. 2000-2018). Variation in the local competitive environment promoted variation in BAI, and larger trees were the fastest-growing individuals, irrespective of treatment. Tree thinning and prescribed fire altered the climatic constraints on growth, decreasing the effects of belowground moisture availability and increasing the effects of atmospheric evaporative demand over multi-year timescales. Our results illustrate that restoration treatments can enhance tree-level growth across sites spanning ponderosa pine's climatic niche, even during recent, extreme drought events. However, shifting climatic constraints, combined with predicted increases in evaporative demand in the southwestern United States, suggest that the beneficial effects of such treatments on tree growth may wane over the upcoming decades.}, }
@article {pmid39627652, year = {2025}, author = {Peltier, DMP and Carbone, MS and Ogle, K and Koch, GW and Richardson, AD}, title = {Decades-old carbon reserves are widespread among tree species, constrained only by sapwood longevity.}, journal = {The New phytologist}, volume = {245}, number = {4}, pages = {1468-1480}, doi = {10.1111/nph.20310}, pmid = {39627652}, issn = {1469-8137}, support = {149//Save the Redwoods League/ ; 1936205//Division of Integrative Organismal Systems/ ; 2053337//Division of Integrative Organismal Systems/ ; 1832218//Division of Environmental Biology/ ; 2213599//Division of Environmental Biology/ ; }, mesh = {*Carbon/metabolism ; *Trees/physiology/metabolism ; *Wood/physiology ; Species Specificity ; *Longevity ; Time Factors ; Droughts ; Carbon Isotopes ; Photosynthesis ; Plant Stems/physiology ; Fires ; Models, Biological ; }, abstract = {Carbon reserves are distributed throughout plant cells allowing past photosynthesis to fuel current metabolism. In trees, comparing the radiocarbon (Δ[14]C) of reserves to the atmospheric bomb spike can trace reserve ages. We synthesized Δ[14]C observations of stem reserves in nine tree species, fitting a new process model of reserve building. We asked how the distribution, mixing, and turnover of reserves vary across trees and species. We also explored how stress (drought and aridity) and disturbance (fire and bark beetles) perturb reserves. Given sufficient sapwood, young (< 1 yr) and old (20-60+ yr) reserves were simultaneously present in single trees, including 'prebomb' reserves in two conifers. The process model suggested that most reserves are deeply mixed (30.2 ± 21.7 rings) and then respired (2.7 ± 3.5-yr turnover time). Disturbance strongly increased Δ[14]C mean ages of reserves (+15-35 yr), while drought and aridity effects on mixing and turnover were species-dependent. Fire recovery in Sequoia sempervirens also appears to involve previously unobserved outward mixing of old reserves. Deep mixing and rapid turnover indicate most photosynthate is rapidly metabolized. Yet ecological variation in reserve ages is enormous, perhaps driven by stress and disturbance. Across species, maximum reserve ages appear primarily constrained by sapwood longevity, and thus old reserves are probably widespread.}, }
@article {pmid39624726, year = {2024}, author = {Tian, T and Zhang, X and Zhang, F and Huang, X and Li, M and Quan, Z and Wang, W and Lei, J and Wang, Y and Liu, Y and Wang, JH}, title = {Harnessing AI for advancing pathogenic microbiology: a bibliometric and topic modeling approach.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1510139}, pmid = {39624726}, issn = {1664-302X}, abstract = {INTRODUCTION: The integration of artificial intelligence (AI) in pathogenic microbiology has accelerated research and innovation. This study aims to explore the evolution and trends of AI applications in this domain, providing insights into how AI is transforming research and practice in pathogenic microbiology.<br><br>METHODS: We employed bibliometric analysis and topic modeling to examine 27,420 publications from the Web of Science Core Collection, covering the period from 2010 to 2024. These methods enabled us to identify key trends, research areas, and the geographical distribution of research efforts.<br><br>RESULTS: Since 2016, there has been an exponential increase in AI-related publications, with significant contributions from China and the USA. Our analysis identified eight major AI application areas: pathogen detection, antibiotic resistance prediction, transmission modeling, genomic analysis, therapeutic optimization, ecological profiling, vaccine development, and data management systems. Notably, we found significant lexical overlaps between these areas, especially between drug resistance and vaccine development, suggesting an interconnected research landscape.<br><br>DISCUSSION: AI is increasingly moving from laboratory research to clinical applications, enhancing hospital operations and public health strategies. It plays a vital role in optimizing pathogen detection, improving diagnostic speed, treatment efficacy, and disease control, particularly through advancements in rapid antibiotic susceptibility testing and COVID-19 vaccine development. This study highlights the current status, progress, and challenges of AI in pathogenic microbiology, guiding future research directions, resource allocation, and policy-making.}, }
@article {pmid39622961, year = {2024}, author = {Jeong, D and Hyun, JY and Marchenkova, T and Matiukhina, D and Cho, S and Lee, J and Kim, DY and Li, Y and Darman, Y and Min, MS and Bardyuk, V and Lee, Y and Pandey, P and Lee, H}, title = {Genetic insights and conservation strategies for Amur tigers in Southwest Primorye Russia.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {29985}, pmid = {39622961}, issn = {2045-2322}, support = {550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 5260-20190100//Brain Korea-21 programme/ ; 5260-20200100//Brain Korea-21 programme/ ; A0449-2020010//Brain Korea-21 programme/ ; 5260-20190100//Brain Korea-21 programme/ ; 5260-20200100//Brain Korea-21 programme/ ; A0449-2020010//Brain Korea-21 programme/ ; 5260-20190100//Brain Korea-21 programme/ ; 5260-20200100//Brain Korea-21 programme/ ; A0449-2020010//Brain Korea-21 programme/ ; Building Tumen River Corridor for Tigers and leopards: Genetic diversity of tigers and leopards using non-invasive technique 2022-2023//Tiger and Leopard Conservation Fund in Korea/ ; Building Tumen River Corridor for Tigers and leopards: Genetic diversity of tigers and leopards using non-invasive technique 2022-2023//Tiger and Leopard Conservation Fund in Korea/ ; Building Tumen River Corridor for Tigers and leopards: Genetic diversity of tigers and leopards using non-invasive technique 2022-2023//Tiger and Leopard Conservation Fund in Korea/ ; }, mesh = {Animals ; *Tigers/genetics ; *Conservation of Natural Resources ; *Genetic Variation ; *Microsatellite Repeats/genetics ; Male ; Female ; *DNA, Mitochondrial/genetics ; Russia ; Genetics, Population ; Population Density ; }, abstract = {Southwest Primorye hosts approximately 9% of the remaining wild Amur tiger population and represents hope for the revival of tigers in Northeast China and the Korean peninsula. Decades of conservation efforts have led to a significant increase in population size, from less than 10 individuals surviving in the region in 1996 to multiple folds today. However, while the population size has recovered since the mid-1900s, the effects of genetic depletion on evolutionary potential are not easily reversed. In this study, a non-invasive genetic analysis of the Amur tiger subpopulation in Southwest Primorye was conducted using microsatellite loci and mitochondrial genes to estimate genetic diversity, relatedness, and determine the impact of historical demographic dynamics. A total of 32 individuals (16 males, 15 females, and 1 unidentified sex) were identified, and signs of bottlenecks were detected, reflecting past demographic events. Low genetic variation observed in mitochondrial DNA also revealed genetic depletion within the population. Most individuals were found to be closely related to each other, raising concerns about inbreeding given the small population size and somewhat isolated environment from the main population in Sikhote-Alin. These findings emphasize the urgent need to establish ecological corridors to neighboring areas to restore genetic diversity and ensure the conservation of the Amur tiger population in Southwest Primorye.}, }
@article {pmid39622813, year = {2024}, author = {Monadjem, A and Montauban, C and Webala, PW and Laverty, TM and Bakwo-Fils, EM and Torrent, L and Tanshi, I and Kane, A and Rutrough, AL and Waldien, DL and Taylor, PJ}, title = {African bat database: curated data of occurrences, distributions and conservation metrics for sub-Saharan bats.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1309}, pmid = {39622813}, issn = {2052-4463}, mesh = {*Chiroptera/classification/physiology ; Animals ; Africa South of the Sahara ; *Conservation of Natural Resources ; *Databases, Factual ; Ecosystem ; Animal Distribution ; }, abstract = {Accurate knowledge of species distributions is foundational for effective conservation efforts. Bats are a diverse group of mammals, with important roles in ecosystem functioning. However, our understanding of bats and their ecological importance is hindered by poorly defined ranges, mostly as a result of under-recording. This issue is exacerbated in Africa by the ongoing rapid discovery of new species, both de novo and splits of existing species, and by inaccessibility to museum specimens that are mostly hosted outside of the continent. Here we present the African bat database - a curated set of 17,285 unique locality records of all 266 species of bats from sub-Saharan Africa, vouched for by specimens and/or genetic sequencing, and aligned with current taxonomy. Based on these records, we also present Maxent-based distribution models and calculate the IUCN Red List metrics for Extent of Occurrence and Area of Occupancy. This database and online visualization tool provide an important open-source resource and is expected to significantly advance studies in ecology, and aid in bat conservation.}, }
@article {pmid39622351, year = {2025}, author = {Nishimura, H and Nawa, N and Ogawa, T and Fushimi, K and Schwartz, BS and Fujiwara, T}, title = {Projections of future heat-related emergency hospitalizations for asthma under climate and demographic change scenarios: A Japanese nationwide time-series analysis.}, journal = {Environmental research}, volume = {266}, number = {}, pages = {120498}, doi = {10.1016/j.envres.2024.120498}, pmid = {39622351}, issn = {1096-0953}, mesh = {Japan/epidemiology ; *Asthma/epidemiology/etiology ; Humans ; *Hospitalization/statistics &amp; numerical data ; *Climate Change ; Child ; *Hot Temperature/adverse effects ; Infant ; Child, Preschool ; Adolescent ; Infant, Newborn ; Adult ; Young Adult ; Middle Aged ; Female ; Male ; Aged ; Forecasting ; East Asian People ; }, abstract = {BACKGROUND: There is growing concern about climate impacts on human health. However, empirical evidence is lacking regarding future projections of heat-related asthma hospitalizations. This study aimed to project excess emergency hospitalizations for heat-related asthma exacerbation in Japan.<br><br>METHODS: Using Japanese nationwide administrative data from 2011 to 2019, we conducted an ecological time-series quasi-Poisson regression analysis to estimate the heat-related relative risk of emergency hospitalization for asthma over a lag of 0-3 days during the warm season (June to September). Heat exposure was defined as the region-specific daily mean temperature exceeding the locally defined minimum morbidity temperature percentile (MMP). Heat-related excess hospitalizations for asthma were projected under future climate and demographic change scenarios based on Shared Socioeconomic Pathways (SSPs).<br><br>RESULTS: We identified 75,829 emergency hospitalizations for asthma. The heat-related relative risk of hospitalization was 1.22 (95% confidence interval (CI): 1.12-1.33) at the 99th percentile temperature relative to the MMP, with the highest estimates for cases aged 0-14 years. Heat-related excess hospitalizations were projected to increase by 6.78 (95%CI: 5.84-7.67) times in 2091-2099 versus 2011-2019 along SSP5-8.5 when constant population structure was assumed. The increasing trend persisted even when the future population decline was considered (4.19 (95%CI: 3.53-4.85) times in 2091-2099 versus 2011-2019 under SSP5-8.5).<br><br>CONCLUSION: Future heat-related impacts on asthma exacerbation are expected to increase in Japan toward the end of this century, even when the future demographic change is considered. Our projections will contribute to resilient health systems adapting to ongoing climate change.}, }
@article {pmid39621910, year = {2024}, author = {Alfaro-Sánchez, R and Richardson, AD and Smith, SL and Johnstone, JF and Turetsky, MR and Cumming, SG and Le Moine, JM and Baltzer, JL}, title = {Permafrost instability negates the positive impact of warming temperatures on boreal radial growth.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {50}, pages = {e2411721121}, pmid = {39621910}, issn = {1091-6490}, support = {15879//Aurora Research Institute (ARI)/ ; permafrost monitoring in the Mackenzie River Valley//Canadian Government | Natural Resources Canada (NRCan)/ ; MZ2021//Mar&#xed;a Zambrano program/ ; Small Research 2021 - SR21/1291//British Ecological Society (BES)/ ; Environmental Studies Research Fund and Cumulative Impacts Monitoring Program (Project 170)//Environment and Natural Resources, Northwest Territories (ENR, NWT)/ ; Discovery Grant support//Canadian Government | NSERC | RES'EAU-WaterNET/ ; Bonanza Creek LTER DEB-2224776//National Science Foundation (NSF)/ ; }, mesh = {*Permafrost ; *Trees/growth &amp; development ; Temperature ; Taiga ; Global Warming ; Climate Change ; Forests ; }, abstract = {Climate warming can alleviate temperature and nutrient constraints on tree growth in boreal regions, potentially enhancing boreal productivity. However, in permafrost environments, warming also disrupts the physical foundation on which trees grow, leading to leaning trees or "drunken" forests. Tree leaning might reduce radial growth, undermining potential benefits of warming. Here, we found widespread radial growth reductions in southern latitude boreal forests since the 1980s. At mid latitudes, radial growth increased from ~1980 to ~2000 but showed recent signs of decline afterward. Increased growth was evident since the 1980 s at higher latitudes, where radial growth appears to be temperature limited. However, recent changes in permafrost stability, and the associated increased frequency of tree leaning events, emerged as a significant stressor, leading to reduced radial growth in boreal trees at the highest latitudes, where permafrost is extensive. We showed that trees growing in unstable permafrost sites allocated more nonstructural carbohydrate reserves to offset leaning which compromised radial growth and potential carbon uptake benefits of warming. This higher allocation of resources in drunken trees is needed to build the high-density reaction wood, rich in lignin, that is required to maintain a vertical position. With continued climate warming, we anticipate widespread reductions in radial growth in boreal forests, leading to lower carbon sequestration. These findings enhance our understanding of how climate warming and indirect effects, such as ground instability caused by warming permafrost, will affect boreal forest productivity in the future.}, }
@article {pmid39621775, year = {2024}, author = {Osiecka, AN and Bryndza, P and Briefer, EF and Wojczulanis-Jakubas, K}, title = {Long distance calls: Negligible information loss of little auk social vocalisations due to high frequency propagation losses.}, journal = {PLoS computational biology}, volume = {20}, number = {12}, pages = {e1011961}, pmid = {39621775}, issn = {1553-7358}, mesh = {Animals ; *Vocalization, Animal/physiology ; Sound Spectrography/methods ; Computational Biology ; Acoustics ; Social Behavior ; }, abstract = {How well does the information contained in vocal signals travel through the environment? To assess the efficiency of information transfer in little auk (Alle alle, an Arctic seabird) calls over distance, we selected two of the social call types with the highest potential for individuality coding. Using available recordings of known individuals, we calculated the apparent source levels, with apparent maximum peak sound pressure level (ASPL) of 63 dB re 20 μPa at 1 m for both call types. Further, we created a sound attenuation model using meteorological data collected in the vicinity of the little auk colony in Hornsund, Spitsbergen. Using this model, we modelled the calls to reflect higher frequency filtering and sound level loss occurring during spherical spreading in perfect local conditions, down to the putative hearing threshold of the species, calculated to equal ASPL of signals "propagated" to roughly one kilometre. Those modelled calls were then used in a permuted discriminant function analysis, support vector machine models, and linear models of Beecher's information statistic, to investigate whether transmission loss will affect the retention of individual information of the signal. Calls could be correctly classified to individuals above chance level independently of the distance, down to and over the putative physiological hearing threshold. Interestingly, the information capacity of the signal did not decrease with its filtering and attenuation. While this study touches on signal properties purely and cannot provide evidence of the actual use by the animals, it shows that little auk signals can theoretically travel long distances with negligible information loss, and supports the hypothesis that vocalisations could facilitate long-distance communication in the species.}, }
@article {pmid39618809, year = {2024}, author = {Boyes, D and Young, MR and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Straw Grass-veneer moth, Agriphila straminella (Denis &amp; Schiffermüller), 1775.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {433}, pmid = {39618809}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Straw Grass-veneer moth, Agriphila straminella (Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence has a length of 511.50 megabases. Most of the assembly is scaffolded into 26 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.36 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,087 protein-coding genes.}, }
@article {pmid39616400, year = {2024}, author = {Asaaga, FA and Shakeer, I and Sriram, A and Chhotaria, K and Dutta, S and Narayanaswamy, D and Amankwaa, G and Chanda, MM and Hoti, SL and Young, JC and Purse, BV}, title = {Ties that bind: understanding One Health networks and participation for zoonoses prevention and control in India.}, journal = {One health outlook}, volume = {6}, number = {1}, pages = {24}, pmid = {39616400}, issn = {2524-4655}, abstract = {BACKGROUND: Cross-sectoral collaborations as exemplified by the One Health approach, are widely endorsed as pragmatic avenues for addressing zoonotic diseases, but operationalisation remain limited in low-and-middle income countries (LMICs). Complexities and competing interests and agendas of key stakeholders and the underlying politico-administrative context can all shape outcomes of collaborative arrangements. Evidence is building that organised collaborations are complex political initiatives where different objectives; individual and institutional agendas need to be reconciled to incentivise collaborations.<br><br>METHODS: Drawing on a qualitative network analysis of published sources on 'One Health' stakeholders supplemented with 26 multi-scale (national-state-district level) key-informant interviews (including policymakers, disease managers and public health experts), this paper characterises the fragmented and complex characteristics of institutional networks involved in zoonoses prevention and control in India.<br><br>RESULTS: Our results highlight how the local socio-political and institutional contexts interact to modulate how and when collaborations occur (or not), the associated contingencies and stakeholder innovations in circumventing existing barriers (e.g. competing interests, distrust between actors, departmental bureaucracy) to cross-sector collaborations and zoonoses management. Aside from principal actors negotiating common ground in some instance, they also capitalised on political/institutional pressure to subtly 'manipulate' their subordinates as a way of fostering collaboration, especially in instances when the institutional and political stakes are high.<br><br>CONCLUSION: Altogether our findings suggest that cross-sectoral collaborations are by-product of political and institutional tinkering as long as individual actors and institutional interests converge and these dynamics must be embraced to embed meaningful and sustainable collaborations in local socio-political and administrative contexts.}, }
@article {pmid39615103, year = {2025}, author = {Sha, J and Liu, X and Wang, H and Song, X and Bao, M and Yu, Q and Wen, G and Wei, M}, title = {Status and habitat suitability evaluation: A case study of the typical temperate seagrass beds in the Bohai Sea, China.}, journal = {Marine environmental research}, volume = {204}, number = {}, pages = {106873}, doi = {10.1016/j.marenvres.2024.106873}, pmid = {39615103}, issn = {1879-0291}, mesh = {China ; *Ecosystem ; *Environmental Monitoring/methods ; Conservation of Natural Resources ; Geographic Information Systems ; Oceans and Seas ; }, abstract = {Seagrass beds serve crucial ecological functions, yet they are facing a severe decline necessitating immediate conservation and restoration efforts. Current assessments of seagrass habitat suitability are insufficient, thus hindering the restoration effects. This study used a combination of field surveys and satellite remote sensing to conduct a three-year monitoring of typical temperate seagrass beds in the Caofeidian and Xingcheng areas of the Bohai Sea. The relationships between seagrass community factors and environmental factors were investigated using Spearman correlation analysis, BIOENV analysis, and redundancy analysis (RDA). Subsequently, the weights of each environmental factor were determined using the Analytic Hierarchy Process (AHP), leading to the development of the Habitat Suitability Index (HSI). Seagrass habitat suitability maps for Caofeidian and Xingcheng areas were then generated using Geographic Information System (GIS). The results indicate that both seagrass ecosystems degraded during the study period, which coincided with a decreasing trend in habitat suitability shown by the suitability maps. This study provides a methodology for seagrass bed habitat suitability assessment, thereby contributing to the conservation and restoration of these vital ecosystems.}, }
@article {pmid39612036, year = {2024}, author = {Ma, D and Huang, Q and Wang, Q and Xu, H and Yan, Y}, title = {Detection of spatiotemporal changes in eco-environmental quality based on RSEI and SG filtering and its driving force analysis: a case study in Sichuan Province, China.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {12}, pages = {1274}, pmid = {39612036}, issn = {1573-2959}, support = {ZR2020MD025//Natural Science Foundation of Shandong Province/ ; 42171435//National Natural Science Foundation of China/ ; }, mesh = {China ; *Environmental Monitoring/methods ; *Remote Sensing Technology ; Forests ; Ecosystem ; Grassland ; Conservation of Natural Resources/methods ; }, abstract = {Landsat images were extracted using Google Earth Engine (GEE) platform and optimized by Savitzky-Golay (SG) filtering. The Remote Sensing Ecological Index (RSEI) method was used to analyze the eco-environmental quality in Sichuan Province in recent 20 years. In addition, Theil-Sen median method and Mann-Kendall (MK) test were used to test the change trend of eco-environmental quality. Furthermore, drivers were evaluated by partial correlation analysis, 2D scatter plots, and t tests. The results showed that (1) in the past 20 years, the eco-environmental quality of Sichuan Province was on the rise, and the eco-environmental quality in the western region was better than that in the eastern region. The eco-environmental quality was positively correlated with forest and grassland types, and negatively correlated with cultivated land and urban and rural construction land types. (2) The eco-environmental quality of Sichuan Province is linearly correlated with the digital elevation model, but poorly correlated with slope and slope direction. In the range of slope 0° ~ 9° and southeast direction, the eco-environmental quality is the worst. (3) The eco-environmental quality of Sichuan Province was most significantly affected by soil moisture and sunshine hours. The study can help us to understand and assess the health of ecosystems in Sichuan Province, provide a scientific basis for protecting and improving the environment, and guide the formulation and implementation of environmental protection policies.}, }
@article {pmid39611775, year = {2025}, author = {Andorf, CM and Ross-Ibarra, J and Seetharam, AS and Hufford, MB and Woodhouse, MR}, title = {A unified VCF dataset from nearly 1,500 diverse maize accessions and resources to explore the genomic landscape of maize.}, journal = {G3 (Bethesda, Md.)}, volume = {15}, number = {2}, pages = {}, pmid = {39611775}, issn = {2160-1836}, support = {5030-21000-072-00-D//US. Department of Agriculture, Agricultural Research Service/ ; //Corn Insects and Crop Genetics Research Unit in Ames, Iowa/ ; //Iowa State University/ ; //SCINet/ ; 0201-88888-003-000D//AI Center of Excellence of the USDA Agricultural Research Service/ ; CA-D-PLS-2066-H//USDA/ ; }, mesh = {*Zea mays/genetics ; *Genome, Plant ; *Genomics/methods ; Polymorphism, Single Nucleotide ; *Databases, Genetic ; Software ; Genotype ; Genetic Variation ; Molecular Sequence Annotation ; Linkage Disequilibrium ; }, abstract = {Efforts to capture and analyze maize nucleotide diversity have ranged widely in scope, but differences in reference genome version and software algorithms used in these efforts inhibit comparison, and these data are generally not available in an easy-to-use visualization platform for quick access and analysis. To address these issues, The Maize Genetics and Genomics Database has collaborated with maize researchers to offer variant data from a diverse set of 1,498 inbred lines, traditional varieties, and teosintes through a standardized variant-calling pipeline against version 5 of the B73 reference genome. The output was filtered for mapping quality, completeness, and linkage disequilibrium, and annotated based on variant effects relative to the B73 RefGen_v5 gene annotations. MaizeGDB has also updated a web tool, SNPversity 2.0, to filter, visualize, and download genotype sets based on genomic locations and accessions of interest, and added external datasets to demonstrate SNPversity 2.0's broad usage. MaizeGDB plans to host annual updates of these resources as additional resequencing data become available, with plans to expand to all publicly available sequence data.}, }
@article {pmid39611246, year = {2025}, author = {Armstrong, EE and Li, C and Campana, MG and Ferrari, T and Kelley, JL and Petrov, DA and Solari, KA and Mooney, JA}, title = {A Pipeline and Recommendations for Population and Individual Diagnostic SNP Selection in Non-Model Species.}, journal = {Molecular ecology resources}, volume = {25}, number = {3}, pages = {e14048}, pmid = {39611246}, issn = {1755-0998}, support = {R35 GM118165/GM/NIGMS NIH HHS/United States ; }, mesh = {*Polymorphism, Single Nucleotide ; *Genetics, Population/methods ; *Computational Biology/methods ; *Genotyping Techniques/methods ; }, abstract = {Despite substantial reductions in the cost of sequencing over the last decade, genetic panels remain relevant due to their cost-effectiveness and flexibility across a variety of sample types. In particular, single nucleotide polymorphism (SNP) panels are increasingly favoured for conservation applications. SNP panels are often used because of their adaptability, effectiveness with low-quality samples, and cost-efficiency for population monitoring and forensics. However, the selection of diagnostic SNPs for population assignment and individual identification can be challenging. The consequences of poor SNP selection are under-powered panels, inaccurate results, and monetary loss. Here, we develop a novel and user-friendly SNP selection pipeline (mPCRselect) that can be used to select SNPs for population assignment and/or individual identification. mPCRselect allows any researcher, who has sufficient SNP-level data, to design a successful and cost-effective SNP panel for a diploid species of conservation concern.}, }
@article {pmid39609505, year = {2024}, author = {Alvarez-Mamani, E and Buettner, F and Beltran-Castanon, CA and Ibanez, AJ}, title = {Exploratory analysis of metabolic changes using mass spectrometry data and graph embeddings.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {29570}, pmid = {39609505}, issn = {2045-2322}, support = {No. 174-2020-FONDECYT "Doctoral Programs in Peruvian Universities"//Consejo Nacional de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n Tecnol&#xf3;gica (CONCYTEC), and Fondo Nacional de Desarrollo Cient&#xed;fico, Tecnol&#xf3;gico y de Innovaci&#xf3;n Tecnol&#xf3;gica (FONDECYT)/ ; "The Max Planck Partner Group" (Max Planck Institute for Chemical Ecology-Jena)//Max-Planck-Gesellschaft/ ; "The Max Planck Partner Group" (Max Planck Institute for Chemical Ecology-Jena)//Max-Planck-Gesellschaft/ ; N&#xba; PE501086715-2024- PROCIENCIA)//CONCYTEC-Prociencia convocatoria E041-2024-01/ ; }, mesh = {*Metabolomics/methods ; *Mass Spectrometry/methods ; *Algorithms ; *Data Mining/methods ; Humans ; Deep Learning ; Metabolic Networks and Pathways ; Metabolome ; }, abstract = {Mass spectrometry (MS)-based metabolomics analysis is a powerful tool, but it comes with its own set of challenges. The MS workflow involves multiple steps before its interpretation in what is denominate data mining. Data mining consists of a two-step process. First, the MS data is ordered, arranged, and presented for filtering before being analyzed. Second, the filtered and reduced data are analyzed using statistics to remove further variability. This holds true particularly for MS-based untargeted metabolomics studies, which focused on understanding fold changes in metabolic networks. Since the task of filtering and identifying changes from a large dataset is challenging, automated techniques for mining untargeted MS-based metabolomic data are needed. The traditional statistics-based approach tends to overfilter raw data, which may result in the removal of relevant data and lead to the identification of fewer metabolomic changes. This limitation of the traditional approach underscores the need for a new method. In this work, we present a novel deep learning approach using node embeddings (powered by GNNs), edge embeddings, and anomaly detection algorithm to analyze the data generated by mass spectrometry (MS)-based metabolomics called GEMNA (Graph Embedding-based Metabolomics Network Analysis), for example for an untargeted volatile study on Mentos candy, the data clusters produced by GEMNA were better than the ones used traditional tools, i.e., GEMNA has [Formula: see text], vs. the traditional approach has [Formula: see text].}, }
@article {pmid39609363, year = {2025}, author = {Xu, S and Akhatayeva, Z and Liu, J and Feng, X and Yu, Y and Badaoui, B and Esmailizadeh, A and Kantanen, J and Amills, M and Lenstra, JA and Johansson, AM and Coltman, DW and Liu, GE and Curik, I and Orozco-terWengel, P and Paiva, SR and Zinovieva, NA and Zhang, L and Yang, J and Liu, Z and Wang, Y and Yu, Y and Li, M}, title = {Genetic advancements and future directions in ruminant livestock breeding: from reference genomes to multiomics innovations.}, journal = {Science China. Life sciences}, volume = {68}, number = {4}, pages = {934-960}, pmid = {39609363}, issn = {1869-1889}, mesh = {Animals ; *Livestock/genetics ; *Genomics/methods ; *Breeding/methods ; *Ruminants/genetics ; *Genome ; Phenotype ; Multiomics ; }, abstract = {Ruminant livestock provide a rich source of products, such as meat, milk, and wool, and play a critical role in global food security and nutrition. Over the past few decades, genomic studies of ruminant livestock have provided valuable insights into their domestication and the genetic basis of economically important traits, facilitating the breeding of elite varieties. In this review, we summarize the main advancements for domestic ruminants in reference genome assemblies, population genomics, and the identification of functional genes or variants for phenotypic traits. These traits include meat and carcass quality, reproduction, milk production, feed efficiency, wool and cashmere yield, horn development, tail type, coat color, environmental adaptation, and disease resistance. Functional genomic research is entering a new era with the advancements of graphical pangenomics and telomere-to-telomere (T2T) gap-free genome assembly. These advancements promise to improve our understanding of domestication and the molecular mechanisms underlying economically important traits in ruminant livestock. Finally, we provide new perspectives and future directions for genomic research on ruminant genomes. We suggest how ever-increasing multiomics datasets will facilitate future studies and molecular breeding in livestock, including the potential to uncover novel genetic mechanisms underlying phenotypic traits, to enable more accurate genomic prediction models, and to accelerate genetic improvement programs.}, }
@article {pmid39606930, year = {2024}, author = {Whyte, M and Wambui, KM and Musenge, E}, title = {Nigeria's malaria prevalence in 2015: a geospatial, exploratory district-level approach.}, journal = {Geospatial health}, volume = {19}, number = {2}, pages = {}, doi = {10.4081/gh.2024.1243}, pmid = {39606930}, issn = {1970-7096}, mesh = {Humans ; Nigeria/epidemiology ; *Malaria/epidemiology ; Prevalence ; Child, Preschool ; Infant ; *Spatial Analysis ; Female ; Male ; *Geographic Information Systems ; Socioeconomic Factors ; Adult ; Adolescent ; Child ; Middle Aged ; Young Adult ; }, abstract = {This study used data from the second Nigeria Malaria Indicator Survey (NMIS) conducted in 2015 to investigate the spatial distribution of malaria prevalence in the country and identify its associated factors. Nigeria is divided into 36 states with 109 senatorial districts, most of which are affected by malaria, a major cause of morbidity and mortality in children under five years of age. We carried out an ecological study with analysis at the senatorial district level. A malaria prevalence map was produced combining geographic information systems data from the Nigeria Malaria Indicator Survey (NMIS) of 2015 with shape files from an open data-sharing platform. Spatial autoregressive models were fitted using a set of key covariates. Malaria prevalence in children under-five was highest in Kebbi South senatorial district (70.6%). It was found that poorest wealth index (β = 0.10 (95% CI: 0.01, 0.20), p = 0.04), mothers having only secondary level of education (β = 0.78 (95% CI: 0.05, 1.51), p = 0.04) and households without mosquito bed nets (β = 0.21 (95% CI: 0.02, 0.39), p = 0.03) were all significantly associated with higher malaria prevalence. Moran's I (54.81, p<0.001) showed spatial dependence of malaria prevalence across contiguous districts and spatial autoregressive modelling demonstrated significant spill-over effect of malaria prevalence. Maps produced in this study provide a useful graphical representation of the spatial distribution of malaria prevalence based on NMIS-2015 data. Clustering of malaria prevalence in certain areas further highlights the need for sustained malaria elimination interventions across affected regions in order to break the chain of transmission.}, }
@article {pmid39602490, year = {2024}, author = {Soares, R and Azevedo, L and Vasconcelos, V and Pratas, D and Sousa, SF and Carneiro, J}, title = {Machine Learning-Driven Discovery and Database of Cyanobacteria Bioactive Compounds: A Resource for Therapeutics and Bioremediation.}, journal = {Journal of chemical information and modeling}, volume = {64}, number = {24}, pages = {9576-9593}, doi = {10.1021/acs.jcim.4c00995}, pmid = {39602490}, issn = {1549-960X}, mesh = {*Cyanobacteria/metabolism ; *Machine Learning ; *Biodegradation, Environmental ; *Drug Discovery ; Molecular Docking Simulation ; Databases, Factual ; Databases, Chemical ; Humans ; Software ; }, abstract = {Cyanobacteria strains have the potential to produce bioactive compounds that can be used in therapeutics and bioremediation. Therefore, compiling all information about these compounds to consider their value as bioresources for industrial and research applications is essential. In this study, a searchable, updated, curated, and downloadable database of cyanobacteria bioactive compounds was designed, along with a machine-learning model to predict the compounds' targets of newly discovered molecules. A Python programming protocol obtained 3431 cyanobacteria bioactive compounds, 373 unique protein targets, and 3027 molecular descriptors. PaDEL-descriptor, Mordred, and Drugtax software were used to calculate the chemical descriptors for each bioactive compound database record. The biochemical descriptors were then used to determine the most promising protein targets for human therapeutic approaches and environmental bioremediation using the best machine learning (ML) model. The creation of our database, coupled with the integration of computational docking protocols, represents an innovative approach to understanding the potential of cyanobacteria bioactive compounds. This resource, adhering to the findability, accessibility, interoperability, and reuse of digital assets (FAIR) principles, is an excellent tool for pharmaceutical and bioremediation researchers. Moreover, its capacity to facilitate the exploration of specific compounds' interactions with environmental pollutants is a significant advancement, aligning with the increasing reliance on data science and machine learning to address environmental challenges. This study is a notable step forward in leveraging cyanobacteria for both therapeutic and ecological sustainability.}, }
@article {pmid39600916, year = {2021}, author = {Boyes, D and Crowley, LM and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the harlequin ladybird, Harmonia axyridis (Pallas, 1773).}, journal = {Wellcome open research}, volume = {6}, number = {}, pages = {300}, pmid = {39600916}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Harmonia axyridis (the harlequin ladybird; Arthropoda; Insecta; Coleoptera; Coccinellidae). The genome sequence is 426 megabases in span. The majority (99.98%) of the assembly is scaffolded into 8 chromosomal pseudomolecules, with the X sex chromosome assembled.}, }
@article {pmid39599286, year = {2024}, author = {Toghan, A and Alduaij, OK and Sanad, MMS and Elessawy, NA}, title = {Scalable Engineering of 3D Printing Filaments Derived from Recycling of Plastic Drinking Water Bottle and Glass Waste.}, journal = {Polymers}, volume = {16}, number = {22}, pages = {}, pmid = {39599286}, issn = {2073-4360}, support = {IMSIU-RG23086//Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University/ ; }, abstract = {The most significant challenge that the world is currently facing is the development of beneficial industrial applications for solid waste. A novel strategy was implemented to produce a composite with varying loadings of glass waste nanoparticles (GWNP) in 5, 10, and 15 wt.% with recycled polyethylene terephthalate drinking water bottle waste (RPET). This strategy was based on glass and drinking water bottle waste. An analysis was conducted to evaluate the performance of the composite as filaments for 3D printer applications. This study evaluated the effect of GWNP addition on the chemical structure, thermal and mechanical characteristics of the composite. The Fourier Transform Infrared (FTIR) spectra of the filament composites and RPET composites exhibited similarities. However, the mechanical strength and thermal stability of the filament composites were enhanced due to the increased GWNP content. Furthermore, the results indicated that the filament developed could be utilized for 3D printing, as demonstrated by the successful fabrication of the filament composite, including 5 wt.% GWNP, using a 3D printer pen. The production of filaments using GWNP and RPET matrix presents a cost-effective, high-yield, and ecologically beneficial alternative. The present study may pave the way for the future advancement and utilization of 3D printing filaments by treating hazardous waste and using more ecologically friendly materials in design applications.}, }
@article {pmid39597377, year = {2024}, author = {Maślanka, P and Korycki, R}, title = {Material, Aerodynamic, and Operational Aspects of Single-Skin Paraglider.}, journal = {Materials (Basel, Switzerland)}, volume = {17}, number = {22}, pages = {}, pmid = {39597377}, issn = {1996-1944}, abstract = {The operating comfort of a paraglider is created by the aerodynamic parameters as well as the mass and packing volume of the wing. A classic paraglider has upper and lower covers. To reduce the material and manufacturing costs as well as protect the environment, it is possible to introduce a single-skin wing. This article conducts an analysis of a single-skin paraglider covered only with upper panels, whereas the lower cover is applied only at the leading and trailing edges. The analysis is theoretically oriented; aerodynamic and structural calculations were performed using the ANSYS environment. The single-skin structure was evaluated in terms of the predicted behavior during flight and the material's deformation under the influence of a specified pressure and the overloads acting on it. The results show that developing these structures may influence the creation of models with comparable aerodynamic characteristics to traditional ones. Additionally, the reduced masses and packing volumes of difficult-to-degrade materials are strongly correlated with saving costs and an ecological approach. No corresponding studies were found in the available literature. Thus, this presented analysis may result in a greater understanding and application of this paraglider type.}, }
@article {pmid39596552, year = {2024}, author = {Signore, IA and Donoso, G and Bocchieri, P and Tobar-Calfucoy, EA and Yáñez, CE and Carvajal-Silva, L and Silva, AX and Otth, C and Cappelli, C and Valenzuela Jorquera, H and Zapata-Contreras, D and Espinosa-Parrilla, Y and Zúñiga-Pacheco, P and Fuentes-Guajardo, M and Monardes-Ramírez, VA and Kochifas Velasquez, P and Muñoz, CA and Dorador, C and García-Araya, J and Campillay-Véliz, CP and Echeverria, C and Santander, RA and Cerpa, LC and Martínez, MF and Quiñones, LA and Lamoza Galleguillos, ER and Saez Hidalgo, J and Nova-Lamperti, E and Sanhueza, S and Giacaman, A and Acosta-Jamett, G and Verdugo, C and Plaza, A and Verdugo, C and Selman, C and Verdugo, RA and Colombo, A}, title = {The Chilean COVID-19 Genomics Network Biorepository: A Resource for Multi-Omics Studies of COVID-19 and Long COVID in a Latin American Population.}, journal = {Genes}, volume = {15}, number = {11}, pages = {}, pmid = {39596552}, issn = {2073-4425}, support = {ANID COVID0961, ANID COVID0789, ANID COVID1005, ANID COVID0585, ACT210085, FONDECYT 1170446, FONDECYT 1211480//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; MAG1995//Ministry of Education/ ; RED21193//Interuniversity Center for Healthy Aging/ ; VRID220.085.041-INI//University of Concepci&#xf3;n/ ; }, mesh = {Humans ; *COVID-19/genetics/virology/epidemiology ; Chile ; *Biological Specimen Banks ; *Genomics/methods ; *SARS-CoV-2/genetics ; Male ; Female ; Adult ; Middle Aged ; Aged ; Latin America ; Multiomics ; }, abstract = {Although a lack of diversity in genetic studies is an acknowledged obstacle for personalized medicine and precision public health, Latin American populations remain particularly understudied despite their heterogeneity and mixed ancestry. This gap extends to COVID-19 despite its variability in susceptibility and clinical course, where ethnic background appears to influence disease severity, with non-Europeans facing higher hospitalization rates. In addition, access to high-quality samples and data is a critical issue for personalized and precision medicine, and it has become clear that the solution lies in biobanks. The creation of the Chilean COVID-19 Biorepository reported here addresses these gaps, representing the first nationwide multicentric Chilean initiative. It operates under rigorous biobanking standards and serves as one of South America's largest COVID cohorts. A centralized harmonization strategy was chosen and included unified standard operating procedures, a sampling coding system, and biobanking staff training. Adults with confirmed SARS-CoV-2 infection provided broad informed consent. Samples were collected to preserve blood, plasma, buffy coat, and DNA. Quality controls included adherence to the standard preanalytical code, incident reporting, and DNA concentration and absorbance ratio 260/280 assessments. Detailed sociodemographic, health, medication, and preexisting condition data were gathered. In five months, 2262 participants were enrolled, pseudonymized, and sorted by disease severity. The average Amerindian ancestry considering all participant was 44.0% [SD 15.5%], and this value increased to 61.2% [SD 19.5%] among those who self-identified as Native South Americans. Notably, 279 participants self-identified with one of 12 ethnic groups. High compliance (>90%) in all assessed quality controls was achieved. Looking ahead, our team founded the COVID-19 Genomics Network (C19-GenoNet) focused on identifying genetic factors influencing SARS-CoV-2 outcomes. In conclusion, this bottom-up collaborative effort aims to promote the integration of Latin American populations into global genetic research and welcomes collaborations supporting this endeavor. Interested parties are invited to explore collaboration opportunities through our catalog, accessible online.}, }
@article {pmid39595758, year = {2024}, author = {Aras, SG and Runyon, JR and Kazman, JB and Thayer, JF and Sternberg, EM and Deuster, PA}, title = {Is Greener Better? Quantifying the Impact of a Nature Walk on Stress Reduction Using HRV and Saliva Cortisol Biomarkers.}, journal = {International journal of environmental research and public health}, volume = {21}, number = {11}, pages = {}, pmid = {39595758}, issn = {1660-4601}, support = {XX//The Institute for Integrative Health and Nature Sacred/ ; }, mesh = {Humans ; *Hydrocortisone/analysis/metabolism ; *Saliva/chemistry ; *Walking/physiology ; *Heart Rate/physiology ; Male ; Adult ; Female ; *Biomarkers/analysis/metabolism ; Stress, Psychological/metabolism/physiopathology ; Affect/physiology ; Stress, Physiological/physiology ; Young Adult ; Nature ; Middle Aged ; }, abstract = {The physiological impact of walking in nature was quantified via continuous heart rate variability (HRV), pre- and post-walk saliva cortisol measures, and self-reported mood and mindfulness scores for N = 17 participants who walked "The Green Road" at Walter Reed National Military Medical Center in Bethesda, Maryland. For N = 15 of the participants, HRV analysis revealed two main groups: group one individuals had a 104% increase (mean) in the root mean square standard deviation (RMSSD) and a 47% increase (mean) in the standard deviation of NN values (SDNN), indicating an overall reduction in physiological stress from walking the Green Road, and group two individuals had a decrease (mean) of 42% and 31% in these respective HRV metrics, signaling an increase in physiological stresses. Post-walk self-reported scores for vigor and mood disturbance were more robust for the Green Road than for a comparable urban road corridor and showed that a higher HRV during the walk was associated with improved overall mood. Saliva cortisol was lower after taking a walk for all participants, and it showed that walking the Green Road elicited a significantly larger reduction in cortisol of 53%, on average, when compared with 37% of walking along an urban road. It was also observed that the order in which individuals walked the Green Road and urban road also impacted their cortisol responses, with those walking the urban road before the Green Road showing a substantial reduction in cortisol, suggesting a possible attenuation effect of walking the Green Road first. These findings provide quantitative data demonstrating the stress-reducing effects of being in nature, thus supporting the health benefit value of providing access to nature more broadly in many settings.}, }
@article {pmid39594004, year = {2024}, author = {Alrhmoun, M and Sulaiman, N and Haq, SM and Abidullah, S and Prakofjewa, J and Krigas, N and Pieroni, A and Sõukand, R}, title = {Is Boiling Bitter Greens a Legacy of Ancient Crete? Contemporary Foraging in the Minoan Refugium of the Lasithi Plateau.}, journal = {Foods (Basel, Switzerland)}, volume = {13}, number = {22}, pages = {}, pmid = {39594004}, issn = {2304-8158}, support = {N/A//University of Gastronomic Sciences, Pollenzo, Italy/ ; N/A//Department of Environmental Sciences, Informatics, and Statistics, Ca' Foscari Uni-versity of Venice, Italy/ ; }, abstract = {Wild greens (WGs) play a significant role in Mediterranean diets (MDs), reflecting botanical and cultural diversities, mainly influenced by a complex conglomerate of local human ecologies. This study investigates local ecological knowledge (LEK) linked to traditional gathering and consumption of WGs in the Lasithi Plateau of eastern Crete, where human genetic studies one decade ago showed very peculiar patterns, hypothesising that the Minoan civilisation took refuge there before it disappeared. A field ethnobotanical study was conducted to document the diversity of WGs and their detailed local culinary uses in the Lasithi area by interviewing 31 study participants. Fifty-nine folk taxa (species and subspecies) were recorded, corresponding to fifty-eight botanical taxa. A quotation index was measured to assess the cultural significance of WGs in the study areas; logistic regression analysis was adopted to understand the impact of sensory classifications of WGs and their local cooking methods. Lasithi's foraging showed a notable prevalence of bitter-tasting WGs, which play a central role in local cognition and culinary practices. This bitterness aspect of WGs, potentially influenced by cultural preferences and genetic factors, probably suggests a connection to the ancient Lasithi's inhabitants, i.e., Minoan dietary habits. We found that bitterness is the predominant sensory attribute in Lasithi, characterising 45.76% of the WGs. These findings underscore the complex interplay between local ecologies and biodiversity, LEK, and dietary traditions, highlighting the importance of WGs in understanding the evolution of foraging and plant culinary diversities across the Mediterranean.}, }
@article {pmid39592922, year = {2024}, author = {Das, VA and Gautam, B and Yadav, PK and Varadwaj, PK and Wadhwa, G and Singh, S}, title = {Computational approach to identify novel genomic features conferring high fitness in Bacillus atrophaeus CNY01 and Bacillus velezensis AK-0 associated with plant growth promotion (PGP) in apple.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {1127}, pmid = {39592922}, issn = {1471-2229}, mesh = {*Bacillus/genetics/physiology ; *Malus/microbiology/genetics ; *Genome, Bacterial ; Genetic Fitness ; Genomics/methods ; Genomic Islands ; Computational Biology/methods ; }, abstract = {A comparative genomic analysis approach provides valuable information about genetic variations and evolutionary relationships among microorganisms, aiding not only in the identification of functional genes responsible for traits such as pathogenicity, antibiotic resistance, and metabolic capabilities but also in enhancing our understanding of microbial genomic diversity and their ecological roles, such as supporting plant growth promotion, thereby enabling the development of sustainable strategies for agriculture. We used two strains from different Bacillus species, Bacillus velezensis AK-0 and Bacillus atrophaeus CNY01, which have previously been reported to have PGP activity in apple, and performed comparative genomic analysis to understand their evolutionary process and obtain a mechanistic understanding of their plant growth-promoting activity. We identified genomic features such as mobile genetic elements (MGEs) that encode key proteins involved in the survival, adaptation and growth of these bacterial strains. The presence of genomic islands and intact prophage DNA in Bacillus atrophaeus CNY01 and Bacillus velezensis AK-0 suggests that horizontal gene transfer has contributed to their diversification and acquisition of adaptive traits, enhancing their evolutionary advantage. We also identified novel DNA motifs that are associated with key physiological processes and metabolic pathways.}, }
@article {pmid39591252, year = {2024}, author = {Baradaran, M and Salabi, F and Mahdavinia, M and Mohammadi, E and Vazirianzadeh, B and Avella, I and Kazemi, SM and Lüddecke, T}, title = {ScorpDb: A Novel Open-Access Database for Integrative Scorpion Toxinology.}, journal = {Toxins}, volume = {16}, number = {11}, pages = {}, pmid = {39591252}, issn = {2072-6651}, mesh = {*Scorpion Venoms/chemistry ; *Scorpions ; Animals ; Humans ; Databases, Factual ; Scorpion Stings/drug therapy ; Databases, Protein ; }, abstract = {Scorpion stings are a significant public health concern globally, particularly in tropical and subtropical regions. Scorpion venoms contain a diverse array of bioactive peptides, and different scorpion species around the world typically exhibit varying venom profiles, resulting in a wide range of envenomation symptoms. Despite their harmful effects, scorpion venom peptides hold immense potential for drug development due to their unique characteristics. Therefore, the establishment of a comprehensive database that catalogs scorpions along with their known venom peptides and proteins is imperative in furthering research efforts in this research area. We hereby present ScorpDb, a novel database that offers convenient access to data related to different scorpion species, the peptides and proteins found in their venoms, and the symptoms they can cause. To this end, the ScorpDb database has been primarily advanced to accommodate data on the Iranian scorpion fauna. From there, we propose future community efforts to include a larger diversity of scorpions and scorpion venom components. ScorpDb holds the promise to become a valuable resource for different professionals from a variety of research fields, like toxinologists, arachnologists, and pharmacologists. The database is available at https://www.scorpdb.com/.}, }
@article {pmid39591213, year = {2024}, author = {Roman-Ramos, H and Ho, PL}, title = {Current Technologies in Snake Venom Analysis and Applications.}, journal = {Toxins}, volume = {16}, number = {11}, pages = {}, pmid = {39591213}, issn = {2072-6651}, support = {2017/18398-1//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 309741/2023-8//National Council for Scientific and Technological Development/ ; }, mesh = {*Snake Venoms/chemistry ; Animals ; *Proteomics ; Humans ; Genomics ; Computational Biology ; Snakes ; }, abstract = {This comprehensive review explores the cutting-edge advancements in snake venom research, focusing on the integration of proteomics, genomics, transcriptomics, and bioinformatics. Highlighting the transformative impact of these technologies, the review delves into the genetic and ecological factors driving venom evolution, the complex molecular composition of venoms, and the regulatory mechanisms underlying toxin production. The application of synthetic biology and multi-omics approaches, collectively known as venomics, has revolutionized the field, providing deeper insights into venom function and its therapeutic potential. Despite significant progress, challenges such as the functional characterization of toxins and the development of cost-effective antivenoms remain. This review also discusses the future directions of venom research, emphasizing the need for interdisciplinary collaborations and new technologies (mRNAs, cryo-electron microscopy for structural determinations of toxin complexes, synthetic biology, and other technologies) to fully harness the biomedical potential of venoms and toxins from snakes and other animals.}, }
@article {pmid39589804, year = {2025}, author = {Arias, M and Behrendt, L and Dreßler, L and Raka, A and Perrier, C and Elias, M and Gomez, D and Renoult, JP and Tedore, C}, title = {Testing the equivalency of human "predators" and deep neural networks in the detection of cryptic moths.}, journal = {Journal of evolutionary biology}, volume = {38}, number = {2}, pages = {214-224}, doi = {10.1093/jeb/voae146}, pmid = {39589804}, issn = {1420-9101}, support = {ANR-16-CE02-0012//Clearwing ANR/ ; ANR-10-LABX-04-01//LabEx CeMEB/ ; }, mesh = {Animals ; *Moths/physiology/anatomy &amp; histology ; *Neural Networks, Computer ; Humans ; *Biological Mimicry ; *Predatory Behavior ; }, abstract = {Researchers have shown growing interest in using deep neural networks (DNNs) to efficiently test the effects of perceptual processes on the evolution of colour patterns and morphologies. Whether this is a valid approach remains unclear, as it is unknown whether the relative detectability of ecologically relevant stimuli to DNNs actually matches that of biological neural networks. To test this, we compare image classification performance by humans and 6 DNNs (AlexNet, VGG-16, VGG-19, ResNet-18, SqueezeNet, and GoogLeNet) trained to detect artificial moths on tree trunks. Moths varied in their degree of crypsis, conferred by different sizes and spatial configurations of transparent wing elements. Like humans, four of six DNN architectures found moths with larger transparent elements harder to detect. However, humans and only one DNN architecture (GoogLeNet) found moths with transparent elements touching one side of the moth's outline harder to detect than moths with untouched outlines. When moths took up a smaller proportion of the image (i.e., were viewed from further away), the camouflaging effect of transparent elements touching the moth's outline was reduced for DNNs but enhanced for humans. Viewing distance can thus interact with camouflage type in opposing directions in humans and DNNs, which warrants a deeper investigation of viewing distance/size interactions with a broader range of stimuli. Overall, our results suggest that human and DNN responses had some similarities, but not enough to justify widespread use of DNNs for studies of camouflage.}, }
@article {pmid39586965, year = {2024}, author = {Gianicolo, E and Russo, A and Di Staso, R and Ronckers, CM and Schmidtmann, I and Wollschläger, D and Blettner, M}, title = {A municipality-specific analysis to investigate persistent increased incidence rates of childhood leukaemia near the nuclear power plant of Krümmel in Germany.}, journal = {European journal of epidemiology}, volume = {39}, number = {12}, pages = {1373-1378}, pmid = {39586965}, issn = {1573-7284}, mesh = {Humans ; Germany/epidemiology ; Child ; *Nuclear Power Plants ; Incidence ; Male ; Child, Preschool ; Female ; *Leukemia/epidemiology ; Adolescent ; Infant ; *Registries ; Leukemia, Radiation-Induced/epidemiology ; Infant, Newborn ; Cities/epidemiology ; Environmental Exposure/adverse effects/statistics &amp; numerical data ; Risk Factors ; }, abstract = {Increased incidence rates for childhood leukaemia have been reported in municipalities close to the nuclear power plant (NPP) Krümmel (Geesthacht, Germany). Methodological challenges arise when analysing this association at ecological level. They include the use of an appropriate reference population, unstable estimates of standardised incidence ratios (SIRs), and the potential role of prevailing winds. The aim of our study is to address these challenges. The German Childhood Cancer Registry provided data on leukaemia in children under 15 years (2004-2019). The German Federal Statistical Office provided the population data. The study region included all municipalities with ≥ 75% surface area within 50 kms from the Krümmel NPP. We calculated SIRs using national and regional reference rates. Smoothed incidence relative rates (IRRs) were calculated and mapped to check for potential patterns associated with prevailing winds. Overall 356 cases of childhood leukaemia were observed in the study region (321 municipalities) during 2004-2019. SIRs based on national reference rates show nearly no difference to those calculated using the regional rates as reference. Increased SIR and IRR were observed in Geesthacht (observed-cases = eight; SIR = 2.29; 95% confidence interval: 0.99-4.51. IRR = 1.80; 95% credibility interval: 0.88-2.79). The analysis of the IRR map does not show patterns associated with prevailing winds. Using a regional population as the reference, we found evidence that there may still be an increased risk for childhood leukaemia in Geesthacht. However, IRR estimates are uncertain and credibility intervals are compatible with the absence of elevated risk. The persistent evidence of risk of childhood leukaemia in Geesthacht warrants further epidemiological surveillance.}, }
@article {pmid39586901, year = {2025}, author = {Ma, Y and Xu, L and Zhuang, H and Abd-Eldaim, FA and Tang, Z and Dewer, Y and Wang, H}, title = {Evaluation of Skin Color Supervision Genes in Chickpea Seeds by Multiomics.}, journal = {Molecular biotechnology}, volume = {67}, number = {11}, pages = {4280-4288}, pmid = {39586901}, issn = {1559-0305}, support = {NICGR2019-029//National Infrastructure for Crop Germplasm Resources of China/ ; PT2030//Xinjiang Uygur Autonomous Region Science and Technology Innovation Base Construction/ ; 2017E01023-1//Xinjiang Uygur Autonomous Region Regional Collaborative Innovation Project/ ; }, mesh = {*Seeds/genetics/metabolism ; Gene Expression Regulation, Plant ; *Cicer/genetics/metabolism ; Plant Proteins/genetics/metabolism ; Flavonoids/metabolism ; Gene Expression Profiling ; Transcriptome ; *Pigmentation/genetics ; Metabolome ; Genes, Plant ; Multiomics ; }, abstract = {Seed samples of two types of chickpea (Cicer arietinum Linn.), including variety A (NRCGR-4452) and variety B (local varieties), with different seed colors, were collected every five days for a total of four times during the seed development period. Non-targeted metabolome and transcriptome sequencing were conducted to identify differentially expressed genes and metabolites associated with chickpea seed coat color. The results indicated that the relative quercetin, pelargonidin, luteolin, rutin, myricetin, kaempferol, glycitin, and naringin contents were higher in variety A than in variety B, and that carbohydrate and amino acid metabolites had a greater impact on flavonoid metabolites. Quercetin, luteolin, and kaempferol were most significantly associated with seed color differences, the associated enzyme genes were LOC101491583 (callose synthase 5-like), LOC101503703 (flavonoid 3',5'-hydroxylase), LOC101514158 (callose synthase 5), LOC101497872 (UDP-glycosyltransferase 74F1-like), LOC101500232 (callose synthase 7 isoform X1), LOC101511206 (UDP-glycosyltransferase 73C3-like), LOC101502065 (galactoside 2-alpha-L-fucosyltransferase), LOC101492791 (sulfoquinovosyl transferase SQD2), and LOC101509377 (flavonol synthase). Additionally, the gene transcription factor MYB44 may regulate UDP-glycosyltransferase 73C3 to affect seed color differences.}, }
@article {pmid39585857, year = {2024}, author = {Adderley-Heron, K and Chow-Fraser, P}, title = {Unsupervised classification of Blanding's turtle (Emydoidea blandingii) behavioural states from multi-sensor biologger data.}, journal = {PloS one}, volume = {19}, number = {11}, pages = {e0314291}, pmid = {39585857}, issn = {1932-6203}, mesh = {Animals ; *Turtles/physiology/classification ; Female ; Male ; *Behavior, Animal/physiology ; Accelerometry ; Markov Chains ; Geographic Information Systems ; Nesting Behavior/physiology ; }, abstract = {Classifying animal behaviors in their natural environments is both challenging and ecologically important, but the use of biologgers with multiple sensors has significantly advanced this research beyond the capabilities of traditional methods alone. Here, we show how biologgers containing an integrated tri-axial accelerometer, GPS logger and immersion sensor were used to infer behavioural states of a cryptic, freshwater turtle, the Blanding's turtle (Emydoidea blandingii). Biologgers were attached to three males and five females that reside in two undisturbed coastal marshes in northeastern Georgian Bay (Ontario, Canada) between May and July 2023. Raw acceleration values were separated into static and dynamic acceleration and subsequently used to calculate overall dynamic body acceleration (ODBA) and pitch. The unsupervised Hidden Markov Model (HMM) successfully differentiated five behavioural states as follows: active in water, resting in water, active out of water, resting in water, and nesting. Overall accuracy of the classification was 93.8%, and except for nesting (79%), all other behaviours were above 92%. There were significant differences in daily activity budgets between male and female turtles, with females spending a greater proportion of time active out of water, and inactive out of the water, while males spent a greater proportion of time active in water. These differences were likely a result of large seasonal life-history requirements such as nesting and mate finding. Accurate classification of behavioural states is important for researchers to understand fine-scale activities carried out during the active season and how environmental variables may influence the behaviours of turtles in their natural habitats.}, }
@article {pmid39585479, year = {2024}, author = {Sahak, AS and Karsli, F and Saraj, MA}, title = {Evaluating the impact of urban sprawl on the urban ecological status using GIS and remote sensing from 2000 to 2021: a case study of Herat City, Afghanistan.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {12}, pages = {1246}, pmid = {39585479}, issn = {1573-2959}, mesh = {*Geographic Information Systems ; *Remote Sensing Technology ; *Environmental Monitoring/methods ; *Urbanization ; *Cities ; Afghanistan ; Conservation of Natural Resources/methods ; Ecosystem ; }, abstract = {Urbanization often incurs environmental costs, as fertile agricultural and forested lands are converted into urban areas. Herat City is currently undergoing significant urban transformation. This research aims to assess the impact of urban sprawl on Herat City's urban ecological status during 2000, 2013, and 2021, using GIS and remote sensing. The urban expansion intensity index was used to measure urban sprawl. The Mean Remote Sensing Ecological Index (MRSEI), integrating known granulation entropy (KGE) and comprehensive distance-based ranking (COBRA) algorithms, was utilized to evaluate urban ecological status. The random forest (RF) supervised machine learning-based algorithm was used to classify the study area into four categories (Built-up, Bare-land, Water, and Vegetation). Findings indicate rapid development from 2000 to 2013, followed by moderate expansion until 2021. Urban ecological quality degradation is observed in various directions over time, with the southeast consistently demonstrating excellent status. Interestingly, while good and excellent urban ecological status decreases over two decades, poor and very poor conditions improve. The research underscores an inverse relationship between urban expansion intensity and ecological status, highlighting the need for improved strategies to mitigate environmental decline. These findings will inform Afghan governmental bodies and international organizations, enabling them to better address resource consumption, ecological disruptions, social inequalities, and foster sustainable development.}, }
@article {pmid39584487, year = {2025}, author = {Daru, BH}, title = {A global database of butterfly species native distributions.}, journal = {Ecology}, volume = {106}, number = {1}, pages = {e4462}, doi = {10.1002/ecy.4462}, pmid = {39584487}, issn = {1939-9170}, support = {2345994//National Science Foundation/ ; 2416314//National Science Foundation/ ; }, mesh = {*Butterflies/physiology ; Animals ; *Animal Distribution ; *Databases, Factual ; Ecosystem ; Species Specificity ; }, abstract = {Butterflies represent a diverse group of insects, playing key ecosystem roles such as pollination and their larval form engage in herbivory. Despite their importance, comprehensive global distribution data for butterfly species are lacking. This lack of comprehensive global data has hindered many large-scale questions in ecology, evolutionary biology, and conservation at the regional and global scales. Here, I use an integrative workflow that combines occurrence records, alpha hull polygons, species' dispersal capacity, and natural habitat and environmental variables within a framework of species distribution models to generate species-level native distributions for butterflies at a global scale in the contemporary period. The database releases native range maps for 10,372 extant species of butterflies at a spatial grain resolution of 5 arcmin (~10 km). This database has the potential to allow unprecedented large-scale analyses in ecology, biogeography, and conservation of butterflies. The maps are available in the WGS84 coordinate reference system (EPSG:4326 code) and stored as vector polygons in the GEOPACKAGE format for maximum compression, allowing easy data manipulation using a standard computer. I additionally provide each species' spatial raster. All maps and R scripts are open access and available for download in Dryad and Zenodo, respectively, and are guided by FAIR (Findable, Accessible, Interoperable, and Reusable) data principles. By making these data available to the scientific community, I aim to advance the sharing of biological data to stimulate more comprehensive research in ecology, biogeography, and conservation of butterflies.}, }
@article {pmid39583330, year = {2024}, author = {Hakkenberg, CR and Clark, ML and Bailey, T and Burns, P and Goetz, SJ}, title = {Ladder fuels rather than canopy volumes consistently predict wildfire severity even in extreme topographic-weather conditions.}, journal = {Communications earth &amp; environment}, volume = {5}, number = {1}, pages = {721}, pmid = {39583330}, issn = {2662-4435}, abstract = {Drivers of forest wildfire severity include fuels, topography and weather. However, because only fuels can be actively managed, quantifying their effects on severity has become an urgent research priority. Here we employed GEDI spaceborne lidar to consistently assess how pre-fire forest fuel structure affected wildfire severity across 42 California wildfires between 2019-2021. Using a spatial-hierarchical modeling framework, we found a positive concave-down relationship between GEDI-derived fuel structure and wildfire severity, marked by increasing severity with greater fuel loads until a decline in severity in the tallest and most voluminous forest canopies. Critically, indicators of canopy fuel volumes (like biomass and height) became decoupled from severity patterns in extreme topographic and weather conditions (slopes >20°; winds > 9.3 m/s). On the other hand, vertical continuity metrics like layering and ladder fuels more consistently predicted severity in extreme conditions - especially ladder fuels, where sparse understories were uniformly associated with lower severity levels. These results confirm that GEDI-derived fuel estimates can overcome limitations of optical imagery and airborne lidar for quantifying the interactive drivers of wildfire severity. Furthermore, these findings have direct implications for designing treatment interventions that target ladder fuels versus entire canopies and for delineating wildfire risk across topographic and weather conditions.}, }
@article {pmid39581005, year = {2024}, author = {Tinsley, E and Froidevaux, JSP and Jones, G}, title = {The location of solar farms within England's ecological landscape: Implications for biodiversity conservation.}, journal = {Journal of environmental management}, volume = {372}, number = {}, pages = {123372}, doi = {10.1016/j.jenvman.2024.123372}, pmid = {39581005}, issn = {1095-8630}, mesh = {*Biodiversity ; England ; *Conservation of Natural Resources ; *Ecosystem ; Solar Energy ; Farms ; Geographic Information Systems ; Ecology ; Agriculture ; }, abstract = {A global energy transition to using sustainable renewable sources is being driven by global agreements. Simultaneously there is a call for increased biodiversity conservation. This creates a green-green dilemma, where the expansion of renewables could lead to the demise of biodiversity if not carefully assessed, managed and monitored. Recognition of the dilemma is central to the development of Sustainable Development Goals. It is therefore important to understand whether renewable energy sources such as solar farms are being sited in areas where they have minimal impact on biodiversity. If solar farms were sited with minimal impacts on biodiversity, we hypothesised that they would be less likely to be sited close to ecologically sensitive areas than near random points. We used Geographic Information System methods to explore the density of solar photovoltaic (PV) farms in England and assessed their siting relative to sensitive ecological features, including priority habitat types, designated sites, and land conservation initiatives. We compared the area of 25 sensitive ecological features around solar farms and random points across three spatial scales (100 m, 1000 m, and 6000 m radius scales). Solar farms were distributed throughout England, with the highest concentration in South West England. Solar sites were primarily surrounded by habitats with anthropogenic influences, such as agricultural and urban settings. Priority habitats, such as woodland, grassland, wetland and heathland, were more extensive around random points across spatial scales (except for woodland at the largest scale). Most designated sites were significantly more extensive around random points. We conclude that, under current planning regulations, solar sites in England are being placed appropriately with regard to sensitive ecological habitats, and are often sited in areas already impacted by farming and development. Adaptive planning should be implemented to ensure that the evolving research around biodiversity and solar farms is incorporated into decision making, and monitoring is completed across the lifespan of solar farms to assess impacts and effective mitigation.}, }
@article {pmid39580513, year = {2024}, author = {Li, J and Weckwerth, W and Waldherr, S}, title = {Network structure and fluctuation data improve inference of metabolic interaction strengths with the inverse Jacobian.}, journal = {NPJ systems biology and applications}, volume = {10}, number = {1}, pages = {137}, pmid = {39580513}, issn = {2056-7189}, support = {201806010428//China Scholarship Council (CSC)/ ; }, mesh = {Humans ; *Algorithms ; *Metabolic Networks and Pathways/genetics ; *Breast Neoplasms/metabolism/genetics ; *Metabolomics/methods ; Cell Line, Tumor ; Models, Biological ; Computational Biology/methods ; Female ; Systems Biology/methods ; }, abstract = {Based on high-throughput metabolomics data, the recently introduced inverse differential Jacobian algorithm can infer regulatory factors and molecular causality within metabolic networks close to steady-state. However, these studies assumed perturbations acting independently on each metabolite, corresponding to metabolic system fluctuations. In contrast, emerging evidence puts forward internal network fluctuations, particularly from gene expression fluctuations, leading to correlated perturbations on metabolites. Here, we propose a novel approach that exploits these correlations to quantify relevant metabolic interactions. By integrating enzyme-related fluctuations in the construction of an appropriate fluctuation matrix, we are able to exploit the underlying reaction network structure for the inverse Jacobian algorithm. We applied this approach to a model-based artificial dataset for validation, and to an experimental breast cancer dataset with two different cell lines. By highlighting metabolic interactions with significantly changed interaction strengths, the inverse Jacobian approach identified critical dynamic regulation points which are confirming previous breast cancer studies.}, }
@article {pmid39578727, year = {2024}, author = {Ang'ang'o, LM and Herren, JK and Tastan Bishop, &#xd6;}, title = {Bioinformatics analysis of the Microsporidia sp. MB genome: a malaria transmission-blocking symbiont of the Anopheles arabiensis mosquito.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1132}, pmid = {39578727}, issn = {1471-2164}, mesh = {*Anopheles/microbiology/parasitology/genetics ; Animals ; *Microsporidia/genetics ; *Symbiosis ; *Computational Biology/methods ; *Genome, Fungal ; Malaria/transmission ; Phylogeny ; Mosquito Vectors/microbiology/genetics ; Genomics/methods ; RNA Interference ; }, abstract = {BACKGROUND: The use of microsporidia as a disease-transmission-blocking tool has garnered significant attention. Microsporidia sp. MB, known for its ability to block malaria development in mosquitoes, is an optimal candidate for supplementing malaria vector control methods. This symbiont, found in Anopheles mosquitoes, can be transmitted both vertically and horizontally with minimal effects on its mosquito host. Its genome, recently sequenced from An. arabiensis, comprises a compact 5.9 Mbp.<br><br>RESULTS: Here, we analyze the Microsporidia sp. MB genome, highlighting its major genomic features, gene content, and protein function. The genome contains 2247 genes, predominantly encoding enzymes. Unlike other members of the Enterocytozoonida group, Microsporidia sp. MB has retained most of the genes in the glycolytic pathway. Genes involved in RNA interference (RNAi) were also identified, suggesting a mechanism for host immune suppression. Importantly, meiosis-related genes (MRG) were detected, indicating potential for sexual reproduction in this organism. Comparative analyses revealed similarities with its closest relative, Vittaforma corneae, despite key differences in host interactions.<br><br>CONCLUSION: This study provides an in-depth analysis of the newly sequenced Microsporidia sp. MB genome, uncovering its unique adaptations for intracellular parasitism, including retention of essential metabolic pathways and RNAi machinery. The identification of MRGs suggests the possibility of sexual reproduction, offering insights into the symbiont's evolutionary strategies. Establishing a reference genome for Microsporidia sp. MB sets the foundation for future studies on its role in malaria transmission dynamics and host-parasite interactions.}, }
@article {pmid39576832, year = {2024}, author = {Devadhasan, A and Kolodny, O and Carja, O}, title = {Competition for resources can reshape the evolutionary properties of spatial structure.}, journal = {PLoS computational biology}, volume = {20}, number = {11}, pages = {e1012542}, pmid = {39576832}, issn = {1553-7358}, support = {R35 GM147445/GM/NIGMS NIH HHS/United States ; T32 EB009403/EB/NIBIB NIH HHS/United States ; }, mesh = {*Ecosystem ; Humans ; *Biological Evolution ; Computational Biology ; Mutation ; Models, Biological ; Computer Simulation ; }, abstract = {Many evolving ecosystems have spatial structures that can be conceptualized as networks, with nodes representing individuals or homogeneous subpopulations and links the patterns of spread between them. Prior models of evolution on networks do not take ecological niche differences and eco-evolutionary interplay into account. Here, we combine a resource competition model with evolutionary graph theory to study how heterogeneous topological structure shapes evolutionary dynamics under global frequency-dependent ecological interactions. We find that the addition of ecological competition for resources can produce a reversal of roles between amplifier and suppressor networks for deleterious mutants entering the population. We show that this effect is a nonlinear function of ecological niche overlap and discuss intuition for the observed dynamics using simulations and analytical approximations. We use these theoretical results together with spatial representations from imaging data to show that, for ductal carcinoma, where tumor growth is highly spatially constrained, with cells confined to a tree-like network of ducts, the topological structure can lead to higher rates of deleterious mutant hitchhiking with metabolic driver mutations, compared to tumors characterized by different spatial topologies.}, }
@article {pmid39570994, year = {2024}, author = {Madden, WG and Jin, W and Lopman, B and Zufle, A and Dalziel, B and E Metcalf, CJ and Grenfell, BT and Lau, MSY}, title = {Deep neural networks for endemic measles dynamics: Comparative analysis and integration with mechanistic models.}, journal = {PLoS computational biology}, volume = {20}, number = {11}, pages = {e1012616}, pmid = {39570994}, issn = {1553-7358}, mesh = {*Measles/epidemiology ; Humans ; *Neural Networks, Computer ; *Disease Outbreaks/statistics &amp; numerical data ; *Endemic Diseases/statistics &amp; numerical data ; England/epidemiology ; Wales/epidemiology ; Computational Biology ; Forecasting/methods ; Epidemiological Models ; }, abstract = {Measles is an important infectious disease system both for its burden on public health and as an opportunity for studying nonlinear spatio-temporal disease dynamics. Traditional mechanistic models often struggle to fully capture the complex nonlinear spatio-temporal dynamics inherent in measles outbreaks. In this paper, we first develop a high-dimensional feed-forward neural network model with spatial features (SFNN) to forecast endemic measles outbreaks and systematically compare its predictive power with that of a classical mechanistic model (TSIR). We illustrate the utility of our model using England and Wales measles data from 1944-1965. These data present multiple modeling challenges due to the interplay between metapopulations, seasonal trends, and nonlinear dynamics related to demographic changes. Our results show that while the TSIR model yields similarly performant short-term (1 to 2 biweeks ahead) forecasts for highly populous cities, our neural network model (SFNN) consistently achieves lower root mean squared error (RMSE) across other forecasting windows. Furthermore, we show that our spatial-feature neural network model, without imposing mechanistic assumptions a priori, can uncover gravity-model-like spatial hierarchy of measles spread in which major cities play an important role in driving regional outbreaks. We then turn our attention to integrative approaches that combine mechanistic and machine learning models. Specifically, we investigate how the TSIR can be utilized to improve a state-of-the-art approach known as Physics-Informed-Neural-Networks (PINN) which explicitly combines compartmental models and neural networks. Our results show that the TSIR can facilitate the reconstruction of latent susceptible dynamics, thereby enhancing both forecasts in terms of mean absolute error (MAE) and parameter inference of measles dynamics within the PINN. In summary, our results show that appropriately designed neural network-based models can outperform traditional mechanistic models for short to long-term forecasts, while simultaneously providing mechanistic interpretability. Our work also provides valuable insights into more effectively integrating machine learning models with mechanistic models to enhance public health responses to measles and similar infectious disease systems.}, }
@article {pmid39570888, year = {2024}, author = {Cuesta-Aguirre, DR and Malgosa, A and Santos, C}, title = {An easy-to-use pipeline to analyze amplicon-based Next Generation Sequencing results of human mitochondrial DNA from degraded samples.}, journal = {PloS one}, volume = {19}, number = {11}, pages = {e0311115}, pmid = {39570888}, issn = {1932-6203}, mesh = {*DNA, Mitochondrial/genetics ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Software ; Forensic Genetics/methods ; DNA, Ancient/analysis ; }, abstract = {Genome and transcriptome examinations have become more common due to Next-Generation Sequencing (NGS), which significantly increases throughput and depth coverage while reducing costs and time. Mitochondrial DNA (mtDNA) is often the marker of choice in degraded samples from archaeological and forensic contexts, as its higher number of copies can improve the success of the experiment. Among other sequencing strategies, amplicon-based NGS techniques are currently being used to obtain enough data to be analyzed. There are some pipelines designed for the analysis of ancient mtDNA samples and others for the analysis of amplicon data. However, these pipelines pose a challenge for non-expert users and cannot often address both ancient and forensic DNA particularities and amplicon-based sequencing simultaneously. To overcome these challenges, a user-friendly bioinformatic tool was developed to analyze the non-coding region of human mtDNA from degraded samples recovered in archaeological and forensic contexts. The tool can be easily modified to fit the specifications of other amplicon-based NGS experiments. A comparative analysis between two tools, MarkDuplicates from Picard and dedup parameter from fastp, both designed for duplicate removal was conducted. Additionally, various thresholds of PMDtools, a specialized tool designed for extracting reads affected by post-mortem damage, were used. Finally, the depth coverage of each amplicon was correlated with its level of damage. The results obtained indicated that, for removing duplicates, dedup is a better tool since retains more non-repeated reads, that are removed by MarkDuplicates. On the other hand, a PMDS = 1 in PMDtools was the threshold that allowed better differentiation between present-day and ancient samples, in terms of damage, without losing too many reads in the process. These two bioinformatic tools were added to a pipeline designed to obtain both haplotype and haplogroup of mtDNA. Furthermore, the pipeline presented in the present study generates information about the quality and possible contamination of the sample. This pipeline is designed to automatize mtDNA analysis, however, particularly for ancient samples, some manual analyses may be required to fully validate results since the amplicons that used to be more easily recovered were the ones that had fewer reads with damage, indicating that special care must be taken for poor recovered samples.}, }
@article {pmid39569566, year = {2025}, author = {Sung, ML and León, C and Reisman, JI and Gordon, KS and Kerns, RD and Li, W and Liu, W and Mitra, A and Yu, H and Becker, WC}, title = {Disparities in Receipt of Medications for Opioid Use Disorder Before and During the COVID-19 Pandemic in the US Veterans Health Administration.}, journal = {Substance use &amp; addiction journal}, volume = {46}, number = {2}, pages = {369-376}, doi = {10.1177/29767342241293334}, pmid = {39569566}, issn = {2976-7350}, support = {I01 HX003711/HX/HSRD VA/United States ; R01 DA056470/DA/NIDA NIH HHS/United States ; }, mesh = {Humans ; *COVID-19/epidemiology ; Male ; United States/epidemiology ; Female ; *Opioid-Related Disorders/drug therapy/epidemiology ; United States Department of Veterans Affairs ; Middle Aged ; *Healthcare Disparities/statistics &amp; numerical data ; *Veterans/statistics &amp; numerical data ; Adult ; Pandemics ; Cross-Sectional Studies ; *Opiate Substitution Treatment/statistics &amp; numerical data ; Comorbidity ; SARS-CoV-2 ; }, abstract = {BACKGROUND: Populations disproportionately impacted by the opioid epidemic are less likely to receive medications for opioid use disorder (MOUD; OUD). The COVID-19 pandemic exacerbated these disparities. We performed an ecological survey of subpopulations to compare differences in MOUD receipt among Veterans with OUD before versus during the pandemic.<br><br>METHODS: Using 2 cross-sections of 2 time periods of national Veterans Health Administration electronic health record data, we calculated proportions of Veterans with any MOUD receipt by demographics, Elixhauser comorbidity index, and natural language processing (NLP)-derived substance use and social determinants of health in each time period. We evaluated differences in MOUD receipt before and during the pandemic by patient characteristics using Chi-square and Cohen's h for effect size.<br><br>RESULTS: Among 62&#x2009;195 patients with OUD before the pandemic, the proportion prescribed MOUD increased from 46.5% before to 47.5% (P&#x2009;=&#x2009;.0003) during the pandemic. Statistically significant increased receipt of MOUD was observed for patients who were &#x2265;55&#x2009;years, men, White, with Elixhauser comorbidity indices of 2 and &#x2265;5, and with NLP-derived indicators of substance use. There was a decrease that did not achieve statistical significance in MOUD receipt from before to during the pandemic for patients who were women, Black, Latinx, and food insecure.<br><br>CONCLUSIONS: The proportions of patients with OUD prescribed MOUD increased from before to during the pandemic. However, Veterans who were women, Black, Latinx, and food insecure did not experience these increases. These patients may benefit from interventions such as targeted outreach efforts to improve MOUD engagement to reduce OUD harms.}, }
@article {pmid39569448, year = {2025}, author = {Yu, Y and Edelson, M and Pham, A and Pekar, JE and Johnson, B and Post, K and Kuo, TT}, title = {Distributed, immutable, and transparent biomedical limited data set request management on multi-capacity network.}, journal = {Journal of the American Medical Informatics Association : JAMIA}, volume = {32}, number = {2}, pages = {296-307}, pmid = {39569448}, issn = {1527-974X}, support = {R01EB031030//U.S. National Institutes of Health/ ; R01EB031030/NH/NIH HHS/United States ; R01 HG011066/HG/NHGRI NIH HHS/United States ; //NIH/ ; T15LM011271/LM/NLM NIH HHS/United States ; //San Diego Biomedical Informatics Education &amp; Research/ ; T15 LM011271/LM/NLM NIH HHS/United States ; R01 EB031030/EB/NIBIB NIH HHS/United States ; }, mesh = {*Blockchain ; *Information Dissemination/methods ; Humans ; *Datasets as Topic ; *Computer Communication Networks ; }, abstract = {OBJECTIVE: Our study aimed to expedite data sharing requests of Limited Data Sets (LDS) through the development of a streamlined platform that allows distributed, immutable management of network activities, provides transparent and intuitive auditing of data access history, and systematically evaluated it on a multi-capacity network setting for meaningful efficiency metrics.<br><br>MATERIALS AND METHODS: We developed a blockchain-based system with six types of smart contracts to automate the LDS sharing process among major stakeholders. Our workflow included metadata initialization, access-request processing, and audit-log querying. We evaluated our system using synthetic data on three machines with varying specifications to emulate real-world scenarios. The data employed included &#x223c;1000 researcher requests and &#x223c;360&#xa0;000 log queries.<br><br>RESULTS: On average, it took &#x223c;2.5&#xa0;s to register and respond to a researcher access request. The average runtime for an audit-log query with non-empty output was &#x223c;3&#xa0;ms. The runtime metrics at each institution showed general trends affiliated with their computational capacity.<br><br>DISCUSSION: Our system can reduce the LDS sharing request time from potentially hours to seconds, while enhancing data access transparency in a multi-institutional setting. There were variations in performance across sites that could be attributed to differences in hardware specifications. The performance gains became marginal beyond certain hardware thresholds, pointing to the influence of external factors such as network speeds.<br><br>CONCLUSION: Our blockchain-based system can potentially accelerate clinical research by strengthening the data access process, expediting access and delivery of data links, increasing transparency with clear audit trails, and reinforcing trust in medical data management. Our smart contracts are available at: https://github.com/graceyufei/LDS-Request-Management.}, }
@article {pmid39568559, year = {2024}, author = {Boyes, D and Hutchinson, F and Crowley, LM and Boyes, C and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Silver-barred Sober moth, Aproaerema taeniolella (Zeller, 1839).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {500}, pmid = {39568559}, issn = {2398-502X}, abstract = {We present a genome assembly of a female Silver-barred Sober moth Aproaerema taeniolella (Arthropoda; Insecta; Lepidoptera; Gelechiidae). The genome sequence has a length of 636.60 megabases. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.19 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,274 protein-coding genes.}, }
@article {pmid39567690, year = {2025}, author = {Borton, MA and McGivern, BB and Willi, KR and Woodcroft, BJ and Mosier, AC and Singleton, DM and Bambakidis, T and Pelly, A and Daly, RA and Liu, F and Freiburger, A and Edirisinghe, JN and Faria, JP and Danczak, R and Leleiwi, I and Goldman, AE and Wilkins, MJ and Hall, EK and Pennacchio, C and Roux, S and Eloe-Fadrosh, EA and Good, SP and Sullivan, MB and Wood-Charlson, EM and Miller, CS and Ross, MRV and Henry, CS and Crump, BC and Stegen, JC and Wrighton, KC}, title = {A functional microbiome catalogue crowdsourced from North American rivers.}, journal = {Nature}, volume = {637}, number = {8044}, pages = {103-112}, pmid = {39567690}, issn = {1476-4687}, support = {P30 CA046934/CA/NCI NIH HHS/United States ; }, mesh = {*Crowdsourcing ; *Microbiota/genetics ; *Rivers/microbiology ; United States ; Water Microbiology ; Transcriptome ; Carbon Cycle ; Metagenome ; Databases, Factual ; }, abstract = {Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires knowledge of the spatial drivers of river microbiomes. However, understanding of the core microbial processes governing river biogeochemistry is hindered by a lack of genome-resolved functional insights and sampling across multiple rivers. Here we used a community science effort to accelerate the sampling, sequencing and genome-resolved analyses of river microbiomes to create the Genome Resolved Open Watersheds database (GROWdb). GROWdb profiles the identity, distribution, function and expression of microbial genomes across river surface waters covering 90% of United States watersheds. Specifically, GROWdb encompasses microbial lineages from 27 phyla, including novel members from 10 families and 128 genera, and defines the core river microbiome at the genome level. GROWdb analyses coupled to extensive geospatial information reveals local and regional drivers of microbial community structuring, while also presenting foundational hypotheses about ecosystem function. Building on the previously conceived River Continuum Concept[1], we layer on microbial functional trait expression, which suggests that the structure and function of river microbiomes is predictable. We make GROWdb available through various collaborative cyberinfrastructures[2,3], so that it can be widely accessed across disciplines for watershed predictive modelling and microbiome-based management practices.}, }
@article {pmid39564491, year = {2024}, author = {Zhang, Y and Wang, M and Huang, M and Zhao, J}, title = {Innovative strategies and challenges mosquito-borne disease control amidst climate change.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1488106}, pmid = {39564491}, issn = {1664-302X}, abstract = {The revival of the transmission dynamics of mosquito-borne diseases grants striking challenges to public health intensified by climate change worldwide. This inclusive review article examines multidimensional strategies and challenges linked to climate change and the epidemiology of mosquito-borne diseases such as malaria, dengue, Zika, chikungunya, and yellow fever. It delves into how the biology, pathogenic dynamics, and vector distribution of mosquitoes are influenced by continuously rising temperatures, modified rainfall patterns, and extreme climatic conditions. We also highlighted the high likelihood of malaria in Africa, dengue in Southeast Asia, and blowout of Aedes in North America and Europe. Modern predictive tools and developments in surveillance, including molecular gears, Geographic Information Systems (GIS), and remote sensing have boosted our capacity to predict epidemics. Integrated data management techniques and models based on climatic conditions provide a valuable understanding of public health planning. Based on recent data and expert ideas, the objective of this review is to provide a thoughtful understanding of existing landscape and upcoming directions in the control of mosquito-borne diseases regarding changing climate. This review determines emerging challenges and innovative vector control strategies in the changing climatic conditions to ensure public health.}, }
@article {pmid39563951, year = {2024}, author = {Sivell, O and Hawkes, WLS and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the silvery leafcutter bee, Megachile leachella Curtis, 1828.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {415}, pmid = {39563951}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Megachile leachella (the silvery leafcutter bee; Arthropoda; Insecta; Hymenoptera; Megachilidae). The genome sequence is 573.0 megabases in span. Most of the assembly is scaffolded into 16 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 21.04 kilobases in length.}, }
@article {pmid39563229, year = {2024}, author = {Toth, AL and Wyatt, CDR and Masonbrink, RE and Geist, KS and Fortune, R and Scott, SB and Favreau, E and Rehan, SM and Sumner, S and Gardiner, MM and Sivakoff, FS}, title = {New genomic resources inform transcriptomic responses to heavy metal toxins in the common Eastern bumble bee Bombus impatiens.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1106}, pmid = {39563229}, issn = {1471-2164}, support = {20176701326595//USDA National Institute of Food and Agriculture/ ; 1929239//NSF DEB-NERC/ ; }, mesh = {Animals ; Bees/genetics/drug effects ; *Metals, Heavy/toxicity ; *Transcriptome ; Genomics/methods ; Molecular Sequence Annotation ; Gene Expression Profiling ; Genome, Insect ; Toxins, Biological/genetics ; }, abstract = {BACKGROUND: The common Eastern bumble bee Bombus impatiens is native to North America and is the main commercially reared pollinator in the Americas. There has been extensive research on this species related to its social biology, applied pollination, and genetics. The genome of this species was previously sequenced using short-read technology, but recent technological advances provide an opportunity for substantial improvements. This species is common in agricultural and urban environments, and heavy metal contaminants produced by industrial processes can negatively impact it. To begin to identify possible mechanisms underlying responses to these toxins, we used RNA-sequencing to examine how exposure to a cocktail of four heavy metals at field-realistic levels from industrial areas affected B. impatiens worker gene expression.<br><br>RESULTS: PacBio long-read sequencing resulted in 544x coverage of the genome, and HiC technology was used to map chromatin contacts. Using Juicer and manual curation, the genome was scaffolded into 18 main pseudomolecules, representing a high quality, chromosome-level assembly. The sequenced genome size is 266.6&#xa0;Mb and BRAKER3 annotation produced 13,938 annotated genes. The genome and annotation show high completeness, with &#x2265;&#x2009;96% of conserved Eukaryota and Hymenoptera genes present in both the assembly and annotated genes. RNA sequencing of heavy metal exposed workers revealed 603 brain and 34 fat body differentially expressed genes. In the brain, differentially expressed genes had biological functions related to chaperone activity and protein folding.<br><br>CONCLUSIONS: Our data represent a large improvement in genomic resources for this important model species-with 10% more genome coverage than previously available, and a high-quality assembly into 18 chromosomes, the expected karyotype for this species. The new gene annotation added 777 new genes. Altered gene expression in response to heavy metal exposure suggests a possible mechanism for how these urban toxins are negatively impacting bee health, specifically by altering protein folding in the brain. Overall, these data are useful as a general high quality genomic resource for this species, and provide insight into mechanisms underlying tissue-specific toxicological responses of bumble bees to heavy metals.}, }
@article {pmid39561196, year = {2024}, author = {Konzen, E and Delahay, RJ and Hodgson, DJ and McDonald, RA and Brooks Pollock, E and Spencer, SEF and McKinley, TJ}, title = {Efficient modelling of infectious diseases in wildlife: A case study of bovine tuberculosis in wild badgers.}, journal = {PLoS computational biology}, volume = {20}, number = {11}, pages = {e1012592}, pmid = {39561196}, issn = {1553-7358}, mesh = {Animals ; *Mustelidae/microbiology ; *Tuberculosis, Bovine/epidemiology/transmission/diagnosis ; Cattle ; *Animals, Wild/microbiology ; United Kingdom/epidemiology ; Models, Biological ; Mycobacterium bovis ; Computational Biology/methods ; Disease Reservoirs/microbiology/veterinary ; Ireland/epidemiology ; }, abstract = {Bovine tuberculosis (bTB) has significant socio-economic and welfare impacts on the cattle industry in parts of the world. In the United Kingdom and Ireland, disease control is complicated by the presence of infection in wildlife, principally the European badger. Control strategies tend to be applied to whole populations, but better identification of key sources of transmission, whether individuals or groups, could help inform more efficient approaches. Mechanistic transmission models can be used to better understand key epidemiological drivers of disease spread and identify high-risk individuals and groups if they can be adequately fitted to observed data. However, this is a significant challenge, especially within wildlife populations, because monitoring relies on imperfect diagnostic test information, and even under systematic surveillance efforts (such as capture-mark-recapture sampling) epidemiological events are only partially observed. To this end we develop a stochastic compartmental model of bTB transmission, and fit this to individual-level data from a unique > 40-year longitudinal study of 2,391 badgers using a recently developed individual forward filtering backward sampling algorithm. Modelling challenges are further compounded by spatio-temporal meta-population structures and age-dependent mortality. We develop a novel estimator for the individual effective reproduction number that provides quantitative evidence for the presence of superspreader badgers, despite the population-level effective reproduction number being less than one. We also infer measures of the hidden burden of infection in the host population through time; the relative likelihoods of competing routes of transmission; effective and realised infectious periods; and longitudinal measures of diagnostic test performance. This modelling framework provides an efficient and generalisable way to fit state-space models to individual-level data in wildlife populations, which allows identification of high-risk individuals and exploration of important epidemiological questions about bTB and other wildlife diseases.}, }
@article {pmid39560426, year = {2025}, author = {Zhu, H-H and Liu, M-M and Boekhout, T and Wang, Q-M}, title = {Improvement of a MALDI-TOF database for the reliable identification of Candidozyma auris (formally Candida auris) and related species.}, journal = {Microbiology spectrum}, volume = {13}, number = {1}, pages = {e0144424}, pmid = {39560426}, issn = {2165-0497}, mesh = {*Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; Humans ; *Candidiasis/microbiology/diagnosis ; Candida auris/chemistry/isolation &amp; purification/classification ; Databases, Factual ; Mycological Typing Techniques/methods ; Candida/classification/isolation &amp; purification/chemistry ; }, abstract = {UNLABELLED: Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a promising technique for the rapid identification microorganisms. The aim of this study was to create a new database for the accurate identification of Candidozyma auris (formerly known as Candida auris) and 11 species of the Candidozyma haemuli species complex, including C. chanthaburiensis, C. duobushaemuli, C. haemuli, C. heveicola, C. khanbhai, C. konsanensis, C. metrosideri, C. ohialehuae, C. pseudohaemuli, C. ruelliae, and C. vulturna. Seventy-one Candidozyma isolates from different national institutions were studied. Thirty-seven strains were used to create a MALDI-TOF (microTyper MS) database using the formic acid extraction method. The validation of this database was performed with 34 other strains of the genus Candidozyma, and the result was compared with the identification results when using DBRs v1.0.0.4 (Tianrui, China). Our library allowed a 100% identification of the evaluated strains with all strains showing log scores of >2.0. Repeatability and reproducibility tests result showed a coefficient of variation of the log score values of less than 5%. The MALDI-TOF MS system can identify C. auris and related species quickly and accurately. This method will play a crucial role in accurately diagnosing infectious agents of the genus Candidozyma in clinical practice.<br><br>IMPORTANCE: Importance Candidozyma auris, also known as Candida auris, has quickly spread across the world, and prompt identification of C. auris from infected individuals is critical. However, a standard identification method is lacking for the identification of C. auris in clinical and public health laboratories. To make matters worse, its biochemical assimilation profile was found to be similar to that of closely related and even no-related species, leading to frequent misidentification. To improve diagnostics of this and closely related species, we created a database of reference mass spectra resulting in the efficient and correct identification of all Candidozyma species by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Moreover, potential pathogenic species of Candidozyma can be effectively identified by MALDI-TOF MS, and differentiated from non-clinically relevant phylogenetic relatives. Thus, MALDI-TOF MS may help expedite laboratory diagnosis and treatment of C. auris and related species of clinical importance and help the clinician to decide on early treatment.}, }
@article {pmid39558756, year = {2025}, author = {Paris, JR and King, RA and Ferrer Obiol, J and Shaw, S and Lange, A and Bourret, V and Hamilton, PB and Rowe, D and Laing, LV and Farbos, A and Moore, K and Urbina, MA and van Aerle, R and Catchen, JM and Wilson, RW and Bury, NR and Santos, EM and Stevens, JR}, title = {The Genomic Signature and Transcriptional Response of Metal Tolerance in Brown Trout Inhabiting Metal-Polluted Rivers.}, journal = {Molecular ecology}, volume = {34}, number = {1}, pages = {e17591}, pmid = {39558756}, issn = {1365-294X}, support = {BB/K003240/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //University of Exeter/ ; WT097835MF/WT_/Wellcome Trust/United Kingdom ; Charityno.1135007,Companyno.06545646//Westcountry Rivers Trust, UK/ ; WT101650MA/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; //Environment Agency, UK/ ; }, mesh = {*Genome ; *Transcription, Genetic/drug effects ; *Adaptation, Physiological/drug effects/genetics ; *Rivers ; *Water Pollutants, Chemical/toxicity ; *Salmon/genetics/physiology ; Gene Expression Profiling ; Gene Expression Regulation/drug effects ; *Metals/toxicity ; United Kingdom ; Genetic Loci ; Gene Library ; Metagenomics ; Organ Specificity/drug effects ; Gene Ontology ; Animals ; }, abstract = {Industrial pollution is a major driver of ecosystem degradation, but it can also act as a driver of contemporary evolution. As a result of intense mining activity during the Industrial Revolution, several rivers across the southwest of England are polluted with high concentrations of metals. Despite the documented negative impacts of ongoing metal pollution, brown trout (Salmo trutta L.) survive and thrive in many of these metal-impacted rivers. We used population genomics, transcriptomics, and metal burdens to investigate the genomic and transcriptomic signatures of potential metal tolerance. RADseq analysis of six populations (originating from three metal-impacted and three control rivers) revealed strong genetic substructuring between impacted and control populations. We identified selection signatures at 122 loci, including genes related to metal homeostasis and oxidative stress. Trout sampled from metal-impacted rivers exhibited significantly higher tissue concentrations of cadmium, copper, nickel and zinc, which remained elevated after 11 days in metal-free water. After depuration, we used RNAseq to quantify gene expression differences between metal-impacted and control trout, identifying 2042 differentially expressed genes (DEGs) in the gill, and 311 DEGs in the liver. Transcriptomic signatures in the gill were enriched for genes involved in ion transport processes, metal homeostasis, oxidative stress, hypoxia, and response to xenobiotics. Our findings reveal shared genomic and transcriptomic pathways involved in detoxification, oxidative stress responses and ion regulation. Overall, our results demonstrate the diverse effects of metal pollution in shaping both neutral and adaptive genetic variation, whilst also highlighting the potential role of constitutive gene expression in promoting metal tolerance.}, }
@article {pmid39556417, year = {2024}, author = {Helgeson, SA and Mudgalkar, RM and Jacobs, KA and Lee, AS and Sanghavi, D and Moreno Franco, P and Brooks, IS and , }, title = {Association Between X/Twitter and Prescribing Behavior During the COVID-19 Pandemic: Retrospective Ecological Study.}, journal = {JMIR infodemiology}, volume = {4}, number = {}, pages = {e56675}, pmid = {39556417}, issn = {2564-1891}, support = {U24 TR002306/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; Retrospective Studies ; *Hydroxychloroquine/therapeutic use ; *Social Media ; United States/epidemiology ; *COVID-19/epidemiology ; *Practice Patterns, Physicians' ; Pandemics ; COVID-19 Drug Treatment ; Male ; Female ; Middle Aged ; SARS-CoV-2/drug effects ; }, abstract = {BACKGROUND: Social media has become a vital tool for health care providers to quickly share information. However, its lack of content curation and expertise poses risks of misinformation and premature dissemination of unvalidated data, potentially leading to widespread harmful effects due to the rapid and large-scale spread of incorrect information.<br><br>OBJECTIVE: We aim to determine whether social media had an undue association with the prescribing behavior of hydroxychloroquine, using the COVID-19 pandemic as the setting.<br><br>METHODS: In this retrospective study, we gathered the use of hydroxychloroquine in 48 hospitals in the United States between January and December 2020. Social media data from X/Twitter was collected using Brandwatch, a commercial aggregator with access to X/Twitter's data, and focused on mentions of "hydroxychloroquine" and "Plaquenil." Tweets were categorized by sentiment (positive, negative, or neutral) using Brandwatch's sentiment analysis tool, with results classified by date. Hydroxychloroquine prescription data from the National COVID Cohort Collaborative for 2020 was used. Granger causality and linear regression models were used to examine relationships between X/Twitter mentions and prescription trends, using optimum time lags determined via vector auto-regression.<br><br>RESULTS: A total of 581,748 patients with confirmed COVID-19 were identified. The median daily number of positive COVID-19 cases was 1318.5 (IQR 1005.75-1940.3). Before the first confirmed COVID-19 case, hydroxychloroquine was prescribed at a median rate of 559 (IQR 339.25-728.25) new prescriptions per day. A day-of-the-week effect was noted in both prescriptions and case counts. During the pandemic in 2020, hydroxychloroquine prescriptions increased significantly, with a median of 685.5 (IQR 459.75-897.25) per day, representing a 22.6% rise from baseline. The peak occurred on April 2, 2020, with 3411 prescriptions, a 397.6% increase. Hydroxychloroquine mentions on X/Twitter peaked at 254,770 per day on April 5, 2020, compared to a baseline of 9124 mentions per day before January 21, 2020. During this study's period, 3,823,595 total tweets were recorded, with 10.09% (n=386,115) positive, 37.87% (n=1,448,030) negative, and 52.03% (n=1,989,450) neutral sentiments. A 1-day lag was identified as the optimal time for causal association between tweets and hydroxychloroquine prescriptions. Univariate analysis showed significant associations across all sentiment types, with the largest impact from positive tweets. Multivariate analysis revealed only neutral and negative tweets significantly affected next-day prescription rates.<br><br>CONCLUSIONS: During the first year of the COVID-19 pandemic, there was a significant association between X/Twitter mentions and the number of prescriptions of hydroxychloroquine. This study showed that X/Twitter has an association with the prescribing behavior of hydroxychloroquine. Clinicians need to be vigilant about their potential unconscious exposure to social media as a source of medical knowledge, and health systems and organizations need to be more diligent in identifying expertise, source, and quality of evidence when shared on social media platforms.}, }
@article {pmid39555185, year = {2024}, author = {Yang, D and Hashizume, M and Tobías, A and Honda, Y and Roye, D and Oh, J and Dang, TN and Kim, Y and Abrutzky, R and Guo, Y and Tong, S and Coelho, MSZS and Saldiva, PHN and Lavigne, E and Correa, PM and Ortega, NV and Osorio, S and Kyselý, J and Urban, A and Orru, H and Indermitte, E and Jaakkola, J and Ryti, N and Pascal, M and Huber, V and Schneider, A and Katsouyanni, K and Analitis, A and Entezari, A and Mayvaneh, F and Goodman, P and Zeka, A and Michelozzi, P and de'Donato, F and Alahmad, B and Diaz, MH and la Cruz Valencia, C and Overcenco, A and Houthuijs, D and Ameling, C and Rao, S and Nunes, B and Madureira, J and Holo-Bâc, IH and Scovronick, N and Acquaotta, F and Kim, H and Lee, W and Íñiguez, C and Forsberg, B and Vicedo-Cabrera, AM and Ragettli, MS and Guo, YL and Pan, SC and Li, S and Sera, F and Zanobetti, A and Schwartz, J and Armstrong, B and Gasparrini, A and Chung, Y}, title = {Temporal change in minimum mortality temperature under changing climate: A multicountry multicommunity observational study spanning 1986-2015.}, journal = {Environmental epidemiology (Philadelphia, Pa.)}, volume = {8}, number = {5}, pages = {e334}, pmid = {39555185}, issn = {2474-7882}, support = {MR/R013349/1/MRC_/Medical Research Council/United Kingdom ; MR/V034162/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {BACKGROUND: The minimum mortality temperature (MMT) or MMT percentile (MMTP) is an indicator of population susceptibility to nonoptimum temperatures. MMT and MMTP change over time; however, the changing directions show region-wide heterogeneity. We examined the heterogeneity of temporal changes in MMT and MMTP across multiple communities and in multiple countries.<br><br>METHODS: Daily time-series data for mortality and ambient mean temperature for 699 communities in 34 countries spanning 1986-2015 were analyzed using a two-stage meta-analysis. First, a quasi-Poisson regression was employed to estimate MMT and MMTP for each community during the designated subperiods. Second, we pooled the community-specific temporally varying estimates using mixed-effects meta-regressions to examine temporal changes in MMT and MMTP in the entire study population, as well as by climate zone, geographical region, and country.<br><br>RESULTS: Temporal increases in MMT and MMTP from 19.5 &#xb0;C (17.9, 21.1) to 20.3 &#xb0;C (18.5, 22.0) and from the 74.5 (68.3, 80.6) to 75.0 (71.0, 78.9) percentiles in the entire population were found, respectively. Temporal change was significantly heterogeneous across geographical regions (P < 0.001). Temporal increases in MMT were observed in East Asia (linear slope [LS] = 0.91, P = 0.02) and South-East Asia (LS = 0.62, P = 0.05), whereas a temporal decrease in MMT was observed in South Europe (LS = -0.46, P = 0.05). MMTP decreased temporally in North Europe (LS = -3.45, P = 0.02) and South Europe (LS = -2.86, P = 0.05).<br><br>CONCLUSIONS: The temporal change in MMT or MMTP was largely heterogeneous. Population susceptibility in terms of optimum temperature may have changed under a warming climate, albeit with large region-dependent variations.}, }
@article {pmid39549265, year = {2025}, author = {Rayamajhi, N and Rivera-Colón, AG and Minhas, BF and Cheng, CHC and Catchen, JM}, title = {The genome of the cryopelagic Antarctic bald notothen, Trematomus borchgrevinki.}, journal = {G3 (Bethesda, Md.)}, volume = {15}, number = {1}, pages = {}, pmid = {39549265}, issn = {2160-1836}, support = {10-69157//NSF DGE/ ; //IGERT/ ; //AGR-C/ ; 1645087//NSF OPP/ ; //JC/ ; //C-HCC/ ; 11-42158//NSF ANT/ ; //C-HCC/ ; }, mesh = {Animals ; *Genome ; Antarctic Regions ; Synteny ; Molecular Sequence Annotation ; Chromosomes/genetics ; Female ; Perciformes/genetics ; Repetitive Sequences, Nucleic Acid ; Genomics/methods ; Phylogeny ; }, abstract = {The Antarctic bald notothen, Trematomus borchgrevinki (family Nototheniidae) occupies a high latitude, ice-laden environment and represents an extreme example of cold-specialization among fishes. We present the first, high-quality, chromosome-scale genome of a female T. borchgrevinki individual comprised of 23 putative chromosomes, the largest of which is 65 megabasepairs (Mbp) in length. The total length of the genome 935.13 Mbp, composed of 2,094 scaffolds, with a scaffold N50 of 42.67 Mbp. Annotation yielded 22,192 protein-coding genes while 54.75% of the genome was occupied by repetitive elements; an analysis of repeats demonstrated that an expansion occurred in recent time. Conserved synteny analysis revealed that the genome architecture of T. borchgrevinki is largely maintained with other members of the notothenioid clade, although several significant translocations and inversions are present, including the fusion of orthologous chromosomes 8 and 11 into a single element. This genome will serve as a cold-specialized model for comparisons to other members of the notothenioid adaptive radiation.}, }
@article {pmid39548719, year = {2024}, author = {Chen, Y and Gao, Y and Zhang, Z and Zhan, A}, title = {Multi-Omics Inform Invasion Risks Under Global Climate Change.}, journal = {Global change biology}, volume = {30}, number = {11}, pages = {e17588}, doi = {10.1111/gcb.17588}, pmid = {39548719}, issn = {1365-2486}, support = {2022GDASZH-2022010106//GDAS Special Project of Science and Technology Development/ ; 2024A1515010914//Guangdong Basic and Applied Basic Research Foundation/ ; 42106098//National Natural Science Foundation of China/ ; 32061143012//National Natural Science Foundation of China/ ; 42276126//National Natural Science Foundation of China/ ; 32371753//National Natural Science Foundation of China/ ; }, mesh = {*Climate Change ; *Introduced Species ; *Genomics ; Urochordata/genetics ; Epigenomics ; Adaptation, Physiological/genetics ; Animals ; Multiomics ; }, abstract = {Global climate change is exacerbating biological invasions; however, the roles of genomic and epigenomic variations and their interactions in future climate adaptation remain underexplored. Using the model invasive ascidian Botryllus schlosseri across the Northern Hemisphere, we investigated genomic and epigenomic responses to future climates and developed a framework to assess future invasion risks. We employed generalized dissimilarity modeling and gradient forest analyses to assess genomic and epigenomic offsets under climate change. Our results showed that populations with genomic maladaptation did not geographically overlap with those experiencing epigenomic maladaptation, suggesting that genomic and epigenomic variations play complementary roles in adaptation to future climate conditions. By integrating genomic and epigenomic offsets into the genome-epigenomic index, we predicted that populations with lower index values were less maladapted, indicating a higher risk of future invasions. Native populations exhibited lower offsets than invasive populations, suggesting greater adaptive potentials and higher invasion risks under future climate change scenarios. These results highlight the importance of incorporating multi-omics data into predictive models to study future climate (mal)adaptation and assess invasion risks under global climate change.}, }
@article {pmid39548060, year = {2024}, author = {Conrad, RE and Brink, CE and Viver, T and Rodriguez-R, LM and Aldeguer-Riquelme, B and Hatt, JK and Venter, SN and Rossello-Mora, R and Amann, R and Konstantinidis, KT}, title = {Microbial species and intraspecies units exist and are maintained by ecological cohesiveness coupled to high homologous recombination.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {9906}, pmid = {39548060}, issn = {2041-1723}, support = {1831582//NSF | BIO | Division of Environmental Biology (DEB)/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; 2129823//U.S. National Science Foundation/ ; }, mesh = {*Homologous Recombination ; *Escherichia coli/genetics/classification ; Genome, Bacterial ; Microbiota/genetics ; Evolution, Molecular ; Gene Flow ; Phylogeny ; Computational Biology/methods ; }, abstract = {Recent genomic analyses have revealed that microbial communities are predominantly composed of persistent, sequence-discrete species and intraspecies units (genomovars), but the mechanisms that create and maintain these units remain unclear. By analyzing closely-related isolate genomes from the same or related samples and identifying recent recombination events using a novel bioinformatics methodology, we show that high ecological cohesiveness coupled to frequent-enough and unbiased (i.e., not selection-driven) horizontal gene flow, mediated by homologous recombination, often underlie these diversity patterns. Ecological cohesiveness was inferred based on greater similarity in temporal abundance patterns of genomes of the same vs. different units, and recombination was shown to affect all sizable segments of the genome (i.e., be genome-wide) and have two times or greater impact on sequence evolution than point mutations. These results were observed in both Salinibacter ruber, an environmental halophilic organism, and Escherichia coli, the model gut-associated organism and an opportunistic pathogen, indicating that they may be more broadly applicable to the microbial world. Therefore, our results represent a departure compared to previous models of microbial speciation that invoke either ecology or recombination, but not necessarily their synergistic effect, and answer an important question for microbiology: what a species and a subspecies are.}, }
@article {pmid39547957, year = {2024}, author = {Kwon, EJ and Lee, H and Shin, U and Kim, ES and Myung, K and Kim, J and Park, JH and Kim, K and Lee, Y and Oh, CK and Kim, YH}, title = {Ionizing radiation inhibits zebrafish embryo hatching through induction of tissue inhibitors of metalloproteinases (TIMPs) expression.}, journal = {The FEBS journal}, volume = {291}, number = {24}, pages = {5470-5485}, doi = {10.1111/febs.17318}, pmid = {39547957}, issn = {1742-4658}, support = {IBS-R022-D1//Institute for Basic Science/ ; RS-2023-00223591//National Research Foundation of Korea/ ; RS-2023-00301938//National Research Foundation of Korea/ ; RS-2024-00439078//National Research Foundation of Korea/ ; //KREONET/ ; }, mesh = {Animals ; *Zebrafish/genetics/embryology/metabolism ; *Radiation, Ionizing ; *Tissue Inhibitor of Metalloproteinases/metabolism/genetics ; *Gene Expression Regulation, Developmental/radiation effects ; *Embryo, Nonmammalian/radiation effects/metabolism ; Zebrafish Proteins/genetics/metabolism ; }, abstract = {Ionizing radiation (IR) has garnered growing attention because of its biological effects on aquatic organisms and humans. Here, we identify the most impacted organs and uncover the molecular mechanisms causing the changes in the context of vertebrate development using single-cell RNA sequencing. Alterations in cellular composition and biological functions were explored using transcriptomic profiling of zebrafish embryos exposed to 5 Gy. Single-cell RNA sequencing analyses unveiled notable shifts in the proportions of brain/central nervous system and hatching gland clusters. Although IR exposure led to increased expression of hatching enzymes, a significant but mild delay in hatching was observed following 5 Gy IR exposure. Gene Ontology analysis showed an increased expression of tissue inhibitors of metalloproteinases (TIMPs), known as matrix metalloproteinase inhibitors, which was confirmed via whole-mount in situ hybridization. Correlation analysis linked TIMPs to transcription factors cebpb and cebpd, which were significantly correlated post-IR exposure. Although no morphological changes were observed in some organs, including the brain, the study reveals substantial alterations in developing vertebrates. Notably, despite increased hatching enzymes, elevated TIMPs in the hatching gland suggest a regulatory mechanism impacting hatching activity. This research contributes to comprehending the ecological repercussions of IR exposure, emphasizing the importance of safety measures for aquatic ecosystems and overall environmental health.}, }
@article {pmid39546825, year = {2025}, author = {Meyer, A and Ndiaye, B and Larkins, A and Chaters, G and Gilbert, W and Huntington, B and Ilboudo, G and Dione, M and Jemberu, WT and Diouf, MN and Fall, AG and Fall, M and Lo, M and Rushton, J}, title = {Economic assessment of animal disease burden in Senegalese small ruminants.}, journal = {Preventive veterinary medicine}, volume = {234}, number = {}, pages = {106382}, doi = {10.1016/j.prevetmed.2024.106382}, pmid = {39546825}, issn = {1873-1716}, mesh = {Animals ; Senegal/epidemiology ; *Goat Diseases/economics/epidemiology ; *Goats ; Sheep ; *Sheep Diseases/economics/epidemiology ; Cost of Illness ; Animal Husbandry/economics/methods ; }, abstract = {Small ruminant production in sub-Saharan Africa is limited by a range of constraints, including animal health issues. This study aimed at estimating the impact of these issues on the small ruminant production in Senegal in a holistic manner, using an approach developed by the Global Burden of Animal Diseases (GBADs) programme. The estimation focused on the mixed crop-livestock system, representing a large proportion (>60 %) of the small ruminant population in the country. It was based on existing data collected via a systematic literature review, acquisition of secondary datasets from local stakeholders, and expert elicitation. A dynamic population model was used to calculate the gross margin of the sector under both the current health constraints and an ideal health state, where animals are not exposed to causes of morbidity and mortality. The difference between the current and ideal health scenarios, termed the Animal Health Loss Envelope (AHLE), provides a quantitative measure of the farm-level cost of disease in the system. The all-cause AHLE was estimated at 292 billion FCFA (468 million USD, with 95 % prediction interval 216 - 366 billion FCFA) per year for 2022, for a population of 8.8 million animals. The contribution of Peste des Petits Ruminants (PPR) was modelled separately, as an example of attributing part of the AHLE to a specific disease cause. PPR was estimated to contribute 5 % of the total AHLE. The animal disease burden experienced by Senegalese livestock keepers was largely due to loss in animals and production, with relatively small amounts of animal health expenditure. Implementation of this study contributed to the further development of the GBADs approach. Such estimates can support decision making at all levels, from investment decisions at the international level to local disease awareness campaigns targeting livestock keepers.}, }
@article {pmid39545367, year = {2024}, author = {Heuck, MK and Powell, JR and Kath, J and Birnbaum, C and Frew, A}, title = {Evaluating the Usefulness of the C-S-R Framework for Understanding AM Fungal Responses to Climate Change in Agroecosystems.}, journal = {Global change biology}, volume = {30}, number = {11}, pages = {e17566}, doi = {10.1111/gcb.17566}, pmid = {39545367}, issn = {1365-2486}, support = {DE220100479//Australian Research Council (ARC) Discovery Early Career Researcher Award (DECRA)/ ; FT190100590//Australian Research Council Future Fellowship/ ; }, mesh = {*Climate Change ; *Mycorrhizae/physiology ; *Agriculture ; *Ecosystem ; Symbiosis ; }, abstract = {Arbuscular mycorrhizal (AM) fungi play a key role in terrestrial ecosystems by forming symbiotic relationships with plants and may confer benefits for sustainable agriculture, by reducing reliance on harmful fertiliser and pesticide inputs and enhancing plant resilience against insect herbivores. Despite their ecological importance, critical gaps in understanding AM fungal ecology limit predictions of their responses to global change in agroecosystems. However, predicting climate change impacts on AM fungi is important for maintaining crop productivity and ecosystem stability. Efforts to classify AM fungi based on functional traits, such as the competitor, stress-tolerator, ruderal (C-S-R) framework, aim to address these gaps but face challenges due to the obligate symbiotic nature of the fungi. As the framework is still widely used, we evaluate its applicability in predicting global change impacts on AM fungal communities in agroecosystems. Chagnon's adaptation of the C-S-R framework for AM fungi aligns with some study outcomes (e.g., under the context of water limitation) but faces challenges when used in complex climate change scenarios, varying agricultural conditions and/or extreme climatic conditions. The reliance on a limited dataset to classify AM fungal families further limits accurate predictions of AM fungal community dynamics. Trait data collection could support a nuanced understanding of AM fungi and leveraging AM fungal databases could streamline data management and analysis, enhancing efforts to clarify AM fungal responses to environmental change and guide ecosystem management practices. Thus, while the C-S-R framework holds promise, it requires additional AM fungal trait data for validation and improvement of its predictive power. Conclusively, before designing experiments based on life-history strategies and developing new frameworks tailored to AM fungi a critical first step is to gain a comprehensive understanding of their traits.}, }
@article {pmid39543597, year = {2024}, author = {Rajovic, N and Grubor, N and Cirkovic, A and Maheswaran, R and Bath, PA and Green, D and Bellantuono, I and Milicevic, O and Kanazir, S and Miljus, D and Zivkovic, S and Vidojevic, D and Mickovski, N and Rakocevic, I and Ivanovic, I and Mladenovic, A and Goyder, E and Milic, N}, title = {Insights into relationship of environmental inequalities and multimorbidity: a population-based study.}, journal = {Environmental health : a global access science source}, volume = {23}, number = {1}, pages = {99}, pmid = {39543597}, issn = {1476-069X}, support = {200110/WT_/Wellcome Trust/United Kingdom ; 200110/WT_/Wellcome Trust/United Kingdom ; 200110/WT_/Wellcome Trust/United Kingdom ; 200110/WT_/Wellcome Trust/United Kingdom ; 200007//Ministry of Science, Innovation and Technological Development of the Republic of Serbia/ ; 200007//Ministry of Science, Innovation and Technological Development of the Republic of Serbia/ ; 200110/WT_/Wellcome Trust/United Kingdom ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; }, mesh = {Humans ; Middle Aged ; *Multimorbidity ; Adult ; Male ; Female ; Serbia/epidemiology ; Aged ; Young Adult ; *Air Pollutants/analysis ; Adolescent ; Environmental Exposure/adverse effects ; Air Pollution/analysis/adverse effects ; Prevalence ; Water Quality ; Socioeconomic Factors ; }, abstract = {BACKGROUND: Substantial inequalities in the overall prevalence and patterns of multimorbidity have been widely reported, but the causal mechanisms are complex and not well understood. This study aimed to identify common patterns of multimorbidity in Serbia and assess their relationship with air pollutant concentrations and water quality indicators.<br><br>METHODS: This ecological study was conducted on a nationally representative sample of the Serbian population. Data were obtained from the European Health Interview (EHIS) Survey, a periodic study designed to assess population health using widely recognized standardized instruments. The study included 13,069 participants aged 15 and older, randomly selected through a multistage stratified sampling design. Multimorbidity was defined as having two or more self-reported diagnoses of chronic non-communicable diseases. Latent class analysis (LCA) was performed to identify clusters of multimorbidity. Concentrations of particulate matter (PM10), sulfur dioxide (SO2), nitrogen dioxide (NO2), carbon monoxide (CO), and ozone (O3), as well as water quality indicators, were obtained from the Serbian Environmental Protection Agency.<br><br>RESULTS: The overall prevalence of multimorbidity was 33.4% [32.6%-34.2%]. Six latent classes of multimorbidity were identified: Healthy, Multicondition, Cardiovascular, Metabolic syndrome, Respiratory, and Musculoskeletal. Annual increases in PM10 and SO2 concentrations, as well as daily increases in O3 concentrations, significantly raised the odds of having multimorbidity (OR&#x2009;=&#x2009;1.02, 95% CI 1.02-1.03; OR&#x2009;=&#x2009;1.01, 95% CI 1.00-1.02 and OR&#x2009;=&#x2009;1.03, 95% CI 1.02-1.03, respectively). A pattern of increased risk was observed with rising levels of water contamination. Exposure to physico-chemical, microbiological and combined contamination was associated with a 3.92%, 5.17% and 5.54% higher probability, respectively, of having multiple chronic conditions. There was strong evidence that air pollutants, as well as chemical and microbial water contamination, were significantly associated with higher odds of the most common clusters of multimorbidity identified by LCA.<br><br>CONCLUSION: There is compelling evidence of an association between multimorbidity and environmental pollution, suggesting that exposure to air pollutants and water contaminants may contribute to disease accumulation and help explain geographically and socioeconomically patterned inequalities. These findings underscore the need for extensive studies that simultaneously measure both multimorbidity and pollution to explore their complex interrelationships.}, }
@article {pmid39543483, year = {2024}, author = {Rzehak, T and Praeg, N and Galla, G and Seeber, J and Hauffe, HC and Illmer, P}, title = {Comparison of commonly used software pipelines for analyzing fungal metabarcoding data.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1085}, pmid = {39543483}, issn = {1471-2164}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Fungi/genetics/classification ; *Software ; Animals ; Cattle ; Computational Biology/methods ; Feces/microbiology ; Soil Microbiology ; }, abstract = {BACKGROUND: Metabarcoding targeting the internal transcribed spacer (ITS) region is commonly used to characterize fungal communities of various environments. Given their size and complexity, raw ITS sequences are necessarily processed and quality-filtered with bioinformatic pipelines. However, such pipelines are not yet standardized, especially for fungal communities, and those available may produce contrasting results. While some pipelines cluster sequences based on a specified percentage of base pair similarity into operational taxonomic units (OTUs), others utilize denoising techniques to infer amplicon sequencing variants (ASVs). While ASVs are now considered a more accurate representation of taxonomic diversity for prokaryote communities based on 16S rRNA amplicon sequencing, the applicability of this method for fungal ITS sequences is still debated.<br><br>RESULTS: Here we compared the performance of two commonly used pipelines DADA2 (inferring ASVs) and mothur (clustering OTUs) on fungal metabarcoding sequences originating from two different environmental sample types (fresh bovine feces and pasture soil). At a 99% OTU similarity threshold, mothur consistently identified a higher fungal richness compared to DADA2. In addition, mothur generated homogenous relative abundances across multiple technical replicates (n&#x2009;=&#x2009;18), while DADA2 results for the same replicates were highly heterogeneous.<br><br>CONCLUSIONS: Our study highlights a potential pipeline-associated bias in fungal metabarcoding data analysis of environmental samples. Based on the homogeneity of relative abundances across replicates and the capacity to detect OTUs/ASVs, we suggest using OTU clustering with a similarity of 97% as the most appropriate option for processing fungal metabarcoding data.}, }
@article {pmid39541885, year = {2024}, author = {Wang, G and Li, X and Deng, J and Cao, J and Meng, H and Dong, J and Zhang, H}, title = {Assessing soil cadmium quality standards for different land use types: A global synthesis.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {136450}, doi = {10.1016/j.jhazmat.2024.136450}, pmid = {39541885}, issn = {1873-3336}, abstract = {The contamination of cadmium (Cd) in soil has become an increasingly serious issue worldwide, presenting significant risks to human health, crop safety, and ecosystems. Despite its importance, there is a lack of standardized soil threshold values for use in regulating exposure to Cd-contaminated surface soil. By synthesizing soil environmental standards for Cd from 61 countries and 75 regions, this study analyzed and categorized these standards by land use types. The distribution of Cd quality standards among various countries was determined, based on available data primarily from the United States, Canada, Europe, Australia, and China. The established soil Cd quality standards were also determined for different land types, including lands for agricultural, residential, industrial, construction, commercial uses, and parks/green spaces. Using the ecological environment criteria - species sensitivity distribution (ECC-SSD) model, Cd levels were analyzed across different land use types, and it was determined that a log-logistic distribution was the best fitted model. Our findings indicated that soil Cd quality standards ranged from 0.11 to 5.20 mg/kg for agricultural land, 1.25 to 171.51 mg/kg for residential land, and 2.58 to 1845.26 mg/kg for industrial land, all within the 5-95 % percentile range. The 5 % hazard concentration (HC5) value was recommended as the latest national quality standards for each land type. This comprehensive assessment of global soil Cd quality standards provides valuable insight for decision-makers tasked with effectively managing and mitigating Cd pollution in soil.}, }
@article {pmid39539549, year = {2024}, author = {Pappa, T and Rivas, AL and Iandiorio, MJ and Hoogesteijn, AL and Fair, JM and Rojas Gil, AP and Burriel, AR and Bagos, PG and Chatzipanagiotou, S and Ioannidis, A}, title = {Personalized, disease-stage specific, rapid identification of immunosuppression in sepsis.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1430972}, pmid = {39539549}, issn = {1664-3224}, mesh = {Humans ; *Sepsis/immunology/mortality/blood/diagnosis ; Male ; Female ; Middle Aged ; Aged ; *Precision Medicine ; Leukocyte Count ; Biomarkers/blood ; Aged, 80 and over ; Adult ; Immunosuppression Therapy ; }, abstract = {INTRODUCTION: Data overlapping of different biological conditions prevents personalized medical decision-making. For example, when the neutrophil percentages of surviving septic patients overlap with those of non-survivors, no individualized assessment is possible. To ameliorate this problem, an immunological method was explored in the context of sepsis.<br><br>METHODS: Blood leukocyte counts and relative percentages as well as the serum concentration of several proteins were investigated with 4072 longitudinal samples collected from 331 hospitalized patients classified as septic (n=286), non-septic (n=43), or not assigned (n=2). Two methodological approaches were evaluated: (i) a reductionist alternative, which analyzed variables in isolation; and (ii) a non-reductionist version, which examined interactions among six (leukocyte-, bacterial-, temporal-, personalized-, population-, and outcome-related) dimensions.<br><br>RESULTS: The reductionist approach did not distinguish outcomes: the leukocyte and serum protein data of survivors and non-survivors overlapped. In contrast, the non-reductionist alternative differentiated several data groups, of which at least one was only composed of survivors (a finding observable since hospitalization day 1). Hence, the non-reductionist approach promoted personalized medical practices: every patient classified within a subset associated with 100% survival subset was likely to survive. The non-reductionist method also revealed five inflammatory or disease-related stages (provisionally named 'early inflammation, early immunocompetence, intermediary immuno-suppression, late immuno-suppression, or other'). Mortality data validated these labels: both 'suppression' subsets revealed 100% mortality, the 'immunocompetence' group exhibited 100% survival, while the remaining sets reported two-digit mortality percentages. While the 'intermediary' suppression expressed an impaired monocyte-related function, the 'late' suppression displayed renal-related dysfunctions, as indicated by high concentrations of urea and creatinine.<br><br>DISCUSSION: The data-driven differentiation of five data groups may foster early and non-overlapping biomedical decision-making, both upon admission and throughout their hospitalization. This approach could evaluate therapies, at personalized level, earlier. To ascertain repeatability and investigate the dynamics of the 'other' group, additional studies are recommended.}, }
@article {pmid39537861, year = {2025}, author = {Noria, SF and Pratt, KJ and Abdel-Rasoul, M and Diaz, K and Shalash, B and Abul-Khoudoud, D and Needleman, B and Magallanes, M}, title = {The impact of social determinants of health (SDOH) on completing bariatric surgery at a single academic institution.}, journal = {Surgical endoscopy}, volume = {39}, number = {2}, pages = {1234-1242}, pmid = {39537861}, issn = {1432-2218}, support = {UL1 TR002733/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; *Bariatric Surgery/statistics &amp; numerical data ; Male ; Female ; *Social Determinants of Health/statistics &amp; numerical data ; Middle Aged ; Adult ; *Obesity, Morbid/surgery ; Socioeconomic Factors ; Retrospective Studies ; }, abstract = {BACKGROUND: Underutilization of bariatric surgery is multifactorial. This study aimed to understand the association of SDOH on not achieving surgery.<br><br>METHODS: 1081 applications for primary MBS from January-December 2021 were stratified into those that completed surgery (COM; n&#x2009;=&#x2009;415), in progress&#x2009;>&#x2009;1-year (IP; n&#x2009;=&#x2009;107), dropped out (DO; n&#x2009;=&#x2009;379), and never started (NS; n&#x2009;=&#x2009;180). Using the American-Community-Survey results (2015-2020) and patient zip-codes, population differences in 4-domains of SDOH (demographic/social/housing/economic) were examined between COM versus the other groups. Additionally, using institutional MBSAQIP and EMR data, patient-specific differences in comorbidities were evaluated for COM versus IP/DO. Univariate analysis using Kruskal-Wallis, chi-squared/Fisher's exact tests were used for continuous and/or categorical variables. For patient-level analysis multinomial logistic regression was used to determine predictors of not achieving surgery. Hypothesis testing was conducted at an overall 5 percent type-I error rate (alpha&#x2009;=&#x2009;0.05) and Bonferroni's method was used to adjust for multiple comparisons.<br><br>RESULTS: Compared to COM, IP-patients resided in zip-codes characterized by fewer married people (43% vs 46%; p&#x2009;=&#x2009;0.019), lower education levels (49% vs 43%; p&#x2009;=&#x2009;0.048), more households where rent was&#x2009;>&#x2009;50% of household income (10% vs 8%, p&#x2009;=&#x2009;0.002), and households below the poverty line (17.6% vs 14.5%, p&#x2009;=&#x2009;0.017). At the patient-level, IP were more likely to be male (27.9% vs 14.9%; p&#x2009;=&#x2009;0.014), publicly insured (44.9% vs 28.4%; p&#x2009;=&#x2009;0.004), Black (35.5% vs 22.2%; p&#x2009;=&#x2009;0.006), an active smoker (8.9% vs 2.2%; p&#x2009;=&#x2009;0.018), have a higher BMI (49.6 vs 47.6; p&#x2009;=&#x2009;0.01), and coronary intervention (5.8% vs 1.7%, p&#x2009;=&#x2009;0.034). Comparison of COM vs DO was similar for both phases. Multinomial multivariable logistic regression demonstrated higher BMI (OR&#x2009;=&#x2009;1.03,[CI]:1.01-1.05, p&#x2009;=&#x2009;0.001), males (OR&#x2009;=&#x2009;1.9,[CI]:1.09-3.32, p&#x2009;=&#x2009;0.024), smoking (OR&#x2009;=&#x2009;4.58,[CI]:1.74-12.02, p&#x2009;=&#x2009;0.002), and Medicaid (OR&#x2009;=&#x2009;2.16,[CI]:1.33-3.49, p&#x2009;=&#x2009;0.002) independently predicted not achieving surgery.<br><br>CONCLUSION: Patient-level data demonstrated social not clinical factors predicted surgery completion. Given zip-codes characterizing the IP/DO groups had a greater prevalence of social risk, more attention needs to be directed patient-level social risks.}, }
@article {pmid39537735, year = {2024}, author = {Ki, J and Lee, JM and Lee, W and Kim, JH and Jin, H and Jung, S and Lee, J}, title = {Dual-encoder architecture for metal artifact reduction for kV-cone-beam CT images in head and neck cancer radiotherapy.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {27907}, pmid = {39537735}, issn = {2045-2322}, support = {NRF-2020R1F1A1073430//National Research Foundation of Korea/ ; NRF-2021R1F1A1057818//National Research Foundation of Korea/ ; HI21C1161//Korea Health Industry Development Institute/ ; RS-2020-II201336//Ministry of Science and ICT, South Korea/ ; }, mesh = {*Cone-Beam Computed Tomography/methods ; Humans ; *Head and Neck Neoplasms/radiotherapy/diagnostic imaging ; *Artifacts ; *Metals/chemistry ; Deep Learning ; Image Processing, Computer-Assisted/methods ; Radiotherapy Planning, Computer-Assisted/methods ; Radiotherapy Dosage ; Phantoms, Imaging ; }, abstract = {During a radiotherapy (RT) course, geometrical variations of target volumes, organs at risk, weight changes (loss/gain), tumor regression and/or progression can significantly affect the treatment outcome. Adaptive RT has become the effective methods along with technical advancements in imaging modalities including cone-beam computed tomography (CBCT). Planning CT (pCT) can be modified via deformable image registration (DIR), which is applied to the pair of pCT and CBCT. However, the artifact existed in both pCT and CBCT is a vulnerable factor in DIR. The dose calculation on CBCT is also suggested. Missing information due to the artifacts hinders the accurate dose calculation on CBCT. In this study, we aim to develop a deep learning-based metal artifact reduction (MAR) model to reduce the metal artifacts in CBCT for head and neck cancer RT. To train the proposed MAR model, we synthesized the kV-CBCT images including metallic implants, with and without metal artifacts (simulated image data pairs) through sinogram image handling process. We propose the deep learning architecture which focuses on both artifact removal and reconstruction of anatomic structure using a dual-encoder architecture. We designed four single-encoder models and three dual-encoder models based on UNet (for an artifact removal) and FusionNet (for a tissue restoration). Each single-encoder model contains either UNet or FusionNet, while the dual-encoder models have both UNet and FusionNet architectures. In the dual-encoder models, we implemented different feature fusion methods, including simple addition, spatial attention, and spatial/channel wise attention. Among the models, a dual-encoder model with spatial/channel wise attention showed the highest scores in terms of peak signal-to-noise ratio, mean squared error, structural similarity index, and Pearson correlation coefficient. CBCT images from 34 head and neck cancer patients were used to test the developed models. The dual-encoder model with spatial/channel wise attention showed the best results in terms of artifact index. By using the proposed model to CBCT, one can achieve more accurate synthetic pCT for head and neck patients as well as better tissue recognition and structure delineation for CBCT image itself.}, }
@article {pmid39537340, year = {2024}, author = {Di Battista, V and Danielsen, PH and Gajewicz-Skretna, A and Kedziorski, A and Seiffert, SB and Ma-Hock, L and Berthing, T and Mortensen, A and Sundermann, A and Skjolding, LM and Vogel, U and Baun, A and Wohlleben, W}, title = {Oxide-Perovskites for Automotive Catalysts Biotransform and Induce Multicomponent Clearance and Hazard.}, journal = {ACS nano}, volume = {18}, number = {47}, pages = {32672-32693}, pmid = {39537340}, issn = {1936-086X}, mesh = {*Oxides/chemistry ; Animals ; Catalysis ; *Lanthanum/chemistry ; Rats ; Mice ; Calcium Compounds/chemistry ; Titanium/chemistry ; Automobiles ; Male ; Biotransformation ; Surface Properties ; Lung/metabolism/drug effects ; }, abstract = {Oxide-perovskites designed for automotive catalysts contain multiple metal elements whose presence is crucial to achieving the targeted performance. They are highly stable in exhaust operating conditions; however, little is known about their stability under physiological conditions. As some of the metallic components are hazardous to humans and the environment, perovskite benefits in cleaner air must be balanced with risks in a Safe and Sustainable Design (SSbD) approach. New approach methodologies (NAMs), including in chemico and in silico methods, were used for testing hazards and benefits, including catalytic activity and tolerance for temporary excess of oxygen under dynamic driving conditions. The composition and surface properties of six different lanthanum-based oxide-perovskites compromised their stability under lung physiological conditions, influencing the oxidative damage of the particles and the bioacessibility of leaching metals. We found consistent biotransformation of the oxide-perovskite materials at pH 4.5. The leached lanthanum ions, but not other metals, respeciated into lanthanum phosphate nanoparticles, which increased the overall oxidative damage in additive synergy. The NAM results in the presented SSbD approach were challenged by in vivo studies in rats and mice, which confirmed multicomponent clearance from lungs into urine and supported the comparative ranking of effects against well-characterized spinel materials. Among the perovskites, the version with reduced nickel content and doped with palladium offered the best SSbD balance, despite not improving the conventional benchmark catalytic performance and related sustainability benefits. Redesign by industry may be necessary to better fulfill all SSbD dimensions.}, }
@article {pmid39536186, year = {2024}, author = {Corrêa-do-Nascimento, GS and Galvão, C and Leite, GR}, title = {Investigating the distribution of a rare Colombo-Venezuelan kissing bug, Rhodnius neivai, Lent, 1953, using geographical information system-based analyses.}, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {119}, number = {}, pages = {e240106}, pmid = {39536186}, issn = {1678-8060}, mesh = {Animals ; *Rhodnius ; *Geographic Information Systems ; Colombia ; *Insect Vectors/classification ; *Animal Distribution ; Venezuela ; Chagas Disease/transmission ; Ecosystem ; }, abstract = {BACKGROUND: Rhodnius neivai, a kissing bug found in the dry regions of Colombia and Venezuela, has limited documented occurrences. While it is not deemed a significant vector for Chagas disease, distributional and ecological studies are essential in monitoring species domiciliation and shedding light on the evolutionary aspects of the Rhodniini tribe.<br><br>OBJECTIVES: The study aims to provide a detailed revision of R. neivai distribution and evaluate general spatial data quality for ecological niche modelling (ENM). It will also provide the first published ENM for the species, which may aid species sampling and future analytical improvement.<br><br>METHODS: Registers and other spatial information were gathered by literature review; data georeferencing, preliminary geographical investigations, and model editing were conducted in GIS platforms; ENMs were built using R and explored the uncertainty of parameters and algorithms.<br><br>FINDINGS: Twenty four unique sites were identified, unearthing 17 previously uncovered records. Data lacks robust spatial and temporal precision; however, ENMs had acceptable validations. The models present some variation in suitability but with objective areas for sampling effort.<br><br>MAIN CONCLUSIONS: Rhodnius neivai distribution is better explained by conditions that characterise dry ecotypes, but further sampling is essential to improve modelling and advance with ecological and evolutive matters.}, }
@article {pmid39536049, year = {2024}, author = {Zhao, Y and Cordero, OX and Tikhonov, M}, title = {Linear-regression-based algorithms can succeed at identifying microbial functional groups despite the nonlinearity of ecological function.}, journal = {PLoS computational biology}, volume = {20}, number = {11}, pages = {e1012590}, pmid = {39536049}, issn = {1553-7358}, mesh = {*Algorithms ; Linear Models ; *Ecosystem ; *Computational Biology/methods ; Models, Biological ; Microbiota/physiology ; Nonlinear Dynamics ; }, abstract = {Microbial communities play key roles across diverse environments. Predicting their function and dynamics is a key goal of microbial ecology, but detailed microscopic descriptions of these systems can be prohibitively complex. One approach to deal with this complexity is to resort to coarser representations. Several approaches have sought to identify useful groupings of microbial species in a data-driven way. Of these, recent work has claimed some empirical success at de novo discovery of coarse representations predictive of a given function using methods as simple as a linear regression, against multiple groups of species or even a single such group (the ensemble quotient optimization (EQO) approach). Modeling community function as a linear combination of individual species' contributions appears simplistic. However, the task of identifying a predictive coarsening of an ecosystem is distinct from the task of predicting the function well, and it is conceivable that the former could be accomplished by a simpler methodology than the latter. Here, we use the resource competition framework to design a model where the "correct" grouping to be discovered is well-defined, and use synthetic data to evaluate and compare three regression-based methods, namely, two proposed previously and one we introduce. We find that regression-based methods can recover the groupings even when the function is manifestly nonlinear; that multi-group methods offer an advantage over a single-group EQO; and crucially, that simpler (linear) methods can outperform more complex ones.}, }
@article {pmid39530726, year = {2024}, author = {Toledo, MJL and Zawadzki, MJ and Scott, SB and Johnson, JA and Marcusson-Clavertz, D and Kim, J and Lanza, S and Almeida, DM and Sliwinski, MJ and Smyth, JM}, title = {Exploring the Utility of a Real-Time Approach to Characterising Within-Person Fluctuations in Everyday Stress Responses.}, journal = {Stress and health : journal of the International Society for the Investigation of Stress}, volume = {40}, number = {6}, pages = {e3501}, pmid = {39530726}, issn = {1532-2998}, support = {/NH/NIH HHS/United States ; /NH/NIH HHS/United States ; }, mesh = {Humans ; Female ; Male ; *Stress, Psychological/psychology ; Adult ; *Ecological Momentary Assessment ; Middle Aged ; Aged ; }, abstract = {Few studies have measured components of stress responses in real time-an essential step in designing just-in-time interventions targeting moments of risk. Using ecological momentary assessment (EMA), we characterised stress response components to everyday stressors, including reactivity (the response following a stressor), recovery (the return towards baseline), and pile-up (the accumulation of stressors) (RRPs) by quantifying the dynamics of response indicators (i.e., subjective stress, negative affect, and perseverative cognition). To determine the utility of these novel measures in capturing and characterising acute moments of the stress response, this study evaluated the proportion of variance in RRPs attributed to (1) between-person, (2) between-days, and (3) within-day (momentary) levels. Healthy adults (n = 123; aged 35-65, 79% women, 91% non-Hispanic White) participated in a 14-day study assessing stress response via EMA 6 times a day. RRPs were constructed from 10,065 EMA reports. Multilevel models with moments nested within days nested within persons were used to partition variance in the RRPs. Reactivity and recovery indicators captured the most variation within-days (i.e., across moments; range 76%-80% and 87%-89%, respectively), with small amounts of variance between-person. For pile-up, variation was mostly observed between-days (range 60%-63%) and between-persons (range 27%-31%). In contrast, raw measures of stress response reflected substantial between-person (range 32%-54%) and within-day (range 34%-53%) variance. These results demonstrated that a person-specific approach to measuring stress response components (i.e., RRPs) can capture the dynamic within-person variation in stress response, as it occurs in real time, making it well-suited for use in novel just-in-time interventions targeting moments of risk.}, }
@article {pmid39526854, year = {2024}, author = {Tan, X and Xue, F and Zhang, C and Wang, T}, title = {mbDriver: identifying driver microbes in microbial communities based on time-series microbiome data.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {6}, pages = {}, pmid = {39526854}, issn = {1477-4054}, support = {12331009//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Microbiota ; Computational Biology/methods ; Algorithms ; Gastrointestinal Microbiome ; }, abstract = {Alterations in human microbial communities are intricately linked to the onset and progression of diseases. Identifying the key microbes driving these community changes is crucial, as they may serve as valuable biomarkers for disease prevention, diagnosis, and treatment. However, there remains a need for further research to develop effective methods for addressing this critical task. This is primarily because defining the driver microbe requires consideration not only of each microbe's individual contributions but also their interactions. This paper introduces a novel framework, called mbDriver, for identifying driver microbes based on microbiome abundance data collected at discrete time points. mbDriver comprises three main components: (i) data preprocessing of time-series abundance data using smoothing splines based on the negative binomial distribution, (ii) parameter estimation for the generalized Lotka-Volterra (gLV) model using regularized least squares, and (iii) quantification of each microbe's contribution to the community's steady state by manipulating the causal graph implied by gLV equations. The performance of nonparametric spline-based denoising and regularized least squares estimation is comprehensively evaluated on simulated datasets, demonstrating superiority over existing methods. Furthermore, the practical applicability and effectiveness of mbDriver are showcased using a dietary fiber intervention dataset and an ulcerative colitis dataset. Notably, driver microbes identified in the dietary fiber intervention dataset exhibit significant effects on the abundances of short-chain fatty acids, while those identified in the ulcerative colitis dataset show a significant correlation with metabolism-related pathways.}, }
@article {pmid39526196, year = {2024}, author = {Boyes, D and Crowley, LM and Boyes, C and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Pale November moth, Epirrita christyi (Allen, 1906).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {540}, pmid = {39526196}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Pale November moth, Epirrita christyi (Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 474.20 megabases. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.99 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,983 protein-coding genes.}, }
@article {pmid39521320, year = {2024}, author = {Coelho, LA and Gonzalez, CLR and Tammurello, C and Campus, C and Gori, M}, title = {Hand and foot overestimation in visually impaired human adults.}, journal = {Neuroscience}, volume = {563}, number = {}, pages = {74-83}, doi = {10.1016/j.neuroscience.2024.10.055}, pmid = {39521320}, issn = {1873-7544}, mesh = {Humans ; Female ; Male ; Adult ; *Hand ; *Foot ; Middle Aged ; *Blindness/physiopathology/psychology ; Persons with Visual Disabilities/psychology ; Body Image/psychology ; Young Adult ; Sex Characteristics ; }, abstract = {Previous research has shown that visual impairment results in reduced audio, tactile and proprioceptive ability. One hypothesis is that these issues arise from inaccurate body representations. Few studies have investigated metric body representations in a visually impaired population. We designed an ecologically valid behavioural task in which visually impaired adults haptically explored various sized gloves or shoes. They were asked to indicate if they perceived each clothing item as bigger than the size of their hand or foot. In the post-hoc analyses we fit psychometric curves to the data to extract the point of subjective equality. We then compared the results to age/sex matched controls. We hypothesized the blind participants body representations should be more distorted. Because previous research has shown that females are more likely to overestimate body size, we predicted sex differences in the sighted participants. However, because blind adults have no exposure to visual ideals of body size, we predicted that there would be no sex differences. Our results showed thatblind participants overestimated their hands and feetto a similar degree. Sighted controls overestimated their hands significantly more than their feet. Taken together, our results partially support our hypothesis and suggest that visual deprivation, even for short periods result in hand size overestimation.}, }
@article {pmid39520764, year = {2025}, author = {Rodriguez-Caturla, MY and Margalho, LP and Graça, JS and Pia, AKR and Xavier, VL and Noronha, MF and Cabral, L and Lemos-Junior, WJF and Castillo, CJC and SantˈAna, AS}, title = {Bacterial dynamics and volatile metabolome changes of vacuum-packaged beef with different pH during chilled storage.}, journal = {International journal of food microbiology}, volume = {427}, number = {}, pages = {110955}, doi = {10.1016/j.ijfoodmicro.2024.110955}, pmid = {39520764}, issn = {1879-3460}, mesh = {*Volatile Organic Compounds/analysis/metabolism ; Hydrogen-Ion Concentration ; Vacuum ; Cattle ; Animals ; *Red Meat/microbiology ; *Food Packaging/methods ; *Food Microbiology ; *Food Storage ; Bacteria/metabolism/growth &amp; development/classification/genetics/isolation &amp; purification ; Metabolome ; Brazil ; RNA, Ribosomal, 16S/genetics ; }, abstract = {This study aimed to assess the growth of spoilage bacteria in Brazilian vacuum-packed beef across different pH ranges (5.4-5.8, 5.8-6.1, ≥6.1) stored at temperatures of 0 °C, 4 °C, and 7 °C. Additionally, the research sought to identify predominant spoilage bacteria at the genus level using 16S rDNA gene sequencing and analyze the principal volatile organic compounds (VOCs) produced by this microbiota through HS-SPME/GC-MS. Lactic acid bacteria (LAB) consistently exhibited counts exceeding 6.0 Log CFU/g, regardless of temperature and pH conditions. The bacterial diversity in the meat samples reflected the influence of slaughterhouse environments, with Pseudomonas and Serratia remaining dominant across different cuts and pH levels. Post-storage, variations in pH and temperature modulated the initial bacterial diversity, leading to a reduction in diversity and an increase in LAB such as Lactobacillus, Lactococcus, Leuconostoc, and Carnobacterium. Notably, these changes were observed within pH ranges of 5.4-5.8 and 5.8-6.1, irrespective of beef cuts and storage temperatures. Based on high throughput sequencing and VOCS, correlation analysis revealed a relationship between the growth of specific spoilage microorganisms under vacuum conditions and the presence of VOCs such as alcohols (e.g., 1-propanol, 2-methyl-) and ketones (e.g., 2-nonanone, 2-octanone, 2-heptanone), identifying them as potential indicators of spoilage bacteria growth.}, }
@article {pmid39516498, year = {2024}, author = {Weistuch, C and Murgas, KA and Zhu, J and Norton, L and Dill, KA and Tannenbaum, AR and Deasy, JO}, title = {Normal tissue transcriptional signatures for tumor-type-agnostic phenotype prediction.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {27230}, pmid = {39516498}, issn = {2045-2322}, support = {BCRF-17-193//Breast Cancer Research Foundation/ ; W911NF2210292//Army Research Office/ ; P30 CA008748/CA/NCI NIH HHS/United States ; FA9550-20-1-0029//Air Force Office of Scientific Research/ ; R01-AG048769/GF/NIH HHS/United States ; R01 AG048769/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; *Transcriptome ; *Phenotype ; *Gene Expression Regulation, Neoplastic ; Female ; Neoplasms/genetics/pathology/metabolism ; Gene Expression Profiling ; Breast Neoplasms/genetics/pathology/metabolism ; }, abstract = {Cancer transcriptional patterns reflect both unique features and shared hallmarks across diverse cancer types, but whether differences in these patterns are sufficient to characterize the full breadth of tumor phenotype heterogeneity remains an open question. We hypothesized that these shared transcriptomic signatures reflect repurposed versions of functional tasks performed by normal tissues. Starting with normal tissue transcriptomic profiles, we use non-negative matrix factorization to derive six distinct transcriptomic phenotypes, called archetypes, which combine to describe both normal tissue patterns and variations across a broad spectrum of malignancies. We show that differential enrichment of these signatures correlates with key tumor characteristics, including overall patient survival and drug sensitivity, independent of clinically actionable DNA alterations. Additionally, we show that in HR+/HER2- breast cancers, metastatic tumors adopt transcriptomic signatures consistent with the invaded tissue. Broadly, our findings suggest that cancer often arrogates normal tissue transcriptomic characteristics as a component of both malignant progression and drug response. This quantitative framework provides a strategy for connecting the diversity of cancer phenotypes and could potentially help manage individual patients.}, }
@article {pmid39513992, year = {2025}, author = {Black, AN and Jeon, JY and Mularo, AJ and Allen, NM and Heenkenda, E and Buchanan-Schwanke, JC and Bickham, JW and Lowe, ZE and DeWoody, JA}, title = {Thematic Layers of Genomic Susceptibility for Conservation Monitoring.}, journal = {Molecular ecology}, volume = {34}, number = {23}, pages = {e17582}, doi = {10.1111/mec.17582}, pmid = {39513992}, issn = {1365-294X}, mesh = {*Conservation of Natural Resources/methods ; *Genetics, Population/methods ; *Genomics/methods ; Hybridization, Genetic ; Heterozygote ; Geographic Information Systems ; Homozygote ; }, abstract = {Population genomics has great potential to inform applied conservation management and associated policy. However, the bioinformatic analyses and interpretation of population genomic datasets can be daunting and difficult to convey to nonspecialists, including on-the-ground conservationists that work with many state, federal and international agencies. We think that individual population genomic metrics of interest can be interpolated and ultimately distilled into thematic GIS layers that represent spatiotemporal genomic potential (or conversely, susceptibility) in conservation monitoring. As examples relevant to ongoing conservation efforts, we use introgressive hybridisation and individual heterozygosity to illustrate a conceptual approach for mapping population genomic susceptibility. The general framework of thematic layers could be extended to integrate key genomic metrics (e.g., runs of homozygosity and genomic load) that are relevant to many conservation efforts.}, }
@article {pmid39512488, year = {2024}, author = {Lewis, JH and Kojima, H and Suenaga, M and Petsopoulos, D and Fujisawa, Y and Truong, XL and Warren, DL}, title = {The era of cybertaxonomy: X-ray microtomography reveals cryptic diversity and concealed cuticular sculpture in Aphanerostethus Voss, 1957 (Coleoptera, Curculionidae).}, journal = {ZooKeys}, volume = {1217}, number = {}, pages = {1-45}, pmid = {39512488}, issn = {1313-2989}, abstract = {Weevils represent one of the most speciose and economically important animal clades, but remain poorly studied across much of the Oriental Region. Here, an integrative revision of the Oriental, flightless genus Aphanerostethus Voss, 1957 (Curculionidae: Molytinae) based on X-ray microtomography, multi-gene DNA barcoding (CO1, Cytb, 16S), and traditional morphological techniques (light microscopy, dissections) is presented. Twelve new species, namely, A.armatus Lewis &amp; Kojima, sp. nov., A.bifidus Kojima &amp; Lewis, sp. nov., A.darlingi Lewis, sp. nov., A.decoratus Lewis &amp; Kojima, sp. nov., A.falcatus Kojima, Lewis &amp; Fujisawa, sp. nov., A.incurvatus Kojima &amp; Lewis, sp. nov., A.japonicus Lewis &amp; Kojima, sp. nov., A.magnus Lewis &amp; Kojima, sp. nov., A.morimotoi Kojima &amp; Lewis, sp. nov., A.nudus Lewis &amp; Kojima, sp. nov., A.spinosus Lewis &amp; Kojima, sp. nov., and A.taiwanus Lewis, Fujisawa &amp; Kojima, sp. nov. are described from Japan, Taiwan, Vietnam, and Malaysia. A neotype is designated for A.vannideki Voss, 1957. The hitherto monotypic genus Darumazo Morimoto &amp; Miyakawa, 1985, syn. nov. is synonymized under Aphanerostethus based on new morphological data and Aphanerostethusdistinctus (Morimoto &amp; Miyakawa, 1985), comb. nov. is transferred accordingly. X-ray microtomography is successfully used to explore for stable interspecific differences in cuticular, internal and micro morphology. Remarkable species-specific sexual dimorphism in the metatibial uncus is described in seven of the newly described Aphanerostethus species and the evolution of this character is discussed.}, }
@article {pmid39511491, year = {2024}, author = {Tang, Y and Tian, C and Yao, D and Yang, S and Shi, L and Yi, L and Peng, Q}, title = {Community assembly and potential function analysis of the endophyte in Eucommia ulmoides.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {460}, pmid = {39511491}, issn = {1471-2180}, mesh = {*Endophytes/genetics/metabolism/classification/physiology/isolation &amp; purification ; *Eucommiaceae/microbiology ; *Ascomycota/genetics/growth &amp; development/physiology ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Iridoid Glucosides/metabolism ; Basidiomycota/genetics/physiology ; Symbiosis ; Fungi/classification/genetics/isolation &amp; purification/metabolism/physiology ; Computational Biology ; }, abstract = {Endophytes play a pivotal role in protecting host plants from both biotic and abiotic stresses, promoting the production of active components (AC) and plant growth. However, the succession of the endophyte community in Eucommia ulmoides (E. ulmoides), particularly the community assembly and function, has not been extensively investigated. In this study, we employed high-throughput sequencing and bioinformatics tools to analyze endophyte diversity across different tree ages, parts, and periods. We examined the population differences, correlations, community assembly mechanisms, and functional roles of these endophytes. Functional predictions via PICRUSt2 revealed that most endophytic fungal functions were linked to biosynthesis, with significant differences in biosynthetic functional abundance across parts and periods. In contrast, the metabolic activity of endophytic bacteria remained stable across different periods and parts. Correlation analysis further confirmed a strong positive relationship between ACs and certain endophytic fungi. Among them, the fungal phyla Ascomycota and Basidiomycota were identified as key contributors to the metabolism of chlorogenic acid (CA), while Aucubin was significantly positively correlated with several endophytic bacteria. These findings provide valuable insights into the functional roles and community assembly mechanism of E. ulmoides endophytes, as well as their symbiotic relationships.}, }
@article {pmid39507254, year = {2024}, author = {Flores, M and Ho, E and Ly, C and Ceberio, N and Guardado, M and Felix, K and Thorner, HM and Paunovich, M and Godek, C and Kalaydjian, C and Rohlfs, RV}, title = {Decreased accuracy of forensic DNA mixture analysis for groups with lower genetic diversity.}, journal = {iScience}, volume = {27}, number = {11}, pages = {111067}, pmid = {39507254}, issn = {2589-0042}, support = {R25 GM059298/GM/NIGMS NIH HHS/United States ; T32 GM148332/GM/NIGMS NIH HHS/United States ; T34 GM008574/GM/NIGMS NIH HHS/United States ; }, abstract = {Forensic investigation of DNA samples from multiple contributors has become commonplace. These complex analyses use statistical frameworks accounting for multiple levels of uncertainty in allelic contributions from different individuals, particularly for samples containing few molecules of DNA. These methods have been thoroughly tested along some axes of variation, but less attention has been paid to accuracy across human genetic variation. Here, we quantify the accuracy of DNA mixture analysis over 83 human groups. We find higher false inclusion rates for mixtures with more contributors and for groups with lower genetic diversity. Even for three-contributor mixtures where two contributors are known and the reference group is correctly specified, false inclusion rates are 1e-5 or higher for 36 out of 83 groups. This means that, depending on multiple testing, some false inclusions may be expected. These false positives could be lessened with more selective and conservative use of DNA mixture analysis.}, }
@article {pmid39503522, year = {2024}, author = {Campelo, F and de Oliveira, ALG and Reis-Cunha, J and Fraga, VG and Bastos, PH and Ashford, J and Ekárt, A and Adelino, TER and Silva, MVF and de Melo Iani, FC and de Jesus, ACP and Bartholomeu, DC and de Souza Trindade, G and Fujiwara, RT and Bueno, LL and Lobo, FP}, title = {Phylogeny-aware linear B-cell epitope predictor detects targets associated with immune response to orthopoxviruses.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {6}, pages = {}, pmid = {39503522}, issn = {1477-4054}, support = {BIP-00123-23//FAPEMIG/ ; INCT-406441/2022-7//Brazilian National Institutes of Science and Technology/ ; RED-00067-23//Rede Mineira de Imunobiol&#xf3;gicos/ ; APQ-4035/17//State of Minas Gerais Research Support Foundation/ ; 310311/2023-3//National Council for Scientific and Technological Development/ ; 405249/2022-5//MCTI/Brazil/ ; MR/T016019/1//UK Medical Research Council/ ; //EPSRC/UK/ ; }, mesh = {*Phylogeny ; Humans ; *Epitopes, B-Lymphocyte/immunology ; Orthopoxvirus/immunology/genetics ; Computational Biology/methods ; Vaccinia virus/immunology/genetics ; Mpox, Monkeypox ; }, abstract = {We introduce a phylogeny-aware framework for predicting linear B-cell epitope (LBCE)-containing regions within proteins. Our approach leverages evolutionary information by using a taxonomic scaffold to build models trained on hierarchically structured data. The resulting models present performance equivalent or superior to generalist methods, despite using simpler features and a fraction of the data volume required by current state-of-the-art predictors. This allows the utilization of available data for major pathogen lineages to facilitate the prediction of LBCEs for emerging infectious agents. We demonstrate the efficacy of our approach by predicting new LBCEs in the monkeypox (MPXV) and vaccinia viruses. Experimental validation of selected targets using sera from infected patients confirms the presence of LBCEs, including candidates for the differential serodiagnosis of recent MPXV infections. These results point to the use of phylogeny-aware predictors as a useful strategy to facilitate the targeted development of immunodiagnostic tools.}, }
@article {pmid39501271, year = {2024}, author = {Sijm-Eeken, M and Ossebaard, HC and Čaluković, A and Temme, B and Peute, LW and Jaspers, MW}, title = {Linking theory and practice to advance sustainable healthcare: the development of maturity model version 1.0.}, journal = {BMC health services research}, volume = {24}, number = {1}, pages = {1350}, pmid = {39501271}, issn = {1472-6963}, mesh = {Humans ; *Delivery of Health Care/organization &amp; administration ; Climate Change ; Sustainable Development ; Conservation of Natural Resources/methods ; Models, Theoretical ; Models, Organizational ; }, abstract = {BACKGROUND: Climate change and increased awareness of planetary health have made reducing ecological footprints a priority for healthcare organizations. However, improving healthcare's environmental impact remains difficult. Numerous researchers argue these difficulties are caused by healthcare's environmental impact being multidimensional, influenced throughout the healthcare chain, and often has downstream consequences that are hard to identify or to measure. Even though existing research describes many successful approaches to reduce healthcare's environmental impact, a robust multidimensional framework to assess this impact is lacking. This research aims at developing a maturity model for sustainable healthcare that could be used for self-assessment by healthcare professionals to identify improvement actions and for sharing best practices in environmental sustainability.<br><br>METHODS: A design-oriented approach for maturity model development was combined with an expert panel and six case studies to develop, refine and expand the maturity model for environmentally sustainable healthcare.<br><br>RESULTS: A maturity model was developed containing four domains: 'Governance', 'Organization Structures', 'Processes', and 'Outcomes and Control'. Applying the model in real-world environments demonstrated the model's understandability, ease of use, usefulness, practicality and ability to identify improvement actions for environmental sustainability in healthcare organizations.<br><br>CONCLUSIONS: This study found that healthcare practitioners could apply the maturity model developed and tested in this study in several hours without training to help them gain valuable insights into the environment footprint of the healthcare setting they worked in. Systematically implementing the model developed in this study could help address the urgent need to mitigate the substantial environmental impact of healthcare. These implementations can help evaluate and improve the maturity model.}, }
@article {pmid39497067, year = {2024}, author = {Moeller, AH and Dillard, BA and Goldman, SL and Real, MVF and Sprockett, DD}, title = {Removal of sequencing adapter contamination improves microbial genome databases.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1033}, pmid = {39497067}, issn = {1471-2164}, support = {R01 DK139214/DK/NIDDK NIH HHS/United States ; R35 GM138284/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Databases, Genetic ; DNA Contamination ; Genome, Microbial ; Humans ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Cattle ; Mice ; Swine ; }, abstract = {Advances in assembling microbial genomes have led to growth of reference genome databases, which have been transformative for applied and basic microbiome research. Here we show that published microbial genome databases from humans, mice, cows, pigs, fish, honeybees, and marine environments contain significant sequencing-adapter contamination that systematically reduces assembly accuracy and contiguousness. By removing the adapter-contaminated ends of contiguous sequences and reassembling MGnify reference genomes, we improve the quality of assemblies in these databases.}, }
@article {pmid39494195, year = {2024}, author = {Boyes, D and Boyes, C and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Case-bearing Clothes moth, Tinea pellionella (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {119}, pmid = {39494195}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Tinea pellionella (the Case-bearing Clothes moth; Arthropoda; Insecta; Lepidoptera; Tineidae). The genome sequence is 245.3 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 25.86 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,811 protein coding genes.}, }
@article {pmid39493766, year = {2024}, author = {Chakraborty, H and Chakraborty, HJ and Das, BK and Maity, J}, title = {Age-specific changes in the serum proteome of female anadromous, hilsa Tenualosa ilisha: a comparative analysis across developmental stages.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1448627}, pmid = {39493766}, issn = {1664-3224}, mesh = {Female ; *Proteome ; Animals ; Proteomics/methods ; Tandem Mass Spectrometry ; Protein Interaction Maps ; Computational Biology/methods ; Age Factors ; Chromatography, Liquid ; Blood Proteins/metabolism ; Fishes/genetics/blood ; Aging/blood/immunology ; }, abstract = {INTRODUCTION: The proteome profile of the female Tenualosa ilisha (Hamilton, 1822), a species of great ecological and economic importance, across various age groups was investigated to comprehend the functional dynamics of the serum proteome for conservation and aquaculture, as well as sustain the population.<br><br>METHODS: Advanced liquid chromatography-tandem mass spectrometry LC-MS/MS-based proteomic data were analysed and submitted to the ProteomeXchange Consortium via PRIDE (PRoteomics IDEntifications database). Bioinformatics analysis of serum proteome have been done and it showed different proteins associated with GO Gene Ontology () terms, and the genes associated with enriched KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways (such as phagosome, mTOR, Apelin signalling pathways, herpes simplex virus) implicated in immune responses.<br><br>RESULTS: The expression levels of important immunological proteins, such as those involved in cellular defence and inflammatory responses, were significantly different age-dependently. In this study, we annotated 952, 494, 415, and 282 proteins in year classes IV, III, II, and I Hilsa, respectively, and analysed their Protein-Protein Interaction (PPI) networks based on their functional characteristics. From year classes I to IV, new proteins appeared and were more than three-fold. Notably, class I hilsa displayed a lower abundance of proteins than class IV hilsa.<br><br>DISCUSSION: This is the first study, to the best of our knowledge, to report the analysis of the serum proteome of hilsa at different developmental stages, and the results can help improve the understanding of the mechanisms underlying the different changes in protein enrichment during migration in hilsa. This analysis also offers crucial insights into the immune system for hilsa conservation and management.}, }
@article {pmid39493638, year = {2024}, author = {Reuken, PA and Besteher, B and Bleidorn, J and Brockmann, D and Finke, K and Freytag, A and Lehmann-Pohl, K and Lemhöfer, C and Mikolajczyk, R and Puta, C and Scherag, A and Wiedermann, M and Zippel-Schultz, B and Stallmach, A}, title = {Web-based telemedicine approach for treatment of post-COVID-19 in Thuringia (WATCH).}, journal = {Digital health}, volume = {10}, number = {}, pages = {20552076241291748}, pmid = {39493638}, issn = {2055-2076}, abstract = {OBJECTIVE: After infection with SARS-CoV-2, a substantial proportion of patients develop long-lasting sequelae. These sequelae include fatigue (potentially as severe as that seen in ME/CFS cases), cognitive dysfunction, and psychiatric symptoms. Because the pathophysiology of these sequelae remains unclear, existing therapeutic concepts address the symptoms through pacing strategies, cognitive training, and psychological therapy.<br><br>METHODS: Here, we present a protocol for a digital multimodal structured intervention addressing common symptoms through three intervention modules: BRAIN, BODY, and SOUL. This intervention includes an assessment conducted via a mobile "post-COVID-19 bus" near the patient's home, as well as the use of wearable devices and mobile applications to support pacing strategies and collection of data, including ecological momentary assessment.<br><br>RESULTS: We will focus on physical component subscore of the SF36 as Quality of Life parameter as the primary outcome parameter for WATCH to take into account the holistic approach that is necessary for care of post-COVID patients.<br><br>CONCLUSION: In the current project, we present a protocol for a holistic and multimodal structured therapeutic concept which is easily accessible, and scalable for post-COVID patients.}, }
@article {pmid39488960, year = {2024}, author = {Tayyab, M and Hussain, M and Zhang, J and Ullah, S and Tong, Z and Rahman, ZU and Al-Aizari, AR and Al-Shaibah, B}, title = {Leveraging GIS-based AHP, remote sensing, and machine learning for susceptibility assessment of different flood types in peshawar, Pakistan.}, journal = {Journal of environmental management}, volume = {371}, number = {}, pages = {123094}, doi = {10.1016/j.jenvman.2024.123094}, pmid = {39488960}, issn = {1095-8630}, mesh = {*Floods ; Pakistan ; *Machine Learning ; *Geographic Information Systems ; Algorithms ; Remote Sensing Technology ; }, abstract = {Due to its diverse topography, Pakistan faces different types of floods each year, which cause substantial physical, environmental, and socioeconomic damage. However, the susceptibility of specific regions to different flood types remains unexplored. To the best of our knowledge for the first time, this study employed an integrated approach by leveraging a GIS-based Analytical Hierarchy Process (AHP), remote sensing, and machine learning (ML) algorithms, to assess susceptibility to three different types of flooding in Peshawar, Pakistan. The study first evaluated the degree of susceptibility to riverine, urban, and flash floods using the GIS-based AHP technique, and then employed ML models, (i.e., specifically Random Forest [RF] and Extreme Gradient Boosting [XG-Boost] to analyze multi-type flood susceptibility in the study region. The performance of the ML models was also evaluated, and the XG-Boost model outperforms RF, demonstrating a higher correlation coefficient (R[2] = 0.561-0.922) and lower mean absolute error (MAE = 0.042-0.354), and root-mean-square error (RMSE = 0.119-0.415) for both training and testing datasets. The superior performance of the XG-Boost was further confirmed by the higher value of the area under the curve (AUC) values, which is relatively higher (0.87) than that of the AHP (0.70) and RF (0.86) models. Based on the relative best performance, the XG-Boost model was chosen for further susceptibility assessment of different types of floods, and the generated flood susceptibility maps revealed that 20.9% of the total area is susceptible to riverine flooding, while 30.27% and 48.68% of the total area is susceptible to urban and flash flooding, respectively. The study's findings are significant, offering valuable insights for relevant stakeholders in guiding future flood risk management and sustainable land use plans in the study area.}, }
@article {pmid39480949, year = {2024}, author = {Goldshtein, A and Chen, X and Amichai, E and Boonman, A and Harten, L and Yinon, O and Orchan, Y and Nathan, R and Toledo, S and Couzin, ID and Yovel, Y}, title = {Acoustic cognitive map-based navigation in echolocating bats.}, journal = {Science (New York, N.Y.)}, volume = {386}, number = {6721}, pages = {561-567}, doi = {10.1126/science.adn6269}, pmid = {39480949}, issn = {1095-9203}, mesh = {Animals ; Acoustics ; *Chiroptera/physiology ; *Cognition ; *Echolocation ; Geographic Information Systems ; Homing Behavior ; *Spatial Navigation ; }, abstract = {Bats are known for their ability to use echolocation for obstacle avoidance and orientation. However, the extent to which bats utilize their highly local and directional echolocation for kilometer-scale navigation is unknown. In this study, we translocated wild Kuhl's pipistrelle bats and tracked their homing abilities while manipulating their visual, magnetic, and olfactory sensing and accurately tracked them using a new reverse GPS system. We show that bats can identify their location after translocation and conduct several-kilometer map-based navigation using solely echolocation. This proposition was further supported by a large-scale echolocation model disclosing how bats use environmental acoustic information to perform acoustic cognitive map-based navigation. We also demonstrate that navigation is improved when using both echolocation and vision.}, }
@article {pmid39480880, year = {2024}, author = {Silva, GAA and Harder, AM and Kirksey, KB and Mathur, S and Willoughby, JR}, title = {Detectability of runs of homozygosity is influenced by analysis parameters and population-specific demographic history.}, journal = {PLoS computational biology}, volume = {20}, number = {10}, pages = {e1012566}, pmid = {39480880}, issn = {1553-7358}, mesh = {*Homozygote ; *Genetics, Population/methods ; *Inbreeding ; Animals ; Models, Genetic ; Computational Biology/methods ; Humans ; Computer Simulation ; Polymorphism, Single Nucleotide/genetics ; }, abstract = {Wild populations are increasingly threatened by human-mediated climate change and land use changes. As populations decline, the probability of inbreeding increases, along with the potential for negative effects on individual fitness. Detecting and characterizing runs of homozygosity (ROHs) is a popular strategy for assessing the extent of individual inbreeding present in a population and can also shed light on the genetic mechanisms contributing to inbreeding depression. Here, we analyze simulated and empirical datasets to demonstrate the downstream effects of program selection and long-term demographic history on ROH inference, leading to context-dependent biases in the results. Through a sensitivity analysis we evaluate how various parameter values impact ROH-calling results, highlighting its utility as a tool for parameter exploration. Our results indicate that ROH inferences are sensitive to factors such as sequencing depth and ROH length distribution, with bias direction and magnitude varying with demographic history and the programs used. Estimation biases are particularly pronounced at lower sequencing depths, potentially leading to either underestimation or overestimation of inbreeding. These results are particularly important for the management of endangered species, as underestimating inbreeding signals in the genome can substantially undermine conservation initiatives. We also found that small true ROHs can be incorrectly lumped together and called as longer ROHs, leading to erroneous inference of recent inbreeding. To address these challenges, we suggest using a combination of ROH detection tools and ROH length-specific inferences, along with sensitivity analysis, to generate robust and context-appropriate population inferences regarding inbreeding history. We outline these recommendations for ROH estimation at multiple levels of sequencing effort, which are typical of conservation genomics studies.}, }
@article {pmid39480818, year = {2024}, author = {Ramesh, S and Rapp, S and Tapias Gomez, J and Levine, B and Tapias-Gomez, D and Chung, D and Truong, Z}, title = {Reference Sequence Browser: An R application with a user-friendly GUI to rapidly query sequence databases.}, journal = {PloS one}, volume = {19}, number = {10}, pages = {e0309707}, pmid = {39480818}, issn = {1932-6203}, mesh = {*User-Computer Interface ; *Software ; *DNA Barcoding, Taxonomic/methods ; Databases, Genetic ; Databases, Nucleic Acid ; Web Browser ; }, abstract = {Land managers, researchers, and regulators increasingly utilize environmental DNA (eDNA) techniques to monitor species richness, presence, and absence. In order to properly develop a biological assay for eDNA metabarcoding or quantitative PCR, scientists must be able to find not only reference sequences (previously identified sequences in a genomics database) that match their target taxa but also reference sequences that match non-target taxa. Determining which taxa have publicly available sequences in a time-efficient and accurate manner currently requires computational skills to search, manipulate, and parse multiple unconnected DNA sequence databases. Our team iteratively designed a Graphic User Interface (GUI) Shiny application called the Reference Sequence Browser (RSB) that provides users efficient and intuitive access to multiple genetic databases regardless of computer programming expertise. The application returns the number of publicly accessible barcode markers per organism in the NCBI Nucleotide, BOLD, or CALeDNA CRUX Metabarcoding Reference Databases. Depending on the database, we offer various search filters such as min and max sequence length or country of origin. Users can then download the FASTA/GenBank files from the RSB web tool, view statistics about the data, and explore results to determine details about the availability or absence of reference sequences.}, }
@article {pmid39483086, year = {2024}, author = {Behera, BP and Naik, H and Konkimalla, VB}, title = {Peptaloid: A Comprehensive Database for Exploring Peptide Alkaloid.}, journal = {Journal of chemical information and modeling}, volume = {64}, number = {22}, pages = {8387-8395}, doi = {10.1021/acs.jcim.4c01667}, pmid = {39483086}, issn = {1549-960X}, mesh = {*Peptides/chemistry ; *Alkaloids/chemistry/pharmacology ; Databases, Protein ; Machine Learning ; Databases, Factual ; Humans ; }, abstract = {Peptaloid is the first dedicated database for peptide alkaloid molecules, a unique class of naturally derived compounds known for their structural diversity and significant biological activities. Despite their promising potential in drug discovery and therapeutic development, research on peptide alkaloids has been limited by the absence of a comprehensive and centralized resource. Fragmented data across various sources have posed a significant challenge, underscoring the need for a specialized database to facilitate more efficient research and application. Peptaloid addresses this critical gap by providing a database with over 161,000 peptide alkaloid entries, each detailed with structural, physicochemical, and pharmacological properties. By leveraging advanced computational tools and machine learning, Peptaloid generates ADMET profiles, aiding in identifying and optimizing therapeutic candidates. Designed for versatility, the database supports various applications beyond drug discovery, including ecology and material sciences. Peptaloid (as a specialized database for peptide alkaloids) will play a crucial role in innovation and collaboration across scientific disciplines. Peptaloid is accessible at https://peptaloid.niser.ac.in.}, }
@article {pmid39481332, year = {2025}, author = {Yao, M and Ren, A and Yang, X and Chen, L and Wang, X and van der Meer, W and van Loosdrecht, MCM and Liu, G and Pabst, M}, title = {Unveiling the influence of heating temperature on biofilm formation in shower hoses through multi-omics.}, journal = {Water research}, volume = {268}, number = {Pt B}, pages = {122704}, doi = {10.1016/j.watres.2024.122704}, pmid = {39481332}, issn = {1879-2448}, mesh = {*Biofilms ; Proteomics ; Heating ; Metagenomics ; Hot Temperature ; Metagenome ; Multiomics ; }, abstract = {Shower systems provide unique environments that are conducive to biofilm formation and the proliferation of pathogens. The water heating temperature is a delicate decision that can impact microbial growth, balancing safety and energy consumption. This study investigated the impact of different heating temperatures (39 °C, 45 °C, 51 °C and 58 °C) on the shower hose biofilm (exposed to a final water temperature of 39 °C) using controlled full-scale shower setups. Whole metagenome sequencing and metaproteomics were employed to unveil the microbial composition and protein expression profiles. Overall, the genes and enzymes associated with disinfectant resistance and biofilm formation appeared largely unaffected. However, metagenomic analysis revealed a sharp decline in the number of total (86,371 to 34,550) and unique genes (32,279 to 137) with the increase in hot water temperature, indicating a significant reduction of overall microbial complexity. None of the unique proteins were detected in the proteomics experiments, suggesting smaller variation among biofilms on the proteome level compared to genomic data. Furthermore, out of 43 pathogens detected by metagenomics, only 5 could actually be detected by metaproteomics. Most interestingly, our study indicates that 45 °C heating temperature may represent an optimal balance. It minimizes active biomass (ATP) and reduces the presence of pathogens while saving heating energy. Our study offered new insights into the impact of heating temperature on shower hose biofilm formation and proposed optimal parameters that ensure biosafety while conserving energy.}, }
@article {pmid39477106, year = {2024}, author = {Manzanedo, RD and Chin, ARO and Ettinger, AK and Pederson, N and Pradhan, K and Guiterman, CH and Su, J and Baumgarten, F and Hille Ris Lambers, J}, title = {Moving ecological tree-ring big data forwards: Limitations, data integration, and multidisciplinarity.}, journal = {The Science of the total environment}, volume = {955}, number = {}, pages = {177244}, doi = {10.1016/j.scitotenv.2024.177244}, pmid = {39477106}, issn = {1879-1026}, mesh = {*Ecology ; *Big Data ; *Trees ; *Databases, Factual ; Environmental Monitoring/methods ; Forests ; Ecosystem ; }, abstract = {In recent years, tree-ring databases have emerged as a remarkable resource for ecological research, allowing us to address ecological questions at unprecedented temporal and spatial scales. However, concerns regarding big tree-ring data limitations and risks have also surfaced, leading to questions about their potential to be representative of long-term forest responses. Here, we highlight three paths of action to improve on tree-ring databases in ecology: 1) Implementing consistent bias analyses in large dendroecological databases and promoting community-driven data to address data limitations, 2) Encouraging the integration of tree-ring data with other ecological datasets, and 3) Promoting theory-driven, mechanistic dendroecological research. These issues are increasingly important for tackling pressing cross-disciplinary research questions. Finally, although we focus here on tree ring databases, these points apply broadly across many aggregative databases in ecology.}, }
@article {pmid39475652, year = {2024}, author = {Chala, D and Endresen, D and Demissew, S and Slaughter, LA and Johnsen, EB and Stenseth, NC}, title = {Stop using racist, unethical, and inappropriate names in taxonomy.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {45}, pages = {e2415490121}, pmid = {39475652}, issn = {1091-6490}, }
@article {pmid39475336, year = {2025}, author = {Menssen, M and Dammann, M and Fneish, F and Ellenberger, D and Schaarschmidt, F}, title = {Prediction Intervals for Overdispersed Poisson Data and Their Application in Medical and Pre-Clinical Quality Control.}, journal = {Pharmaceutical statistics}, volume = {24}, number = {2}, pages = {e2447}, pmid = {39475336}, issn = {1539-1612}, mesh = {Humans ; *Quality Control ; Poisson Distribution ; Monte Carlo Method ; Algorithms ; Computer Simulation ; Models, Statistical ; Multiple Sclerosis ; Data Interpretation, Statistical ; }, abstract = {In pre-clinical and medical quality control, it is of interest to assess the stability of the process under monitoring or to validate a current observation using historical control data. Classically, this is done by the application of historical control limits (HCL) graphically displayed in control charts. In many applications, HCL are applied to count data, for example, the number of revertant colonies (Ames assay) or the number of relapses per multiple sclerosis patient. Count data may be overdispersed, can be heavily right-skewed and clusters may differ in cluster size or other baseline quantities (e.g., number of petri dishes per control group or different length of monitoring times per patient). Based on the quasi-Poisson assumption or the negative-binomial distribution, we propose prediction intervals for overdispersed count data to be used as HCL. Variable baseline quantities are accounted for by offsets. Furthermore, we provide a bootstrap calibration algorithm that accounts for the skewed distribution and achieves equal tail probabilities. Comprehensive Monte-Carlo simulations assessing the coverage probabilities of eight different methods for HCL calculation reveal, that the bootstrap calibrated prediction intervals control the type-1-error best. Heuristics traditionally used in control charts (e.g., the limits in Shewhart c- or u-charts or the mean ± 2 SD) fail to control a pre-specified coverage probability. The application of HCL is demonstrated based on data from the Ames assay and for numbers of relapses of multiple sclerosis patients. The proposed prediction intervals and the algorithm for bootstrap calibration are publicly available via the R package predint.}, }
@article {pmid39475188, year = {2025}, author = {Kemmler, E and Lemfack, MC and Goede, A and Gallo, K and Toguem, SMT and Ahmed, W and Millberg, I and Preissner, S and Piechulla, B and Preissner, R}, title = {mVOC 4.0: a database of microbial volatiles.}, journal = {Nucleic acids research}, volume = {53}, number = {D1}, pages = {D1692-D1696}, pmid = {39475188}, issn = {1362-4962}, support = {Pi153/36-1//German Research Foundation/ ; //University of Rostock/ ; 428445448//Food allergy and tolerance (FOOD@)/ ; }, mesh = {*Volatile Organic Compounds/metabolism/chemistry ; *Bacteria/metabolism/genetics ; Microbiota ; Metabolomics/methods ; Databases, Factual ; Humans ; Metabolome ; Terpenes/metabolism/chemistry ; Databases, Chemical ; }, abstract = {Metabolomic microbiome research has become an important topic for understanding agricultural, ecological as well as health correlations. Only the determination of both the non-volatile and the volatile organic compound (mVOC) production by microorganisms allows a holistic view for understanding the complete potential of metabolomes and metabolic capabilities of bacteria. In the recent past, more and more bacterial headspaces and culture media were analyzed, leading to an accumulation of about 3500 mVOCs in the updated mVOC 4.0 database, including compounds synthesized by the newly discovered non-canonical terpene pathway. Approximately 10% of all mVOCs can be assigned with a biological function, some mVOCs have the potential to impact agriculture in the future (e.g. eco-friendly pesticides) or animal and human health care. mVOC 4.0 offers various options for exploring extensively annotated mVOC data from different perspectives, including improved mass spectrometry matching. The mVOC 4.0 database includes literature searches with additional relevant keywords, making it the most up-to-date and comprehensive publicly available mVOC platform at: http://bioinformatics.charite.de/mvoc.}, }
@article {pmid39473806, year = {2024}, author = {Ayadi, H and Elbéji, A and Despotovic, V and Fagherazzi, G}, title = {Digital Vocal Biomarker of Smoking Status Using Ecological Audio Recordings: Results from the Colive Voice Study.}, journal = {Digital biomarkers}, volume = {8}, number = {1}, pages = {159-170}, pmid = {39473806}, issn = {2504-110X}, abstract = {INTRODUCTION: The complex health, social, and economic consequences of tobacco smoking underscore the importance of incorporating reliable and scalable data collection on smoking status and habits into research across various disciplines. Given that smoking impacts voice production, we aimed to develop a gender and language-specific vocal biomarker of smoking status.<br><br>METHODS: Leveraging data from the Colive Voice study, we used statistical analysis methods to quantify the effects of smoking on voice characteristics. Various voice feature extraction methods combined with machine learning algorithms were then used to produce a gender and language-specific (English and French) digital vocal biomarker to differentiate smokers from never-smokers.<br><br>RESULTS: A total of 1,332&#x202c; participants were included after propensity score matching (mean age = 43.6 [13.65], 64.41% are female, 56.68% are English speakers, 50% are smokers and 50% are never-smokers). We observed differences in voice features distribution: for women, the fundamental frequency F0, the formants F1, F2, and F3 frequencies and the harmonics-to-noise ratio were lower in smokers compared to never-smokers (p < 0.05) while for men no significant disparities were noted between the two groups. The accuracy and AUC of smoking status prediction reached 0.71 and 0.76, respectively, for the female participants, and 0.65 and 0.68, respectively, for the male participants.<br><br>CONCLUSION: We have shown that voice features are impacted by smoking. We have developed a novel digital vocal biomarker that can be used in clinical and epidemiological research to assess smoking status in a rapid, scalable, and accurate manner using ecological audio recordings.}, }
@article {pmid39473051, year = {2024}, author = {Wang, Y and Chen, J and Ni, Y and Liu, Y and Gao, X and Tse, MA and Panagiotou, G and Xu, A}, title = {Exercise-changed gut mycobiome as a potential contributor to metabolic benefits in diabetes prevention: an integrative multi-omics study.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2416928}, pmid = {39473051}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; *Exercise ; Middle Aged ; *Mycobiome ; *Fungi/classification/genetics/isolation &amp; purification ; *Feces/microbiology ; Proteomics ; Prediabetic State/microbiology/metabolism ; Metabolomics ; Bacteria/classification/isolation &amp; purification/genetics/metabolism ; Adult ; Diabetes Mellitus, Type 2/microbiology/prevention &amp; control ; Metagenomics ; Multiomics ; }, abstract = {BACKGROUND: The importance of gut microbes in mediating the benefits of lifestyle intervention is increasingly recognized. However, compared to the bacterial microbiome, the role of intestinal fungi in exercise remains elusive. With our established randomized controlled trial of exercise intervention in Chinese males with prediabetes (n = 39, ClinicalTrials.gov:NCT03240978), we investigated the dynamics of human gut mycobiome and further interrogated their associations with exercise-elicited outcomes using multi-omics approaches.<br><br>METHODS: Clinical variations and biological samples were collected before and after training. Fecal fungal composition was analyzed using the internal transcribed spacer 2 (ITS2) sequencing and integrated with paired shotgun metagenomics, untargeted metabolomics, and Olink proteomics.<br><br>RESULTS: Twelve&#x2009;weeks of exercise training profoundly promoted fungal ecological diversity and intrakingdom connection. We further identified exercise-responsive genera with potential metabolic benefits, including Verticillium, Sarocladium, and Ceratocystis. Using multi-omics approaches, we elucidated comprehensive associations between changes in gut mycobiome and exercise-shaped metabolic phenotypes, bacterial microbiome, and circulating metabolomics and proteomics profiles. Furthermore, a machine-learning algorithm built using baseline microbial signatures and clinical characteristics predicted exercise responsiveness in improvements of insulin sensitivity, with an area under the receiver operating characteristic (AUROC) of 0.91 (95% CI: 0.85-0.97) in the discovery cohort and of 0.79 (95% CI: 0.74-0.86) in the independent validation cohort (n&#x2009;=&#x2009;30).<br><br>CONCLUSIONS: Our findings suggest that intense exercise training significantly remodels the human fungal microbiome composition. Changes in gut fungal composition are associated with the metabolic benefits of exercise, indicating gut mycobiome is a possible molecular transducer of exercise. Moreover, baseline gut fungal signatures predict exercise responsiveness for diabetes prevention, highlighting that targeting the gut mycobiome emerges as a prospective strategy in tailoring personalized training for diabetes prevention.}, }
@article {pmid39472185, year = {2025}, author = {Orr, MC and Albert, G and Hughes, AC and Koludarov, I and Luo, A and Qiao, H and Wang, MQ and Chesters, D and Zhu, CD}, title = {Dark data limit the biological sciences.}, journal = {Science bulletin}, volume = {70}, number = {4}, pages = {452-453}, doi = {10.1016/j.scib.2024.10.021}, pmid = {39472185}, issn = {2095-9281}, }
@article {pmid39470965, year = {2024}, author = {Sandin, P and Baard, P and Bülow, W and Helgesson, G}, title = {Authorship and Citizen Science: Seven Heuristic Rules.}, journal = {Science and engineering ethics}, volume = {30}, number = {6}, pages = {53}, pmid = {39470965}, issn = {1471-5546}, support = {2019-00548//Svenska Forskningsr&#xe5;det Formas/ ; }, mesh = {*Authorship/standards ; Humans ; *Citizen Science/ethics ; *Heuristics ; *Guidelines as Topic ; *Ethics, Research ; *Publishing/ethics/standards ; Editorial Policies ; Research Personnel/ethics ; Volunteers ; Social Responsibility ; }, abstract = {Citizen science (CS) is an umbrella term for research with a significant amount of contributions from volunteers. Those volunteers can occupy a hybrid role, being both 'researcher' and 'subject' at the same time. This has repercussions for questions about responsibility and credit, e.g. pertaining to the issue of authorship. In this paper, we first review some existing guidelines for authorship and their applicability to CS. Second, we assess the claim that the guidelines from the International Committee of Medical Journal Editors (ICMJE), known as 'the Vancouver guidelines', may lead to exclusion of deserving citizen scientists as authors. We maintain that the idea of including citizen scientists as authors is supported by at least two arguments: transparency and fairness. Third, we argue that it might be plausible to include groups as authors in CS. Fourth and finally, we offer a heuristic list of seven recommendations to be considered when deciding about whom to include as an author of a CS publication.}, }
@article {pmid39470730, year = {2025}, author = {Bağcı, C and Nuhamunada, M and Goyat, H and Ladanyi, C and Sehnal, L and Blin, K and Kautsar, SA and Tagirdzhanov, A and Gurevich, A and Mantri, S and von Mering, C and Udwary, D and Medema, MH and Weber, T and Ziemert, N}, title = {BGC Atlas: a web resource for exploring the global chemical diversity encoded in bacterial genomes.}, journal = {Nucleic acids research}, volume = {53}, number = {D1}, pages = {D618-D624}, pmid = {39470730}, issn = {1362-4962}, support = {161L0284C//Federal Ministry of Research and Education (BMBF)/ ; TTU09.716//German Centre for Infection Research (DZIF)/ ; NNF20CC0035580//Novo Nordisk Foundation/ ; //Saarland University/ ; //National Agri-Food Biotechnology Institute/ ; 101064285//Horizon Europe-Research and Innovation Framework Programme/ ; //Office of Science/ ; DE-AC02-05CH11231//Department of Energy/ ; }, mesh = {*Genome, Bacterial/genetics ; *Internet ; *Multigene Family ; Databases, Genetic ; Bacteria/genetics/metabolism/classification ; Metagenomics/methods ; Metagenome/genetics ; Biosynthetic Pathways/genetics ; Secondary Metabolism/genetics ; Software ; }, abstract = {Secondary metabolites are compounds not essential for an organism's development, but provide significant ecological and physiological benefits. These compounds have applications in medicine, biotechnology and agriculture. Their production is encoded in biosynthetic gene clusters (BGCs), groups of genes collectively directing their biosynthesis. The advent of metagenomics has allowed researchers to study BGCs directly from environmental samples, identifying numerous previously unknown BGCs encoding unprecedented chemistry. Here, we present the BGC Atlas (https://bgc-atlas.cs.uni-tuebingen.de), a web resource that facilitates the exploration and analysis of BGC diversity in metagenomes. The BGC Atlas identifies and clusters BGCs from publicly available datasets, offering a centralized database and a web interface for metadata-aware exploration of BGCs and gene cluster families (GCFs). We analyzed over 35 000 datasets from MGnify, identifying nearly 1.8 million BGCs, which were clustered into GCFs. The analysis showed that ribosomally synthesized and post-translationally modified peptides are the most abundant compound class, with most GCFs exhibiting high environmental specificity. We believe that our tool will enable researchers to easily explore and analyze the BGC diversity in environmental samples, significantly enhancing our understanding of bacterial secondary metabolites, and promote the identification of ecological and evolutionary factors shaping the biosynthetic potential of microbial communities.}, }
@article {pmid39470715, year = {2025}, author = {Miao, Z and Ren, Y and Tarabini, A and Yang, L and Li, H and Ye, C and Liti, G and Fischer, G and Li, J and Yue, JX}, title = {ScRAPdb: an integrated pan-omics database for the Saccharomyces cerevisiae reference assembly panel.}, journal = {Nucleic acids research}, volume = {53}, number = {D1}, pages = {D852-D863}, pmid = {39470715}, issn = {1362-4962}, support = {32070592//National Natural Science Foundation of China/ ; 2022A1515010717//Guangdong Basic and Applied Basic Research Foundation/ ; 2019QN01Y183//Guangdong Pearl River Talents Program/ ; YTP-SYSUCC-0042//Sun Yat-sen University Cancer Center/ ; 24qnpy293//Fundamental Research Funds for the Central Universities/ ; }, mesh = {*Saccharomyces cerevisiae/genetics/metabolism ; *Genome, Fungal ; *Databases, Genetic ; *Genomics/methods ; Telomere/genetics ; Molecular Sequence Annotation ; Proteomics ; Multiomics ; }, abstract = {As a unicellular eukaryote, the budding yeast Saccharomyces cerevisiae strikes a unique balance between biological complexity and experimental tractability, serving as a long-standing classic model for both basic and applied studies. Recently, S. cerevisiae further emerged as a leading system for studying natural diversity of genome evolution and its associated functional implication at population scales. Having high-quality comparative and functional genomics data are critical for such efforts. Here, we exhaustively expanded the telomere-to-telomere (T2T) S. cerevisiae reference assembly panel (ScRAP) that we previously constructed for 142 strains to cover high-quality genome assemblies and annotations of 264 S. cerevisiae strains from diverse geographical and ecological niches and also 33 outgroup strains from all the other Saccharomyces species complex. We created a dedicated online database, ScRAPdb (https://www.evomicslab.org/db/ScRAPdb/), to host this expanded pangenome collection. Furthermore, ScRAPdb also integrates an array of population-scale pan-omics atlases (pantranscriptome, panproteome and panphenome) and extensive data exploration toolkits for intuitive genomics analyses. All curated data and downstream analysis results can be easily downloaded from ScRAPdb. We expect ScRAPdb to become a highly valuable platform for the yeast community and beyond, leading to a pan-omics understanding of the global genetic and phenotypic diversity.}, }
@article {pmid39469132, year = {2024}, author = {Bernstein, JM and Bautista, JB and Clores, MA and Brown, RM and Ruane, S and Sanguila, MB and Alis-Besenio, MGJ and Pejo, CLF and Cuesta, MA}, title = {Using mangrove and field observation data to identify fine-scale species distributions: a case study in bockadams (Serpentes: Homalopsidae: Cerberus).}, journal = {Royal Society open science}, volume = {11}, number = {10}, pages = {240483}, pmid = {39469132}, issn = {2054-5703}, abstract = {Characterization of species distributions is a fundamental challenge in biodiversity science, with particular significance for downstream evolutionary studies, conservation efforts, field-based faunal studies and estimates of species diversity. Checklists and phylogenetic studies often focus on poorly known, rare taxa with limited ranges. However, studies of widely distributed, ecologically important species that are abundant in their preferred microhabitats are also important for systematics and local conservation efforts, but less often studied. We collected novel natural history data during fieldwork (2019-2023) for Philippine populations of bockadams (Homalopsidae: Cerberus), one of the most abundant vertebrates in Southeast Asian aquatic systems. Considered a coastal snake, many studies report Cerberus inland. We report the frequency of encounters of Cerberus schneiderii, and the IUCN data-deficient, Philippine-endemic Cerberus microlepis during six expeditions (62 days; 1041 person-hours). We report new occurrence data for 69 C. schneiderii and 6 C. microlepis for coastal and inland populations, water measurements and dietary observations. Regression analyses and ecological niche models show the importance of coastal and mangrove habitats for Cerberus. Our study is the most comprehensive assessment of Philippine Cerberus populations to date and provides critical baseline natural history data for downstream research on widespread and range-restricted species of Southeast Asian snakes.}, }
@article {pmid39469049, year = {2024}, author = {Chávez-Luzanía, RA and Ortega-Urquieta, ME and Aguilera-Ibarra, J and Morales-Sandoval, PH and Hernández-Coss, JA and González-Vázquez, LA and Jara-Morales, VB and Arredondo-Márquez, SH and Olea-Félix, MJ and de Los Santos-Villalobos, S}, title = {Transdisciplinary approaches for the study of cyanobacteria and cyanotoxins.}, journal = {Current research in microbial sciences}, volume = {7}, number = {}, pages = {100289}, pmid = {39469049}, issn = {2666-5174}, abstract = {Cyanobacteria, ancient aerobic and photoautotrophic prokaryotes, thrive in diverse ecosystems due to their extensive morphological and physiological adaptations. They play crucial roles in aquatic ecosystems as primary producers and resource providers but also pose significant ecological and health risks through blooms that produce harmful toxins, called cyanotoxins. The taxonomic affiliation of cyanobacteria has evolved from morphology-based methods to genomic analysis, which offers detailed structural and physiological insights that are essential for accurate taxonomic affiliation and monitoring. However, challenges posed by uncultured species have been extrapolated to the detection and quantification of cyanotoxins. Current advances in molecular biology and informatics improve the precision of monitoring and allow the analysis of groups of genes related to toxin production, providing crucial information for environmental biosafety and public health. Unfortunately, public genomic databases heavily underrepresent cyanobacteria, which limits the understanding of their diversity and metabolic capabilities. Despite the increasing availability of cyanobacterial genome sequences, research is still largely focused on a few model strains, narrowing the scope of genetic and metabolic studies. The challenges posed by cyanobacterial blooms and cyanotoxins necessitate improved molecular, cultivation, and polyphasic techniques for comprehensive classification and quantification, highlighting the need for advanced genomic approaches to better understand and manage cyanobacteria and toxins. This review explores the application of transdisciplinary approaches for the study of cyanobacteria and cyanotoxins focused on diversity analysis, population quantification, and cyanotoxin monitoring, emphasizing their genomic resources and their potential in the genomic mining of toxin-related genes.}, }
@article {pmid39467848, year = {2024}, author = {Büttiker, P and Boukherissa, A and Weissenberger, S and Ptacek, R and Anders, M and Raboch, J and Stefano, GB}, title = {Cognitive Impact of Neurotropic Pathogens: Investigating Molecular Mimicry through Computational Methods.}, journal = {Cellular and molecular neurobiology}, volume = {44}, number = {1}, pages = {72}, pmid = {39467848}, issn = {1573-6830}, mesh = {Humans ; *Molecular Mimicry ; Computational Biology/methods ; Cognition/physiology ; Protein Binding ; Amino Acid Sequence ; Viral Proteins/metabolism/chemistry ; Models, Molecular ; }, abstract = {Neurotropic pathogens, notably, herpesviruses, have been associated with significant neuropsychiatric effects. As a group, these pathogens can exploit molecular mimicry mechanisms to manipulate the host central nervous system to their advantage. Here, we present a systematic computational approach that may ultimately be used to unravel protein-protein interactions and molecular mimicry processes that have not yet been solved experimentally. Toward this end, we validate this approach by replicating a set of pre-existing experimental findings that document the structural and functional similarities shared by the human cytomegalovirus-encoded UL144 glycoprotein and human tumor necrosis factor receptor superfamily member 14 (TNFRSF14). We began with a thorough exploration of the Homo sapiens protein database using the Basic Local Alignment Search Tool (BLASTx) to identify proteins sharing sequence homology with UL144. Subsequently, we used AlphaFold2 to predict the independent three-dimensional structures of UL144 and TNFRSF14. This was followed by a comprehensive structural comparison facilitated by Distance-Matrix Alignment and Foldseek. Finally, we used AlphaFold-multimer and PPIscreenML to elucidate potential protein complexes and confirm the predicted binding activities of both UL144 and TNFRSF14. We then used our in silico approach to replicate the experimental finding that revealed TNFRSF14 binding to both B- and T-lymphocyte attenuator (BTLA) and glycoprotein domain and UL144 binding to BTLA alone. This computational framework offers promise in identifying structural similarities and interactions between pathogen-encoded proteins and their host counterparts. This information will provide valuable insights into the cognitive mechanisms underlying the neuropsychiatric effects of viral infections.}, }
@article {pmid39466727, year = {2024}, author = {Charniga, K and Park, SW and Akhmetzhanov, AR and Cori, A and Dushoff, J and Funk, S and Gostic, KM and Linton, NM and Lison, A and Overton, CE and Pulliam, JRC and Ward, T and Cauchemez, S and Abbott, S}, title = {Best practices for estimating and reporting epidemiological delay distributions of infectious diseases.}, journal = {PLoS computational biology}, volume = {20}, number = {10}, pages = {e1012520}, pmid = {39466727}, issn = {1553-7358}, support = {MR/R015600/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; *Communicable Diseases/epidemiology ; *Disease Outbreaks/statistics &amp; numerical data ; Models, Statistical ; Computational Biology/methods ; Epidemiological Models ; }, abstract = {Epidemiological delays are key quantities that inform public health policy and clinical practice. They are used as inputs for mathematical and statistical models, which in turn can guide control strategies. In recent work, we found that censoring, right truncation, and dynamical bias were rarely addressed correctly when estimating delays and that these biases were large enough to have knock-on impacts across a large number of use cases. Here, we formulate a checklist of best practices for estimating and reporting epidemiological delays. We also provide a flowchart to guide practitioners based on their data. Our examples are focused on the incubation period and serial interval due to their importance in outbreak response and modeling, but our recommendations are applicable to other delays. The recommendations, which are based on the literature and our experience estimating epidemiological delay distributions during outbreak responses, can help improve the robustness and utility of reported estimates and provide guidance for the evaluation of estimates for downstream use in transmission models or other analyses.}, }
@article {pmid39464503, year = {2023}, author = {Weir, JC and ,  and ,  and ,  and ,  and ,  and ,  and Boyes, D}, title = {The genome sequence of the Vapourer moth, Orgyia antiqua (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {314}, pmid = {39464503}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Orgyia antiqua specimen (the Vapourer moth; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 480.1 megabases in span. Most of the assembly is scaffolded into 14 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,475 protein coding genes.}, }
@article {pmid39464235, year = {2022}, author = {Boyes, D and ,  and ,  and ,  and ,  and ,  and Lewin, T and , }, title = {The genome sequence of the acorn piercer, Pammene fasciana (Linnaeus, 1761).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {258}, pmid = {39464235}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Pammene fasciana (acorn piercer; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 564 megabases in span. Most of the assembly (99.94%) is scaffolded into 28 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 16.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,224 protein-coding genes.}, }
@article {pmid39461044, year = {2024}, author = {Wu, Y and Wei, C and Zhang, Y and Gu, C and Fang, Y}, title = {Investigating intrinsic and situational predictors of depression among older adults: An analysis of the CHARLS database.}, journal = {Asian journal of psychiatry}, volume = {102}, number = {}, pages = {104279}, doi = {10.1016/j.ajp.2024.104279}, pmid = {39461044}, issn = {1876-2026}, mesh = {Humans ; Female ; Male ; Aged ; Middle Aged ; Aged, 80 and over ; *Depression/epidemiology ; Databases, Factual ; China/epidemiology ; Risk Factors ; Follow-Up Studies ; Depressive Disorder/epidemiology ; Chronic Disease ; }, abstract = {BACKGROUND: This study aimed to investigate the intrinsic and situational predictors of depression under the health ecological model.<br><br>METHODS: Two waves (2011 and 2013) of survey data were collected from the CHARLS. A total of 5845 older adults (&#x2267;60) were included, and depression was defined as CESD-10 score &#x2267;10. Random forest combined with interpretable methods were utilized to select important predictors of depression. Multilevel logit model was used to examine the associations of intrinsic and situational predictors with depression.<br><br>RESULTS: After a 2-year follow up, 1822 individuals (31.17&#x202f;%) developed depression. Interpretable analyses showed that both intrinsic and situational variables were predictive for depression. Multilevel logit model showed that age, gender, number of chronic diseases, number of pain areas, life satisfaction, and toilet distance were significantly associated with depression.<br><br>CONCLUSION: Both intrinsic and situational factors were found to be associated with depression among community older population, highlighting their significance for early prevention from the perspective of public health.}, }
@article {pmid39460934, year = {2024}, author = {Frazer, SA and Baghbanzadeh, M and Rahnavard, A and Crandall, KA and Oakley, TH}, title = {Discovering genotype-phenotype relationships with machine learning and the Visual Physiology Opsin Database (VPOD).}, journal = {GigaScience}, volume = {13}, number = {}, pages = {}, pmid = {39460934}, issn = {2047-217X}, support = {DEB-2153773//National Science Foundation/ ; }, mesh = {*Machine Learning ; *Opsins/genetics/metabolism ; Animals ; *Phenotype ; *Databases, Genetic ; Genetic Association Studies ; Genotype ; Humans ; Mutation ; }, abstract = {BACKGROUND: Predicting phenotypes from genetic variation is foundational for fields as diverse as bioengineering and global change biology, highlighting the importance of efficient methods to predict gene functions. Linking genetic changes to phenotypic changes has been a goal of decades of experimental work, especially for some model gene families, including light-sensitive opsin proteins. Opsins can be expressed in vitro to measure light absorption parameters, including λmax-the wavelength of maximum absorbance-which strongly affects organismal phenotypes like color vision. Despite extensive research on opsins, the data remain dispersed, uncompiled, and often challenging to access, thereby precluding systematic and comprehensive analyses of the intricate relationships between genotype and phenotype.<br><br>RESULTS: Here, we report a newly compiled database of all heterologously expressed opsin genes with &#x3bb;max phenotypes that we call the Visual Physiology Opsin Database (VPOD). VPOD_1.0 contains 864 unique opsin genotypes and corresponding &#x3bb;max phenotypes collected across all animals from 73 separate publications. We use VPOD data and deepBreaks to show regression-based machine learning (ML) models often reliably predict &#x3bb;max, account for nonadditive effects of mutations on function, and identify functionally critical amino acid sites.<br><br>CONCLUSION: The ability to reliably predict functions from gene sequences alone using ML will allow robust exploration of molecular-evolutionary patterns governing phenotype, will inform functional and evolutionary connections to an organism's ecological niche, and may be used more broadly for de novo protein design. Together, our database, phenotype predictions, and model comparisons lay the groundwork for future research applicable to families of genes with quantifiable and comparable phenotypes.}, }
@article {pmid39460811, year = {2024}, author = {Hasan, A and Ibrahim, M and Alonazi, WB and Yu, R and Li, B}, title = {Pangenome analysis of five representative Tropheryma whipplei strains following multiepitope-based vaccine design via immunoinformatic approaches.}, journal = {Molecular genetics and genomics : MGG}, volume = {299}, number = {1}, pages = {101}, pmid = {39460811}, issn = {1617-4623}, mesh = {Humans ; *Tropheryma/genetics/immunology ; *Bacterial Vaccines/immunology/genetics ; Whipple Disease/immunology/microbiology/genetics ; Computational Biology/methods ; Bacterial Proteins/genetics/immunology ; Genome, Bacterial ; Epitopes/immunology/genetics ; Vaccine Development ; Immunodominant Epitopes/immunology/genetics ; Proteomics/methods ; Proteome/genetics/immunology ; }, abstract = {Whipple disease caused by Tropheryma whipplei a gram-positive bacterium is a systemic disorder that impacts not only the gastrointestinal tract but also the vascular system, joints, central nervous system, and cardiovascular system. Due to the lack of an approved vaccine, this study aimed to utilize immunoinformatic approaches to design multiepitope -based vaccine by utilizing the proteomes of five representative T. whipplei strains. The genomes initially comprised a total of 4,844 proteins ranging from 956 to 1012 proteins per strain. We collected 829 nonredundant lists of core proteins, that were shared among all the strains. Following subtractive proteomics, one extracellular protein, WP_033800108.1, a WhiB family transcriptional regulator, was selected for the chimeric-based multiepitope vaccine. Five immunodominant epitopes were retrieved from the WhiB family transcriptional regulator protein, indicating MHC-I and MHC-II with a global population coverage of 70.61%. The strong binding affinity, high solubility, nontoxicity, nonallergenic properties and high antigenicity scores make the selected epitopes more appropriate. Integration of the epitopes into a chimeric vaccine was carried out by applying appropriate adjuvant molecules and linkers, leading to the vaccine construct having enhanced immunogenicity and successfully eliciting both innate and adaptive immune responses. Moreover, the abilityof the vaccine to bind TLR4, a core innate immune receptor, was confirmed. Molecular dynamics simulations have also revealed the promising potential stability of the designed vaccine at 400 ns. In summary, we have designed a potential vaccine construct that has the ability not only to induce targeted immunogenicity for one strain but also for global T. whipplei strains. This study proposes a potential universal vaccine, reducing Whipple's disease risk and laying the groundwork for future research on multi-strain pathogens.}, }
@article {pmid39454020, year = {2025}, author = {Wong, R and Matulewicz, RS and Talwar, R and Shoenbill, KA and Goldstein, AO and Bjurlin, MA}, title = {Increased Tobacco Taxation Associated With Decreased Consumption and Bladder Cancer Incidence.}, journal = {Urology practice}, volume = {12}, number = {2}, pages = {250-256}, pmid = {39454020}, issn = {2352-0787}, support = {K08 CA259452/CA/NCI NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Taxes/statistics &amp; numerical data ; *Urinary Bladder Neoplasms/epidemiology/etiology ; Incidence ; United States/epidemiology ; *Tobacco Products/economics ; *Tobacco Use/epidemiology/economics ; Male ; Female ; }, abstract = {INTRODUCTION: The temporal relationship between smoking exposure and bladder cancer (BC) diagnosis remains ill defined. This study aims to cross-correlate and temporally associate changes in US tobacco tax and consumption with BC incidence.<br><br>METHODS: US tobacco consumption, tobacco tax data, and BC incidence rates from 1975 to 2019 were retrieved. A cross-correlation lag time for tobacco tax and consumption on BC incidence was calculated while controlling for national health expenditure. Proxied lag weighted semi-log linear models were used to determine the rate of change in BC incidence rates associated with a 1% change in tobacco tax percentages on a national and state level.<br><br>RESULTS: A 1% increase in tobacco tax was associated with a 1.77% decrease in BC incidence over a 6-year period (R[2] = 0.9687, P = .00044). Twenty-two states had a statistically significant decline in BC incidences correlated with increasing tobacco taxation. Reduction in BC incidence > 0.5% was observed in states along the western and eastern US borders. Montana, Utah, Nebraska, Arkansas, and Tennessee did not have decreasing BC incidences from tobacco tax increases. California had the most drastic decline in BC incidence (1.98%). Nationally, tobacco consumption decrease in 1 pack per capita was associated with a 0.47% decrease in BC incidence over a 28-year period (R[2] = 0.984, P = .00011).<br><br>CONCLUSIONS: Declining US tobacco consumption may indicate significant reduction in BC incidence through 2047. Primary prevention through adaptation of state-legislated tax changes may contribute to a reduction in BC incidence in states lying within the Central United States. A national tobacco tax initiative can be considered given the improvement in population health.}, }
@article {pmid39449983, year = {2023}, author = {Boyes, D and Holland, PWH and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Currant Clearwing moth, Synanthedon tipuliformis (Clerck, 1759).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {300}, pmid = {39449983}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Synanthedon tipuliformis (the Currant Clearwing; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 295.8 megabases in span. Most of the assembly (99.98%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 27.05 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,878 protein-coding genes.}, }
@article {pmid39448189, year = {2024}, author = {Konečný, L and Peterková, K}, title = {Unveiling the peptidases of parasites from the office chair - The endothelin-converting enzyme case study.}, journal = {Advances in parasitology}, volume = {126}, number = {}, pages = {1-52}, doi = {10.1016/bs.apar.2024.05.003}, pmid = {39448189}, issn = {2163-6079}, mesh = {Animals ; *Computational Biology ; Endothelin-Converting Enzymes/genetics ; Schistosoma mansoni/enzymology/genetics ; Humans ; Peptide Hydrolases/genetics/metabolism ; Proteomics ; }, abstract = {The emergence of high-throughput methodologies such as next-generation sequencing and proteomics has necessitated significant advancements in biological databases and bioinformatic tools, therefore reshaping the landscape of research into parasitic peptidases. In this review we outline the development of these resources along the -omics technologies and their transformative impact on the field. Apart from extensive summary of general and specific databases and tools, we provide a general pipeline on how to use these resources effectively to identify candidate peptidases from these large datasets and how to gain as much information about them as possible without leaving the office chair. This pipeline is then applied in an illustrative case study on the endothelin-converting enzyme 1 homologue from Schistosoma mansoni and attempts to highlight the contemporary capabilities of bioinformatics. The case study demonstrate how such approach can aid to hypothesize enzyme functions and interactions through computational analysis alone effectively and emphasizes how such virtual investigations can guide and optimize subsequent wet lab experiments therefore potentially saving precious time and resources. Finally, by showing what can be achieved without traditional wet laboratory methods, this review provides a compelling narrative on the use of bioinformatics to bridge the gap between big data and practical research applications, highlighting the key role of these technologies in furthering our understanding of parasitic diseases.}, }
@article {pmid39446479, year = {2024}, author = {Oliveira, J and Aires Dias, J and Correia, R and Pinheiro, R and Reis, V and Sousa, D and Agostinho, D and Simões, M and Castelo-Branco, M}, title = {Exploring Immersive Multimodal Virtual Reality Training, Affective States, and Ecological Validity in Healthy Firefighters: Quasi-Experimental Study.}, journal = {JMIR serious games}, volume = {12}, number = {}, pages = {e53683}, pmid = {39446479}, issn = {2291-9279}, abstract = {BACKGROUND: Firefighters face stressful life-threatening events requiring fast decision-making. To better prepare for those situations, training is paramount, but errors in real-life training can be harmful. Virtual reality (VR) simulations provide the desired realism while enabling practice in a secure and controlled environment. Firefighters' affective states are also crucial as they are a higher-risk group.<br><br>OBJECTIVE: To assess the impact on affective states of 2 simulated immersive experiences in a sample of healthy firefighters (before, during, and after the simulation), we pursued a multivariate approach comprising cognitive performance, situational awareness, depression, anxiety, stress, number of previous adverse events experienced, posttraumatic stress disorder (PTSD) severity, and emotions. The efficacy and ecological validity of an innovative VR haptic system were also tested, exploring its impact on performance.<br><br>METHODS: In collaboration with the Portuguese National Fire Service School, we exposed 22 healthy firefighters to 2 immersive scenarios using the FLAIM Trainer VR system (neutral and arousing scenarios) while recording physiological data in a quasi-experimental study. Baseline cognitive performance, depression, anxiety, stress, number of adverse events, and severity of PTSD symptoms were evaluated. Positive and negative affective states were measured before, between, and after each scenario. Situational awareness, sense of presence, ecological validity, engagement, and negative effects resulting from VR immersion were tested.<br><br>RESULTS: Baseline positive affect score was high (mean 32.4, SD 7.2) and increased after the VR tasks (partial &#x3b7;[2]=0.52; Greenhouse-Geisser F1.82,32.78=19.73; P<.001). Contrarily, mean negative affect score remained low (range 11.0-11.9) throughout the study (partial &#x3b7;[2]=0.02; Greenhouse-Geisser F2.13,38.4=0.39; P=.69). Participants' feedback on the VR sense of presence was also positive, reporting a high sense of physical space (mean score 3.9, SD 0.8), ecological validity (mean score 3.8, SD 0.6), and engagement (mean score 3.8, SD 0.6). Engagement was related to the number of previously experienced adverse events (r=0.49; P=.02) and positive affect (after the last VR task; r=0.55; P=.02). Conversely, participants reported few negative effects (mean score 1.7, SD 0.6). The negative effects correlated positively with negative affect (after the last VR task; r=0.53; P=.03); and avoidance (r=0.73; P<.001), a PTSD symptom, controlling for relevant baseline variables. Performance related to situational awareness was positive (mean 46.4, SD 34.5), although no relation was found to metacognitively perceived situational awareness (r=-0.12; P=.59).<br><br>CONCLUSIONS: We show that VR is an effective alternative to in-person training as it was considered ecologically valid and engaging while promoting positive emotions, with few negative repercussions. This corroborates the use of VR to test firefighters' performance and situational awareness. Further research is needed to ascertain that firefighters with PTSD symptomatology are not negatively affected by VR. This study favors the use of VR training and provides new insights on its emotional and cognitive impact on the trainee.}, }
@article {pmid39445720, year = {2025}, author = {Compton, ZT and Mellon, W and Harris, VK and Rupp, S and Mallo, D and Kapsetaki, SE and Wilmot, M and Kennington, R and Noble, K and Baciu, C and Ramirez, LN and Peraza, A and Martins, B and Sudhakar, S and Aksoy, S and Furukawa, G and Vincze, O and Giraudeau, M and Duke, EG and Spiro, S and Flach, E and Davidson, H and Li, CI and Zehnder, A and Graham, TA and Troan, BV and Harrison, TM and Tollis, M and Schiffman, JD and Aktipis, CA and Abegglen, LM and Maley, CC and Boddy, AM}, title = {Cancer Prevalence across Vertebrates.}, journal = {Cancer discovery}, volume = {15}, number = {1}, pages = {227-244}, pmid = {39445720}, issn = {2159-8290}, support = {T32 CA272303/CA/NCI NIH HHS/United States ; P01 CA091955/CA/NCI NIH HHS/United States ; OTKA K143421//Agence Nationale de la Recherche (ANR)/ ; COVER ANR-23-CE02-0019//Agence Nationale de la Recherche (ANR)/ ; U54 CA217376/CA/NCI NIH HHS/United States ; ADHS18-198847//Arizona Biomedical Research Commission (ABRC)/ ; U2C CA233254/CA/NCI NIH HHS/United States ; //Hyundai Hope On Wheels (Hope On Wheels)/ ; BC132057//Congressionally Directed Medical Research Programs (CDMRP)/ ; R01 CA140657/CA/NCI NIH HHS/United States ; R21 CA257980/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; *Neoplasms/epidemiology/genetics/veterinary ; Prevalence ; *Vertebrates ; Humans ; }, abstract = {Cancer is pervasive across multicellular species, but what explains the differences in cancer prevalence across species? Using 16,049 necropsy records for 292 species spanning three clades of tetrapods (amphibians, sauropsids, and mammals), we found that neoplasia and malignancy prevalence increases with adult mass (contrary to Peto's paradox) and somatic mutation rate but decreases with gestation time. The relationship between adult mass and malignancy prevalence was only apparent when we controlled for gestation time. Evolution of cancer susceptibility appears to have undergone sudden shifts followed by stabilizing selection. Outliers for neoplasia prevalence include the common porpoise (<1.3%), the Rodrigues fruit bat (<1.6%), the black-footed penguin (<0.4%), ferrets (63%), and opossums (35%). Discovering why some species have particularly high or low levels of cancer may lead to a better understanding of cancer syndromes and novel strategies for the management and prevention of cancer. Significance: Evolution has discovered mechanisms for suppressing cancer in a wide variety of species. By analyzing veterinary necropsy records, we can identify species with exceptionally high or low cancer prevalence. Discovering the mechanisms of cancer susceptibility and resistance may help improve cancer prevention and explain cancer syndromes. See related commentary by Metzger, p. 14.}, }
@article {pmid39442119, year = {2024}, author = {Castro-Nunes, P and Palmieri, P and Bellas, H and Soares, A and Viana, J and Carvalho, PVR and Jatobá, A}, title = {Effects of pay for performance in primary care in an under-registration scenario.}, journal = {Revista de saude publica}, volume = {58}, number = {}, pages = {44}, pmid = {39442119}, issn = {1518-8787}, mesh = {Humans ; *Primary Health Care/economics ; Brazil ; *Reimbursement, Incentive/economics ; Female ; National Health Programs/economics ; }, abstract = {OBJECTIVE: To propose a method for detecting and analyzing under-registration and highlight its potential financial effect in view of the implementation of the Previne Brasil Program.<br><br>METHODS: An ecological study was carried out to analyze cytopathological exams in programmatic area 3.1 in the municipality of Rio de Janeiro. The data was collected from the Departamento de Inform&#xe1;tica do Sistema &#xda;nico de Sa&#xfa;de (DATASUS - Department of Informatics of the Unified Health System) database, including information on reports from outsourced cytopathology laboratories and those available in the Sistema de Informa&#xe7;&#xe3;o em Sa&#xfa;de para a Aten&#xe7;&#xe3;o B&#xe1;sica (SISAB - Health Information System for Primary Care) and the Sistema de Informa&#xe7;&#xe3;o do C&#xe2;ncer do Colo do &#xda;tero (SISCOLO - Cervical Cancer Information System) of DATASUS/Ministry of Health.<br><br>RESULTS: The estimated under-registrations per health unit totaled 108,511 exams in the last two years in the programmatic area 3.1 area, which corresponds to an estimated total of R$ 435,129.00 that would have been foregone if the Previne Brasil Program had been in place during the period studied.<br><br>CONCLUSION: The article's main contribution lies in the presentation of empirical evidence of the potential effects of under-registration on Primary Health Care financing. In addition, there are two other significant findings - firstly, it highlights weaknesses in the process of recording health information inherent to vulnerable regions; secondly, it indicates a vicious circle potentially fueled by sudden changes in Primary Health Care funding conditions, in addition to potential consequences for other levels of care.}, }
@article {pmid39441382, year = {2025}, author = {Canzler, S and Schubert, K and Rolle-Kampczyk, UE and Wang, Z and Schreiber, S and Seitz, H and Mockly, S and Kamp, H and Haake, V and Huisinga, M and Bergen, MV and Buesen, R and Hackermüller, J}, title = {Evaluating the performance of multi-omics integration: a thyroid toxicity case study.}, journal = {Archives of toxicology}, volume = {99}, number = {1}, pages = {309-332}, pmid = {39441382}, issn = {1432-0738}, support = {C5 - XomeTox//European Chemical Industry Council/ ; 101057014//HORIZON EUROPE Framework Programme/ ; }, mesh = {Animals ; *Thyroid Gland/drug effects/pathology/metabolism ; Rats ; Risk Assessment ; Proteomics/methods ; Transcriptome/drug effects ; Male ; Metabolomics/methods ; *Genomics/methods ; Humans ; Toxicity Tests/methods ; Multiomics ; }, abstract = {Multi-omics data integration has been repeatedly discussed as the way forward to more comprehensively cover the molecular responses of cells or organisms to chemical exposure in systems toxicology and regulatory risk assessment. In Canzler et al. (Arch Toxicol 94(2):371-388. https://doi.org/10.1007/s00204-020-02656-y), we reviewed the state of the art in applying multi-omics approaches in toxicological research and chemical risk assessment. We developed best practices for the experimental design of multi-omics studies, omics data acquisition, and subsequent omics data integration. We found that multi-omics data sets for toxicological research questions were generally rare, with no data sets comprising more than two omics layers adhering to these best practices. Due to these limitations, we could not fully assess the benefits of different data integration approaches or quantitatively evaluate the contribution of various omics layers for toxicological research questions. Here, we report on a multi-omics study on thyroid toxicity that we conducted in compliance with these best practices. We induced direct and indirect thyroid toxicity through Propylthiouracil (PTU) and Phenytoin, respectively, in a 28-day plus 14-day recovery oral rat toxicity study. We collected clinical and histopathological data and six omics layers, including the long and short transcriptome, proteome, phosphoproteome, and metabolome from plasma, thyroid, and liver. We demonstrate that the multi-omics approach is superior to single-omics in detecting responses at the regulatory pathway level. We also show how combining omics data with clinical and histopathological parameters facilitates the interpretation of the data. Furthermore, we illustrate how multi-omics integration can hint at the involvement of non-coding RNAs in post-transcriptional regulation. Also, we show that multi-omics facilitates grouping, and we assess how much information individual and combinations of omics layers contribute to this approach.}, }
@article {pmid39440963, year = {2024}, author = {Wang, Y and Sun, Y and Huang, K and Gao, Y and Lin, Y and Yuan, B and Wang, X and Xu, G and Nussio, LG and Yang, F and Ni, K}, title = {Multi-omics analysis reveals the core microbiome and biomarker for nutrition degradation in alfalfa silage fermentation.}, journal = {mSystems}, volume = {9}, number = {11}, pages = {e0068224}, pmid = {39440963}, issn = {2379-5077}, support = {32171686//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {*Medicago sativa/microbiology/metabolism ; *Silage/microbiology ; *Fermentation ; *Microbiota/genetics ; Animals ; Biomarkers/metabolism ; Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; Cattle ; Multiomics ; }, abstract = {UNLABELLED: Alfalfa (Medicago sativa L.) is one of the most extensively cultivated forage crops globally, and its nutritional quality critically influences the productivity of dairy cows. Silage fermentation is recognized as a crucial technique for the preservation of fresh forage, ensuring the retention of its vital nutrients. However, the detailed microbial components and their functions in silage fermentation are not fully understood. This study integrated large-scale microbial culturing with high-throughput sequencing to thoroughly examine the microbial community structure in alfalfa silage and explored the potential pathways of nutritional degradation via metagenomic analysis. The findings revealed an enriched microbial diversity in silage, indicated by the identification of amplicon sequence variants. Significantly, the large-scale culturing approach recovered a considerable number of unique microbes undetectable by high-throughput sequencing. Predominant genera, such as Lactiplantibacillus, Leuconostoc, Lentilactobacillus, Weissella, and Liquorilactobacillus, were identified based on their abundance and prevalence. Additionally, genes associated with Enterobacteriaceae were discovered, which might be involved in pathways leading to the production of ammonia-N and butyric acid. Overall, this study offers a comprehensive insight into the microbial ecology of silage fermentation and provides valuable information for leveraging microbial consortia to enhance fermentation quality.<br><br>IMPORTANCE: Silage fermentation is a microbial-driven anaerobic process that efficiently converts various substrates into nutrients readily absorbable and metabolizable by ruminant animals. This study, integrating culturomics and metagenomics, has successfully identified core microorganisms involved in silage fermentation, including those at low abundance. This discovery is crucial for the targeted cultivation of specific microorganisms to optimize fermentation processes. Furthermore, our research has uncovered signature microorganisms that play pivotal roles in nutrient metabolism, significantly advancing our understanding of the intricate relationships between microbial communities and nutrient degradation during silage fermentation.}, }
@article {pmid39439296, year = {2025}, author = {Rosche, C and Broennimann, O and Novikov, A and Mrázová, V and Boiko, GV and Danihelka, J and Gastner, MT and Guisan, A and Kožić, K and Lehnert, M and Müller-Schärer, H and Nagy, DU and Remelgado, R and Ronikier, M and Selke, JA and Shiyan, NM and Suchan, T and Thoma, AE and Zdvořák, P and Mráz, P}, title = {Herbarium specimens reveal a cryptic invasion of polyploid Centaurea stoebe in Europe.}, journal = {The New phytologist}, volume = {245}, number = {1}, pages = {392-405}, pmid = {39439296}, issn = {1469-8137}, mesh = {*Centaurea/genetics/physiology ; Europe ; *Polyploidy ; *Introduced Species ; Phylogeography ; Ecosystem ; Diploidy ; }, abstract = {Numerous plant species are expanding their native ranges due to anthropogenic environmental change. Because cytotypes of polyploid complexes often show similar morphologies, there may be unnoticed range expansions (i.e. cryptic invasions) of one cytotype into regions where only the other cytotype is native. We critically revised herbarium specimens of diploid and tetraploid Centaurea stoebe, collected across Europe between 1790 and 2023. Based on their distribution in natural and relict habitats and phylogeographic data, we estimated the native ranges of both cytotypes. Diploids are native across their entire European range, whereas tetraploids are native only to South-Eastern Europe and have recently expanded their range toward Central Europe. The proportion of tetraploids has exponentially increased over time in their expanded but not in their native range. This cryptic invasion predominantly occurred in ruderal habitats and enlarged the climatic niche of tetraploids toward a more oceanic climate. We conclude that spatio-temporally explicit assessments of range shifts, habitat preferences and niche evolution can improve our understanding of cryptic invasions. We also emphasize the value of herbarium specimens for accurate estimation of species´ native ranges, with fundamental implications for the design of research studies and the assessment of biodiversity trends.}, }
@article {pmid39438357, year = {2024}, author = {Little, AJ and Matthee, CA and Ueckermann, EA and Horak, IG and Hui, C and Matthee, S}, title = {Host and habitat shape ectoparasite diversity on Mastomys natalensis and Mastomys coucha (Muridae).}, journal = {Parasitology}, volume = {151}, number = {8}, pages = {769-783}, pmid = {39438357}, issn = {1469-8161}, support = {R01 AI136832/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Rodent Diseases/parasitology/epidemiology ; *Ecosystem ; *Murinae/parasitology ; Male ; *Ectoparasitic Infestations/parasitology/veterinary ; Female ; Host-Parasite Interactions ; Mites/physiology/classification ; Siphonaptera/classification/physiology ; Biodiversity ; Ticks/classification/physiology ; }, abstract = {Mastomys natalensis and M. coucha are commensal rodent species endemic to Africa. A recent taxonomic revision within Mastomys leaves the parasite–host list of M. natalensis questionable and that of M. coucha incomplete. The current study aimed to develop a better understanding of the ectoparasite diversity associated with the 2 distinct but closely related rodent species and to explore the influence of host and habitat type on ectoparasite infestations. Between 2014 and 2020, 590 rodents were trapped in 3 habitat types (village, agriculture and natural) across a wildlife-human/domestic animal interface. In total 48 epifaunistic species (45 ectoparasitic and 3 predatory) represented by 29 genera from 4 taxonomic groups (fleas, lice, mites and ticks) were recorded. Only 50% of the epifauna were shared between the 2 rodent species, with mites the most speciose taxon in both host species. The abundance of epifaunistic individuals, and also those of mites and fleas, were significantly higher on male M. natalensis, while ticks were significantly higher on reproductively active M. natalensis. For both rodent species, infestations by most epifaunistic taxa (on M. natalensis) and some taxa (on M. coucha) were significantly lower in the village as opposed to the less disturbed agricultural and natural habitat types. The study highlights the importance of host life history, even in closely related rodent species, in shaping parasite profiles and a loss of parasite diversity in more extreme anthropogenic habitats.}, }
@article {pmid39436938, year = {2024}, author = {Rocha, U and Kasmanas, JC and Toscan, R and Sanches, DS and Magnusdottir, S and Saraiva, JP}, title = {Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in prokaryotic metagenome-assembled genome recovery.}, journal = {PLoS computational biology}, volume = {20}, number = {10}, pages = {e1012530}, pmid = {39436938}, issn = {1553-7358}, mesh = {*Metagenome/genetics ; *Microbiota/genetics ; *Computer Simulation ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Bacteria/genetics/classification ; Genome, Bacterial/genetics ; }, abstract = {We hypothesize that sample species abundance, sequencing depth, and taxonomic relatedness influence the recovery of metagenome-assembled genomes (MAGs). To test this hypothesis, we assessed MAG recovery in three in silico microbial communities composed of 42 species with the same richness but different sample species abundance, sequencing depth, and taxonomic distribution profiles using three different pipelines for MAG recovery. The pipeline developed by Parks and colleagues (8K) generated the highest number of MAGs and the lowest number of true positives per community profile. The pipeline by Karst and colleagues (DT) showed the most accurate results (~ 92%), outperforming the 8K and Multi-Metagenome pipeline (MM) developed by Albertsen and collaborators. Sequencing depth influenced the accurate recovery of genomes when using the 8K and MM, even with contrasting patterns: the MM pipeline recovered more MAGs found in the original communities when employing sequencing depths up to 60 million reads, while the 8K recovered more true positives in communities sequenced above 60 million reads. DT showed the best species recovery from the same genus, even though close-related species have a low recovery rate in all pipelines. Our results highlight that more bins do not translate to the actual community composition and that sequencing depth plays a role in MAG recovery and increased community resolution. Even low MAG recovery error rates can significantly impact biological inferences. Our data indicates that the scientific community should curate their findings from MAG recovery, especially when asserting novel species or metabolic traits.}, }
@article {pmid39436510, year = {2024}, author = {Zinicovscaia, I and Chernyagina, O and Chaligava, O and Yushin, N and Devyatova, E and Grozov, D}, title = {Moss biomonitoring in areas affected by ashfalls of Shiveluch volcano (Kamchatka).}, journal = {Environmental science and pollution research international}, volume = {31}, number = {52}, pages = {61730-61739}, pmid = {39436510}, issn = {1614-7499}, mesh = {*Bryophyta/chemistry ; *Volcanic Eruptions ; *Environmental Monitoring/methods ; *Biological Monitoring ; Air Pollutants/analysis ; }, abstract = {The moss bag technique was applied on Kamchatka to assess the effect of Shiveluch volcano on the air quality. Moss bags were exposed in settlements located at different distances from the volcano and affected by ashfall to varying degrees. The inductively coupled plasma optical emission spectrometry was used for the determination of the content of Al, Ba, Co, Cd, Cr, Cu, Fe, Mn, P, Pb, Sr, S, V, and Zn in both exposed and unexposed moss samples. Relative accumulation factor revealed enrichment of mosses exposed in the area affected by ashfall with Al, Cr, V, and Zn. Correlation and principal component analysis allowed to identify elements of volcanogenic, geogenic, and anthropogenic origin. Ecological risk values less than 150 indicate low potential ecological risk in the region. Active moss biomonitoring can be considered a cheap and efficient tool for in-depth study of the influence of volcanic activity on air quality on the peninsula.}, }
@article {pmid39435526, year = {2025}, author = {Kan-Lingwood, NY and Sagi, L and Mazie, S and Shahar, N and Zecherle Bitton, L and Templeton, A and Rubenstein, D and Bouskila, A and Bar-David, S}, title = {Genotyping Error Detection and Customised Filtration for SNP Datasets.}, journal = {Molecular ecology resources}, volume = {25}, number = {1}, pages = {e14033}, doi = {10.1111/1755-0998.14033}, pmid = {39435526}, issn = {1755-0998}, support = {2011384//United States-Israel Binational Science Foundation/ ; }, mesh = {*Polymorphism, Single Nucleotide ; *Genotyping Techniques/methods ; Animals ; Genotype ; Computational Biology/methods ; }, abstract = {A major challenge in analysing single-nucleotide polymorphism (SNP) genotype datasets is detecting and filtering errors that bias analyses and misinterpret ecological and evolutionary processes. Here, we present a comprehensive method to estimate and minimise genotyping error rates (deviations from the 'true' genotype) in any SNP datasets using triplicates (three repeats of the same sample) in a four-step filtration pipeline. The approach involves: (1) SNP filtering by missing data; (2) SNP filtering by error rates; (3) sample filtering by missing data and (4) detection of recaptured individuals by using estimated SNP error rates. The modular pipeline is provided in an R script that allows customised adjustments. We demonstrate the applicability of the method using non-invasive sampling from the Asiatic wild ass (Equus hemionus) population in Israel. We genotyped 756 samples using 625 SNPs, of which 255 were triplicates of 85 samples. The average SNP error rate, calculated based on the number of mismatching genotypes across triplicates before filtration, was 0.0034 and was reduced to 0.00174 following filtration. Evaluating genetic distance (GD) and relatedness (r) between triplicates before and after filtration (expected to be at the minimum and maximum respectively) showed a significant reduction in the average GD, from 58.1 to 25.3 (p = 0.0002) and a significant increase in relatedness, from r = 0.98 to r = 0.991 (p = 0.00587). We demonstrate how error rate estimation enhances recapture detection and improves genotype quality.}, }
@article {pmid39434036, year = {2024}, author = {Li, C and Zhang, X and Zhao, L and Liu, S}, title = {Multi-omics profiling reveals the molecular mechanisms of H2O2-induced detrimental effects on Thamnaconus septentrionalis.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {984}, pmid = {39434036}, issn = {1471-2164}, mesh = {Animals ; *Hydrogen Peroxide/metabolism ; Fishes/metabolism/genetics ; Transcriptome/drug effects ; Gene Expression Profiling ; Metabolomics ; Signal Transduction/drug effects ; Metabolome/drug effects ; Multiomics ; }, abstract = {BACKGROUND: Hydrogen peroxide (H2O2), a novel water treatment agent, can be used for disinfection, water quality adjustment, and disease prevention, while excessive H2O2 can injure farm animals, even leading to death. Hydrogen peroxide is a recommended disinfectant and bactericide for treating gill diseases and vibriosis in the greenfin horse-faced filefish Thamnaconus septentrionalis. However, its cumulative effect, toxic molecular mechanism and relevant signal transduction/metabolic networks in marine fishes are largely unknown.<br><br>RESULTS: We employed a multi-omics approach to investigate the detrimental effects of 50&#xa0;mg/L H2O2 exposure (2&#xa0;h/d) on filefish for 2 d, 4 d, and 6 d. Transcriptome sequencing showed that differentially expressed genes (DEGs) were mainly classified into functions such as signal transduction, nervous system, liver and bile acid metabolism, energy metabolism, cell adhesion and communication, inflammation and immune response. Metabolomic analysis found that the significantly changed metabolites (SCMs) were involved in phenylalanine metabolism, inflammatory mediator regulation, linoleic acid metabolism, and necroptosis. The main SCMs were cholic acid, carnitine C12:1, dimethylmalonic acid, glutamic acid, L-lactic acid, shikimic acid, 2-methylsuccinic acid, and others. Moreover, H2O2-induced oxidative stress also disturbs the balance of the gut microbiota, altering the microbial composition and affecting digestive processes.<br><br>CONCLUSIONS: Integrated multiomics analysis revealed that H2O2-induced detrimental impacts include mucosal damage, inflammatory and immune responses, altered energy metabolism, and gut microbiota disorders. These findings offer novel insights into the harmful effects and signal transduction/metabolic pathways triggered by H2O2 exposure in marine fishes.}, }
@article {pmid39432055, year = {2025}, author = {Zhao, L and Henriksen, RA and Ramsøe, A and Nielsen, R and Korneliussen, TS}, title = {Revisiting the Briggs Ancient DNA Damage Model: A Fast Maximum Likelihood Method to Estimate Post-Mortem Damage.}, journal = {Molecular ecology resources}, volume = {25}, number = {1}, pages = {e14029}, pmid = {39432055}, issn = {1755-0998}, support = {CF19-0712//Carlsberg Foundation/ ; CF20-0071//Carlsberg Foundation/ ; R302-2018-2155//Lundbeck Foundation/ ; }, mesh = {*DNA, Ancient/analysis ; DNA Damage ; Sequence Analysis, DNA/methods ; Likelihood Functions ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; Humans ; }, abstract = {One essential initial step in the analysis of ancient DNA is to authenticate that the DNA sequencing reads are actually from ancient DNA. This is done by assessing if the reads exhibit typical characteristics of post-mortem damage (PMD), including cytosine deamination and nicks. We present a novel statistical method implemented in a fast multithreaded programme, ngsBriggs that enables rapid quantification of PMD by estimation of the Briggs ancient damage model parameters (Briggs parameters). Using a multinomial model with maximum likelihood fit, ngsBriggs accurately estimates the parameters of the Briggs model, quantifying the PMD signal from single and double-stranded DNA regions. We extend the original Briggs model to capture PMD signals for contemporary sequencing platforms and show that ngsBriggs accurately estimates the Briggs parameters across a variety of contamination levels. Classification of reads into ancient or modern reads, for the purpose of decontamination, is significantly more accurate using ngsBriggs than using other methods available. Furthermore, ngsBriggs is substantially faster than other state-of-the-art methods. ngsBriggs offers a practical and accurate method for researchers seeking to authenticate ancient DNA and improve the quality of their data.}, }
@article {pmid39430511, year = {2024}, author = {Shamrat, FMJM and Idna Idris, MY and Zhou, X and Khalid, M and Sharmin, S and Sharmin, Z and Ahmed, K and Moni, MA}, title = {PollenNet: A novel architecture for high precision pollen grain classification through deep learning and explainable AI.}, journal = {Heliyon}, volume = {10}, number = {19}, pages = {e38596}, pmid = {39430511}, issn = {2405-8440}, abstract = {Pollen grains play a critical role in environmental, agricultural, and allergy research despite their tiny dimensions. The accurate classification of pollen grains remains a significant challenge, mainly attributable to their intricate structures and the extensive diversity of species. Traditional methods often lack accuracy and effectiveness, prompting the need for advanced solutions. This study introduces a novel deep learning framework, PollenNet, designed to tackle the intricate challenge of pollen grain image classification. The efficiency of PollenNet is thoroughly evaluated through stratified 5-fold cross-validation, comparing it with cutting-edge methods to demonstrate its superior performance. A comprehensive data preparation phase is conducted, including removing duplicates and low-quality images, applying Non-local Means Denoising for noise reduction, and Gamma correction to adjust image brightness. Furthermore, Explainable AI (XAI) is utilized to enhance the interpretability of the model, while Receiver Operating Characteristic (ROC) curve analysis serves as a quantitative method for evaluating the model's capabilities. PollenNet demonstrates superior performance when compared to existing models, with an accuracy of 98.45 %, precision of 98.20 %, specificity of 98.40 %, recall of 98.30 %, and f1-score of 98.25 %. The model also maintains low Mean Squared Error (0.03) and Mean Absolute Error (0.02) rates. The ROC curve analysis, the low False Positive Rate (0.016), and the False Negative Rate (0.017) highlight the reliability and dependability of the model. This study significantly improves the efficacy of classifying pollen grains, indicating an important advancement in the application of deep learning for ecological research.}, }
@article {pmid39429633, year = {2024}, author = {Boyes, D and Holland, PWH and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Hebrew Character, Orthosia gothica (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {90}, pmid = {39429633}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Orthosia gothica (the Hebrew character; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 1,065.1 megabases in span. Most of the assembly is scaffolded into 37 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.38 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,691 protein coding genes.}, }
@article {pmid39429632, year = {2024}, author = {Li, R and Li, J and Lopez, JV and Oatley, G and Clayton-Lucey, IA and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the smooth giant clam, Tridacna derasa Röding, 1798.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {375}, pmid = {39429632}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual Tridacna derasa (the smooth giant clam; Mollusca; Bivalvia;Cardiida; Cardiidae). The genome sequence is 1,060.2 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 24.95 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,638 protein coding genes.}, }
@article {pmid39424895, year = {2024}, author = {Melo, MS and Lima, SVMA and Dos Santos, AD and Ribeiro, CJN and Júnior, PAB and Silva, TKS and de Resende, LT and Corrêa, F and Migowski, A and Schiffman, M and Rodriguez, AC and Ribeiro, A and Raiol, T}, title = {Temporal trends, spatial and spatiotemporal clusters of cervical cancer mortality in Brazil from 2000 to 2021.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {24436}, pmid = {39424895}, issn = {2045-2322}, support = {Grant number GEREB-Fiocruz/CNPq 440204/2019-4.//Oswaldo Cruz Foundation (Fiocruz) and National Council for Scientific and Technological Development (CNPq)/ ; }, mesh = {Humans ; Female ; Brazil/epidemiology ; *Uterine Cervical Neoplasms/mortality/epidemiology ; Adult ; Middle Aged ; *Spatio-Temporal Analysis ; Aged ; Young Adult ; Adolescent ; Mortality/trends ; }, abstract = {Cervical cancer, despite being preventable through primary and secondary prevention strategies, remains one of the leading causes of morbidity and mortality among women in Brazil. This study aimed to analyze the temporal, spatial, and space-time patterns of cervical cancer mortality in Brazil. An ecological study was conducted using temporal, spatial, and space-time analysis techniques, using death certificates with cervical cancer as the underlying cause or associated condition among females in Brazil from 2000 to 2021. Death certificate and population data were provided by the Department of Health Informatics of the Unified Health System (DATASUS) and the Brazilian Institute of Geography and Statistics (IBGE), respectively. A total of 123,306 deaths associated with cervical cancer among women were registered during the study period. A rising trend in mortality was detected since 2014 onwards, after 14 years of decline. Particularly, an increase in mortality was observed among the younger age groups, and in the North and Northeast regions regardless of age. Heterogeneity in the spatial distribution of cervical cancer mortality was observed, with high mortality clusters around the country, but mostly concentrated in the North and Northeast regions. These findings suggest a need and an opportunity to develop efficient and effective health policies targeting those regions and groups of women at higher risk which in turn will allow for fast and significant reductions in cervical cancer mortality in Brazil.}, }
@article {pmid39423319, year = {2025}, author = {Tian, Y and Yang, L and Ding, S and Zhang, D and Yuan, L and Liu, Z and Hu, QN}, title = {BioTRY: A Comprehensive Knowledge Base for Titer, Rate, and Yield of Biosynthesis.}, journal = {ACS synthetic biology}, volume = {14}, number = {1}, pages = {285-289}, doi = {10.1021/acssynbio.4c00347}, pmid = {39423319}, issn = {2161-5063}, mesh = {*Synthetic Biology/methods ; *Knowledge Bases ; *Computational Biology/methods ; Fermentation ; Databases, Factual ; }, abstract = {Synthetic biology is rapidly evolving into a data-intensive science that increasingly relies on massive data sets; one of its applications is the evaluation of the economic viability of fermentation processes. However, the key economic indicators, namely titer, rate, and yield (TRY), which respectively reflect the downstream processing, reactor size, and raw material costs, are not well captured in bioinformatics databases. In this paper, we present BioTRY, an intuitive and user-friendly tool that contains >5,000 biochemicals and >3,800 strains, along with over 52,000 corresponding TRY entries with original references. It is freely available at http://www.synbiohealth.cn/biotry. To our knowledge, BioTRY is the first available database on biosynthesis TRY data from original research. We anticipate that BioTRY will become a useful tool that aids researchers and decision-makers in understanding the current development state of biosynthesis and allows them to foresee potential prospects and applications for biosynthesis.}, }
@article {pmid39421415, year = {2024}, author = {Ion, MC and Bloomer, CC and Bărăscu, TI and Oficialdegui, FJ and Shoobs, NF and Williams, BW and Scheers, K and Clavero, M and Grandjean, F and Collas, M and Baudry, T and Loughman, Z and Wright, JJ and Ruokonen, TJ and Chucholl, C and Guareschi, S and Koese, B and Banyai, ZM and Hodson, J and Hurt, M and Kaldre, K and Lipták, B and Fetzner, JW and Cancellario, T and Weiperth, A and Birzaks, J and Trichkova, T and Todorov, M and Balalaikins, M and Griffin, B and Petko, ON and Acevedo-Alonso, A and D'Elía, G and Śliwińska, K and Alekhnovich, A and Choong, H and South, J and Whiterod, N and Zorić, K and Haase, P and Soto, I and Brady, DJ and Haubrock, PJ and Torres, PJ and Şadrin, D and Vlach, P and Kaya, C and Woo Jung, S and Kim, JY and Vermeersch, XHC and Bonk, M and Guiaşu, R and Harlioğlu, MM and Devlin, J and Kurtul, I and Błońska, D and Boets, P and Masigol, H and Cabe, PR and Jussila, J and Vrålstad, T and Beresford, DV and Reid, SM and Patoka, J and Strand, DA and Tarkan, AS and Steen, F and Abeel, T and Harwood, M and Auer, S and Kelly, S and Giantsis, IA and Maciaszek, R and Alvanou, MV and Aksu, &#xd6; and Hayes, DM and Kawai, T and Tricarico, E and Chakandinakira, A and Barnett, ZC and Kudor, &#x15e;G and Beda, AE and Vîlcea, L and Mizeranschi, AE and Neagul, M and Licz, A and Cotoarbă, AD and Petrusek, A and Kouba, A and Taylor, CA and Pârvulescu, L}, title = {World of Crayfish™: a web platform towards real-time global mapping of freshwater crayfish and their pathogens.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e18229}, pmid = {39421415}, issn = {2167-8359}, mesh = {Animals ; *Astacoidea/microbiology ; *Fresh Water ; Aphanomyces ; Internet ; Ecosystem ; Databases, Factual ; }, abstract = {Freshwater crayfish are amongst the largest macroinvertebrates and play a keystone role in the ecosystems they occupy. Understanding the global distribution of these animals is often hindered due to a paucity of distributional data. Additionally, non-native crayfish introductions are becoming more frequent, which can cause severe environmental and economic impacts. Management decisions related to crayfish and their habitats require accurate, up-to-date distribution data and mapping tools. Such data are currently patchily distributed with limited accessibility and are rarely up-to-date. To address these challenges, we developed a versatile e-portal to host distributional data of freshwater crayfish and their pathogens (using Aphanomyces astaci, the causative agent of the crayfish plague, as the most prominent example). Populated with expert data and operating in near real-time, World of Crayfish™ is a living, publicly available database providing worldwide distributional data sourced by experts in the field. The database offers open access to the data through specialized standard geospatial services (Web Map Service, Web Feature Service) enabling users to view, embed, and download customizable outputs for various applications. The platform is designed to support technical enhancements in the future, with the potential to eventually incorporate various additional features. This tool serves as a step forward towards a modern era of conservation planning and management of freshwater biodiversity.}, }
@article {pmid39420601, year = {2024}, author = {Li, Z and Zhang, Y and Peng, B and Qin, S and Zhang, Q and Chen, Y and Chen, C and Bao, Y and Zhu, Y and Hong, Y and Liu, B and Liu, Q and Xu, L and Chen, X and Ma, X and Wang, H and Xie, L and Yao, Y and Deng, B and Li, J and De, B and Chen, Y and Wang, J and Li, T and Liu, R and Tang, Z and Cao, J and Zuo, E and Mei, C and Zhu, F and Shao, C and Wang, G and Sun, T and Wang, N and Liu, G and Ni, JQ and Liu, Y}, title = {A novel interpretable deep learning-based computational framework designed synthetic enhancers with broad cross-species activity.}, journal = {Nucleic acids research}, volume = {52}, number = {21}, pages = {13447-13468}, pmid = {39420601}, issn = {1362-4962}, support = {2021YFF1200500//China National Key R&amp;D Program/ ; 32070595//National Natural Science Foundation of China/ ; 20221250020//Ministry of Science and Technology/ ; 20181300988//National Natural Science Foundation of China/ ; }, mesh = {*Enhancer Elements, Genetic ; Animals ; *Deep Learning ; Drosophila melanogaster/genetics ; Drosophila/genetics ; Humans ; Computational Biology/methods ; Gene Expression Regulation ; }, abstract = {Enhancers play a critical role in dynamically regulating spatial-temporal gene expression and establishing cell identity, underscoring the significance of designing them with specific properties for applications in biosynthetic engineering and gene therapy. Despite numerous high-throughput methods facilitating genome-wide enhancer identification, deciphering the sequence determinants of their activity remains challenging. Here, we present the DREAM (DNA cis-Regulatory Elements with controllable Activity design platforM) framework, a novel deep learning-based approach for synthetic enhancer design. Proficient in uncovering subtle and intricate patterns within extensive enhancer screening data, DREAM achieves cutting-edge sequence-based enhancer activity prediction and highlights critical sequence features implicating strong enhancer activity. Leveraging DREAM, we have engineered enhancers that surpass the potency of the strongest enhancer within the Drosophila genome by approximately 3.6-fold. Remarkably, these synthetic enhancers exhibited conserved functionality across species that have diverged more than billion years, indicating that DREAM was able to learn highly conserved enhancer regulatory grammar. Additionally, we designed silencers and cell line-specific enhancers using DREAM, demonstrating its versatility. Overall, our study not only introduces an interpretable approach for enhancer design but also lays out a general framework applicable to the design of other types of cis-regulatory elements.}, }
@article {pmid39419226, year = {2024}, author = {Liu, J and Zhu, M and Shi, X and Hui, C and Sun, Y and Zhang, R and Jin, D and Li, Z and Chen, H and Zhao, Z}, title = {Cascading impacts of nitrogen deposition on soil microbiome and herbivore communities in desert steppes.}, journal = {The Science of the total environment}, volume = {955}, number = {}, pages = {176892}, doi = {10.1016/j.scitotenv.2024.176892}, pmid = {39419226}, issn = {1879-1026}, mesh = {*Nitrogen ; *Soil Microbiology ; *Microbiota/drug effects ; *Herbivory ; Animals ; *Insecta/physiology ; Desert Climate ; Soil/chemistry ; Biodiversity ; Grassland ; Ecosystem ; China ; }, abstract = {Human activities in the last century have intensified global nitrogen deposition, resulting in the degradation of ecosystem function and loss of biodiversity worldwide. Nitrogen addition is a crucial method for examining the effects of atmospheric nitrogen deposition on species composition and structure of soil microbiome and biotic community, as exogenous nitrogen inputs can trigger cascading effects on ecosystem functions. In a 6-year experiment, we evaluated the impact of nitrogen addition on soil microbial-plant-insect systems in desert steppes. Our results show that nitrogen addition significantly altered soil microbial composition and ecological function, leading to a decrease in nitrogen-fixing bacteria and an increase in saprophytic fungi. High levels of nitrogen addition increased total plant biomass while decreasing species diversity. Additionally, high nitrogen addition levels suppressed below-ground biomass of gramineae and legumes compared to low nitrogen addition. Nitrogen addition also increased herbivore abundance by altering insect community structure, particularly benefiting chewing pests over sucking pests, thus heightening the risk of biological disasters through trophic cascading effects. Consequently, excessive nitrogen addition may destabilize desert steppe ecosystems by disturbing soil microbial-plant-insect interactions, hindering the maintenance of biotic community diversity and steppe productivity.}, }
@article {pmid39417898, year = {2024}, author = {Khalaf, SMH and Alqahtani, MSM and Ali, MRM and Abdelalim, ITI and Hodhod, MS}, title = {Modeling climate-related global risk maps of rice bacterial blight caused by Xanthomonas oryzae (Ishiyama 1922) using geographical information system (GIS).}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {11}, pages = {1064}, pmid = {39417898}, issn = {1573-2959}, mesh = {*Xanthomonas ; *Oryza/microbiology ; *Climate Change ; *Plant Diseases/microbiology/statistics &amp; numerical data ; *Geographic Information Systems ; Environmental Monitoring ; Climate ; }, abstract = {Rice is a critical staple crop that feeds more than half of the world's population. Still, its production confronts various biotic risks, notably the severe bacterial blight disease produced by Xanthomonas oryzae. Understanding the possible effects of climate change on the geographic distribution of this virus is critical to ensuring food security. This work used ecological niche modeling and the Maxent algorithm to create future risk maps for the range of X. oryzae under several climate change scenarios between 2050 and 2070. The model was trained using 93 occurrence records of X. oryzae and five critical bioclimatic variables. It has an excellent predictive performance, with an AUC of 0.889. The results show that X. oryzae's potential geographic range and habitat suitability are expected to increase significantly under low (RCP2.6) and high (RCP8.5) emission scenarios. Key climatic drivers allowing this development include increased yearly precipitation, precipitation during the wettest quarter, and the wettest quarter's mean temperature. These findings are consistent with broader research revealing that climate change is allowing many plant diseases and other dangerous microbes to spread across the globe. Integrating these spatial predictions with data on host susceptibility, agricultural practices, and socioeconomic vulnerabilities can help to improve targeted surveillance, preventative, and management methods for reducing the growing threat of bacterial blight to rice production. Proactive, multidisciplinary efforts to manage the changing disease dynamics caused by climate change will be critical to assuring global food security in the future decades.}, }
@article {pmid39417330, year = {2025}, author = {Kershenbaum, A and Akçay, &#xc7; and Babu-Saheer, L and Barnhill, A and Best, P and Cauzinille, J and Clink, D and Dassow, A and Dufourq, E and Growcott, J and Markham, A and Marti-Domken, B and Marxer, R and Muir, J and Reynolds, S and Root-Gutteridge, H and Sadhukhan, S and Schindler, L and Smith, BR and Stowell, D and Wascher, CAF and Dunn, JC}, title = {Automatic detection for bioacoustic research: a practical guide from and for biologists and computer scientists.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {100}, number = {2}, pages = {620-646}, pmid = {39417330}, issn = {1469-185X}, support = {//A*MIDEX/ ; //Cambridge Centre for Data-Driven Discovery/ ; //African Institute for Mathematical Sciences/ ; NE/W005468/1//Natural Environment Research Council/ ; //Global Affairs Canada/ ; ANR-20-CE23-0012-01 MIM//Agence Nationale de la Recherche/ ; ANR-20-CHIA-0014//Agence Nationale de la Recherche/ ; ANR-16-CONV-0002//Institute of Convergence ILCB/ ; //International Development Research Centre/ ; }, mesh = {*Acoustics ; Animals ; Machine Learning ; }, abstract = {Recent years have seen a dramatic rise in the use of passive acoustic monitoring (PAM) for biological and ecological applications, and a corresponding increase in the volume of data generated. However, data sets are often becoming so sizable that analysing them manually is increasingly burdensome and unrealistic. Fortunately, we have also seen a corresponding rise in computing power and the capability of machine learning algorithms, which offer the possibility of performing some of the analysis required for PAM automatically. Nonetheless, the field of automatic detection of acoustic events is still in its infancy in biology and ecology. In this review, we examine the trends in bioacoustic PAM applications, and their implications for the burgeoning amount of data that needs to be analysed. We explore the different methods of machine learning and other tools for scanning, analysing, and extracting acoustic events automatically from large volumes of recordings. We then provide a step-by-step practical guide for using automatic detection in bioacoustics. One of the biggest challenges for the greater use of automatic detection in bioacoustics is that there is often a gulf in expertise between the biological sciences and the field of machine learning and computer science. Therefore, this review first presents an overview of the requirements for automatic detection in bioacoustics, intended to familiarise those from a computer science background with the needs of the bioacoustics community, followed by an introduction to the key elements of machine learning and artificial intelligence that a biologist needs to understand to incorporate automatic detection into their research. We then provide a practical guide to building an automatic detection pipeline for bioacoustic data, and conclude with a discussion of possible future directions in this field.}, }
@article {pmid39415784, year = {2024}, author = {Lohse, K and Vila, R and Hayward, A and Laetsch, DR and Harnqvist, S and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Essex Skipper butterfly, Thymelicus lineola (Ochsenheimer, 1808).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {452}, pmid = {39415784}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Essex Skipper butterfly, Thymelicus lineola (Arthropoda; Insecta; Lepidoptera; Hesperiidae). The genome sequence spans 511.80 megabases. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 17.24 kilobases in length.}, }
@article {pmid39414803, year = {2024}, author = {Lončarević, N and Liu, U and Stefanaki, A and Carapeto, A and Ensslin, A and Meade, C and Metzing, D and Peci, D and Fantinato, E and Colling, G and Pankova, H and Akmane, I and Tsvetkov, IN and Sibik, J and Szitár, K and Van Meerbeek, K and Daco, L and Boudagher, M and Klisz, M and Walczak, M and Evju, M and Lužnik, M and Kiehn, M and Sarginci, M and Aksoy, N and Koçer, N and Barazani, O and Anastasiu, P and Stroh, P and Vit, P and Vergeer, P and Puchałka, R and Kahale, R and Godefroid, S and Lanfranco, S and Parpan, T and Kull, T and Rašomavičius, V and Fišer, &#x17d; and Glasnović, P}, title = {Database of European vascular plants red lists as a contribution to more coherent plant conservation.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1138}, pmid = {39414803}, issn = {2052-4463}, support = {R25 CA018201/CA/NCI NIH HHS/United States ; CA18201//European Cooperation in Science and Technology (COST)/ ; }, mesh = {Europe ; *Databases, Factual ; *Conservation of Natural Resources ; *Plants/classification ; Biodiversity ; }, abstract = {We introduce the database of European vascular plant red lists, a compilation of red list categories designated to taxa during in-country conservation assessments. Version 1.0 of the database is a standalone static dataset with open access in an end-user friendly format. Its aim is to fulfil the objectives of European Cooperation in Science and Technology (COST) Action 18201, ConservePlants. The database synthesizes data across 42 red lists from 41 countries, with participation of 39 out of a total of 44 European countries and two additional Mediterranean countries. The database contains 51,109 records representing 21,481 original taxonomic names with 37 different red list categories. During data harmonisation, 20,312 of the original taxonomic names were assigned to 17,873 unique accepted taxonomic names with scientific authorships across 184 families, 1650 genera and 15,593 species; and red list categories were standardised to 13 unique categories. We see this database as a source of information in diverse plant conservation activities and suitable for various stakeholders.}, }
@article {pmid39409485, year = {2024}, author = {Jechow, A and Bumberger, J and Palm, B and Remmler, P and Schreck, G and Ogashawara, I and Kiel, C and Kohnert, K and Grossart, HP and Singer, GA and Nejstgaard, JC and Wollrab, S and Berger, SA and Hölker, F}, title = {Characterizing and Implementing the Hamamatsu C12880MA Mini-Spectrometer for Near-Surface Reflectance Measurements of Inland Waters.}, journal = {Sensors (Basel, Switzerland)}, volume = {24}, number = {19}, pages = {}, pmid = {39409485}, issn = {1424-8220}, support = {Leibniz Competition No. K45/2017 (CONNECT-Connectivity and synchronization of lake ecosystems in space and time)//Leibniz Association/ ; IGB Frontiers project (2017)//Leibniz Institute of Freshwater Ecology and Inland Fisheries/ ; }, abstract = {In recent decades, inland water remote sensing has seen growing interest and very strong development. This includes improved spatial resolution, increased revisiting times, advanced multispectral sensors and recently even hyperspectral sensors. However, inland waters are more challenging than oceanic waters due to their higher complexity of optically active constituents and stronger adjacency effects due to their small size and nearby vegetation and built structures. Thus, bio-optical modeling of inland waters requires higher ground-truthing efforts. Large-scale ground-based sensor networks that are robust, self-sufficient, non-maintenance-intensive and low-cost could assist this otherwise labor-intensive task. Furthermore, most existing sensor systems are rather expensive, precluding their employability. Recently, low-cost mini-spectrometers have become widely available, which could potentially solve this issue. In this study, we analyze the characteristics of such a mini-spectrometer, the Hamamatsu C12880MA, and test it regarding its application in measuring water-leaving radiance near the surface. Overall, the measurements performed in the laboratory and in the field show that the system is very suitable for the targeted application.}, }
@article {pmid39407030, year = {2024}, author = {Mc Cartney, AM and Formenti, G and Mouton, A and De Panis, D and Marins, LS and Leitão, HG and Diedericks, G and Kirangwa, J and Morselli, M and Salces-Ortiz, J and Escudero, N and Iannucci, A and Natali, C and Svardal, H and Fernández, R and De Pooter, T and Joris, G and Strazisar, M and Wood, JMD and Herron, KE and Seehausen, O and Watts, PC and Shaw, F and Davey, RP and Minotto, A and Fernández, JM and Böhne, A and Alegria, C and Alioto, T and Alves, PC and Amorim, IR and Aury, JM and Backstrom, N and Baldrian, P and Baltrunaite, L and Barta, E and BedHom, B and Belser, C and Bergsten, J and Bertrand, L and Bilandija, H and Binzer-Panchal, M and Bista, I and Blaxter, M and Borges, PAV and Dias, GB and Bosse, M and Brown, T and Bruggmann, R and Buena-Atienza, E and Burgin, J and Buzan, E and Cariani, A and Casadei, N and Chiara, M and Chozas, S and Čiampor, F and Crottini, A and Cruaud, C and Cruz, F and Dalen, L and De Biase, A and Del Campo, J and Delic, T and Dennis, AB and Derks, MFL and Diroma, MA and Djan, M and Duprat, S and Eleftheriadi, K and Feulner, PGD and Flot, JF and Forni, G and Fosso, B and Fournier, P and Fournier-Chambrillon, C and Gabaldon, T and Garg, S and Gissi, C and Giupponi, L and Gomez-Garrido, J and González, J and Grilo, ML and Grüning, B and Guerin, T and Guiglielmoni, N and Gut, M and Haesler, MP and Hahn, C and Halpern, B and Harrison, PW and Heintz, J and Hindrikson, M and Höglund, J and Howe, K and Hughes, GM and Istace, B and Cock, MJ and Janžekovič, F and Jonsson, ZO and Joye-Dind, S and Koskimäki, JJ and Krystufek, B and Kubacka, J and Kuhl, H and Kusza, S and Labadie, K and Lähteenaro, M and Lantz, H and Lavrinienko, A and Leclère, L and Lopes, RJ and Madsen, O and Magdelenat, G and Magoga, G and Manousaki, T and Mappes, T and Marques, JP and Redondo, GIM and Maumus, F and McCarthy, SA and Megens, HJ and Melo-Ferreira, J and Mendes, SL and Montagna, M and Moreno, J and Mosbech, MB and Moura, M and Musilova, Z and Myers, E and Nash, WJ and Nater, A and Nicholson, P and Niell, M and Nijland, R and Noel, B and Noren, K and Oliveira, PH and Olsen, RA and Ometto, L and Oomen, RA and Ossowski, S and Palinauskas, V and Palsson, S and Panibe, JP and Pauperio, J and Pavlek, M and Payen, E and Pawlowska, J and Pellicer, J and Pesole, G and Pimenta, J and Pippel, M and Pirttilä, AM and Poulakakis, N and Rajan, J and M C Rego, R and Resendes, R and Resl, P and Riesgo, A and Rodin-Morch, P and Soares, AER and Fernandes, CR and Romeiras, MM and Roxo, G and Rüber, L and Ruiz-Lopez, MJ and Saarma, U and da Silva, LP and Sim-Sim, M and Soler, L and Sousa, VC and Santos, CS and Spada, A and Stefanovic, M and Steger, V and Stiller, J and Stöck, M and Struck, TH and Sudasinghe, H and Tapanainen, R and Tellgren-Roth, C and Trindade, H and Tukalenko, Y and Urso, I and Vacherie, B and Van Belleghem, SM and Van Oers, K and Vargas-Chavez, C and Velickovic, N and Vella, N and Vella, A and Vernesi, C and Vicente, S and Villa, S and Pettersson, OV and Volckaert, FAM and Voros, J and Wincker, P and Winkler, S and Ciofi, C and Waterhouse, RM and Mazzoni, CJ}, title = {Author Correction: The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.}, journal = {npj biodiversity}, volume = {3}, number = {1}, pages = {31}, doi = {10.1038/s44185-024-00065-3}, pmid = {39407030}, issn = {2731-4243}, }
@article {pmid39404811, year = {2024}, author = {Litavský, J and Majzlan, O and Langraf, V and Žarnovičan, H}, title = {Influence of habitat management and selected environmental parameters on the ground-living communities of harvestmen (Opiliones) in the historical park in Rusovce (Slovakia).}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {11}, pages = {1056}, pmid = {39404811}, issn = {1573-2959}, support = {No. 1/0007/21//Slovak Grant Agency of the Ministry of Education, Science, Research and Sport of the Slovak Republic/ ; No. 1/0007/21//Slovak Grant Agency of the Ministry of Education, Science, Research and Sport of the Slovak Republic/ ; No. 1/0255/23//Slovak Grant Agency of the Ministry of Education, Science, Research and Sport of the Slovak Republic/ ; }, mesh = {*Ecosystem ; *Parks, Recreational ; *Environmental Monitoring ; Animals ; Slovakia ; Biodiversity ; Arachnida ; Conservation of Natural Resources/methods ; Forests ; Microclimate ; }, abstract = {City parks serve as valuable refuges for invertebrates in the urban environment, which are constantly exposed to human influence caused by management practices in the parks. Many harvestman species are suitable bioindicators for monitoring ecological change; however, their effective use in environmental assessment necessitates to expand the insufficient knowledge of ecological environmental specificities of their communities. We studied the diversity and dynamics of harvestman (Opiliones) communities in the historical park in Rusovce, situated in the southwestern part of Bratislava (Slovakia). Seven study sites were investigated, representing areas subjected to different management practices. The research was conducted from March 2019 to April 2020, using pitfall traps. We evaluated the impact of microclimatic variables (soil and air temperature), environmental characteristics (plant diversity and cover of vegetation layers, age of forest stands, thickness of the litter layer), and management practices on the structure of harvestman communities. The study revealed the response of specific harvestman species to temperature variations, emphasizing the importance of microclimatic conditions. Environmental variables, such as the richness of plant species in the shrub layer, the cover of the herb and shrub vegetation layers, and the age of the forest stands, were identified as key factors that influence the dispersal of harvestman species. Furthermore, management practices, especially the presence of monoculture tree plantations, significantly affected the species composition of harvestmen. Examining the sensitivity of Opiliones, important bioindicators, to these factors is crucial for implementing effective conservation strategies in urban green spaces and anthropogenically influenced ecosystems.}, }
@article {pmid39403498, year = {2024}, author = {Hung, RJ and Low, I and Yeh, HC and Wang, PY and Chen, YS and Chen, LF}, title = {Feedback matters: EEG correlates of empathy involved in the naturalistic communication of emotions.}, journal = {Heliyon}, volume = {10}, number = {19}, pages = {e38574}, pmid = {39403498}, issn = {2405-8440}, abstract = {Empathy involves the processing of complex information related to dynamic interactions between the empathizer and target. One neural signature of empathy is the suppression of electroencephalographic mu rhythm (8-13 Hz) over the sensorimotor region. It is important to consider that few researchers have studied the effects of empathizer feedback on empathy and its underlying neural mechanism, and most previous research has lacked ecological validity due to standardized emotional stimuli and constraints on the experiment environment. Our objective in this study was to investigate the means by which empathizer feedback influences one's own empathy in naturalistic social situations. Our results revealed that empathizer feedback decreases empathic accuracy but does not affect the emotional contagion nor the emotional intensity of the empathizer. We also found that the ability to accurately infer sadness is hindered by empathizer feedback. Empathizers presented lower alpha activity in the sensorimotor cortical areas only while receiving sad narratives and not providing feedback. This study contributes to the emerging research on the influence of empathizer feedback in naturalistic social settings.}, }
@article {pmid39403309, year = {2024}, author = {Sivell, O and Sivell, D and Webb, JA and Mitchell, R and Ashworth, M and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the acalyptrate fly Dryomyza anilis Fallén, 1820.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {440}, pmid = {39403309}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male acalyptrate fly Dryomyza anilis (Arthropoda; Insecta; Diptera; Dryomyzidae). The genome sequence has a total length of 656.60 megabases. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.48 kilobases in length.}, }
@article {pmid39401552, year = {2024}, author = {Yan, X and Zhao, Z and Feng, S and Zhang, Y and Wang, Z and Li, Z}, title = {Multi-omics analysis reveal the fall armyworm Spodoptera frugiperda tolerate high temperature by mediating chitin-related genes.}, journal = {Insect biochemistry and molecular biology}, volume = {174}, number = {}, pages = {104192}, doi = {10.1016/j.ibmb.2024.104192}, pmid = {39401552}, issn = {1879-0240}, mesh = {Animals ; *Spodoptera/genetics/growth &amp; development/metabolism/physiology ; *Chitin/metabolism ; Hot Temperature ; Larva/genetics/growth &amp; development/metabolism ; CRISPR-Cas Systems ; Insect Proteins/metabolism/genetics ; Thermotolerance ; Transcriptome ; RNA Interference ; Multiomics ; }, abstract = {Climate change facilitates the rapid invasion of agricultural pests, threatening global food security. The fall armyworm Spodoptera frugiperda is a highly polyphagous migratory pest tolerant to high temperatures, allowing its proliferation in harsh thermal environments. We aimed to demonstrate mechanisms of its high-temperature tolerance, particularly transcriptional and metabolic regulation, which are poorly understood. To achieve the aim, we examined the impact and mechanism of heat events on S. frugiperda by using multiple approaches: ecological measurements, transcriptomics, metabolomics, RNAi, and CRISPR/Cas9 technology. We observed that several physiological indices (larval survival rate, larval period, pupation rate, pupal weight, eclosion rate, and average fecundity) decreased as the temperature increased, with the 32 °C treatment displaying a significant difference from the control group at 26 °C. Significantly upregulated expression of genes encoding endochitinase and chitin deacetylase was observed in the chitin-binding, extracellular region, and carbohydrate metabolic process GO terms of hemolymph, fat body, and brain, exhibiting a tissue-specific pattern. Significantly enriched pathways (e.g., cutin, suberin, and wax biosynthesis; oxidative phosphorylation and cofactor biosynthesis; diverse amino acid biosynthesis and degradation; carbon metabolism; and energy metabolism), all of which are essential for S. frugiperda larvae to tolerate temperature, were found in metabolites that were expressed differently. Successful RNA interference targeting of the three chitin-related genes reduced gene expression levels and larval survival rate. Knockout of the endochitinase gene by using the CRISPR/Cas9 system significantly reduced the relative gene expression and increased sensitivity to high-temperature exposure. On the basis of our findings, theoretical foundations for understanding the high-temperature tolerance of S. frugiperda populations and latent genetic control strategies were established.}, }
@article {pmid39401366, year = {2024}, author = {Posch, BC and Bush, SE and Koepke, DF and Schuessler, A and Anderegg, LLD and Aparecido, LMT and Blonder, BW and Guo, JS and Kerr, KL and Moran, ME and Cooper, HF and Doughty, CE and Gehring, CA and Whitham, TG and Allan, GJ and Hultine, KR}, title = {Intensive leaf cooling promotes tree survival during a record heatwave.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {43}, pages = {e2408583121}, pmid = {39401366}, issn = {1091-6490}, support = {IOS-2140427//NSF (NSF)/ ; IOS-2140428//NSF (NSF)/ ; IOS-2140429//NSF (NSF)/ ; IOS-2003205//NSF (NSF)/ ; IOS-2216855//NSF (NSF)/ ; DEB-1340852//NSF (NSF)/ ; DEB-1340856//NSF (NSF)/ ; DEB-2017895//NSF (NSF)/ ; }, mesh = {*Plant Leaves/physiology ; *Populus/physiology/genetics ; *Trees/physiology/genetics ; *Water ; Soil ; Genotype ; Extreme Heat ; Hot Temperature ; Ecosystem ; }, abstract = {Increasing heatwaves are threatening forest ecosystems globally. Leaf thermal regulation and tolerance are important for plant survival during heatwaves, though the interaction between these processes and water availability is unclear. Genotypes of the widely distributed foundation tree species Populus fremontii were studied in a controlled common garden during a record summer heatwave-where air temperature exceeded 48 °C. When water was not limiting, all genotypes cooled leaves 2 to 5 °C below air temperatures. Homeothermic cooling was disrupted for weeks following a 72-h reduction in soil water, resulting in leaf temperatures rising 3 °C above air temperature and 1.3 °C above leaf thresholds for physiological damage, despite the water stress having little effect on leaf water potentials. Tradeoffs between leaf thermal safety and hydraulic safety emerged but, regardless of water use strategy, all genotypes experienced significant leaf mortality following water stress. Genotypes from warmer climates showed greater leaf cooling and less leaf mortality after water stress in comparison with genotypes from cooler climates. These results illustrate how brief soil water limitation disrupts leaf thermal regulation and potentially compromises plant survival during extreme heatwaves, thus providing insight into future scenarios in which ecosystems will be challenged with extreme heat and unreliable soil water access.}, }
@article {pmid39399683, year = {2024}, author = {Martin, C and Gitter, A and Anantharaman, K}, title = {Protein Set Transformer: A protein-based genome language model to power high diversity viromics.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {39399683}, issn = {2693-5015}, support = {R35 GM143024/GM/NIGMS NIH HHS/United States ; }, abstract = {Exponential increases in microbial and viral genomic data demand transformational advances in scalable, generalizable frameworks for their interpretation. Standard homology-based functional analyses are hindered by the rapid divergence of microbial and especially viral genomes and proteins that significantly decreases the volume of usable data. Here, we present Protein Set Transformer (PST), a protein-based genome language model that models genomes as sets of proteins without considering sparsely available functional labels. Trained on >100k viruses, PST outperformed other homology- and language model-based approaches for relating viral genomes based on shared protein content. Further, PST demonstrated protein structural and functional awareness by clustering capsid-fold-containing proteins with known capsid proteins and uniquely clustering late gene proteins within related viruses. Our data establish PST as a valuable method for diverse viral genomics, ecology, and evolutionary applications. We posit that the PST framework can be a foundation model for microbial genomics when trained on suitable data.}, }
@article {pmid39399250, year = {2024}, author = {Arliyani, I and Noori, MT and Ammarullah, MI and Tangahu, BV and Mangkoedihardjo, S and Min, B}, title = {Constructed wetlands combined with microbial fuel cells (CW-MFCs) as a sustainable technology for leachate treatment and power generation.}, journal = {RSC advances}, volume = {14}, number = {44}, pages = {32073-32100}, pmid = {39399250}, issn = {2046-2069}, abstract = {The physical and chemical treatment processes of leachate are not only costly but can also possibly produce harmful by products. Constructed wetlands (CW) has been considered a promising alternative technology for leachate treatment due to less demand for energy, economic, ecological benefits, and simplicity of operations. Various trends and approaches for the application of CW for leachate treatment have been discussed in this review along with offering an informatics peek of the recent innovative developments in CW technology and its perspectives. In addition, coupling CW with microbial fuel cells (MFCs) has proven to produce renewable energy (electricity) while treating contaminants in leachate wastewaters (CW-MFC). The combination of CW-MFC is a promising bio electrochemical that plays symbiotic among plant microorganisms in the rhizosphere of an aquatic plant that convert sun electricity is transformed into bioelectricity with the aid of using the formation of radical secretions, as endogenous substrates, and microbial activity. Several researchers study and try to find out the application of CW-MFC for leachate treatment, along with this system and performance. Several key elements for the advancement of CW-MFC technology such as bioelectricity, reactor configurations, plant species, and electrode materials, has been comprehensively discussed and future research directions were suggested for further improving the performance. Overall, CW-MFC may offer an eco-friendly approach to protecting the aquatic environment and come with built-in advantages for visual appeal and animal habitats using natural materials such as gravel, soil, electroactive bacteria, and plants under controlled condition.}, }
@article {pmid39398940, year = {2024}, author = {Boyes, D and Hutchinson, F and Crowley, LM and Holland, PWH and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Common Flat-body moth, Agonopterix heracliana Linnaeus, 1758.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {329}, pmid = {39398940}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Agonopterix heracliana (the Common Flat-body; Arthropoda; Insecta; Lepidoptera; Depressariidae). The genome sequence is 539.1 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.36 kilobases in length.}, }
@article {pmid39398938, year = {2024}, author = {Li, R and Li, J and Lemer, S and Lopez, JV and Oatley, G and Sinclair, E and Clayton-Lucey, IA and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the heart cockle, Fragum sueziense (Issel, 1869).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {366}, pmid = {39398938}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual Fragum sueziense (the heart cockle; Mollusca; Bivalvia; Cardiida; Cardiidae). The genome sequence is 1,206.1 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 92.77 kilobases in length. Gene annotation of this assembly on Ensembl identified 70,309 protein-coding genes.}, }
@article {pmid39398937, year = {2024}, author = {Boyes, D and Crowley, LM and Morley, LM and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Green Oak Leaf Roller, Tortrix viridana (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {260}, pmid = {39398937}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from a female Tortrix viridana (the Green Oak Leaf Roller; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 456.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 16.43 kilobases in length.}, }
@article {pmid39396151, year = {2025}, author = {Burger, J and Gochfeld, M and Brown, KG and Cortes, M and Ng, K and Kosson, D}, title = {Using the National Land Cover Database as an indicator of shrub-steppe habitat: comparing two large United States federal lands with surrounding regions.}, journal = {Journal of toxicology and environmental health. Part A}, volume = {88}, number = {1}, pages = {1-19}, doi = {10.1080/15287394.2024.2412659}, pmid = {39396151}, issn = {2381-3504}, mesh = {*Ecosystem ; *Conservation of Natural Resources ; Idaho ; Washington ; Databases, Factual ; United States ; Grassland ; Environmental Monitoring/methods ; }, abstract = {There is a need to assess whether ecological resources are being protected on large, federal lands. The aim of this study was to present a methodology which consistently and transparently determines whether two large Department of Energy (U.S. DOE) facilities have protected valuable ecological lands on their sites compared to the surrounding region. The National Land Cover Database (2019) was used to examine the % shrub-scrub (shrub-steppe) and other habitats on the DOE's Hanford Site (HS, Washington) and on the Idaho National Laboratory (INL), compared to a 10-km and 30-km diameter band of land surrounding each site. On both sites, over 95% is in shrub-scrub or grassland, compared to the surrounding region. Approximately 70% of 10 km and 30-km bands around INL, and less than 50% of land surrounding HS is located in these two habitat types. INL has preserved a significantly higher % shrub/scrub habitat than HS, but INL allows grazing on 60% of its land. HS has preserved a significantly higher % grassland than INL but no grazing on site is present. The methodology presented may be used to compare key ecological habitat types such as grasslands, forest, and desert among sites in different parts of the country. This methodology enables managers, resource trustees, and the public to (1) make remediation decisions that protect resources, (2) assess whether landowners and managers have adequately characterized and protected environmental resources on their sites, and (3) whether landowners and managers have protected the integrity of that land as well as its climax vegetation.}, }
@article {pmid39395210, year = {2025}, author = {Pachade, S and Porwal, P and Kokare, M and Deshmukh, G and Sahasrabuddhe, V and Luo, Z and Han, F and Sun, Z and Qihan, L and Kamata, SI and Ho, E and Wang, E and Sivajohan, A and Youn, S and Lane, K and Chun, J and Wang, X and Gu, Y and Lu, S and Oh, YT and Park, H and Lee, CY and Yeh, H and Cheng, KW and Wang, H and Ye, J and He, J and Gu, L and Müller, D and Soto-Rey, I and Kramer, F and Arai, H and Ochi, Y and Okada, T and Giancardo, L and Quellec, G and Mériaudeau, F}, title = {RFMiD: Retinal Image Analysis for multi-Disease Detection challenge.}, journal = {Medical image analysis}, volume = {99}, number = {}, pages = {103365}, doi = {10.1016/j.media.2024.103365}, pmid = {39395210}, issn = {1361-8423}, mesh = {Humans ; *Retinal Diseases/diagnostic imaging ; Image Interpretation, Computer-Assisted/methods ; Deep Learning ; Fundus Oculi ; Datasets as Topic ; Diabetic Retinopathy/diagnostic imaging ; Databases, Factual ; }, abstract = {In the last decades, many publicly available large fundus image datasets have been collected for diabetic retinopathy, glaucoma, and age-related macular degeneration, and a few other frequent pathologies. These publicly available datasets were used to develop a computer-aided disease diagnosis system by training deep learning models to detect these frequent pathologies. One challenge limiting the adoption of a such system by the ophthalmologist is, computer-aided disease diagnosis system ignores sight-threatening rare pathologies such as central retinal artery occlusion or anterior ischemic optic neuropathy and others that ophthalmologists currently detect. Aiming to advance the state-of-the-art in automatic ocular disease classification of frequent diseases along with the rare pathologies, a grand challenge on "Retinal Image Analysis for multi-Disease Detection" was organized in conjunction with the IEEE International Symposium on Biomedical Imaging (ISBI - 2021). This paper, reports the challenge organization, dataset, top-performing participants solutions, evaluation measures, and results based on a new "Retinal Fundus Multi-disease Image Dataset" (RFMiD). There were two principal sub-challenges: disease screening (i.e. presence versus absence of pathology - a binary classification problem) and disease/pathology classification (a 28-class multi-label classification problem). It received a positive response from the scientific community with 74 submissions by individuals/teams that effectively entered in this challenge. The top-performing methodologies utilized a blend of data-preprocessing, data augmentation, pre-trained model, and model ensembling. This multi-disease (frequent and rare pathologies) detection will enable the development of generalizable models for screening the retina, unlike the previous efforts that focused on the detection of specific diseases.}, }
@article {pmid39395131, year = {2024}, author = {Atesoglu, A and Ayyildiz, E and Karakaya, I and Bulut, FS and Serengil, Y}, title = {Land cover and drought risk assessment in Türkiye's mountain regions using neutrosophic decision support system.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {11}, pages = {1046}, pmid = {39395131}, issn = {1573-2959}, mesh = {*Droughts ; *Environmental Monitoring/methods ; *Climate Change ; Risk Assessment ; Ecosystem ; Turkey ; Decision Support Techniques ; Remote Sensing Technology ; Conservation of Natural Resources/methods ; }, abstract = {Earth observation (EO) provides dynamic scientific methods for tracking and defining ecological parameters in mountainous regions. Open-source platforms are frequently utilized in this context to efficiently collect and evaluate spatial data. In this study, we used Collect Earth (CE), an open-source land monitoring platform, to reveal and assess land cover, land cover change, and relevant ecological parameters such as drought risk. Mountain ecosystems were subject to an evaluation for the first time by combining remote sensing with a hybridization of Decision-Making Trial and Evaluation Laboratory (DEMATEL), analytic hierarchy process (AHP), and Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS) for neutrosophic sets in risk assessment problems of several connected criteria. The high and dispersed high alpine environment of Türkiye accommodates land with relatively less human influence, making it suitable to observe climate change impacts. In the framework of the study, we evaluated more than two decades (2000-2022) of land use and land cover (LULC) changes in the mountain regions of the country. Using nine identified ecological parameters, we also evaluated drought risk. The parameters included were the LULC classes and their change, elevation, slope, aspect, precipitation, temperature, normalized difference vegetation index (NDVI), water deficit, and evapotranspiration (ET). The risk map we produced revealed a high to very high drought risk for almost throughout the Türkiye's mountainous areas. We concluded that integrating geospatial techniques with hybridization is promising for mapping drought risk, helping policymakers prepare effective drought mitigation measures to reasonably adapt to climate change impacts.}, }
@article {pmid39392918, year = {2024}, author = {Kopania, EEK and Thomas, GWC and Hutter, CR and Mortimer, SME and Callahan, CM and Roycroft, E and Achmadi, AS and Breed, WG and Clark, NL and Esselstyn, JA and Rowe, KC and Good, JM}, title = {Sperm competition intensity shapes divergence in both sperm morphology and reproductive genes across murine rodents.}, journal = {Evolution; international journal of organic evolution}, volume = {79}, number = {1}, pages = {11-27}, pmid = {39392918}, issn = {1558-5646}, support = {R01 HD094787/HD/NICHD NIH HHS/United States ; R01 HD073439/HD/NICHD NIH HHS/United States ; R01 HG009299/HG/NHGRI NIH HHS/United States ; DEB-1754096//National Science Foundation/ ; R01-HG009299/HG/NHGRI NIH HHS/United States ; R01-HD073439//National Institute of Child Health and Human Development/ ; }, mesh = {Animals ; Male ; *Spermatozoa/physiology ; Mice/genetics ; *Evolution, Molecular ; *Testis/anatomy &amp; histology ; Phylogeny ; Selection, Genetic ; Sexual Selection ; Spermatogenesis/genetics ; Murinae/genetics/physiology ; Rats ; Reproduction/genetics ; }, abstract = {It remains unclear how variation in the intensity of sperm competition shapes phenotypic and molecular evolution across clades. Mice and rats in the subfamily Murinae are a rapid radiation exhibiting incredible diversity in sperm morphology and production. We combined phenotypic and genomic data to perform phylogenetic comparisons of male reproductive traits and genes across 78 murine species. We identified several shifts towards smaller relative testes mass (RTM), presumably reflecting reduced sperm competition. Several sperm traits were associated with RTM, suggesting that mating system evolution selects for convergent suites of traits related to sperm competitive ability. We predicted that sperm competition would also drive more rapid molecular divergence in species with large testes. Contrary to this, we found that many spermatogenesis genes evolved more rapidly in species with smaller RTM due to relaxed purifying selection. While some reproductive genes evolved rapidly under recurrent positive selection, relaxed selection played a greater role in underlying rapid evolution in small testes species. Our work demonstrates that postcopulatory sexual selection can impose strong purifying selection shaping the evolution of male reproduction and that broad patterns of molecular evolution may help identify genes that contribute to male fertility.}, }
@article {pmid39390673, year = {2024}, author = {Udaondo, Z and Ramos, JL and Abram, K}, title = {Unraveling the genomic diversity of the Pseudomonas putida group: exploring taxonomy, core pangenome, and antibiotic resistance mechanisms.}, journal = {FEMS microbiology reviews}, volume = {48}, number = {6}, pages = {}, pmid = {39390673}, issn = {1574-6976}, support = {PID2021-123469OB-I00//Plan Nacional sobre Drogas/ ; }, mesh = {*Pseudomonas putida/genetics/classification/drug effects ; *Genome, Bacterial/genetics ; *Genetic Variation ; Drug Resistance, Bacterial/genetics ; Genomics ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The genus Pseudomonas is characterized by its rich genetic diversity, with over 300 species been validly recognized. This reflects significant progress made through sequencing and computational methods. Pseudomonas putida group comprises highly adaptable species that thrive in diverse environments and play various ecological roles, from promoting plant growth to being pathogenic in immunocompromised individuals. By leveraging the GRUMPS computational pipeline, we scrutinized 26 363 genomes labeled as Pseudomonas in the NCBI GenBank, categorizing all Pseudomonas spp. genomes into 435 distinct species-level clusters or cliques. We identified 224 strains deposited under the taxonomic identifier "Pseudomonas putida" distributed within 31 of these species-level clusters, challenging prior classifications. Nine of these 31 cliques contained at least six genomes labeled as "Pseudomonas putida" and were analysed in depth, particularly clique_1 (P. alloputida) and clique_2 (P. putida). Pangenomic analysis of a set of 413 P. putida group strains revealed over 2.2 million proteins and more than 77 000 distinct protein families. The core genome of these 413 strains includes 2226 protein families involved in essential biological processes. Intraspecific genetic homogeneity was observed within each clique, each possessing a distinct genomic identity. These cliques exhibit distinct core genes and diverse subgroups, reflecting adaptation to specific environments. Contrary to traditional views, nosocomial infections by P. alloputida, P. putida, and P. monteilii have been reported, with strains showing varied antibiotic resistance profiles due to diverse mechanisms. This review enhances the taxonomic understanding of key P. putida group species using advanced population genomics approaches and provides a comprehensive understanding of their genetic diversity, ecological roles, interactions, and potential applications.}, }
@article {pmid39390511, year = {2024}, author = {Li, Y and Thomas, GWC and Richards, S and Waterhouse, RM and Zhou, X and Pfrender, ME}, title = {Rapid evolution of mitochondrion-related genes in haplodiploid arthropods.}, journal = {BMC biology}, volume = {22}, number = {1}, pages = {229}, pmid = {39390511}, issn = {1741-7007}, mesh = {Animals ; *Evolution, Molecular ; *Arthropods/genetics ; *Genes, Mitochondrial/genetics ; Phylogeny ; Haploidy ; Diploidy ; Oxidative Phosphorylation ; Cell Nucleus/genetics ; }, abstract = {BACKGROUND: Mitochondrial genes and nuclear genes cooperate closely to maintain the functions of mitochondria, especially in the oxidative phosphorylation (OXPHOS) pathway. However, mitochondrial genes among arthropod lineages have dramatic evolutionary rate differences. Haplodiploid arthropods often show fast-evolving mitochondrial genes. One hypothesis predicts that the small effective population size of haplodiploid species could enhance the effect of genetic drift leading to higher substitution rates in mitochondrial and nuclear genes. Alternatively, positive selection or compensatory changes in nuclear OXPHOS genes could lead to the fast-evolving mitochondrial genes. However, due to the limited number of arthropod genomes, the rates of evolution for nuclear genes in haplodiploid species, besides hymenopterans, are largely unknown. To test these hypotheses, we used data from 76 arthropod genomes, including 5 independently evolved haplodiploid lineages, to estimate the evolutionary rates and patterns of gene family turnover of mitochondrial and nuclear genes.<br><br>RESULTS: We show that five haplodiploid lineages tested here have fast-evolving mitochondrial genes and fast-evolving nuclear genes related to mitochondrial functions, while nuclear genes not related to mitochondrion showed no significant evolutionary rate differences. Among hymenopterans, bees and ants show faster rates of molecular evolution in mitochondrial genes and mitochondrion-related nuclear genes than sawflies and wasps. With genome data, we also find gene family expansions and contractions in mitochondrion-related genes of bees and ants.<br><br>CONCLUSIONS: Our results reject the small population size hypothesis in haplodiploid species. A combination of positive selection and compensatory changes could lead to the observed patterns in haplodiploid species. The elevated evolutionary rates in OXPHOS complex 2 genes of bees and ants suggest a unique evolutionary history of social hymenopterans.}, }
@article {pmid39387871, year = {2024}, author = {Smith, SJ and Cummins, SF and Motti, CA and Wang, T}, title = {A mass spectrometry database for the identification of marine animal saponin-related metabolites.}, journal = {Analytical and bioanalytical chemistry}, volume = {416}, number = {29}, pages = {6893-6907}, pmid = {39387871}, issn = {1618-2650}, mesh = {*Saponins/analysis/metabolism ; Animals ; *Aquatic Organisms/chemistry/metabolism ; *Mass Spectrometry/methods ; Databases, Factual ; }, abstract = {Saponins encompass a diverse group of naturally occurring glycoside molecules exhibiting amphiphilic properties and a broad range of biological activities. There is a resurgence of interest in those saponins produced by marine organisms based on their potential therapeutic benefits, application in food products and most recently their potential involvement in intra- and inter-species chemical communication. The continual advancements in liquid chromatography techniques and mass spectrometry technologies have allowed for greater detection rates, as well as improved isolation and elucidation of saponins. These factors have significantly contributed to the expansion in the catalogue of known saponin structures isolated from marine invertebrates; however, there currently exists no specific chemical library resource to accelerate the discovery process. In this study, a Marine Animal Saponin Database (MASD v1.0) has been developed to serve as a valuable chemical repository for known marine saponin-related data, including chemical formula, molecular mass and biological origin of nearly 1000 secondary metabolites associated with saponins produced by marine invertebrates. We demonstrate its application with an exemplar asteroid extract (Acanthaster cf. solaris, also known as crown-of-thorns starfish; COTS), identifying saponins from the MASD v1.0 that have been previously reported from COTS, as well as 21 saponins isolated from multiple other related asteroid species. This database will help facilitate future research endeavours, aiding researchers in exploring the vast chemical diversity of saponins produced by marine organisms and providing ecological insights, and the realisation of their potential for various applications, including as pharmaceuticals.}, }
@article {pmid39386964, year = {2024}, author = {Martin, SH and Lohse, K and Ebdon, S and Mackintosh, A and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Pearl-bordered Fritillary, Boloria euphrosyne (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {267}, pmid = {39386964}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Boloria euphrosyne (the Pearl-bordered Fritillary; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 400.4 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.17 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,138 protein coding genes.}, }
@article {pmid39385455, year = {2024}, author = {Wu, H and Li, Q and Wu, JC}, title = {Bioinformatics-aided function exploration of GH29 fucosidases from human gut Parabacteroides.}, journal = {Glycobiology}, volume = {34}, number = {12}, pages = {}, doi = {10.1093/glycob/cwae086}, pmid = {39385455}, issn = {1460-2423}, support = {2023GDASZH-2023010102//GDAS' Project of Science and Technology Development/ ; SL2023A04J01435//Guangzhou Basic and Applied Basic Research Foundation/ ; 2022A1515110917//Guangdong Basic and Applied Basic Research Foundation/ ; 32302033//National Natural Science Foundation of China/ ; 2023A04J1494//Guangzhou Basic and Applied Basic Research Foundation/ ; 2022GDASZH-2022010110//GDAS' Project of Science and Technology Development/ ; }, mesh = {Humans ; *alpha-L-Fucosidase/metabolism/genetics/chemistry ; *Computational Biology ; Gastrointestinal Microbiome ; Bacteroidetes/enzymology/genetics ; Polysaccharides/metabolism/chemistry ; Substrate Specificity ; Mucins/metabolism/chemistry ; }, abstract = {Gut microbes produce α-l-fucosidases critical for utilizing human milk oligosaccharides, mucosal and dietary glycans. Although gut Parabacteroides have garnered attention for their impact on host health and disease, their CAZymes remain poorly studied. CAZome analysis of eleven gut Parabacteroides type strains revealed their capacity to degrade mucin O-glycans. Their abundance of GH29 fucosidases caught our attention, and we predicted the functional profiles of 46 GH29 fucosidases using in silico approaches. Our findings showed diverse linkages specificities and species-specific distributions, with over half of GH29 enzymes functioning as α1,3/4 fucosidases, essential for acting on Lewis antigen epitopes of mucin O-glycans. We further enzymatically validated 4 novel GH29 sequences from poorly characterized groups. PgoldGH29A (cluster37GH29BERT, GH29:75.1CUPP) does not act on tested natural substrates. PgoldGH29B (cluster1GH29BERT, GH29:84.1CUPP) functions as a strict α1,3/4 fucosidase. PgoldGH29C (cluster14GH29BERT, GH29:29.1CUPP) displays unprecedented substrate specificity for α1,2/3/4 disaccharides. PgoldGH29D (cluster4GH29BERT, GH29:6.2CUPP) acts on α1,2/3/4/6 linkages similar to enzymes from GH29:6.1CUPP but prefers disaccharides over trisaccharides. These results suggest that PgoldGH29B and PgoldGH29D can contribute to mucin O-glycan degradation via their α1,3/4 and α1,2 fucosidase activity, respectively, while the natural substrates of PgoldGH29A and PgoldGH29C may be irrelevant to host-glycans. These insights enhance our understanding of the ecological niches inhabited by gut Parabacteroides and may guide similar exploration in other intriguing gut microbial species.}, }
@article {pmid39381069, year = {2024}, author = {Boyes, D and Lees, DC and Sims, I and Phillips, D and Boyes, C and ,  and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Yellow-dotted Stilt, Euspilapteryx auroguttella Stephens, 1835.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {226}, pmid = {39381069}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Euspilapteryx auroguttella (the Yellow-dotted Stilt; Arthropoda; Insecta; Lepidoptera; Gracillariidae). The genome sequence is 331.9 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.94 kilobases in length.}, }
@article {pmid39379720, year = {2024}, author = {Klopper, A}, title = {GPS tracking reveals how hares shape lynx populations.}, journal = {Nature}, volume = {634}, number = {8033}, pages = {301}, doi = {10.1038/d41586-024-03272-x}, pmid = {39379720}, issn = {1476-4687}, mesh = {Animals ; *Geographic Information Systems ; *Lynx/physiology ; Population Density ; Population Dynamics ; Alaska ; *Predatory Behavior ; *Hares/physiology ; }, }
@article {pmid39376700, year = {2024}, author = {Chelliah, DS and Ray, AE and Zhang, E and Terauds, A and Ferrari, BC}, title = {The Vestfold Hills are alive: characterising microbial and environmental dynamics in Old Wallow, eastern Antarctica.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1443491}, pmid = {39376700}, issn = {1664-302X}, abstract = {Old Wallow is an underexplored, hyper-arid coastal desert in Antarctica's Vestfold Hills. Situated near an elephant seal wallow, we examined how stochastic nutrient inputs from the seal wallow affect soil communities amid environmental changes along a spatially explicit sampling transect. We hypothesized that nutrient levels would be elevated due to proximity to the seal wallow, influencing community distributions. While the soil bacterial and eukaryotic communities at the phylum level were similar to other terrestrial environments, analysis at class and family levels revealed a dominance of unclassified taxa that are often linked to marine environments. Elevated nutrient concentrations (NO3 [-], SO4 [2-], SO3) were found at Old Wallow, with conductivity and Cl[-] levels up to 10-fold higher at the lowest elevation soils, correlating with significantly (p < 0.05) higher abundances of halophilic (Halomonadaceace) and uncultivated lineages (Ca Actinomarinales, unclassified Bacillariophyta and unclassified Opisthonkonta). An improved Gradient Forest model was used to quantify microbial responses to 26 soil gradients at OW, revealing variable responses to environmental predictors and identifying critical environmental thresholds or drivers of community turnover. Major tipping points were projected for eukaryotes with SO4 [2-], pH, and SO3, and for bacteria with moisture, Na2O, and Cl[-]. Thus, the Old Wallow ecosystem is primarily shaped by salt, sulphate, and moisture and is dominated by uncultivated taxa, which may be sensitive to environmental changes once critical tipping points are reached. This study provides critical baseline data for future regional monitoring under threats of environmental change.}, }
@article {pmid39374677, year = {2024}, author = {Ikeda, T and Cooray, U and Matsugaki, R and Suzuki, Y and Takagi, M and Muramatsu, K and Fushimi, K and Murakami, M and Osaka, K and Matsuda, S}, title = {Associations of hypothetical early intensive in-hospital rehabilitation with activities of daily living after hip fracture surgery in patients with and without dementia: emulating a randomized controlled trial using medical claims data.}, journal = {Journal of clinical epidemiology}, volume = {176}, number = {}, pages = {111550}, doi = {10.1016/j.jclinepi.2024.111550}, pmid = {39374677}, issn = {1878-5921}, mesh = {Humans ; *Hip Fractures/surgery/rehabilitation ; Female ; Male ; *Dementia/rehabilitation ; Aged ; *Activities of Daily Living ; Japan ; Aged, 80 and over ; Middle Aged ; Hospitalization/statistics &amp; numerical data ; Recovery of Function ; }, abstract = {OBJECTIVES: To investigate the impact of early intensive in-hospital rehabilitation, initiated within 2 days of surgery and lasting up to 7 days, on the recovery of activities of daily living in patients with and without dementia.<br><br>STUDY DESIGN AND SETTING: Medical claims data from 925 hospitals in Japan were analyzed. We enrolled patients aged &#x2265;50&#xa0;years who underwent hip fracture surgery within 2&#xa0;days of admission between April 1, 2018, and December 31, 2019. Low- (20&#xa0;minutes per day starting on day 2), highest- (60&#xa0;minutes per day starting on day 1), and gradually increasing (20&#xa0;minutes on day 1, 40&#xa0;minutes on days 2-4, and 60&#xa0;minutes per day thereafter) intensity regimens were used as exposures. The outcomes were Barthel Index (BI) scores at 14 and 30&#xa0;days postoperatively. For per-protocol analysis, a target trial emulation framework with the sequential doubly robust estimator was used.<br><br>RESULTS: Among patients without dementia (N&#xa0;=&#xa0;11,461), no significant differences in BI scores were observed at 14&#xa0;days postoperatively across regimens. At 30&#xa0;days postoperatively, significant differences in BI scores were noted between highest- and low-intensity regimens and between gradually increasing intensity and low-intensity regimens, with additive BI scores of 15.2 (95% CI, 10.7-19.7) and 14.7 (95% CI, 9.2-20.2), respectively. In patients with dementia (N&#xa0;=&#xa0;14,302), significant differences in BI scores were noted at 14&#xa0;days postoperatively between highest- and low-intensity regimens and between gradually increasing intensity and low-intensity regimens, with additive BI scores of 8.7 (95% CI, 5.2-12.2) and 10.7 (95% CI, 5.8-15.6), respectively. At 30&#xa0;days postoperatively, a significant difference in BI scores was observed between gradually increasing intensity and low-intensity regimens, with an additive BI score of 17.9 (95% CI, 11.3-24.5).<br><br>CONCLUSION: Early intensive in-hospital rehabilitation is highly relevant and beneficial for dementia patients.}, }
@article {pmid39373887, year = {2024}, author = {Dittrich, SP and Adithya, S and Ajith, Y and Athira, N and Athira, KS and Safeer, MS and Preena, P and Aishwarya, A and Athira, K and Nisha, AR and Devi, G and Mäder, M and Beena, V and Jacob, SS}, title = {Parasite diversity among domestic goats of tropical monsoon climatic zone in India.}, journal = {Parasitology research}, volume = {123}, number = {10}, pages = {342}, pmid = {39373887}, issn = {1432-1955}, support = {IN-ME_BI-5550//Deutscher Akademischer Austauschdienst/ ; SRG/2022/000837//Science and Engineering Research Board/ ; SRG/2022/000837//Science and Engineering Research Board/ ; }, mesh = {Animals ; *Goats/parasitology ; India/epidemiology ; *Goat Diseases/parasitology/epidemiology ; *Tropical Climate ; Phylogeny ; Parasitic Diseases, Animal/parasitology/epidemiology ; Parasites/classification/isolation &amp; purification/genetics ; Biodiversity ; }, abstract = {Among different climatic zones in India, the tropical monsoon region comprises a diverse ecosystem characterized by the endemic nature of several parasites including certain emerging and re-emerging vector-borne pathogens of humans, whereas a systematic investigation of the occurrence of different parasites among domestic goats in this area is not yet explored. The goal of the present study is to explore the parasite diversity focusing on molecular identification of vector-borne hemoparasites and its health impacts on domestic goats reared in the tropical monsoon climate zone of Kerala, India. Among 227 goats presented to the Teaching Veterinary Clinical Complex (TVCC) in the monsoon months of 2023, thirty animals were recruited for the study. The animals were screened for the presence of different hemoparasites (Anaplasma spp., Theileria spp., and Babesia spp.), ectoparasites (ticks, lice, and fleas), and gastrointestinal (GI) parasites (hookworms, threadworms, tapeworms, whipworms, and coccidia). The isolated hemoparasites were further characterized by sequencing and phylogenetic analysis. The correlation studies to elucidate the association between the occurrence of different parasites and clinical manifestations (hyperthermia, pallor of mucous membrane, circulatory failure, respiratory signs, neurological instability, and GI signs), blood picture (anemia, leukopenia, thrombocytopenia), demographics (sex and age), and treatment history (hemoparasitic therapy, ectoparasiticidal application, and prophylactic deworming) were conducted. The co-infection status of these parasites was also evaluated. A substantial portion of the goats in the study group was found to be affected by vector-borne hemoparasitic diseases and their arthropod vectors or GI parasites or both. This can be attributed to the constantly warm and humid climate of the region, which is favorable for the survival and growth of different life cycle stages of these parasites and vectors. A strategic parasitic disease surveillance-cum-control program is the need of the hour for ensuring climate resilience and profitable goat farming in the region.}, }
@article {pmid39373541, year = {2025}, author = {Zuo, YW and Quan, MH and Liu, GH and Zhang, X and Long, NN and You, SQ and Peng, Y and Deng, HP}, title = {Multi-Omics Analysis Reveals Molecular Responses of Alkaloid Content Variations in Lycoris aurea Across Different Locations.}, journal = {Plant, cell &amp; environment}, volume = {48}, number = {2}, pages = {953-964}, doi = {10.1111/pce.15187}, pmid = {39373541}, issn = {1365-3040}, support = {//This study was supported by General Program of the Chongqing Natural Science Foundation and National Natural Science Foundation of China./ ; }, mesh = {*Lycoris/metabolism/genetics ; *Alkaloids/metabolism ; Gene Expression Regulation, Plant ; Metabolomics ; Transcriptome ; Soil Microbiology ; Protein Interaction Maps ; Gene Expression Profiling ; Photosynthesis ; Metabolome ; Genes, Plant ; Multiomics ; }, abstract = {Lycoris aurea, celebrated for its visually striking flowers and significant medicinal value due to the presence of alkaloids such as lycorine and galanthamine, has intricate yet poorly understood regulatory mechanisms. This study provides a detailed examination of the transcriptomic, metabolomic and ecological dynamics of L. aurea, aiming to elucidate the underlying molecular mechanisms of alkaloid biosynthesis. Our comparative analysis across different ecological settings highlighted key genes involved in alkaloid biosynthesis, such as genes encoding aldehyde dehydrogenase and norbelladine 4'-O-methyltransferase, which were distinctively increased in the high alkaloids-producing group. We identified a total of 6871 differentially expressed genes and 915 metabolites involved in pathways like terpenoid backbone biosynthesis, phenylalanine, tyrosine and tryptophan biosynthesis. Protein interaction network analysis revealed significant upregulation of photosynthesis, photosystem and photosynthetic membrane pathways in the alkaloids-producing region. Furthermore, our research delineated the interactions among soil microbial communities, genes and plant and soil biochemical properties, noting that bacterial populations correlate with soil properties that favour the activation of metabolic pathways essential for alkaloid production. Collectively, this study advances our understanding of the genetic and metabolic alkaloid biosynthesis pathways in L. aurea, shedding light on the complex interactions that govern alkaloid production.}, }
@article {pmid39373528, year = {2024}, author = {Ros-Rocher, N}, title = {The evolution of multicellularity and cell differentiation symposium: bridging evolutionary cell biology and computational modelling using emerging model systems.}, journal = {Biology open}, volume = {13}, number = {10}, pages = {}, pmid = {39373528}, issn = {2046-6390}, support = {101106415//European Union's Horizon Europe research and innovation funding program/ ; //Institute Pasteur: Institut Pasteur; Baylor College of Medicine/ ; }, mesh = {*Cell Differentiation/genetics ; *Biological Evolution ; Animals ; Computational Biology/methods ; Humans ; Cell Biology ; Models, Biological ; Computer Simulation ; Genomics/methods ; }, abstract = {'The evolution of multicellularity and cell differentiation' symposium, organized as part of the EuroEvoDevo 2024 meeting on June 25-28th in Helsinki (Finland), addressed recent advances on the molecular and mechanistic basis for the evolution of multicellularity and cell differentiation in eukaryotes. The symposium involved over 100 participants and brought together 10 speakers at diverse career stages. Talks covered various topics at the interface of developmental biology, evolutionary cell biology, comparative genomics, computational biology, and ecology using animal, protist, algal and mathematical models. This symposium offered a unique opportunity for interdisciplinary dialog among researchers working on different systems, especially in promoting collaborations and aligning strategies for studying emerging model species. Moreover, it fostered opportunities to promote early career researchers in the field and opened discussions of ongoing work and unpublished results. In this Meeting Review, we aim to promote the research, capture the spirit of the meeting, and present key topics discussed within this dynamic, growing and open community.}, }
@article {pmid39373052, year = {2024}, author = {Xie, X and Gui, L and Qiao, B and Wang, G and Huang, S and Zhao, Y and Sun, S}, title = {Deep learning in template-free de novo biosynthetic pathway design of natural products.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {6}, pages = {}, pmid = {39373052}, issn = {1477-4054}, support = {2572022BD04//Fundamental Research Funds for the Central Universities/ ; 62001088//National Natural Science Foundation of China/ ; }, mesh = {*Biological Products/metabolism ; *Deep Learning ; *Biosynthetic Pathways ; Algorithms ; Computational Biology/methods ; Humans ; }, abstract = {Natural products (NPs) are indispensable in drug development, particularly in combating infections, cancer, and neurodegenerative diseases. However, their limited availability poses significant challenges. Template-free de novo biosynthetic pathway design provides a strategic solution for NP production, with deep learning standing out as a powerful tool in this domain. This review delves into state-of-the-art deep learning algorithms in NP biosynthesis pathway design. It provides an in-depth discussion of databases like Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome, and UniProt, which are essential for model training, along with chemical databases such as Reaxys, SciFinder, and PubChem for transfer learning to expand models' understanding of the broader chemical space. It evaluates the potential and challenges of sequence-to-sequence and graph-to-graph translation models for accurate single-step prediction. Additionally, it discusses search algorithms for multistep prediction and deep learning algorithms for predicting enzyme function. The review also highlights the pivotal role of deep learning in improving catalytic efficiency through enzyme engineering, which is essential for enhancing NP production. Moreover, it examines the application of large language models in pathway design, enzyme discovery, and enzyme engineering. Finally, it addresses the challenges and prospects associated with template-free approaches, offering insights into potential advancements in NP biosynthesis pathway design.}, }
@article {pmid39367377, year = {2024}, author = {Qiao, L and Zhang, C and Zhang, M and Jiang, H and Shi, Y and Zhang, W and Mei, Y and Li, Y and Wang, H}, title = {High-risk spatiotemporal patterns of leprosy in the southeastern region of Yunnan province from 2010 to 2022: an analysis at the township level.}, journal = {BMC public health}, volume = {24}, number = {1}, pages = {2707}, pmid = {39367377}, issn = {1471-2458}, support = {82103748//National Natural Science Foundation of China/ ; 81972950//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Leprosy/epidemiology ; China/epidemiology ; Female ; Male ; *Spatio-Temporal Analysis ; Adult ; Middle Aged ; *Geographic Information Systems ; Adolescent ; Young Adult ; Aged ; Child ; Risk Factors ; }, abstract = {BACKGROUND: Despite being preventable and curable, leprosy remains endemic in some undeveloped regions, including China. Wenshan Zhuang and Miao Autonomous Prefecture (Wenshan prefecture) currently bears the highest leprosy burden in China. In this ecological study, we aimed to analyze the epidemiological characteristics as well as identify and visualize the high-risk townships of Wenshan prefecture using the most updated leprosy data from 2010 to 2022.<br><br>METHODS: Geographical information system combined with spatial scan statistics was used for newly detected leprosy cases abstracted from the Leprosy Management Information System in China. Global Moran's I index was used to uncover the spatial pattern of leprosy at the township level. Spatial scan statistics, encompassing purely temporal, purely spatial, spatial variation in temporal trends, and space-time analysis, were implemented for detecting the risk clusters.<br><br>RESULTS: Between 2010 and 2022, Wenshan prefecture detected 532 new leprosy cases, comprising 352 (66.17%) males and 180 (33.83%) females. The aggregated time primarily occurred between October 2010 and March 2014. The distribution pattern of newly detected leprosy cases was spatially clustered. We identified four high-risk spatial clusters encompassing 54.51% of the new cases. Furthermore, spatial variation in temporal trends highlighted one cluster as a potential high-risk area. Finally, two space-time clusters were detected, and the most likely cluster was predominantly located in the central and northwest regions of Wenshan prefecture, spanning from January 2010 to September 2013.<br><br>CONCLUSIONS: In this ecology study, we characterized the epidemiological features and temporal and spatial patterns of leprosy in Wenshan prefecture using the most recent leprosy data between 2010 and 2022. Our findings offer scientific insights into the epidemiological profiles and spatiotemporal dynamics of leprosy in Wenshan prefecture. Clinicians and policymakers should pay particular attention to the identified clusters for the prevention and control of leprosy.}, }
@article {pmid39367017, year = {2024}, author = {Zhou, M and Guo, F}, title = {Mechanism and spatial spillover effect of digital economy on common prosperity in the Yellow River Basin of China.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {23086}, pmid = {39367017}, issn = {2045-2322}, support = {41801105//National Natural Science Foundation of China/ ; 2022RW040//Shandong Province Higher Education Youth Innovation Technology Support Program/ ; 23CGLJ15//Shandong Province Social Science Planning and Research Project/ ; }, abstract = {The digital economy has emerged as a new trend in economic development and has profoundly influenced the process of achieving common prosperity. However, current research on the correlation between the digital economy and common prosperity from the perspective of a river basin still needs to be strengthened. Based on this, the present study first theoretically elaborates the conceptual meanings of "digital economy" and "common prosperity", as well as the mechanism by which the digital economy empowers common prosperity. Subsequently, a scientifically-constructed performance evaluation index system for the digital economy and common prosperity is established. Considering the Yellow River Basin as an empirical case study area, this study investigates the mechanism and spatial spillover effects of the digital economy in empowering common prosperity from 2005 to 2020. The research findings reveal that: (1) The Yellow River Basin exhibits a basin characteristic with downstream > midstream > upstream areas regarding the level of common prosperity and digital economy. It indicates that a distinct spatial correlation exists between the two factors. However, the ongoing decrease in both high-level and very high-level areas reflects the lengthy and challenging journey of enhancing the quality and efficiency of the digital economy in empowering common prosperity. (2) The digital economy not only directly impacts common prosperity, but also fosters its development through spatial spillover effects. Among the control factors, informatization and housing levels have a major stimulating effect. (3) There exists a clear regional heterogeneity in how the digital economy affects common prosperity in the Yellow River Basin. Specifically, common prosperity of downstream cities is significantly impacted by the digital economy. The spatial spillover effects of the digital economy on common prosperity exhibit a pronounced "neighborhood as a moat" characteristic. (4) The digital economy facilitates the achievement of shared prosperity through the implementation of mechanisms centered on sharing, affluence, and sustainability. These research findings illuminate the empowering mechanisms and spatial spillover pathways of the digital economy in promoting shared prosperity, aligning with national strategies for ecological conservation and high-quality development in the Yellow River Basin.}, }
@article {pmid39364368, year = {2024}, author = {Bullion, CM and Bahlai, CA}, title = {Data gap or biodiversity gap? Evaluating apparent spatial biases in community science observations of Odonata in the east-central United States.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e18115}, pmid = {39364368}, issn = {2167-8359}, mesh = {Animals ; *Biodiversity ; *Odonata ; Humans ; Bias ; United States ; Databases, Factual ; }, abstract = {Odonates (dragonflies and damselflies) have become popular study organisms for insect-based climate studies, due to the taxon's strong sensitivity to environmental conditions, and an enthusiastic following by community scientists due to their charismatic appearance and size. Where formal records of this taxon can be limited, public efforts have provided nearly 1,500,000 open-sourced odonate records through online databases, making real-time spatio-temporal monitoring more feasible. While these databases can be extensive, concerns regarding these public endeavors have arisen from a variety of sources: records may be biased by human factors (ex: density, technological access) which may cause erroneous interpretations. Indeed, records of odonates in the east-central US documented in the popular database iNaturalist bear striking patterns corresponding to political boundaries and other human activities. We conducted a 'ground-truthing' study using a structured sampling method to examine these patterns in an area where community science reports indicated variable abundance, richness, and diversity which appeared to be linked to observation biases. Our observations were largely consistent with patterns recorded by community scientists, suggesting these databases were indeed capturing representative biological trends and raising further questions about environmental drivers in the observed data gaps.}, }
@article {pmid39363544, year = {2024}, author = {Panayi, P and Peters, E and Bentall, R and Hardy, A and Berry, K and Sellwood, W and Dudley, R and Longden, E and Underwood, R and Steel, C and Jafari, H and Emsley, R and Mason, L and Elliott, R and Varese, F}, title = {Complex PTSD symptoms predict positive symptoms of psychosis in the flow of daily life.}, journal = {Psychological medicine}, volume = {54}, number = {12}, pages = {1-12}, pmid = {39363544}, issn = {1469-8978}, support = {NIHR128623//Health Technology Assessment Programme/ ; NIHR130971//Efficacy and Mechanism Evaluation Programme/ ; N/A//NIHR Maudsley Biomedical Research Centre/ ; }, abstract = {BACKGROUND: Post-traumatic stress disorder (PTSD) has been shown to predict psychotic symptomology. However, few studies have examined the relative contribution of PTSD compared to broader post-traumatic sequelae in maintaining psychosis. Complex PTSD (cPTSD), operationalized using ICD-11 criteria, includes core PTSD (intrusions, avoidance, hyperarousal) as well as additional "disturbances of self-organisation" (DSO; emotional dysregulation, interpersonal difficulties, negative self-concept) symptoms, more likely to be associated with complex trauma histories. It was hypothesized that DSOs would be associated with positive psychotic symptoms (paranoia, voices, and visions) in daily life, over and above core PTSD symptoms.<br><br>METHODS: This study (N = 153) employed a baseline subsample of the Study of Trauma And Recovery (STAR), a clinical sample of participants with comorbid post-traumatic stress and psychosis symptoms. Core PTSD, DSO and psychosis symptoms were assessed up to 10 times per day at quasi-random intervals over six consecutive days using Experience Sampling Methodology.<br><br>RESULTS: DSOs within the preceding 90 min predicted paranoia, voices, and visions at subsequent moments. These relationships persisted when controlling for core PTSD symptoms within this timeframe, which were themselves significant. The associations between DSOs and paranoia but not voices or visions, were significantly stronger than those between psychosis and core PTSD symptoms.<br><br>CONCLUSIONS: Consistent with an affective pathway to psychosis, the findings suggest that DSOs may be more important than core PTSD symptoms in maintaining psychotic experiences in daily life among people with comorbid psychosis and cPTSD, and indicate the potential importance of addressing broad post-traumatic sequelae in trauma-focused psychosis interventions.}, }
@article {pmid39363203, year = {2024}, author = {Viana, PAB and Tschoeke, DA and de Moraes, L and Santos, LA and Barral-Netto, M and Khouri, R and Ramos, PIP and Meirelles, PM}, title = {Design and implementation of a metagenomic analytical pipeline for respiratory pathogen detection.}, journal = {BMC research notes}, volume = {17}, number = {1}, pages = {291}, pmid = {39363203}, issn = {1756-0500}, support = {2023-PPI-007//Rockefeller Foundation/ ; }, mesh = {*Metagenomics/methods ; Humans ; *Respiratory Tract Infections/microbiology/diagnosis ; Metagenome/genetics ; Computational Biology/methods ; Reproducibility of Results ; Nasopharynx/microbiology/virology ; }, abstract = {OBJECTIVE: We developed an in-house bioinformatics pipeline to improve the detection of respiratory pathogens in metagenomic sequencing data. This pipeline addresses the need for short-time analysis, high accuracy, scalability, and reproducibility in a high-performance computing environment.<br><br>RESULTS: We evaluated our pipeline using ninety synthetic metagenomes designed to simulate nasopharyngeal swab samples. The pipeline successfully identified 177 out of 204 respiratory pathogens present in the compositions, with an average processing time of approximately 4&#xa0;min per sample (processing 1&#xa0;million paired-end reads of 150 base pairs). For the estimation of all the 470 taxa included in the compositions, the pipeline demonstrated high accuracy, identifying 420 and achieving a correlation of 0.9 between their actual and predicted relative abundances. Among the identified taxa, 27 were significantly underestimated or overestimated, including only three clinically relevant pathogens. We also validated the pipeline by applying it to a clinical dataset from a study on metagenomic pathogen characterization in patients with acute respiratory infections and successfully identified all pathogens responsible for the diagnosed infections. These findings underscore the pipeline's effectiveness in pathogen detection and highlight its potential utility in respiratory pathogen surveillance.}, }
@article {pmid39362872, year = {2024}, author = {Fu, SW and Feng, MC and Chi, PW and Ding, TS}, title = {Combining citizen science data and literature to build a traits dataset of Taiwan's birds.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1076}, pmid = {39362872}, issn = {2052-4463}, mesh = {Animals ; Taiwan ; *Birds ; *Citizen Science ; *Ecosystem ; Databases, Factual ; }, abstract = {Trait-based methodologies are gaining traction in the field of ecology, providing deeper insights into ecosystem structure and functions. To this end, trait databases tailored to specific taxonomic groups have become foundational. In Taiwan, the collaborative efforts of avian researchers and dedicated citizen scientists have led to the compilation of a vast array of data. This includes web-sourced images from social media, spatial distribution records from eBird, and morphological metrics from banded birds and specimens. Enriched by peer-reviewed literature, we have meticulously assembled a comprehensive trait dataset encompassing 454 bird species across 73 families. This dataset covers a wide range of traits, including foraging ecology, morphological characteristics, territorial behaviors, breeding attributes, and the roles of bird species in ecosystem regulation. As an invaluable resource, this dataset lays the foundation for in-depth exploration of functional diversity, trait-based community ecology, ecosystem function, and critical insights needed to shape conservation strategies.}, }
@article {pmid39362167, year = {2024}, author = {Fardullah, M and Hossain, MT and Islam, MS and Islam, MR and Rahman, MR and Akther, K and Uddin, A and Morshed, S and Sultana, N and Alam, MA and Bahadur, NM and Robel, FN}, title = {Occurrence and spatial distribution of microplastics in water and sediments of Hatiya Island, Bangladesh and their risk assessment.}, journal = {Journal of environmental management}, volume = {370}, number = {}, pages = {122697}, doi = {10.1016/j.jenvman.2024.122697}, pmid = {39362167}, issn = {1095-8630}, mesh = {*Microplastics/analysis ; Risk Assessment ; Bangladesh ; *Environmental Monitoring ; *Water Pollutants, Chemical/analysis ; Geologic Sediments/chemistry/analysis ; Islands ; }, abstract = {This research has evaluated the MPs distribution, characteristics, and potential threats of MPs in surface water and sediments from Hatiya Island. The results showed that the abundance of MPs was 139 ± 44 items/m[3] in surface water and 493 ± 80 items/kg dw in sediments, indicating higher levels of MPs contamination in sediment samples. Fibers were the predominant kind of microplastics, and microscopic sizes (0.3-1.5 mm) MPs were generally more frequent and largely present in both the surface water and sediments. Fourier-transform infrared spectroscopy (FTIR) confirmed that polyethylene terephthalate was the major polymer component of microplastics in surface water, whereas polyethylene was the most abundant polymer in sediments. MPs contamination risk was examined based on multiple risk assessment models. Nemerow pollution index (NPI) and pollutant load index (PLI) show minimal pollution levels of MPs. But potential hazard index (PHI), potential ecological risk factor (Er), and potential ecological risk index (RI), indicate severe MPs contamination due to the presence of polyurethane, polycarbonate, polyvinyl chloride, epoxy that were hazardous MPs and exhibited a critical concern for MPs risk. These statistics will help to understand the environmental difficulties generated by MPs and which hazard is waiting for mankind in the future.}, }
@article {pmid39360250, year = {2024}, author = {Soni, N and Eyre, MT and Souza, FN and Diggle, PJ and Ko, AI and Begon, M and Pickup, R and Childs, JE and Khalil, H and Carvalho-Pereira, TSA and Pertile, AC and Carvalho, M and de Oliveira, D and Nery, N and Giorgi, E and Costa, F}, title = {Disentangling the influence of reservoir abundance and pathogen shedding on zoonotic spillover of the Leptospira agent in urban informal settlements.}, journal = {Frontiers in public health}, volume = {12}, number = {}, pages = {1447592}, pmid = {39360250}, issn = {2296-2565}, support = {U01 AI088752/AI/NIAID NIH HHS/United States ; F31 AI114245/AI/NIAID NIH HHS/United States ; R01 TW009504/TW/FIC NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; R01 AI052473/AI/NIAID NIH HHS/United States ; R25 TW009338/TW/FIC NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Leptospirosis/epidemiology/microbiology/transmission ; *Leptospira/isolation &amp; purification ; *Disease Reservoirs/microbiology ; Brazil/epidemiology ; Rats ; *Zoonoses/microbiology ; Male ; Female ; Adult ; Bacterial Shedding ; Longitudinal Studies ; Middle Aged ; Risk Factors ; Urban Population/statistics &amp; numerical data ; Adolescent ; Young Adult ; }, abstract = {Rats are major reservoirs for pathogenic Leptospira, the bacteria causing leptospirosis, particularly in urban informal settlements. However, the impact of variation in rat abundance and pathogen shedding rates on spillover transmission to humans remains unclear. This study aimed to investigate how spatial variation in reservoir abundance and pathogen pressure affect Leptospira spillover transmission to humans in a Brazilian urban informal settlement. A longitudinal eco-epidemiological study was conducted from 2013 to 2014 to characterize the spatial distribution of rat abundance and Leptospira shedding rates in rats and determine the association with human infection risk in a cohort of 2,206 community residents. Tracking plates and live-trapping were used to measure rat abundance and quantify rat shedding status and load. In parallel, four sequential biannual serosurveys were used to identify human Leptospira infections. To evaluate the role of shedding on human risk, we built three statistical models for: (1) the relative abundance of rats, (2) the shedding rate by individual rats, and (3) human Leptospira infection, in which "total shedding", obtained by multiplying the predictions from those two models, was used as a risk factor. We found that Leptospira shedding was associated with older and sexually mature rats and varied spatially and temporally-higher at valley bottoms and with seasonal rainfall (December to March). The point estimate for "total shedding" by rat populations was positive, i.e., Leptospira infection risk increased with total shedding, but the association was not significant [odds ratio (OR) = 1.1; 95% confidence interval (CI): 0.9, 1.4]. This positive trend was mainly driven by rat abundance, rather than individual rat shedding (OR = 1.8; 95% CI: 0.6, 5.4 vs. OR = 1.0; 95% CI: 0.7, 1.4]. Infection risk was higher in areas with more vegetative land cover (OR = 2.4; 95% CI: 1.2, 4.8), and when floodwater entered the house (OR = 2.4; 95% CI: 1.6, 3.4). Our findings indicate that environmental and hydrological factors play a more significant role in Leptospira spillover than rat associated factors. Furthermore, we developed a novel approach combining several models to elucidate complex links between animal reservoir abundance, pathogen shedding and environmental factors on zoonotic spillover in humans that can be extended to other environmentally transmitted diseases.}, }
@article {pmid39359327, year = {2023}, author = {Boyes, D and Boyes, C and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Crescent Plume, Marasmarcha lunaedactyla (Haworth, 1811).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {431}, pmid = {39359327}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Marasmarcha lunaedactyla (the Crescent Plume; Arthropoda; Insecta; Lepidoptera; Pterophoridae). The genome sequence is 771.1 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 16.43 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,571 protein coding genes.}, }
@article {pmid39355992, year = {2024}, author = {Auffret, AG and Ladouceur, E and Haussmann, NS and Daouti, E and Elumeeva, TG and Kačergytė, I and Knape, J and Kotowska, D and Low, M and Onipchenko, VG and Paquet, M and Rubene, D and Plue, J}, title = {A global database of soil seed bank richness, density, and abundance.}, journal = {Ecology}, volume = {105}, number = {11}, pages = {e4438}, doi = {10.1002/ecy.4438}, pmid = {39355992}, issn = {1939-9170}, mesh = {*Seed Bank ; *Soil ; *Databases, Factual ; *Biodiversity ; *Seeds ; Ecosystem ; Plants/classification ; }, abstract = {A soil seed bank is the collective name for viable seeds that are stored naturally in the soil. At the species or population level, the ability to form a seed bank represents a strategy for (re)colonization following a disturbance or other change in the local environmental conditions. At the community level, seed banks are thought to buffer local diversity during periods of environmental change and are often studied in relation to the potential for passive habitat restoration. The role that seed banks play in plant population and community dynamics, as well as their importance in the agricultural sector, means that they have been widely studied in ecological research. This database is the result of a comprehensive literature search, including all seed bank studies from the Web of Science from which data could be extracted, as well as an additional search of the Russian language literature. The database contains information on the species richness, seed density, and/or seed abundance in 3096 records from at least 1929 locations across the world's seven continents, extracted from 1442 studies published between 1940 and 2020. Records are grouped into five broad habitat categories (aquatic, arable, forest, grassland-including shrubland-and wetland), including information relating to habitat degradation from, or restoration to other habitats (total 14 combinations). Sampling protocols were also extracted for each record, and the database was extensively checked for errors. The location of each record was then used to extract summary climate data and biome classification from external published databases. The database has several potential uses. The large geographical spread relative to many other global biodiversity datasets is relevant for investigating patterns of diversity in biogeographical or macroecological contexts. Habitat type and status (intact, degraded, and restored) can be used to provide insights for biodiversity conservation, while the potential effects of sampling method and effort can be used to inform optimized data collection for future seed bank studies. This database is released under the CC-BY license.}, }
@article {pmid39354608, year = {2024}, author = {Navratilova, HF and Whetton, AD and Geifman, N}, title = {Artificial intelligence driven definition of food preference endotypes in UK Biobank volunteers is associated with distinctive health outcomes and blood based metabolomic and proteomic profiles.}, journal = {Journal of translational medicine}, volume = {22}, number = {1}, pages = {881}, pmid = {39354608}, issn = {1479-5876}, support = {202205080261//Lembaga Pengelola Dana Pendidikan/ ; }, mesh = {Humans ; *Food Preferences ; United Kingdom ; Male ; Female ; *Biological Specimen Banks ; Middle Aged ; *Proteomics/methods ; *Metabolomics ; *Artificial Intelligence ; Metabolome ; Adult ; Aged ; Surveys and Questionnaires ; Health ; UK Biobank ; }, abstract = {BACKGROUND: Specific food preferences can determine an individual's dietary patterns and therefore, may be associated with certain health risks and benefits.<br><br>METHODS: Using food preference questionnaire (FPQ) data from a subset comprising over 180,000 UK Biobank participants, we employed Latent Profile Analysis (LPA) approach to identify the main patterns or profiles among participants. blood biochemistry across groups/profiles was compared using the non-parametric Kruskal-Wallis test. We applied the Limma algorithm for differential abundance analysis on 168 metabolites and 2923 proteins, and utilized the Database for Annotation, Visualization and Integrated Discovery (DAVID) to identify enriched biological processes and pathways. Relative risks (RR) were calculated for chronic diseases and mental conditions per group, adjusting for sociodemographic factors.<br><br>RESULTS: Based on their food preferences, three profiles were termed: the putative Health-conscious group (low preference for animal-based or sweet foods, and high preference for vegetables and fruits), the Omnivore group (high preference for all foods), and the putative Sweet-tooth group (high preference for sweet foods and sweetened beverages). The Health-conscious group exhibited lower risk of heart failure (RR&#x2009;=&#x2009;0.86, 95%CI 0.79-0.93) and chronic kidney disease (RR&#x2009;=&#x2009;0.69, 95%CI 0.65-0.74) compared to the two other groups. The Sweet-tooth group had greater risk of depression (RR&#x2009;=&#x2009;1.27, 95%CI 1.21-1.34), diabetes (RR&#x2009;=&#x2009;1.15, 95%CI 1.01-1.31), and stroke (RR&#x2009;=&#x2009;1.22, 95%CI 1.15-1.31) compared to the other two groups. Cancer (overall) relative risk showed little difference across the Health-conscious, Omnivore, and Sweet-tooth groups with RR of 0.98 (95%CI 0.96-1.01), 1.00 (95%CI 0.98-1.03), and 1.01 (95%CI 0.98-1.04), respectively. The Health-conscious group was associated with lower levels of inflammatory biomarkers (e.g., C-reactive Protein) which are also known to be elevated in those with common metabolic diseases (e.g., cardiovascular disease). Other markers modulated in the Health-conscious group, ketone bodies, insulin-like growth factor-binding protein (IGFBP), and Growth Hormone 1 were more abundant, while leptin was less abundant. Further, the IGFBP pathway, which influences IGF1 activity, may be significantly enhanced by dietary choices.<br><br>CONCLUSIONS: These observations align with previous findings from studies focusing on weight loss interventions, which include a reduction in leptin levels. Overall, the Health-conscious group, with preference to healthier food options, has better health outcomes, compared to Sweet-tooth and Omnivore groups.}, }
@article {pmid39352141, year = {2024}, author = {Coclet, C and Camargo, AP and Roux, S}, title = {MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes.}, journal = {mSystems}, volume = {9}, number = {10}, pages = {e0088824}, pmid = {39352141}, issn = {2379-5077}, mesh = {*Metagenome/genetics ; *Genome, Viral/genetics ; *Metagenomics/methods ; *Viruses/genetics/classification/isolation &amp; purification ; Software ; Virome/genetics ; Computational Biology/methods ; Molecular Sequence Annotation ; }, abstract = {While numerous computational frameworks and workflows are available for recovering prokaryote and eukaryote genomes from metagenome data, only a limited number of pipelines are designed specifically for viromics analysis. With many viromics tools developed in the last few years alone, it can be challenging for scientists with limited bioinformatics experience to easily recover, evaluate quality, annotate genes, dereplicate, assign taxonomy, and calculate relative abundance and coverage of viral genomes using state-of-the-art methods and standards. Here, we describe Modular Viromics Pipeline (MVP) v.1.0, a user-friendly pipeline written in Python and providing a simple framework to perform standard viromics analyses. MVP combines multiple tools to enable viral genome identification, characterization of genome quality, filtering, clustering, taxonomic and functional annotation, genome binning, and comprehensive summaries of results that can be used for downstream ecological analyses. Overall, MVP provides a standardized and reproducible pipeline for both extensive and robust characterization of viruses from large-scale sequencing data including metagenomes, metatranscriptomes, viromes, and isolate genomes. As a typical use case, we show how the entire MVP pipeline can be applied to a set of 20 metagenomes from wetland sediments using only 10 modules executed via command lines, leading to the identification of 11,656 viral contigs and 8,145 viral operational taxonomic units (vOTUs) displaying a clear beta-diversity pattern. Further, acting as a dynamic wrapper, MVP is designed to continuously incorporate updates and integrate new tools, ensuring its ongoing relevance in the rapidly evolving field of viromics. MVP is available at https://gitlab.com/ccoclet/mvp and as versioned packages in PyPi and Conda.IMPORTANCEThe significance of our work lies in the development of Modular Viromics Pipeline (MVP), an integrated and user-friendly pipeline tailored exclusively for viromics analyses. MVP stands out due to its modular design, which ensures easy installation, execution, and integration of new tools and databases. By combining state-of-the-art tools such as geNomad and CheckV, MVP provides high-quality viral genome recovery and taxonomy and host assignment, and functional annotation, addressing the limitations of existing pipelines. MVP's ability to handle diverse sample types, including environmental, human microbiome, and plant-associated samples, makes it a versatile tool for the broader microbiome research community. By standardizing the analysis process and providing easily interpretable results, MVP enables researchers to perform comprehensive studies of viral communities, significantly advancing our understanding of viral ecology and its impact on various ecosystems.}, }
@article {pmid39352117, year = {2024}, author = {Gu, S and Shao, Y and Rehm, K and Bigler, L and Zhang, D and He, R and Xu, R and Shao, J and Jousset, A and Friman, VP and Bian, X and Wei, Z and Kümmerli, R and Li, Z}, title = {Feature sequence-based genome mining uncovers the hidden diversity of bacterial siderophore pathways.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {39352117}, issn = {2050-084X}, support = {No. 2021YFF1200500//National Key Research and Development Program of China/ ; No. 42107140//National Natural Science Foundation of China/ ; No.41922053//National Natural Science Foundation of China/ ; No. 32071255//National Natural Science Foundation of China/ ; No. T2321001//National Natural Science Foundation of China/ ; No. BX2021012//National Postdoctoral Program for Innovative Talents/ ; no. 310030_212266/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {*Siderophores/metabolism/genetics ; *Genome, Bacterial ; *Pseudomonas/genetics/metabolism ; *Computational Biology/methods ; Metabolic Networks and Pathways/genetics ; Phylogeny ; Oligopeptides/metabolism/genetics ; Secondary Metabolism/genetics ; Iron/metabolism ; }, abstract = {Microbial secondary metabolites are a rich source for pharmaceutical discoveries and play crucial ecological functions. While tools exist to identify secondary metabolite clusters in genomes, precise sequence-to-function mapping remains challenging because neither function nor substrate specificity of biosynthesis enzymes can accurately be predicted. Here, we developed a knowledge-guided bioinformatic pipeline to solve these issues. We analyzed 1928 genomes of Pseudomonas bacteria and focused on iron-scavenging pyoverdines as model metabolites. Our pipeline predicted 188 chemically different pyoverdines with nearly 100% structural accuracy and the presence of 94 distinct receptor groups required for the uptake of iron-loaded pyoverdines. Our pipeline unveils an enormous yet overlooked diversity of siderophores (151 new structures) and receptors (91 new groups). Our approach, combining feature sequence with phylogenetic approaches, is extendable to other metabolites and microbial genera, and thus emerges as powerful tool to reconstruct bacterial secondary metabolism pathways based on sequence data.}, }
@article {pmid39351379, year = {2024}, author = {Leavy, OC and Russell, RJ and Harrison, EM and Lone, NI and Kerr, S and Docherty, AB and Sheikh, A and Richardson, M and Elneima, O and Greening, NJ and Harris, VC and Houchen-Wolloff, L and McAuley, HJC and Saunders, RM and Sereno, M and Shikotra, A and Singapuri, A and Aul, R and Beirne, P and Bolton, CE and Brown, JS and Choudhury, G and Diar Bakerly, N and Easom, N and Echevarria, C and Fuld, J and Hart, N and Hurst, JR and Jones, M and Parekh, D and Pfeffer, P and Rahman, NM and Rowland-Jones, S and Shah, AM and Wootton, DG and Jolley, C and Thompson, AAR and Chalder, T and Davies, MJ and De Soyza, A and Geddes, JR and Greenhalf, W and Heller, S and Howard, L and Jacob, J and Jenkins, RG and Lord, JM and Man, WD and McCann, GP and Neubauer, S and Openshaw, PJM and Porter, J and Rowland, MJ and Scott, JT and Semple, MG and Singh, SJ and Thomas, D and Toshner, M and Lewis, K and Heaney, LG and Briggs, A and Zheng, B and Thorpe, M and Quint, JK and Chalmers, JD and Ho, LP and Horsley, A and Marks, M and Poinasamy, K and Raman, B and Wain, LV and Brightling, CE and Evans, RA}, title = {1-year health outcomes associated with systemic corticosteroids for COVID-19: a longitudinal cohort study.}, journal = {ERJ open research}, volume = {10}, number = {5}, pages = {}, pmid = {39351379}, issn = {2312-0541}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {BACKGROUND: In patients with coronavirus disease 2019 (COVID-19) requiring supplemental oxygen, dexamethasone reduces acute severity and improves survival, but longer-term effects are unknown. We hypothesised that systemic corticosteroid administration during acute COVID-19 would be associated with improved health-related quality of life (HRQoL) 1 year after discharge.<br><br>METHODS: Adults admitted to hospital between February 2020 and March 2021 for COVID-19 and meeting current guideline recommendations for dexamethasone treatment were included using two prospective UK cohort studies (Post-hospitalisation COVID-19 and the International Severe Acute Respiratory and emerging Infection Consortium). HRQoL, assessed by the EuroQol-Five Dimensions-Five Levels utility index (EQ-5D-5L UI), pre-hospital and 1 year after discharge were compared between those receiving corticosteroids or not after propensity weighting for treatment. Secondary outcomes included patient-reported recovery, physical and mental health status, and measures of organ impairment. Sensitivity analyses were undertaken to account for survival and selection bias.<br><br>FINDINGS: Of the 1888 participants included in the primary analysis, 1149 received corticosteroids. There was no between-group difference in EQ-5D-5L UI at 1 year (mean difference 0.004, 95% CI -0.026-0.034). A similar reduction in EQ-5D-5L UI was seen at 1 year between corticosteroid exposed and nonexposed groups (mean&#xb1;sd change -0.12&#xb1;0.22 versus -0.11&#xb1;0.22). Overall, there were no differences in secondary outcome measures. After sensitivity analyses modelled using a cohort of 109&#x2009;318 patients admitted to hospital with COVID-19, EQ-5D-5L UI at 1 year remained similar between the two groups.<br><br>INTERPRETATION: Systemic corticosteroids for acute COVID-19 have no impact on the large reduction in HRQoL 1 year after hospital discharge. Treatments to address the persistent reduction in HRQoL are urgently needed.}, }
@article {pmid39351031, year = {2024}, author = {Wei, C and Cai, Y and Liu, J and Guo, Y and Wu, X and He, X and Hu, D}, title = {Factors influencing user's health information discernment abilities in online health communities: based on SEM and fsQCA.}, journal = {Frontiers in public health}, volume = {12}, number = {}, pages = {1379094}, pmid = {39351031}, issn = {2296-2565}, mesh = {Humans ; Surveys and Questionnaires ; Female ; Male ; Adult ; *Internet ; Consumer Health Information ; Latent Class Analysis ; Information Seeking Behavior ; Fuzzy Logic ; Young Adult ; Middle Aged ; }, abstract = {INTRODUCTION: Online health communities have become the main source for people to obtain health information. However, the existence of poor-quality health information, misinformation, and rumors in online health communities increases the challenges in governing information quality. It not only affects users' health decisions but also undermines social stability. It is of great significance to explore the factors that affect users' ability to discern information in online health communities.<br><br>METHODS: This study integrated the Stimulus-Organism-Response Theory, Information Ecology Theory and the Mindsponge Theory to constructed a model of factors influencing users' health information discernment abilities in online health communities. A questionnaire was designed based on the variables in the model, and data was collected. Utilizing Structural Equation Modeling (SEM) in conjunction with fuzzy-set Qualitative Comparative Analysis (fsQCA), the study analyzed the complex causal relationships among stimulus factors, user perception, and the health information discernment abilities.<br><br>RESULTS: The results revealed that the dimensions of information, information environment, information technology, and information people all positively influenced health information discernment abilities. Four distinct configurations were identified as triggers for users' health information discernment abilities. The core conditions included information source, informational support, technological security, technological facilitation, and perceived risk. It was also observed that information quality and emotional support can act as substitutes for one another, as can informational support and emotional support.<br><br>DISCUSSION: This study provides a new perspective to study the influencing factors of health information discernment abilities of online health community users. It can provide experiences and references for online health community information services, information resource construction and the development of users' health information discernment abilities.}, }
@article {pmid39349447, year = {2024}, author = {Zhou, L and Wu, S and Chen, Y and Huang, R and Cheng, B and Mao, Q and Liu, T and Liu, Y and Zhao, K and Pan, H and Yu, C and Gao, X and Luo, L and Zhang, Q}, title = {Multi-omics analyzes of Rosa gigantea illuminate tea scent biosynthesis and release mechanisms.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {8469}, pmid = {39349447}, issn = {2041-1723}, mesh = {*Rosa/genetics/metabolism ; *Volatile Organic Compounds/metabolism ; *Odorants/analysis ; *Genome, Plant ; *Gene Expression Regulation, Plant ; Gene Regulatory Networks ; Genomics/methods ; Eugenol/analogs &amp; derivatives/metabolism ; Plant Proteins/genetics/metabolism ; Pollination ; Multiomics ; }, abstract = {Rose is an important ornamental crop cultivated globally for perfume production. However, our understanding of the mechanisms underlying scent production and molecular breeding for fragrance is hindered by the lack of a reference genome for tea roses. We present the first complete telomere-to-telomere (T2T) genome of Rosa gigantea, with high quality (QV > 60), including detailed characterization of the structural features of repetitive regions. The expansion of genes associated with phenylpropanoid biosynthesis may account for the unique tea scent. We uncover the release rhythm of aromatic volatile organic compounds and their gene regulatory networks through comparative genomics and time-ordered gene co-expression networks. Analyzes of eugenol homologs demonstrate how plants attract pollinators using specialized phenylpropanoids in specific tissues. This study highlights the conservation and utilization of genetic diversity from wild endangered species through multi-omics approaches, providing a scientific foundation for enhancing rose fragrance via de novo domestication.}, }
@article {pmid39346055, year = {2024}, author = {Knobloch, S and Salimi, F and Buaya, A and Ploch, S and Thines, M}, title = {RAPiD: a rapid and accurate plant pathogen identification pipeline for on-site nanopore sequencing.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e17893}, pmid = {39346055}, issn = {2167-8359}, mesh = {*Nanopore Sequencing/methods ; Metagenomics/methods ; Plant Diseases/microbiology ; Bacteria/genetics/isolation &amp; purification/classification ; Sequence Analysis, DNA/methods ; Fungi/genetics/isolation &amp; purification/classification ; Plants/microbiology ; Computational Biology/methods ; }, abstract = {Nanopore sequencing technology has enabled the rapid, on-site taxonomic identification of samples from anything and anywhere. However, sequencing errors, inadequate databases, as well as the need for bioinformatic expertise and powerful computing resources, have hampered the widespread use of the technology for pathogen identification in the agricultural sector. Here we present RAPiD, a lightweight and accurate real-time taxonomic profiling pipeline. Compared to other metagenomic profilers, RAPiD had a higher classification precision achieved through the use of a curated, non-redundant database of common agricultural pathogens and extensive quality filtering of alignments. On a fungal, bacterial and mixed mock community RAPiD was the only pipeline to detect all members of the communities. We also present a protocol for in-field sample processing enabling pathogen identification from plant sample to sequence within 3 h using low-cost equipment. With sequencing costs continuing to decrease and more high-quality reference genomes becoming available, nanopore sequencing provides a viable method for rapid and accurate pathogen identification in the field. A web implementation of the RAPiD pipeline for real-time analysis is available at https://agrifuture.senckenberg.de.}, }
@article {pmid39345378, year = {2025}, author = {McDaniel, JH and Patel, V and Olson, ND and He, HJ and He, Z and Cole, KD and Gooden, AA and Schmitt, A and Sikkink, K and Sedlazeck, FJ and Doddapaneni, H and Jhangiani, SN and Muzny, DM and Gingras, MC and Mehta, H and Behera, S and Paulin, LF and Hastie, AR and Yu, HC and Weigman, V and Rojas, A and Kennedy, K and Remington, J and Salas-González, I and Sudkamp, M and Wiseman, K and Lajoie, BR and Levy, S and Jain, M and Akeson, S and Narzisi, G and Steinsnyder, Z and Reeves, C and Shelton, J and Kingan, SB and Lambert, C and Bayabyan, P and Wenger, AM and McLaughlin, IJ and Adamson, A and Kingsley, C and Wescott, M and Kim, Y and Paten, B and Park, J and Violich, I and Miga, KH and Gardner, J and McNulty, B and Rosen, GL and McCoy, R and Brundu, F and Sayyari, E and Scheffler, K and Truong, S and Catreux, S and Hannah, LC and Lipson, D and Benjamin, H and Iremadze, N and Soifer, I and Krieger, G and Eacker, S and Wood, M and Cross, E and Husar, G and Gross, S and Vernich, M and Kolmogorov, M and Ahmad, T and Keskus, A and Bryant, A and Thibaud-Nissen, F and Trow, J and Proszynski, J and Hirschberg, JW and Ryon, K and Mason, CE and Bhakta, MS and Zachary Sanborn, J and Munding, EM and Wagner, J and Xiao, C and Liss, AS and Zook, JM}, title = {Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39345378}, issn = {2692-8205}, support = {OT2 OD034190/OD/NIH HHS/United States ; U01 CA253405/CA/NCI NIH HHS/United States ; R01 HG011274/HG/NHGRI NIH HHS/United States ; S10 OD028587/OD/NIH HHS/United States ; U24 HG011853/HG/NHGRI NIH HHS/United States ; R35 GM133747/GM/NIGMS NIH HHS/United States ; R44 HG014126/HG/NHGRI NIH HHS/United States ; }, abstract = {The Genome in a Bottle Consortium (GIAB), hosted by the National Institute of Standards and Technology (NIST), is developing new matched tumor-normal samples, the first to be explicitly consented for public dissemination of genomic data and cell lines. Here, we describe a comprehensive genomic dataset from the first individual, HG008, including DNA from an adherent, epithelial-like pancreatic ductal adenocarcinoma (PDAC) tumor cell line and matched normal cells from duodenal and pancreatic tissues. Data for the tumor-normal matched samples comes from seventeen distinct state-of-the-art whole genome measurement technologies, including high depth short and long-read bulk whole genome sequencing (WGS), single cell WGS, and Hi-C, and karyotyping. In future publications, these data will be used by the GIAB Consortium to develop matched tumor-normal benchmarks for somatic variant detection. We expect these data to facilitate innovation for whole genome measurement technologies, de novo assembly of tumor and normal genomes, and bioinformatic tools to identify small and structural somatic mutations. This first-of-its-kind broadly consented open-access resource will facilitate further understanding of sequencing methods used for cancer biology.}, }
@article {pmid39345343, year = {2024}, author = {Halpern, B and Vörös, J and Mc Cartney, AM and Formenti, G and Mouton, A and ,  and ,  and ,  and , }, title = {The genome sequence of the Hungarian meadow viper, Vipera ursinii rakosiensis (Méhely, 1893).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {404}, pmid = {39345343}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Vipera ursinii rakosiensis (the Hungarian meadow viper; Chordata; Lepidosauria; Squamata; Viperidae). The genome sequence is 1,625.0 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 17.38 kilobases in length.}, }
@article {pmid39343505, year = {2024}, author = {Eneli, I and Heeren, FAN and Cason-Wilkerson, RL and Pratt, KJ}, title = {Metabolic and Bariatric Surgery for Adolescents.}, journal = {Pediatric clinics of North America}, volume = {71}, number = {5}, pages = {981-998}, doi = {10.1016/j.pcl.2024.06.007}, pmid = {39343505}, issn = {1557-8240}, mesh = {Humans ; Adolescent ; *Bariatric Surgery/methods ; *Pediatric Obesity/surgery ; Obesity, Morbid/surgery/psychology ; Gastrectomy/methods ; }, abstract = {Obesity is a chronic, complex, and multifactorial disease. Currently, approximately 6% have severe obesity with higher rates seen among racial/ethnic minority subgroups and in rural communities. Severe obesity is associated with cardiometabolic, psychologic, and musculoskeletal comorbidities. Metabolic and bariatric surgery is an effective treatment option for adolescents endorsed by major pediatric organizations. The most common procedure is the vertical sleeve gastrectomy. Pre-operative evaluation includes an in-depth medical, nutrition, physical activity and psychosocial assessment, with a care plan developed by a multidicplinary team with the adolescent and caregiver. The post-operative plan should include monitoring for surgical complications, weight regain, micronutrient deficiencies, psychologic challenges, and transition to adult care.}, }
@article {pmid39341239, year = {2024}, author = {Adomako, MO and Jin, L and Li, C and Liu, J and Adu, D and Seshie, VI and Yu, FH}, title = {Mechanisms underpinning microplastic effects on the natural climate solutions of wetland ecosystems.}, journal = {The Science of the total environment}, volume = {954}, number = {}, pages = {176491}, doi = {10.1016/j.scitotenv.2024.176491}, pmid = {39341239}, issn = {1879-1026}, abstract = {Wetland ecosystems are vital carbon dioxide (CO2) sinks, offering significant nature-based solutions for global climate mitigation. However, the recent influx of microplastic (MP) into wetlands substantially impacts key drivers (e.g., plants and microorganisms) underpinning these wetland functions. While MP-induced greenhouse gas (GHG) emissions and effects on soil organic carbon (SOC) mineralization potentially threaten the long-term wetland C-climate feedbacks, the exact mechanisms and linkage are unclear. This review provides a conceptual framework to elaborate on the interplay between MPs, wetland ecosystems, and the atmospheric milieu. We also summarize published studies that validate possible MP impacts on natural climate solutions of wetlands, as well as provide extensive elaboration on underlying mechanisms. We briefly highlight the relationships between MP influx, wetland degradation, and climate change and conclude by identifying key gaps for future research priorities. Globally, plastic production, MP entry into aquatic systems, and wetland degradation-related emissions are predicted to increase. This means that MP-related emissions and wetland-climate feedback should be addressed in the context of the UN Paris Climate Agreement on net-zero emissions by 2050. This overview serves as a wake-up call on the alarming impacts of MPs on wetland ecosystems and urges a global reconsideration of nature-based solutions in the context of climate mitigation.}, }
@article {pmid39340701, year = {2024}, author = {Gang, J and Ping, Y and Du, C}, title = {Anti-Magnaporthe oryzae Activity of Streptomyces bikiniensis HD-087 In Vitro and Bioinformatics Analysis of Polyketide Synthase Gene pksL.}, journal = {Current microbiology}, volume = {81}, number = {11}, pages = {379}, pmid = {39340701}, issn = {1432-0991}, support = {32172468//National Natural Science Foundation of China/ ; }, mesh = {*Polyketide Synthases/genetics/metabolism ; *Streptomyces/genetics/metabolism/enzymology ; *Computational Biology ; *Multigene Family ; Bacterial Proteins/genetics/metabolism ; Erythromycin/pharmacology ; Antifungal Agents/pharmacology/metabolism ; Polyketides/metabolism/pharmacology ; Anti-Bacterial Agents/pharmacology ; Molecular Docking Simulation ; Ascomycota ; }, abstract = {Streptomyces bikiniensis HD-087 is capable of synthesizing various antimicrobial substances to counter the detrimental effects of hazardous microorganisms. To elucidate whether it produces polyketide antibiotics and the synthesis mechanism of antibiotic substances, the metabolites and related genes of S. bikiniensis HD-087 were analyzed through LC-MS, anti-Magnaporthe oryzae activity detection, and bioinformatics approaches. The result indicated that the strain HD-087 could produce erythromycin, a polyketide antibiotic. The inhibitory zones of the fermentation supernatant of strain HD-087 and methanol solution of erythromycin extract against M. oryzae were 40.84 ± 0.68 mm and 33.18 ± 0.81 mm, respectively. The IC50 value of erythromycin extract for inhibiting spore germination of erythromycin extract was 220.43 μg/mL. There are two polyketide synthesis gene clusters in the genome of strain HD-087, namely t1pks-nrps and t3pks-lantipeptide-t1pks-nrps. The key gene pksL in the t3pks-lantipeptide-t1pks-nrps gene cluster was predicted. The results suggested that it encodes a stable, hydrophilic, and acidic protein, mainly composed of α-helix and random coil. The PksL protein contains dehydrogenase (DH), ketone reductase (KR), acyl carrier protein (ACP), and ketone synthase (KS) domains. Moreover, it can form interaction networks with 11 proteins containing domains, such as polyketide synthase and ACP synthase. The molecular docking between PksL and acetyl-CoA is stable and strong, suggesting that PksL protein could catalyze the synthesis of polyketides with CoA as a substrate. This study provides a theoretical basis for further exploring the polyketides synthesis mechanism and developing antifungal metabolites in S. bikiniensis HD-087.}, }
@article {pmid39337302, year = {2024}, author = {Romano Spica, V and Volpini, V and Valeriani, F and Carotenuto, G and Arcieri, M and Platania, S and Castrignanò, T and Clementi, ME and Michetti, F}, title = {In Silico Predicting the Presence of the S100B Motif in Edible Plants and Detecting Its Immunoreactive Materials: Perspectives for Functional Foods, Dietary Supplements and Phytotherapies.}, journal = {International journal of molecular sciences}, volume = {25}, number = {18}, pages = {}, pmid = {39337302}, issn = {1422-0067}, mesh = {*Dietary Supplements ; *S100 Calcium Binding Protein beta Subunit/metabolism ; *Functional Food ; *Plants, Edible/chemistry ; Computer Simulation ; Amino Acid Motifs ; Phytotherapy/methods ; Computational Biology/methods ; Humans ; Fruit/chemistry/metabolism ; Phylogeny ; Plant Proteins/metabolism ; }, abstract = {The protein S100B is a part of the S100 protein family, which consists of at least 25 calcium-binding proteins. S100B is highly conserved across different species, supporting important biological functions. The protein was shown to play a role in gut microbiota eubiosis and is secreted in human breast milk, suggesting a physiological trophic function in newborn development. This study explores the possible presence of the S100B motif in plant genomes, and of S100B-like immunoreactive material in different plant extracts, opening up potential botanical uses for dietary supplementation. To explore the presence of the S100B motif in plants, a bioinformatic workflow was used. In addition, the immunoreactivity of S100B from vegetable and fruit samples was tested using an ELISA assay. The S100B motif was expected in silico in the genome of different edible plants belonging to the Viridiplantae clade, such as Durio zibethinus or Malus domestica and other medicinal species. S100B-like immunoreactive material was also detected in samples from fruits or leaves. The finding of S100B-like molecules in plants sheds new light on their role in phylogenesis and in the food chain. This study lays the foundation to elucidate the possible beneficial effects of plants or derivatives containing the S100B-like principle and their potential use in nutraceuticals.}, }
@article {pmid39332349, year = {2024}, author = {Sun, Q and Zhang, Z and Ping, Q and Wang, L and Li, Y}, title = {Insight into using multi-omics analysis to elucidate nitrogen removal mechanisms in a novel improved constructed rapid infiltration system: Functional gene and metabolite signatures.}, journal = {Water research}, volume = {267}, number = {}, pages = {122502}, doi = {10.1016/j.watres.2024.122502}, pmid = {39332349}, issn = {1879-2448}, mesh = {*Nitrogen/metabolism ; *Wastewater/chemistry ; Waste Disposal, Fluid/methods ; Denitrification ; Nitrification ; Metabolomics ; Metagenomics ; Ammonium Compounds/metabolism ; Multiomics ; }, abstract = {In this study, a laboratory-scale improved constructed rapid infiltration (imCRI) system with non-saturated and saturated layers was constructed, and corn cobs as solid carbon source were added to the saturated layer to enhance the removal of nitrogen. Combined analyses of metagenomics and metabolomics were conducted to elucidate the nitrogen removal mechanism in the imCRI system. The results showed that the hydraulic load significantly influenced the treatment performance of the imCRI system, and a hydraulic load of 1.25 m[3]/(m[2]⋅d) was recommended. Under optimal conditions, the imCRI system using simulated wastewater achieved average removal efficiencies of 97.8 % for chemical oxygen demand, 85.7 % for total nitrogen (TN), and 97.6 % for ammonia nitrogen. Metagenomic and metabolomic analyses revealed that besides nitrification and denitrification, dissimilatory nitrate reduction to ammonium (DNRA), anammox, etc., are also involved in nitrogen metabolism in the imCRI system. Although nitrification was the predominant pathway in the non-saturated layer, aerobic denitrification also occurred, accounting for 22.59 % of the TN removal. In the saturated layer, nitrogen removal was attributed to synergistic effects of denitrification, DNRA and anammox. Moreover, correlation analysis among nitrogen removal, functional genes and metabolites suggested that metabolites related to the tricarboxylic acid cycle generated from the glycolysis of corn cobs provided sufficient energy for denitrification. Our results can offer a promising technology for decentralized wastewater treatment with stringent nitrogen removal requirements, and provide a foundation for understanding the underlying nitrogen transformation and removal mechanism.}, }
@article {pmid39331699, year = {2024}, author = {Yang, Z and Shan, Y and Liu, X and Chen, G and Pan, Y and Gou, Q and Zou, J and Chang, Z and Zeng, Q and Yang, C and Kong, J and Sun, Y and Li, S and Zhang, X and Wu, WC and Li, C and Peng, H and Holmes, EC and Guo, D and Shi, M}, title = {VirID: Beyond Virus Discovery-An Integrated Platform for Comprehensive RNA Virus Characterization.}, journal = {Molecular biology and evolution}, volume = {41}, number = {10}, pages = {}, pmid = {39331699}, issn = {1537-1719}, support = {82341118//National Natural Science Foundation of China/ ; 2022A1515011854//Natural Science Foundation of Guangdong Province of China/ ; JCYJ20210324124414040//Shenzhen Science and Technology Program/ ; //Hong Kong Innovation and Technology Fund (ITF/ ; GZNL2023A01001//Major Project of Guangzhou National Laboratory/ ; 2019ZT08Y464//Guangdong Province "Pearl River Talent Plan" Innovation, Entrepreneurship Team Project/ ; ZDSYS20220606100803007//Fund of Shenzhen Key Laboratory/ ; GNT2017197//NHMRC (Australia) Investigator Award/ ; //Innovation and Technology Commission, Hong Kong Special Administrative Region, China/ ; }, mesh = {*RNA Viruses/genetics ; *Software ; *Metagenomics/methods ; *Phylogeny ; Humans ; RNA-Dependent RNA Polymerase/genetics ; Computational Biology/methods ; }, abstract = {RNA viruses exhibit vast phylogenetic diversity and can significantly impact public health and agriculture. However, current bioinformatics tools for viral discovery from metagenomic data frequently generate false positive virus results, overestimate viral diversity, and misclassify virus sequences. Additionally, current tools often fail to determine virus-host associations, which hampers investigation of the potential threat posed by a newly detected virus. To address these issues we developed VirID, a software tool specifically designed for the discovery and characterization of RNA viruses from metagenomic data. The basis of VirID is a comprehensive RNA-dependent RNA polymerase database to enhance a workflow that includes RNA virus discovery, phylogenetic analysis, and phylogeny-based virus characterization. Benchmark tests on a simulated data set demonstrated that VirID had high accuracy in profiling viruses and estimating viral richness. In evaluations with real-world samples, VirID was able to identify RNA viruses of all types, but also provided accurate estimations of viral genetic diversity and virus classification, as well as comprehensive insights into virus associations with humans, animals, and plants. VirID therefore offers a robust tool for virus discovery and serves as a valuable resource in basic virological studies, pathogen surveillance, and early warning systems for infectious disease outbreaks.}, }
@article {pmid39331660, year = {2024}, author = {Pasqualini, J and Facchin, S and Rinaldo, A and Maritan, A and Savarino, E and Suweis, S}, title = {Emergent ecological patterns and modelling of gut microbiomes in health and in disease.}, journal = {PLoS computational biology}, volume = {20}, number = {9}, pages = {e1012482}, pmid = {39331660}, issn = {1553-7358}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; Models, Biological ; Computational Biology ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Recent advancements in next-generation sequencing have revolutionized our understanding of the human microbiome. Despite this progress, challenges persist in comprehending the microbiome's influence on disease, hindered by technical complexities in species classification, abundance estimation, and data compositionality. At the same time, the existence of macroecological laws describing the variation and diversity in microbial communities irrespective of their environment has been recently proposed using 16s data and explained by a simple phenomenological model of population dynamics. We here investigate the relationship between dysbiosis, i.e. in unhealthy individuals there are deviations from the "regular" composition of the gut microbial community, and the existence of macro-ecological emergent law in microbial communities. We first quantitatively reconstruct these patterns at the species level using shotgun data, and addressing the consequences of sampling effects and statistical errors on ecological patterns. We then ask if such patterns can discriminate between healthy and unhealthy cohorts. Concomitantly, we evaluate the efficacy of different statistical generative models, which incorporate sampling and population dynamics, to describe such patterns and distinguish which are expected by chance, versus those that are potentially informative about disease states or other biological drivers. A critical aspect of our analysis is understanding the relationship between model parameters, which have clear ecological interpretations, and the state of the gut microbiome, thereby enabling the generation of synthetic compositional data that distinctively represent healthy and unhealthy individuals. Our approach, grounded in theoretical ecology and statistical physics, allows for a robust comparison of these models with empirical data, enhancing our understanding of the strengths and limitations of simple microbial models of population dynamics.}, }
@article {pmid39331576, year = {2024}, author = {Qiao, B and Wang, S and Hou, M and Chen, H and Zhou, Z and Xie, X and Pang, S and Yang, C and Yang, F and Zou, Q and Sun, S}, title = {Identifying nucleotide-binding leucine-rich repeat receptor and pathogen effector pairing using transfer-learning and bilinear attention network.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {10}, pages = {}, pmid = {39331576}, issn = {1367-4811}, support = {62273086//National Natural Science Foundation of China/ ; }, mesh = {*Deep Learning ; *NLR Proteins/metabolism ; *Computational Biology/methods ; Algorithms ; }, abstract = {MOTIVATION: Nucleotide-binding leucine-rich repeat (NLR) family is a class of immune receptors capable of detecting and defending against pathogen invasion. They have been widely used in crop breeding. Notably, the correspondence between NLRs and effectors (CNE) determines the applicability and effectiveness of NLRs. Unfortunately, CNE data is very scarce. In fact, we've found a substantial 91 291 NLRs confirmed via wet experiments and bioinformatics methods but only 387 CNEs are recognized, which greatly restricts the potential application of NLRs.<br><br>RESULTS: We propose a deep learning algorithm called ProNEP to identify NLR-effector pairs in a high-throughput manner. Specifically, we conceptualized the CNE prediction task as a protein-protein interaction (PPI) prediction task. Then, ProNEP predicts the interaction between NLRs and effectors by combining the transfer learning with a bilinear attention network. ProNEP achieves superior performance against state-of-the-art models designed for PPI predictions. Based on ProNEP, we conduct extensive identification of potential CNEs for 91&#xa0;291 NLRs. With the rapid accumulation of genomic data, we expect that this tool will be widely used to predict CNEs in new species, advancing biology, immunology, and breeding.<br><br>The ProNEP is available at http://nerrd.cn/#/prediction. The project code is available at https://github.com/QiaoYJYJ/ProNEP.}, }
@article {pmid39328967, year = {2024}, author = {Dey, B and Ferdous, J and Ahmed, R}, title = {Comprehensive stomata image dataset of Sundarbans Mangrove and Ratargul Swamp forest tree species in Bangladesh.}, journal = {Data in brief}, volume = {57}, number = {}, pages = {110908}, pmid = {39328967}, issn = {2352-3409}, abstract = {Plants' leaf stomata are crucial for various scientific research, including identifying species, studying ecology, conserving ecosystems, improving agriculture, and advancing the field of deep learning. This dataset, containing 1083 images, encompasses 11 species from two distinct locations in Bangladesh: nine from the Sundarbans mangrove forest and two from the Ratargul Swamp Forest. It is a valuable tool for refining machine learning algorithms that specialize in detecting stomata and categorizing species accurately. Researchers can explore a deeper understanding of plant physiology, adaptation mechanisms, and environmental interactions by employing pattern recognition, deep learning, and feature extraction techniques. Additionally, this dataset could be a potential tool for enhancing research in macroscopic metamaterials, extending its impact beyond traditional biological studies into interdisciplinary fields of technology and material science.}, }
@article {pmid39326744, year = {2024}, author = {Wang, Y and Feng, Z and Ghani, MI and Wang, Q and Zeng, L and Yang, X and Zhang, X and Chen, C and Li, S and Cao, P and Chen, X and Cernava, T}, title = {Co-exposure to microplastics and soil pollutants significantly exacerbates toxicity to crops: Insights from a global meta and machine-learning analysis.}, journal = {The Science of the total environment}, volume = {954}, number = {}, pages = {176490}, doi = {10.1016/j.scitotenv.2024.176490}, pmid = {39326744}, issn = {1879-1026}, mesh = {*Soil Pollutants/toxicity ; *Microplastics/toxicity ; *Crops, Agricultural ; *Machine Learning ; Environmental Monitoring/methods ; Soil/chemistry ; Environmental Pollution/statistics &amp; numerical data ; }, abstract = {Environmental contamination of microplastics (MPs) is ubiquitous worldwide, and co-contamination of arable soils with MPs and other pollutants is of increasing concern, and may lead to unexpected consequences on crop production. However, the overall implications of this combined effect, whether beneficial or detrimental, remain a subject of current debate. Here, we conducted a global meta and machine-learning analysis to evaluate the effects of co-exposure to MPs and other pollutants on crops, utilizing 3346 biological endpoints derived from 68 different studies. Overall, compared with control groups that only exposure to conventional soil contaminants, co-exposure significantly exacerbated toxicity to crops, particularly with MPs intensifying adverse effects on crop morphology, oxidative damage, and photosynthetic efficiency. Interestingly, our analysis demonstrated a significant reduction in the accumulation of pollutants in the crop due to the presence of MPs. In addition, the results revealed that potential adverse effects were primarily associated with crop species, MPs mass concentration, and exposure duration. Our study reaffirms the substantial consequences of MPs as emerging pollutants on crops within the context of integrated pollution, providing novel insights into improving sustainability in agro-ecosystems.}, }
@article {pmid39326182, year = {2024}, author = {Li, D and Ping, Q and Mo, R and Guo, W and Zhang, S and Wang, L and Li, Y}, title = {Revealing synergistic mechanisms of biochar-assisted microbial electrolysis cells in enhancing the anaerobic digestion performance of waste activated sludge: Extracellular polymeric substances characterization, enzyme activity assay, and multi-omics analysis.}, journal = {Water research}, volume = {267}, number = {}, pages = {122501}, doi = {10.1016/j.watres.2024.122501}, pmid = {39326182}, issn = {1879-2448}, mesh = {*Sewage/microbiology ; Anaerobiosis ; *Extracellular Polymeric Substance Matrix/metabolism ; Charcoal/chemistry ; Waste Disposal, Fluid/methods ; Electrolysis ; Methane/metabolism ; Multiomics ; }, abstract = {Although biochar (BC)-assisted microbial electrolysis cells (MEC) has been shown to improve anaerobic digestion (AD) performance of waste activated sludge (WAS), the underlying mechanisms remain unclear. This study conducted an in-depth investigation into the mechanism based on analyses of extracellular polymeric substances (EPS) characteristics, enzyme activities and multi-omics. The results showed that compared with the control group, methane production improved by 16.73 %, 21.32 %, and 29.37 % in the BC, MEC, and BC-assisted MEC (BC-MEC) groups, respectively. The reconfiguration of the protein secondary structure increased the hydrophobicity of the EPS, thereby promoting microbial aggregation. In addition, partial least-squares path modeling (PLS-PM) and mantel test based on the enzyme activity and multi-omics analyses revealed that the promotional effect of MEC on the hydrolysis of WAS was superior to that of BC, while BC was more advantageous in promoting electron transfer and biofilm formation regulated by quorum sensing. The synergistic effects of BC and MEC were exemplified in the BC-MEC group. g_norank_Aminicenantales responsible for the hydrolysis of WAS was enriched (29.6 %), and the activities of hydrolytic enzymes including α-glucosidases and proteases were increased by 29.1 % and 43.6 %, respectively. Further, the expressions of genes related to acyl homoserine lactones (AHLs) and diffusible signal factor (DSF) in quorum sensing systems, as well as the genes related to hydrogenase involved in electron transfer (mbhJKL, hyfB-JR, hypA-F, and hoxFHUY), were up-regulated in the BC-MEC group. This facilitated electron transfer and microbial communication, consequently enhancing methane production. This research significantly advances the understanding of the mechanism by which BC-assisted MEC enhances AD performance and provides valuable insights into strategies for improving energy recovery from WAS.}, }
@article {pmid39325874, year = {2024}, author = {Zhu, Y and Chen, G and Sun, Y}, title = {VirTAXA: enhancing RNA virus taxonomic classification with remote homology search and tree-based validation.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {10}, pages = {}, pmid = {39325874}, issn = {1367-4811}, support = {11206819//City University of Hong Kong, Hong Kong Research Grants Council/ ; //Hong Kong Innovation and Technology Fund/ ; }, mesh = {*RNA Viruses/genetics/classification ; *Software ; RNA, Viral/genetics ; Phylogeny ; Sequence Analysis, RNA/methods ; Genome, Viral ; Algorithms ; Computational Biology/methods ; }, abstract = {SUMMARY: RNA viruses are ubiquitous across a broad spectrum of ecosystems. Therefore, beyond their significant implications for public health, RNA viruses are also key players in ecological processes. High-through sequencing has accelerated the discovery of RNA viruses. Nevertheless, many of these viruses lack taxonomic annotation, posing a challenge to functional inference and evolutionary study. In particular, virus classification at the genus level remains difficult due to the limited reference data and ambiguous boundaries between some closely related genera. We introduce VirTAXA, a robust classification tool that combines remote homology search and tree-based validation to enhance the genus-level taxonomic classification of RNA viruses. VirTAXA is able to predict the genus label of an assembled viral contig and provide evidence type for each prediction. It achieves comparable accuracy to state-of-the-art methods while assigning genus labels to a greater number of sequences. Specifically, on the Global Ocean RNA metatranscriptomic data, VirTAXA can assign genus labels for 18% more contigs than the second-best classification tool. Furthermore, we demonstrated that VirTAXA can be conveniently extended to other types of viruses.<br><br>The source code and data of VirTAXA are available via https://github.com/JudithEllyn/VirTAXA.}, }
@article {pmid39323974, year = {2022}, author = {Boyes, D and Crowley, LM and ,  and ,  and ,  and ,  and ,  and Skojec, C and Plotkin, D and Kawahara, AY and , }, title = {The genome sequence of the 6-spot burnet, Zygaena filipendulae (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {197}, pmid = {39323974}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Zygaena filipendulae (6-spot burnet; Arthropoda; Insecta; Lepidoptera; Zygaenidae). The genome sequence is 365.9 megabases in span. The majority of the assembly (99.99%) is scaffolded into 31 chromosomal pseudomolecules, with the W and Z sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 15.6 kilobases in length. Gene annotation of this assembly on Ensembl has identified 12,493 protein coding genes.}, }
@article {pmid39323166, year = {2024}, author = {Lin, ML and Hu, ZQ and Peng, WH and Ye, WL and Zhang, CL and Huang, XR and Chen, S and Gui, HR}, title = {[Pollution Assessment and Source Apportionment of Heavy Metals in the Surrounding Soil of Typical Mining Areas in Tongling, Anhui Province].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {45}, number = {9}, pages = {5494-5505}, doi = {10.13227/j.hjkx.202307274}, pmid = {39323166}, issn = {0250-3301}, abstract = {To study the level of heavy metal pollution and ecological risks in the soil around typical mining areas in Tongling, a total of 150 soil samples were collected from the study area. The content characteristics of 10 elements, namely, As, Cd, Cr, Cu, Hg, Mn, Ni, Pb, Fe, and Zn, in the soils were analyzed. Methods including enrichment factor, the geo-accumulation index, single-factor pollution index, Nemero comprehensive pollution index, and potential ecological risk index were used to evaluate the pollution status of heavy metals in the soil of the study area. The pollution sources of heavy metals in the soil were also analyzed using correlation analysis, cluster analysis, and principal component analysis. The results showed that except for Cr and Fe, the average contents of the other eight heavy metal elements were higher than the soil background values in the study area. Pb, Zn, As, Cu, and Cd had a high degree of variation and were significantly affected by external interference. The spatial distribution showed that both Cr and Ni showed a decreasing trend from the edge to the central region, whereas the other eight heavy metals showed a decreasing trend from the central region to the surrounding areas. The pollution level of Cd and Cu in the soil of the research area was relatively severe. The overall ecological risk was at a medium to low level. Cd and Hg were the main contributing factors. As, Cd, Cu, Fe, Mn, Pb, and Zn mainly came from agricultural, industrial, and transportation sources, whereas Cr and Ni were mainly from natural sources. However, the sources of Hg were relatively complex. The research results can provide a scientific basis for the prevention and control of soil heavy metal pollution in metal mining areas, as well as the remediation of mine pollution.}, }
@article {pmid39321538, year = {2024}, author = {Cao, J and Lei, Y and Li, W and Jiang, X and Li, M}, title = {Coupled digital visualization and multi-omics uncover neurobehavioral dysfunction in zebrafish induced by resorcinol bis(diphenylphosphate).}, journal = {Environment international}, volume = {192}, number = {}, pages = {109023}, doi = {10.1016/j.envint.2024.109023}, pmid = {39321538}, issn = {1873-6750}, mesh = {Animals ; *Zebrafish/physiology ; Water Pollutants, Chemical/toxicity ; Blood-Brain Barrier/drug effects ; Resorcinols/toxicity ; Brain/drug effects/metabolism ; Behavior, Animal/drug effects ; Gastrointestinal Microbiome/drug effects ; Multiomics ; }, abstract = {Resorcinol bis(diphenylphosphate) (RDP) is an emerging pollutant that has been frequently detected in aquatic environments, although its toxicity is poorly characterized. To understand how RDP affects the neural system, two-month-old zebrafish were exposed to RDP at concentrations of 0.1 and 10 μg/L for 60 days. Following exposure, behavioral assessments were conducted, revealing the emergence of anxiety-like symptoms and memory deficits among the adult fish exposed to RDP, especially at the higher concentration. The increased blood-brain barrier (BBB) permeability (4.67-5.58-fold higher than the control group), reduced expression of tight junction proteins and the rapid brain RDP bioaccumulation (15.63 ± 2.34 ng/g wet weight) indicated the neurotoxicity of RDP. Excess reactive oxygen species synthesis (2.20-2.50-fold) was induced by RDP, leading to mitochondrial dysfunction and decreased production of neurotransmitters in the brain, specifically serotonin (5-HT; 16.3 %) and dopamine (DA; 18.1 %). Metabolomic analysis revealed that the low-toxicity RDP dose up-regulated lipid-related metabolites, while the high-toxicity dose up-regulated arachidonic acid metabolism and disrupted amino acid metabolism, including tryptophan and tyrosine metabolism related to dopaminergic and serotonergic pathways. The dysregulation of genes in various cellular processes was identified by transcriptomics, mainly involved in cell adhesion molecules and gap junctions, and oxidative phosphorylation, which were directly associated with BBB permeability and oxidative stress, respectively. Correlation analysis of microbiome-metabolite-host links built a mechanistic hypothesis for alterations in gut microbiota (Actinobacteriota and Proteobacteria) induced by high-dose RDP leading to the alteration of tryptophan, tyrosine, and arachidonic acid metabolism, decreasing the production of 5-HT and DA through the gut-brain axis. This study provides valuable insights into the mechanism underlying RDP-induced neurotoxicity in zebrafish, which can inform ecological risk assessments.}, }
@article {pmid39320588, year = {2024}, author = {Oroud, IM}, title = {The implications of climate change on freshwater resources in the arid and semiarid Mediterranean environments using hydrological modeling, GIS tools, and remote sensing.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {10}, pages = {979}, pmid = {39320588}, issn = {1573-2959}, mesh = {*Climate Change ; *Environmental Monitoring/methods ; *Hydrology ; *Remote Sensing Technology ; *Geographic Information Systems ; Fresh Water/chemistry ; Groundwater/chemistry ; Models, Theoretical ; Mediterranean Region ; Desert Climate ; Water Resources ; }, abstract = {Precipitation partitioning in arid and semiarid environments is not well understood due to scanty precipitation, its temporal distribution, and the lack/absence of adequate measurements of the hydrometeorological components. Simulation methods have the potential to bridge the data gap, thereby providing a window to estimate the water balance components. The present investigation evaluates the water balance components of a typical watershed situated in the southeastern Mediterranean for the period 1979 through 2019 using daily meteorological data and a grid spacing of 250 m. Generated runoff results were commensurate with corresponding values obtained using the SWAT model. Computed groundwater recharge is also compatible with recharge values calculated using the chloride mass balance method. Results show that average runoff and groundwater recharge for the entire period was ⁓24 mm a[-1] and 19 mm a[-1], giving a precipitation ratio of 9.5% and 7.5%, respectively. Substantial interannual variability in the water balance components was observed during the study period which reflected the significant precipitation fluctuations typifying the Eastern Mediterranean. Results show that the period extending from 1998/1999 through 2018/2019 witnessed an 18% drop in annual precipitation, while surface runoff and groundwater recharge experienced a reduction of ⁓34% and ⁓67%, respectively. Although groundwater recharge is a complex function of numerous meteorological and geological factors, the NDVI can provide an excellent indicator of groundwater recharge in marginal Mediterranean environments. This is highly beneficial in areas where climate records are scanty or absent. The presented results emphasize the significant impacts of global warming and aridification on the future availability of water resources in the semiarid marginal climates in the Eastern Mediterranean and point out clearly that water resources in this area will become scarcer, leading to multiple security threats at national and regional levels.}, }
@article {pmid39313745, year = {2024}, author = {Dabrowski, JK and Yang, EJ and Crofts, SJC and Hillary, RF and Simpson, DJ and McCartney, DL and Marioni, RE and Kirschner, K and Latorre-Crespo, E and Chandra, T}, title = {Probabilistic inference of epigenetic age acceleration from cellular dynamics.}, journal = {Nature aging}, volume = {4}, number = {10}, pages = {1493-1507}, pmid = {39313745}, issn = {2662-8465}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Epigenesis, Genetic ; *Aging/genetics ; *DNA Methylation ; CpG Islands/genetics ; Genome-Wide Association Study ; Aged ; Female ; Male ; Middle Aged ; Models, Statistical ; }, abstract = {The emergence of epigenetic predictors was a pivotal moment in geroscience, propelling the measurement and concept of biological aging into a quantitative era; however, while current epigenetic clocks show strong predictive power, they are data-driven in nature and are not based on the underlying biological mechanisms driving methylation dynamics. We show that predictions of these clocks are susceptible to several confounding non-age-related phenomena that make interpretation of these estimates and associations difficult. To address these limitations, we developed a probabilistic model describing methylation transitions at the cellular level. Our approach reveals two measurable components, acceleration and bias, which directly reflect perturbations of the underlying cellular dynamics. Acceleration is the proportional increase in the speed of methylation transitions across CpG sites, whereas bias corresponds to global changes in methylation levels. Using data from 15,900 participants from the Generation Scotland study, we develop a robust inference framework and show that these are two distinct processes confounding current epigenetic predictors. Our results show improved associations of acceleration and bias with physiological traits known to impact healthy aging, such as smoking and alcohol consumption, respectively. Furthermore, a genome-wide association study of epigenetic age acceleration identified seven genomic loci.}, }
@article {pmid39312537, year = {2024}, author = {Malamud, J and Guloksuz, S and van Winkel, R and Delespaul, P and De Hert, MAF and Derom, C and Thiery, E and Jacobs, N and Rutten, BPF and Huys, QJM}, title = {Characterizing the dynamics, reactivity and controllability of moods in depression with a Kalman filter.}, journal = {PLoS computational biology}, volume = {20}, number = {9}, pages = {e1012457}, pmid = {39312537}, issn = {1553-7358}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Affect/physiology ; *Depression/physiopathology ; *Computational Biology ; Algorithms ; Ecological Momentary Assessment ; Psychometrics/methods ; Male ; Female ; }, abstract = {BACKGROUND: Mood disorders involve a complex interplay between multifaceted internal emotional states, and complex external inputs. Dynamical systems theory suggests that this interplay between aspects of moods and environmental stimuli may hence determine key psychopathological features of mood disorders, including the stability of mood states, the response to external inputs, how controllable mood states are, and what interventions are most likely to be effective. However, a comprehensive computational approach to all these aspects has not yet been undertaken.<br><br>METHODS: Here, we argue that the combination of ecological momentary assessments (EMA) with a well-established dynamical systems framework-the humble Kalman filter-enables a comprehensive account of all these aspects. We first introduce the key features of the Kalman filter and optimal control theory and their relationship to aspects of psychopathology. We then examine the psychometric and inferential properties of combining EMA data with Kalman filtering across realistic scenarios. Finally, we apply the Kalman filter to a series of EMA datasets comprising over 700 participants with and without symptoms of depression.<br><br>RESULTS: The results show a naive Kalman filter approach performs favourably compared to the standard vector autoregressive approach frequently employed, capturing key aspects of the data better. Furthermore, it suggests that the depressed state involves alterations to interactions between moods; alterations to how moods responds to external inputs; and as a result an alteration in how controllable mood states are. We replicate these findings qualitatively across datasets and explore an extension to optimal control theory to guide therapeutic interventions.<br><br>CONCLUSIONS: Mood dynamics are richly and profoundly altered in depressed states. The humble Kalman filter is a well-established, rich framework to characterise mood dynamics. Its application to EMA data is valid; straightforward; and likely to result in substantial novel insights both into mechanisms and treatments.}, }
@article {pmid39309423, year = {2023}, author = {Boyes, D and Blaxter, ML and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Beautiful Hook-tip, Laspeyria flexula (Denis &amp; Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {529}, pmid = {39309423}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Laspeyria flexula (the Beautiful Hook-tip; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 450.9 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.58 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,281 protein coding genes.}, }
@article {pmid39309224, year = {2024}, author = {Boyes, D and Lees, DC and Wawman, DC and ,  and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Blue-bordered Carpet moth Plemyria rubiginata (Denis &amp; Schiffermüller) 1775.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {271}, pmid = {39309224}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Plemyria rubiginata (the Blue-bordered Carpet moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 356.2 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 17.64 kilobases in length.}, }
@article {pmid39309222, year = {2024}, author = {Boyes, D and Wawman, DC and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Figure of Eighty moth Tethea ocularis Linnaeus, 1767.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {348}, pmid = {39309222}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Tethea ocularis (the Figure of Eighty; Arthropoda; Insecta; Lepidoptera; Drepanidae). The genome sequence is 339.1 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.28 kilobases in length.}, }
@article {pmid39304763, year = {2025}, author = {Pakkir Shah, AK and Walter, A and Ottosson, F and Russo, F and Navarro-Diaz, M and Boldt, J and Kalinski, JJ and Kontou, EE and Elofson, J and Polyzois, A and González-Marín, C and Farrell, S and Aggerbeck, MR and Pruksatrakul, T and Chan, N and Wang, Y and Pöchhacker, M and Brungs, C and Cámara, B and Caraballo-Rodríguez, AM and Cumsille, A and de Oliveira, F and Dührkop, K and El Abiead, Y and Geibel, C and Graves, LG and Hansen, M and Heuckeroth, S and Knoblauch, S and Kostenko, A and Kuijpers, MCM and Mildau, K and Papadopoulos Lambidis, S and Portal Gomes, PW and Schramm, T and Steuer-Lodd, K and Stincone, P and Tayyab, S and Vitale, GA and Wagner, BC and Xing, S and Yazzie, MT and Zuffa, S and de Kruijff, M and Beemelmanns, C and Link, H and Mayer, C and van der Hooft, JJJ and Damiani, T and Pluskal, T and Dorrestein, P and Stanstrup, J and Schmid, R and Wang, M and Aron, A and Ernst, M and Petras, D}, title = {Statistical analysis of feature-based molecular networking results from non-targeted metabolomics data.}, journal = {Nature protocols}, volume = {20}, number = {1}, pages = {92-162}, pmid = {39304763}, issn = {1750-2799}, support = {EXC 2124//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; U24 DK133658/DK/NIDDK NIH HHS/United States ; R03 DE021437/DE/NIDCR NIH HHS/United States ; }, mesh = {Chromatography, Liquid/methods ; Data Interpretation, Statistical ; *Metabolomics/methods ; Software ; Tandem Mass Spectrometry/methods ; }, abstract = {Feature-based molecular networking (FBMN) is a popular analysis approach for liquid chromatography-tandem mass spectrometry-based non-targeted metabolomics data. While processing liquid chromatography-tandem mass spectrometry data through FBMN is fairly streamlined, downstream data handling and statistical interrogation are often a key bottleneck. Especially users new to statistical analysis struggle to effectively handle and analyze complex data matrices. Here we provide a comprehensive guide for the statistical analysis of FBMN results, focusing on the downstream analysis of the FBMN output table. We explain the data structure and principles of data cleanup and normalization, as well as uni- and multivariate statistical analysis of FBMN results. We provide explanations and code in two scripting languages (R and Python) as well as the QIIME2 framework for all protocol steps, from data clean-up to statistical analysis. All code is shared in the form of Jupyter Notebooks (https://github.com/Functional-Metabolomics-Lab/FBMN-STATS). Additionally, the protocol is accompanied by a web application with a graphical user interface (https://fbmn-statsguide.gnps2.org/) to lower the barrier of entry for new users and for educational purposes. Finally, we also show users how to integrate their statistical results into the molecular network using the Cytoscape visualization tool. Throughout the protocol, we use a previously published environmental metabolomics dataset for demonstration purposes. Together, the protocol, code and web application provide a complete guide and toolbox for FBMN data integration, cleanup and advanced statistical analysis, enabling new users to uncover molecular insights from their non-targeted metabolomics data. Our protocol is tailored for the seamless analysis of FBMN results from Global Natural Products Social Molecular Networking and can be easily adapted to other mass spectrometry feature detection, annotation and networking tools.}, }
@article {pmid39304543, year = {2024}, author = {Hossen, MF and Sultana, N}, title = {Landscape transition-induced ecological risk modeling using GIS and remote sensing techniques: a case of Saint Martin Island, Bangladesh.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {10}, pages = {964}, pmid = {39304543}, issn = {1573-2959}, mesh = {Bangladesh ; *Environmental Monitoring/methods ; *Remote Sensing Technology ; *Geographic Information Systems ; *Conservation of Natural Resources ; *Islands ; *Ecosystem ; Risk Assessment/methods ; Humans ; Bayes Theorem ; }, abstract = {Uncontrolled human activity and nature are causing the deterioration of Saint Martin Island, Bangladesh's only tropical island, necessitating sustainable land use strategies and ecological practices. Therefore, the present study measures the land use/cover transition from 1974 to 2021, predicts 2032 and 2042, and constructs the spatiotemporal features of the Landscape Ecological Risk Index based on land use changes. The study utilized Maximum Likelihood Classification (MLC) on Landsat images from 1974, 1988, 2001, 2013, and Sentinel 2B in 2021, achieving ≥ 80% accuracy. The MLP-MC approach was also used to predict 2032 and 2042 LULC change patterns. The eco-risk index was developed using landscape disturbance and vulnerability indices, Bayesian Kriging interpolation, and spatial autocorrelations to indicate spatial clustering. The research found that settlements increased from 2.06 to 28.62 ha between 1974 and 2021 and would cover 41.22 ha in 2042, causing considerable losses in agricultural areas, waterbodies, sand, coral reefs, and vegetation. The area under study showed a more uniform and homogenous environment as Shannon's diversity and evenness scores decreased. The ecological risk of Saint Martin Island increased from 4.31 to 31.05 ha between 1974 and 2042 due to natural and human factors like erosion, tidal bores, population growth, coral mining, habitat destruction, and intensive agricultural practices and tourism, primarily in Nazrul Para, Galachipa, and Western Dakhin Para. The findings will benefit St. Martin Island stakeholders and policymakers by providing insights into current and potential landscape changes and land eco-management.}, }
@article {pmid39303692, year = {2024}, author = {Crits-Christoph, A and Levy, JI and Pekar, JE and Goldstein, SA and Singh, R and Hensel, Z and Gangavarapu, K and Rogers, MB and Moshiri, N and Garry, RF and Holmes, EC and Koopmans, MPG and Lemey, P and Peacock, TP and Popescu, S and Rambaut, A and Robertson, DL and Suchard, MA and Wertheim, JO and Rasmussen, AL and Andersen, KG and Worobey, M and Débarre, F}, title = {Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic.}, journal = {Cell}, volume = {187}, number = {19}, pages = {5468-5482.e11}, pmid = {39303692}, issn = {1097-4172}, support = {U19 AI135995/AI/NIAID NIH HHS/United States ; R01 AI153044/AI/NIAID NIH HHS/United States ; T15 LM011271/LM/NLM NIH HHS/United States ; T32 AI007244/AI/NIAID NIH HHS/United States ; 75N93021C00015/AI/NIAID NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; U01 AI151812/AI/NIAID NIH HHS/United States ; R01 AI135992/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *COVID-19/epidemiology/virology ; *SARS-CoV-2/genetics/isolation &amp; purification ; *Animals, Wild/virology ; *Phylogeny ; Humans ; Pandemics ; }, abstract = {Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start of the COVID-19 pandemic was traced epidemiologically to the Huanan Seafood Wholesale Market. Here, we analyze environmental qPCR and sequencing data collected in the Huanan market in early 2020. We demonstrate that market-linked severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic diversity is consistent with market emergence and find increased SARS-CoV-2 positivity near and within a wildlife stall. We identify wildlife DNA in all SARS-CoV-2-positive samples from this stall, including species such as civets, bamboo rats, and raccoon dogs, previously identified as possible intermediate hosts. We also detect animal viruses that infect raccoon dogs, civets, and bamboo rats. Combining metagenomic and phylogenetic approaches, we recover genotypes of market animals and compare them with those from farms and other markets. This analysis provides the genetic basis for a shortlist of potential intermediate hosts of SARS-CoV-2 to prioritize for serological and viral sampling.}, }
@article {pmid39301440, year = {2024}, author = {Morales, HE and Groombridge, JJ and Tollington, S and Henshaw, S and Tatayah, V and Ruhomaun, K and van Oosterhout, C and Gilbert, MTP and ,  and ,  and ,  and , }, title = {The genome sequence of the Mauritius parakeet, Alexandrinus eques (formerly Psittacula eques) (A.Newton &amp; E. Newton, 1876).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {378}, pmid = {39301440}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Alexandrinus eques, formerly Psittacula eques (the Mauritius Parakeet; Chordata; Aves; Psittaciformes; Psittacidae). The genome sequence is 1203.8 megabases in span. Most of the assembly is scaffolded into 35 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 18.86 kilobases in length.}, }
@article {pmid39297890, year = {2025}, author = {Daich Varela, M and Sanders Villa, A and Pontikos, N and Crossland, MD and Michaelides, M}, title = {Digital health and wearable devices for retinal disease monitoring.}, journal = {Graefe's archive for clinical and experimental ophthalmology = Albrecht von Graefes Archiv fur klinische und experimentelle Ophthalmologie}, volume = {263}, number = {2}, pages = {279-289}, pmid = {39297890}, issn = {1435-702X}, support = {/WT_/Wellcome Trust/United Kingdom ; 206619/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Wearable Electronic Devices ; *Retinal Diseases/diagnosis/physiopathology ; *Telemedicine/instrumentation ; Artificial Intelligence ; Monitoring, Physiologic/instrumentation ; Digital Health ; }, abstract = {Digital health is wielding a growing influence across all areas of healthcare, encompassing various facets such as telemedicine, artificial intelligence (AI), and electronic healthcare records. In Ophthalmology, digital health innovations can be broadly divided into four categories: (i) self-monitoring home devices and apps, (ii) virtual and augmented reality visual aids, (iii) AI software, and (iv) wearables. Wearable devices can work in the background, collecting large amounts of objective data while we do our day-to-day activities, which may be ecologically more valid and meaningful to patients than that acquired in traditional hospital settings. They can be a watch, wristband, piece of clothing, glasses, cane, smartphone in our pocket, earphones, or any other device with a sensor that we carry with us. Focusing on retinal diseases, a key challenge in developing novel therapeutics has been to prove a meaningful benefit in patients' lives and the creation of objective patient-centred endpoints in clinical trials. In this review, we will discuss wearable devices collecting different aspects of visual behaviour, visual field, central vision, and functional vision, as well as their potential implementation as outcome measures in research/clinical trial settings. The healthcare landscape is facing a paradigm shift. Clinicians have a key role of collaborating with the development and fine-tuning of digital health innovations, as well as identifying opportunities where they can be leveraged to enhance our understanding of retinal diseases and improve patient outcomes.}, }
@article {pmid39295890, year = {2023}, author = {Boyes, D and Januszczak, I and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Lunar-spotted Pinion, Cosmia pyralina (Denis &amp; Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {545}, pmid = {39295890}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Cosmia pyralina (the Lunar-spotted Pinion; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 803.3 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.39 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,901 protein coding genes.}, }
@article {pmid39294496, year = {2024}, author = {Khaliq, AM and Rajamohan, M and Saeed, O and Mansouri, K and Adil, A and Zhang, C and Turk, A and Carstens, JL and House, M and Hayat, S and Nagaraju, GP and Pappas, SG and Wang, YA and Zyromski, NJ and Opyrchal, M and Lee, KP and O'Hagan, H and El Rayes, B and Masood, A}, title = {Spatial transcriptomic analysis of primary and metastatic pancreatic cancers highlights tumor microenvironmental heterogeneity.}, journal = {Nature genetics}, volume = {56}, number = {11}, pages = {2455-2465}, pmid = {39294496}, issn = {1546-1718}, mesh = {Humans ; *Tumor Microenvironment/genetics ; *Pancreatic Neoplasms/genetics/pathology ; *Carcinoma, Pancreatic Ductal/genetics/pathology ; *Transcriptome ; *Neoplasm Metastasis/genetics ; Gene Expression Regulation, Neoplastic ; Gene Expression Profiling/methods ; Female ; }, abstract = {Although the spatial, cellular and molecular landscapes of resected pancreatic ductal adenocarcinoma (PDAC) are well documented, the characteristics of its metastatic ecology remain elusive. By applying spatially resolved transcriptomics to matched primary and metastatic PDAC samples, we discovered a conserved continuum of fibrotic, metabolic and immunosuppressive spatial ecotypes across anatomical regions. We observed spatial tumor microenvironment heterogeneity spanning beyond that previously appreciated in PDAC. Through comparative analysis, we show that the spatial ecotypes exhibit distinct enrichment between primary and metastatic sites, implying adaptability to the local environment for survival and progression. The invasive border ecotype exhibits both pro-tumorigenic and anti-tumorigenic cell-type enrichment, suggesting a potential immunotherapy target. The ecotype heterogeneity across patients emphasizes the need to map individual patient landscapes to develop personalized treatment strategies. Collectively, our findings provide critical insights into metastatic PDAC biology and serve as a valuable resource for future therapeutic exploration and molecular investigations.}, }
@article {pmid39294488, year = {2024}, author = {Zhang, WH and Gao, JW and Lau, CC and Jiang, ZF and Yeong, YS and Mok, WJ and Zhou, W}, title = {Effects of different trophic conditions on total fatty acids, amino acids, pigment and gene expression profiles in Euglena gracilis.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {40}, number = {10}, pages = {325}, pmid = {39294488}, issn = {1573-0972}, support = {22zxbtsn00020//Tianjin Municipal Science and Technology Bureau/ ; }, mesh = {*Euglena gracilis/genetics/growth &amp; development/metabolism/ultrastructure ; *Gene Expression Profiling ; *Amino Acids/metabolism ; *Fatty Acids/metabolism ; *Pigments, Biological/metabolism ; Biomass ; Gene Ontology ; Gene Expression Regulation, Developmental ; Heterotrophic Processes ; }, abstract = {Euglena gracilis is a unique microalga that lacks a cell wall and is able to grow under different trophic culture conditions. In this study, cell growth, biomass production, and changes in the ultrastructure of E. gracilis cells cultivated photoautotrophically, mixotrophically, and under sequential-heterotrophy-photoinduction (SHP) were assessed. Mixotrophy induced the highest cell growth and biomass productivity (6.27 ± 0.59 mg/L/d) in E. gracilis, while the highest content of fatty acids, 2.69 ± 0.04% of dry cell weight (DCW) and amino acids, 38.16 ± 0.08% of DCW was obtained under SHP condition. E. gracilis also accumulated significantly higher saturated fatty acids and lower unsaturated fatty acids when cultivated under SHP condition. Transcriptomic analysis showed that the expression of photosynthetic genes (PsbA, PsbC, F-type ATPase alpha and beta) was lower, carbohydrate and protein synthetic genes (glnA, alg14 and fba) were expressed higher in SHP-culture cells when compared to other groups. Different trophic conditions also induced changes in the cell ultrastructure, where paramylon and starch granules were more abundant in SHP-cultured cells. The findings generated in this study illustrated that aerobic SHP cultivation of E. gracilis possesses great potential in human and animal feed applications.}, }
@article {pmid39292721, year = {2024}, author = {Bastien, GE and Cable, RN and Batterbee, C and Wing, AJ and Zaman, L and Duhaime, MB}, title = {Virus-host interactions predictor (VHIP): Machine learning approach to resolve microbial virus-host interaction networks.}, journal = {PLoS computational biology}, volume = {20}, number = {9}, pages = {e1011649}, pmid = {39292721}, issn = {1553-7358}, mesh = {*Machine Learning ; Humans ; *Viruses/genetics ; *Computational Biology/methods ; *Host-Pathogen Interactions/genetics/physiology ; Host Microbial Interactions/genetics/physiology ; }, abstract = {Viruses of microbes are ubiquitous biological entities that reprogram their hosts' metabolisms during infection in order to produce viral progeny, impacting the ecology and evolution of microbiomes with broad implications for human and environmental health. Advances in genome sequencing have led to the discovery of millions of novel viruses and an appreciation for the great diversity of viruses on Earth. Yet, with knowledge of only "who is there?" we fall short in our ability to infer the impacts of viruses on microbes at population, community, and ecosystem-scales. To do this, we need a more explicit understanding "who do they infect?" Here, we developed a novel machine learning model (ML), Virus-Host Interaction Predictor (VHIP), to predict virus-host interactions (infection/non-infection) from input virus and host genomes. This ML model was trained and tested on a high-value manually curated set of 8849 virus-host pairs and their corresponding sequence data. The resulting dataset, 'Virus Host Range network' (VHRnet), is core to VHIP functionality. Each data point that underlies the VHIP training and testing represents a lab-tested virus-host pair in VHRnet, from which meaningful signals of viral adaptation to host were computed from genomic sequences. VHIP departs from existing virus-host prediction models in its ability to predict multiple interactions rather than predicting a single most likely host or host clade. As a result, VHIP is able to infer the complexity of virus-host networks in natural systems. VHIP has an 87.8% accuracy rate at predicting interactions between virus-host pairs at the species level and can be applied to novel viral and host population genomes reconstructed from metagenomic datasets.}, }
@article {pmid39292164, year = {2024}, author = {Sakai, K and Nagata, T and Mori, T and Inoue, S and Fujiwara, H and Odagami, K and Adi, NP and Tatemichi, M and Mori, K}, title = {Research topics in occupational medicine, 1990-2022: A text-mining-applied bibliometric study.}, journal = {Scandinavian journal of work, environment &amp; health}, volume = {50}, number = {7}, pages = {567-576}, pmid = {39292164}, issn = {1795-990X}, support = {240801-01//Industrial Disease Clinical Research Grants from the Ministry of Health, Labor and Welfare/ ; }, mesh = {*Bibliometrics ; *Data Mining ; Humans ; *Occupational Medicine ; Occupational Health ; }, abstract = {OBJECTIVE: Occupational health has been influenced by societal and industrial changes. This study aimed to clarify topic trends in occupational health research in 1990-2022.<br><br>METHODS: We conducted a text-mining-adjusted bibliometric study using research titles in occupational health. Data on research titles and the years of publication were collected from 26 peer-reviewed journals on PubMed. Using morphological and correspondence analyses in text mining, we structured research topics into multiple categories and visualized the relationship between all categories and publication years. Statistical analyses were conducted using the text mining software - KH Coder 3.0.<br><br>RESULTS: We obtained 48 645 articles containing 714 890 words in their titles. The research topics were classified into 4 categories and 17 subcategories, of which those of occupations; countries; non-intervention; psychosocial factors; lifestyle factors; safety; symptoms; therapy and care; and productivity have recently shown an increasing trend. In contrast, the subcategories of risk, chemical factors, disease, and organ damage showed decreasing trends. Chemical factors, which were the main topics in the 1990s, included risk, organ damage, and disease. Productivity, the main topic in the 2020s, co-occurred with lifestyle factors, symptoms, and intervention.<br><br>CONCLUSIONS: Focal areas in occupational-health research shift according to societal trends. Occupational-health research has primarily analyzed issues in developed countries with capitalist values and may not have sufficiently covered issues in developing countries. It is imperative for policymakers and public funding bodies to determine priorities for investigation in the field.}, }
@article {pmid39292040, year = {2024}, author = {Vasconcelos, NM and Bernal, RTI and Souza, JB and Bordoni, PHC and Stein, C and Coll, CVN and Murray, J and Malta, DC}, title = {Underreporting of violence against women: an analysis of two data sources.}, journal = {Ciencia &amp; saude coletiva}, volume = {29}, number = {10}, pages = {e07732023}, doi = {10.1590/1413-812320242910.07732023}, pmid = {39292040}, issn = {1678-4561}, mesh = {Humans ; Brazil/epidemiology ; Female ; Adult ; Young Adult ; Adolescent ; *Sex Offenses/statistics &amp; numerical data ; Middle Aged ; Health Surveys ; Gender-Based Violence/statistics &amp; numerical data ; Information Systems/statistics &amp; numerical data ; Information Sources ; }, abstract = {This article aims to estimate the underreporting of violence against women (VAW) in the Notifiable Diseases Information System (SINAN), based on data from the National Survey of Health (NSH), in Brazil and subnational units (SU). This work was an ecological study using SINAN and NSH, both from 2019. In SINAN, reports of sexual, physical, and psychological VAW, aged 18 years or older, were selected. In the NSH, women of the same age group who reported psychological, physical, or sexual violence, and who had sought health care due to consequences of the violence were selected. SINAN underreporting was calculated in reference to the NSH's estimated population, for Brazil and each SU. Underreporting of VAW in Brazil was 98.5%, 75.9%, and 89.4% for psychological, physical, and sexual violence, respectively. The North and Northeast states presented the lowest reporting rates among the states. VAW in Brazil is highly underreported by the health sector, showing the need for adequate training of health professionals to recognize situations of violence and raise awareness of the importance of reporting.}, }
@article {pmid39290666, year = {2024}, author = {Guclu, C and Luk, CL and Ashton, LA and Abbas, S and Boyle, MJW}, title = {Beta diversity subcomponents of plant species turnover and nestedness reveal drivers of community assembly in a regenerating subtropical forest.}, journal = {Ecology and evolution}, volume = {14}, number = {9}, pages = {e70233}, pmid = {39290666}, issn = {2045-7758}, abstract = {Secondary forests represent a significant proportion of global forest cover, with over 70% of forests in East Asia classified as regenerating. While succession has been studied extensively in temperate systems, trajectories of subtropical succession remain poorly characterized in highly disturbed, urban-adjacent forests. Investigating the additive beta diversity components of turnover and nestedness may reveal community assembly mechanisms driving secondary succession. The present study investigates plant community assembly along a successional gradient from 7 to 70 years following the onset of succession in secondary subtropical forests in Hong Kong, China. Plant survey data for 28 plots were analysed, generating additive Simpsons turnover and nestedness beta diversity metrics. Dissimilarity matrices were generated and modelled as a function of environmental matrices including forest plant community age (years following onset of secondary succession), inter-community distance (metres), and soil moisture saturation (%) across three elevational bands using generalized dissimilarity models. Nonmetric multidimensional scaling of plant communities was conducted with Bray-Curtis dissimilarity matrices. Inter-community distance and successional age differentially influenced plant species turnover between lowland and Montane forest types. Models of nestedness found that plot age and soil moisture saturation were significant drivers of nestedness patterns in plant communities across elevational classes. Turnover represented a higher proportion of Sorensen beta diversity than nestedness, while ANOSIM found significant differentiation between plant communities at different successional stages. Turnover patterns suggest a deterministic model of community assembly, with strong patterns of species replacement between communities at fine spatial scales and successional stages, as well as clear compositional shifts between lowland and montane forest types. NMDS analysis and functional compositional assessments suggested a transition from early successional communities with a high proportion of shrub species, to later successional communities with a higher proportion of tree species, with an increase in species turnover with greater age dissimilarity.}, }
@article {pmid39290433, year = {2024}, author = {Castrillo, M and Aguilar, F and García-Díaz, D}, title = {Dataset on sub-daily vertical profiles of physicochemical parameters and chlorophyll concentration in El Val reservoir, together with its daily meteorological data, storage state and downstream flow (2018-2022).}, journal = {Data in brief}, volume = {57}, number = {}, pages = {110839}, pmid = {39290433}, issn = {2352-3409}, abstract = {The dataset addressed in this article contains parameters about El Val reservoir (province of Zaragoza, Spain). It includes physicochemical variables, the water level, the stored water volume, its meteorological conditions and the flow rate of its effluent, the Queiles River, a few metres downstream of the dam. The El Val reservoir stores water from the Val River, but it also receives water from the Queiles River through a pipeline and from several ravines. The dam releases on the Queiles River, which is a tributary of the Ebro River (the second one in Spain in length and discharge rate). A multiparametric probe (aquaDam, Adasa Systems), hanging from a structure located in the dam, every 6 h makes a vertical profile taking the measurements at each metre of depth from the surface to approximately 573 m above sea level (m.a.s.l.), in other words, between 2 and 3 m above the bottom outlet. This probe collects data of water temperature, pH, ORP, conductivity, dissolved oxygen, turbidity and chlorophyll concentration. Meteorological data are collected in the nearest weather station, located in the municipality of Los Fayos which is about 500 m downstream of the dam. These include daily accumulated precipitation, daily maximum and average solar irradiance, daily maximum, minimum and average air temperature and daily average wind speed. The water level and volume of stored water and the flow rate of the Queiles River are collected in the El Val monitoring station and the Queiles River gauge station respectively, and are also provided on a daily basis. These data are useful to feed deterministic, data driven or hybrid hydrological models with different purposes, like the identification of the impact of meteorological conditions on the physicochemical properties of the reservoir as well as the assessment of different management strategies in the reservoir. This is a data article that additionally supports the work published in Ecological Informatics [1] where the use of common and readily available open data is promoted through its use to feed data driven models, in particular to infer the depth of the thermocline in reservoirs that are periodically or permanently thermally stratified. In that article a dataset derived from the one presented in this article is used.}, }
@article {pmid39290364, year = {2024}, author = {Boyes, D and Holland, PWH and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Red Chestnut moth, Cerastis rubricosa (Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {88}, pmid = {39290364}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Cerastis rubricosa (the Red Chestnut moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 678.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.39 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,784 protein coding genes.}, }
@article {pmid39290036, year = {2024}, author = {Monreal-Di Bello, M and González-Bermejo, D and Castillo-Cano, B and Rodriguez-Pascual, A and Montero-Corominas, D}, title = {Impact of Regulatory Interventions on Ulipristal Acetate 5 mg (Esmya) Use in Spain: An Interrupted Time-Series Analysis.}, journal = {Pharmacoepidemiology and drug safety}, volume = {33}, number = {9}, pages = {e70004}, doi = {10.1002/pds.70004}, pmid = {39290036}, issn = {1099-1557}, support = {//Spanish Agency on Medicines and Medical Devices (AEMPS)/ ; }, mesh = {Humans ; Spain/epidemiology ; *Norpregnadienes/administration &amp; dosage/adverse effects/therapeutic use ; *Interrupted Time Series Analysis ; Female ; Databases, Factual ; Electronic Health Records/statistics &amp; numerical data ; Risk Evaluation and Mitigation ; Male ; Adult ; Middle Aged ; }, abstract = {PURPOSE: Since late 2017, the use of ulipristal acetate 5 mg (UPA; Proprietary name: Esmya) has been under review in the European Union, due to an emerging hepatic risk. In February 2018 and in July 2018, the Spanish Agency of Medicines and Medical Devices and the marketing authorization holder put two risk minimization measures (RMM) in place, in order to inform about new safety information and to mitigate this risk. This study aims to assess RMM effectiveness in Spain, by performing an interrupted time-series (ITS) analyses, between 2014 and 2019.<br><br>METHOD: Two quasi-experimental ITS analyses to examine the use of UPA before and after the RMM release were performed: (a) an ecological study using aggregated data from a drug consumption database; and (b) a study using primary healthcare data gathered from electronic clinical records.<br><br>RESULTS: Regulatory interventions were associated with an immediate and significant decrease level of DID (the number of DDD dispensed per 100&#x2009;000 inhabitants and day) and incidence. The DID was 70% less than expected 12&#x2009;months after the interventions. This value was 59% for the incidence. However, a change in the slope was not observed and the use started rising again in the last segment of the study period.<br><br>CONCLUSION: Despite RMM had an immediate strong impact on UPA use, the last segment upward trend in the long-term might have been affected by the lack of comparable therapeutic alternatives. Further studies should be performed to confirm the increase trend observed and analyze subsequent measures and additional data.}, }
@article {pmid39289538, year = {2024}, author = {Mc Cartney, AM and Formenti, G and Mouton, A and De Panis, D and Marins, LS and Leitão, HG and Diedericks, G and Kirangwa, J and Morselli, M and Salces-Ortiz, J and Escudero, N and Iannucci, A and Natali, C and Svardal, H and Fernández, R and De Pooter, T and Joris, G and Strazisar, M and Wood, JMD and Herron, KE and Seehausen, O and Watts, PC and Shaw, F and Davey, RP and Minotto, A and Fernández, JM and Böhne, A and Alegria, C and Alioto, T and Alves, PC and Amorim, IR and Aury, JM and Backstrom, N and Baldrian, P and Baltrunaite, L and Barta, E and BedHom, B and Belser, C and Bergsten, J and Bertrand, L and Bilandija, H and Binzer-Panchal, M and Bista, I and Blaxter, M and Borges, PAV and Dias, GB and Bosse, M and Brown, T and Bruggmann, R and Buena-Atienza, E and Burgin, J and Buzan, E and Cariani, A and Casadei, N and Chiara, M and Chozas, S and Čiampor, F and Crottini, A and Cruaud, C and Cruz, F and Dalen, L and De Biase, A and Del Campo, J and Delic, T and Dennis, AB and Derks, MFL and Diroma, MA and Djan, M and Duprat, S and Eleftheriadi, K and Feulner, PGD and Flot, JF and Forni, G and Fosso, B and Fournier, P and Fournier-Chambrillon, C and Gabaldon, T and Garg, S and Gissi, C and Giupponi, L and Gomez-Garrido, J and González, J and Grilo, ML and Grüning, B and Guerin, T and Guiglielmoni, N and Gut, M and Haesler, MP and Hahn, C and Halpern, B and Harrison, PW and Heintz, J and Hindrikson, M and Höglund, J and Howe, K and Hughes, GM and Istace, B and Cock, MJ and Janžekovič, F and Jonsson, ZO and Joye-Dind, S and Koskimäki, JJ and Krystufek, B and Kubacka, J and Kuhl, H and Kusza, S and Labadie, K and Lähteenaro, M and Lantz, H and Lavrinienko, A and Leclère, L and Lopes, RJ and Madsen, O and Magdelenat, G and Magoga, G and Manousaki, T and Mappes, T and Marques, JP and Redondo, GIM and Maumus, F and McCarthy, SA and Megens, HJ and Melo-Ferreira, J and Mendes, SL and Montagna, M and Moreno, J and Mosbech, MB and Moura, M and Musilova, Z and Myers, E and Nash, WJ and Nater, A and Nicholson, P and Niell, M and Nijland, R and Noel, B and Noren, K and Oliveira, PH and Olsen, RA and Ometto, L and Oomen, RA and Ossowski, S and Palinauskas, V and Palsson, S and Panibe, JP and Pauperio, J and Pavlek, M and Payen, E and Pawlowska, J and Pellicer, J and Pesole, G and Pimenta, J and Pippel, M and Pirttilä, AM and Poulakakis, N and Rajan, J and M C Rego, R and Resendes, R and Resl, P and Riesgo, A and Rodin-Morch, P and Soares, AER and Fernandes, CR and Romeiras, MM and Roxo, G and Rüber, L and Ruiz-Lopez, MJ and Saarma, U and da Silva, LP and Sim-Sim, M and Soler, L and Sousa, VC and Santos, CS and Spada, A and Stefanovic, M and Steger, V and Stiller, J and Stöck, M and Struck, TH and Sudasinghe, H and Tapanainen, R and Tellgren-Roth, C and Trindade, H and Tukalenko, Y and Urso, I and Vacherie, B and Van Belleghem, SM and Van Oers, K and Vargas-Chavez, C and Velickovic, N and Vella, N and Vella, A and Vernesi, C and Vicente, S and Villa, S and Pettersson, OV and Volckaert, FAM and Voros, J and Wincker, P and Winkler, S and Ciofi, C and Waterhouse, RM and Mazzoni, CJ}, title = {The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.}, journal = {npj biodiversity}, volume = {3}, number = {1}, pages = {28}, pmid = {39289538}, issn = {2731-4243}, support = {/WT_/Wellcome Trust/United Kingdom ; P 32691/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {A genomic database of all Earth's eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP.}, }
@article {pmid39287883, year = {2024}, author = {Stolz, BJ and Dhesi, J and Bull, JA and Harrington, HA and Byrne, HM and Yoon, IHR}, title = {Relational Persistent Homology for Multispecies Data with Application to the Tumor Microenvironment.}, journal = {Bulletin of mathematical biology}, volume = {86}, number = {11}, pages = {128}, pmid = {39287883}, issn = {1522-9602}, support = {EP/R018472/1//EPSRC/ ; EP/R018472/1, EP/K041096/1, EP/R005125/1, EP/T001968/1//EPSRC/ ; EP/R018472/1//EPSRC/ ; EP/R018472/1//EPSRC/ ; RGF EA 201074, UF150238//Royal Society/ ; CTRQQR-2021/100002/CRUK_/Cancer Research UK/United Kingdom ; }, mesh = {*Tumor Microenvironment/immunology ; Humans ; *Mathematical Concepts ; *Models, Biological ; *Neoplasms/pathology/immunology ; Computer Simulation ; Computational Biology ; Macrophages/immunology/pathology ; }, abstract = {Topological data analysis (TDA) is an active field of mathematics for quantifying shape in complex data. Standard methods in TDA such as persistent homology (PH) are typically focused on the analysis of data consisting of a single entity (e.g., cells or molecular species). However, state-of-the-art data collection techniques now generate exquisitely detailed multispecies data, prompting a need for methods that can examine and quantify the relations among them. Such heterogeneous data types arise in many contexts, ranging from biomedical imaging, geospatial analysis, to species ecology. Here, we propose two methods for encoding spatial relations among different data types that are based on Dowker complexes and Witness complexes. We apply the methods to synthetic multispecies data of a tumor microenvironment and analyze topological features that capture relations between different cell types, e.g., blood vessels, macrophages, tumor cells, and necrotic cells. We demonstrate that relational topological features can extract biological insight, including the dominant immune cell phenotype (an important predictor of patient prognosis) and the parameter regimes of a data-generating model. The methods provide a quantitative perspective on the relational analysis of multispecies spatial data, overcome the limits of traditional PH, and are readily computable.}, }
@article {pmid39287032, year = {2024}, author = {Meaume, S and Senet, P and Thomé, B and Aragno, VA and Serge, B and Fortin, S and Boucley, I and Michon-Pasturel, U and Colboc, H}, title = {Impact of primary dressings on healing of venous leg ulcers: a French cohort study from the healthcare insurance database.}, journal = {Journal of wound care}, volume = {33}, number = {9}, pages = {678-686}, doi = {10.12968/jowc.2024.0189}, pmid = {39287032}, issn = {0969-0700}, mesh = {Humans ; Female ; Male ; *Wound Healing ; France ; *Varicose Ulcer/therapy/economics ; Aged ; *Bandages/economics ; Middle Aged ; Cohort Studies ; Databases, Factual ; Aged, 80 and over ; Insurance, Health/statistics &amp; numerical data ; Treatment Outcome ; Health Care Costs/statistics &amp; numerical data ; }, abstract = {OBJECTIVE: Multicomponent bandages (MCBs) are recommended by the French Authority for Health (Haute Autorité de Santé) as first-line treatment for venous leg ulcers (VLUs). A first analysis of the data collected from the French administrative healthcare database (Système National des Données de Santé (SNDS)) on 25,255 patients with a VLU supported superiority of MCBs versus short stretch bandages when considering the healing outcomes and costs associated with closure of these wounds. The aim of this study was to assess how beneficial the primary dressing (technology lipido-colloid nano-oligosaccharide factor (TLC NOSF) or control dressing group (CDG)) could be, when used in combination with MCBs in the treatment of VLUs.<br><br>METHOD: Data from the SNDS were collected for patients meeting the following inclusion criteria: treatment for a VLU with MCBs and with the same dressing type (TLC-NOSF or CDG) during the whole treatment period. Healing outcomes were documented on the global cohorts and propensity score-matched cohorts. The mean healthcare cost and the ecological impact were calculated for those patients healed within the study period.<br><br>RESULTS: In total, 12,507 patients met the criteria for treatment with both MCBs and TLC-NOSF dressings (n=1134) versus MCBs and CDG (n=11,373); with 1134 and 2268 patients per group following propensity score matching. Healing outcomes were favourable for the TLC-NOSF group in the global cohort and were enhanced in the propensity score-matched cohorts. At every point of the analysis, the adjusted healing rates were significantly higher in the TLC-NOSF group than in the CDG group (p<0.001). In the propensity score-matched cohorts (n=3402), the healing rate at three months was 52% in the TLC-NOSF group versus 37% in the CDG group (p<0.001). The median healing time was 87 days versus 125.5 days in the TLC-NOSF and CDG groups, respectively (p<0.0001). TLC-NOSF dressings significantly reduced the average treatment cost per healed ulcer (&#x20ac;2099) by 23.7% compared with dressings without TLC-NOSF (&#x20ac;2751) (p<0.001), as well as the resources used.<br><br>CONCLUSION: This SNDS analysis confirms, in the largest real-life study performed in VLU management, the superiority of the TLC-NOSF dressings versus those not impregnated with the NOSF compound. Better clinical outcomes associated with cost savings and a positive ecological impact support the combination of MCBs and TLC-NOSF dressings and should be considered as an optimal standard of care for the global management of VLUs. These outcomes reinforce the current positions of the international guidelines on the use of NOSF impregnated dressings (UrgoStart range; Laboratoires Urgo, France) in this pathology.}, }
@article {pmid39283951, year = {2024}, author = {Amaral, AS and Devos, DP}, title = {The neglected giants: Uncovering the prevalence and functional groups of huge proteins in proteomes.}, journal = {PLoS computational biology}, volume = {20}, number = {9}, pages = {e1012459}, pmid = {39283951}, issn = {1553-7358}, mesh = {*Proteome/metabolism ; Databases, Protein ; Computational Biology ; Proteins/metabolism/chemistry ; Humans ; Proteomics/methods ; Bacteria/metabolism/genetics ; Animals ; }, abstract = {An often-overlooked aspect of biology is formed by the outliers of the protein length distribution, specifically those proteins with more than 5000 amino acids, which we refer to as huge proteins (HPs). By examining UniprotKB, we discovered more than 41 000 HPs throughout the tree of life, with the majority found in eukaryotes. Notably, the phyla with the highest propensity for HPs are Apicomplexa and Fornicata. Moreover, we observed that certain bacteria, such as Elusimicrobiota or Planctomycetota, have a higher tendency for encoding HPs, even more than the average eukaryote. To investigate if these macro-polypeptides represent "real" proteins, we explored several indirect metrics. Additionally, orthology analyses reveals thousands of clusters of homologous sequences of HPs, revealing functional groups related to key cellular processes such as cytoskeleton organization and functioning as chaperones or as E3-ubiquitin ligases in eukaryotes. In the case of bacteria, the major clusters have functions related to non-ribosomomal peptide synthesis/polyketide synthesis, followed by pathogen-host attachment or recognition surface proteins. Further exploration of the annotations for each HPs supported the previously identified functional groups. These findings underscore the need for further investigation of the cellular and ecological roles of these HPs and their potential impact on biology and biotechnology.}, }
@article {pmid39283104, year = {2024}, author = {Tedim, AP and Almeida-Santos, AC and Lanza, VF and Novais, C and Coque, TM and Freitas, AR and Peixe, L and , }, title = {Bacteriocin distribution patterns in Enterococcus faecium and Enterococcus lactis: bioinformatic analysis using a tailored genomics framework.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {10}, pages = {e0137624}, pmid = {39283104}, issn = {1098-5336}, support = {EXPL/SAU-INF/0261/2021, UIDP/04378/2020, UIDB/04378/2020, LA/P/0140/2020, UI/BD/151317/2021//MCTES | Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia (FCT)/ ; }, mesh = {*Bacteriocins/genetics/metabolism ; *Enterococcus faecium/genetics/metabolism/drug effects ; *Genomics ; *Computational Biology ; Genome, Bacterial ; Anti-Bacterial Agents/pharmacology ; Enterococcus/genetics/metabolism/drug effects ; }, abstract = {UNLABELLED: Multidrug-resistant Enterococcus faecium strains represent a major concern due to their ability to thrive in diverse environments and cause life-threatening infections. While antimicrobial resistance and virulence mechanisms have been extensively studied, the contribution of bacteriocins to E. faecium's adaptability remains poorly explored. E. faecium, within the Bacillota phylum, is a prominent bacteriocin producer. Here, we developed a tailored database of 76 Bacillota bacteriocins (217 sequences, including 40 novel bacteriocins) and applied it to uncover bacteriocin distribution patterns in 997 quality-filtered E. faecium and Enterococcus lactis (former E. faecium clade B) genomes. Curated using computational pipelines and literature mining, our database demonstrates superior precision versus leading public tools in identifying diverse bacteriocins. Distinct bacteriocin profiles emerged between E. faecium and E. lactis, highlighting species-specific adaptations. E. faecium strains from hospitalized patients were significantly enriched in bacteriocins as enterocin A and bacteriocins 43 (or T8), AS5, and AS11. These bacteriocin genes were strongly associated with antibiotic resistance, particularly vancomycin and ampicillin, and Inc18 rep2_pRE25-derivative plasmids, classically associated with vancomycin resistance transposons. Such bacteriocin arsenal likely enhances the adaptability and competitive fitness of E. faecium in the nosocomial environment. By combining a novel tailored database, whole-genome sequencing, and epidemiological data, our work elucidates meaningful connections between bacteriocin determinants, antimicrobial resistance, mobile genetic elements, and ecological origins in E. faecium and provides a framework for elucidating bacteriocin landscapes in other organisms. Characterizing species- and strain-level differences in bacteriocin profiles may reveal determinants of ecological adaptation, and translating these discoveries could further inform strategies to exploit bacteriocins against high-risk clones.<br><br>IMPORTANCE: This work significantly expands the knowledge on the understudied bacteriocin diversity in opportunistic enterococci, revealing their contribution in the adaptation to different environments. It underscores the importance of placing increased emphasis on genetic platforms carrying bacteriocins as well as on cryptic plasmids that often exclusively harbor bacteriocins since bacteriocin production can significantly contribute to plasmid maintenance, potentially facilitating their stable transmission across generations. Further characterization of strain-level bacteriocin landscapes could inform strategies to combat high-risk clones. Overall, these insights provide a framework for unraveling the therapeutic and biotechnological potential of bacteriocins.}, }
@article {pmid39277496, year = {2025}, author = {van der Feltz-Cornelis, CM and Turk, F and Sweetman, J and Khunti, K and Gabbay, M and Shepherd, J and Montgomery, H and Strain, WD and Lip, GYH and Wootton, D and Watkins, CL and Cuthbertson, DJ and Williams, N and Banerjee, A}, title = {Corrigendum to "Prevalence of mental health conditions and brain fog in people with long COVID: A systematic review and meta-analysis" [General Hospital Psychiatry volume 88 (2024)10-22 10.1016/j.genhosppsych.2024.02.009].}, journal = {General hospital psychiatry}, volume = {92}, number = {}, pages = {112}, doi = {10.1016/j.genhosppsych.2024.09.006}, pmid = {39277496}, issn = {1873-7714}, }
@article {pmid39275913, year = {2024}, author = {Takada, K and Nakagawa, S and Kryukov, K and Ozawa, M and Watanabe, T}, title = {Metagenomic analysis of the gut microbiota of hooded cranes (Grus monacha) on the Izumi plain in Japan.}, journal = {FEBS open bio}, volume = {14}, number = {12}, pages = {1972-1984}, pmid = {39275913}, issn = {2211-5463}, support = {//Crane Conservation by the City of Izumi/ ; //Tokyo Biochemical Research Foundation/ ; JPMJCR20H6//Core Research for Evolutional Science and Technology/ ; //2020 Tokai University School of Medicine Research Aid/ ; 22gm1610010h0001//Japan Agency for Medical Research and Development/ ; JP223fa627002h//Japan Agency for Medical Research and Development/ ; //Takeda Science Foundation/ ; 16H06429//Japan Society for the Promotion of Science/ ; 16H06434//Japan Society for the Promotion of Science/ ; 16K21723//Japan Society for the Promotion of Science/ ; 19H04843//Japan Society for the Promotion of Science/ ; 19fk0108171//Japan Society for the Promotion of Science/ ; 21J01036//Japan Society for the Promotion of Science/ ; 22K15469//Japan Society for the Promotion of Science/ ; JP19fk0108113//Japan Society for the Promotion of Science/ ; JP22H02521//Japan Society for the Promotion of Science/ ; }, mesh = {Animals ; Japan ; *Gastrointestinal Microbiome/genetics ; *Birds/microbiology/virology ; *Metagenomics/methods ; Feces/microbiology ; Bacteria/genetics/classification/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Metagenome/genetics ; }, abstract = {Recent advances in DNA sequencing technology have dramatically improved our understanding of the gut microbiota of various animal species. However, research on the gut microbiota of birds lags behind that of many other vertebrates, and information about the gut microbiota of wild birds such as migratory waterfowl is particularly lacking. Because the ecology of migratory waterfowl (e.g., lifestyle, diet, physiological characteristics) differs from that of other birds, the gut microbiota of migratory waterfowl likely also differs, but much is still unknown. The hooded crane (Grus monacha) is an important representative migratory waterbird species and is listed as endangered on the International Union for Conservation of Nature and Natural Resources Red List of Threatened Species. In this study, we analyzed the bacterial and viral microbiota in the gut of hooded cranes by using deep sequencing data from fecal samples of hooded cranes that winter on the Izumi plain in Japan, and found that Cetobacterium, Clupeiformes, and Pbunavirus were clearly present in the fecal samples of hooded cranes. These findings advance our understanding of the ecology of hooded cranes.}, }
@article {pmid39274728, year = {2024}, author = {Sąsiadek-Andrzejczak, E and Maras, P and Kozicki, M}, title = {Flexible and Ecological Cotton-Based Dosimeter for 2D UV Surface Dose Distribution Measurements.}, journal = {Materials (Basel, Switzerland)}, volume = {17}, number = {17}, pages = {}, pmid = {39274728}, issn = {1996-1944}, abstract = {This work presents a 2D radiochromic dosimeter for ultraviolet (UV) radiation measurements, based on cotton fabric volume-modified with nitroblue tetrazolium chloride (NBT) as a radiation-sensitive compound. The developed dosimeter is flexible, which allows it to adapt to various shapes and show a color change from yellowish to purple-brown during irradiation. The intensity of the color change depends on the type of UV radiation and is the highest for UVC (253.7 nm). It has been shown that the developed dosimeters (i) can be used for UVC radiation dose measurements in the range of up to 10 J/cm[2]; (ii) can be measured in 2D using a flatbed scanner; and (iii) can have the obtained images after scanning be filtered with a medium filter to improve their quality by reducing noise from the fabric structure. The developed cotton-NBT dosimeters can measure UVC-absorbed radiation doses on objects of various shapes, and when combined with a dedicated computer software package and a data processing method, they form a comprehensive system for measuring dose distributions for objects with complex shapes. The developed system can also serve as a comprehensive method for assessing the quality and control of UV radiation sources used in various industrial processes.}, }
@article {pmid39273837, year = {2024}, author = {Gatina, E and Zinicovscaia, I and Yushin, N and Chaligava, O and Frontasyeva, M and Sharipova, A}, title = {Assessment of the Atmospheric Deposition of Potentially Toxic Elements Using Moss Pleurozium schreberi in an Urban Area: The Perm (Perm Region, Russia) Case Study.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {17}, pages = {}, pmid = {39273837}, issn = {2223-7747}, abstract = {Assessment of air quality in urban areas is very important because pollutants affect both the environment and human health. In Perm (Russia), a moss biomonitoring method was used to assess the level of air pollution. The concentrations of 15 elements in 87 samples of moss Pleurozium schreberi in the city territory were determined using a direct mercury analyzer and an inductively coupled plasma atomic emission spectroscopy. Using factor and correlation analyses, the grouping of elements and their relationship with emission sources were established. The main sources of emissions of potentially toxic elements are the transportation (road and rail), metallurgical, and chemical industries. The level of atmospheric air pollution was assessed by calculating the environmental risk index, pollutant load index, and pollution coefficient. Based on the values of the pollution index, the level of atmospheric air pollution in Perm varies from unpolluted to highly polluted, with moderate environmental risk.}, }
@article {pmid39273245, year = {2024}, author = {Damarov, IS and Korbolina, EE and Rykova, EY and Merkulova, TI}, title = {Multi-Omics Analysis Revealed the rSNPs Potentially Involved in T2DM Pathogenic Mechanism and Metformin Response.}, journal = {International journal of molecular sciences}, volume = {25}, number = {17}, pages = {}, pmid = {39273245}, issn = {1422-0067}, support = {23-15-00113//Russian Science Foundation/ ; }, mesh = {Humans ; *Metformin/pharmacology/therapeutic use ; *Diabetes Mellitus, Type 2/genetics/drug therapy/metabolism ; *Polymorphism, Single Nucleotide ; *Genome-Wide Association Study ; Hypoglycemic Agents/therapeutic use/pharmacology ; Quantitative Trait Loci ; Computational Biology/methods ; Leukocytes, Mononuclear/metabolism/drug effects ; Gene Expression Regulation/drug effects ; Promoter Regions, Genetic ; Multiomics ; }, abstract = {The goal of our study was to identify and assess the functionally significant SNPs with potentially important roles in the development of type 2 diabetes mellitus (T2DM) and/or their effect on individual response to antihyperglycemic medication with metformin. We applied a bioinformatics approach to identify the regulatory SNPs (rSNPs) associated with allele-asymmetric binding and expression events in our paired ChIP-seq and RNA-seq data for peripheral blood mononuclear cells (PBMCs) of nine healthy individuals. The rSNP outcomes were analyzed using public data from the GWAS (Genome-Wide Association Studies) and Genotype-Tissue Expression (GTEx). The differentially expressed genes (DEGs) between healthy and T2DM individuals (GSE221521), including metformin responders and non-responders (GSE153315), were searched for in GEO RNA-seq data. The DEGs harboring rSNPs were analyzed using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). We identified 14,796 rSNPs in the promoters of 5132 genes of human PBMCs. We found 4280 rSNPs to associate with both phenotypic traits (GWAS) and expression quantitative trait loci (eQTLs) from GTEx. Between T2DM patients and controls, 3810 rSNPs were detected in the promoters of 1284 DEGs. Based on the protein-protein interaction (PPI) network, we identified 31 upregulated hub genes, including the genes involved in inflammation, obesity, and insulin resistance. The top-ranked 10 enriched KEGG pathways for these hubs included insulin, AMPK, and FoxO signaling pathways. Between metformin responders and non-responders, 367 rSNPs were found in the promoters of 131 DEGs. Genes encoding transcription factors and transcription regulators were the most widely represented group and many were shown to be involved in the T2DM pathogenesis. We have formed a list of human rSNPs that add functional interpretation to the T2DM-association signals identified in GWAS. The results suggest candidate causal regulatory variants for T2DM, with strong enrichment in the pathways related to glucose metabolism, inflammation, and the effects of metformin.}, }
@article {pmid39271937, year = {2024}, author = {Hansen, AJ and Burns, P and Ervin, J and Goetz, SJ and Hansen, M and Venter, O and Watson, JEM and Jantz, PA and Virnig, ALS and Barnett, K and Pillay, R and Atkinson, S and Supples, C and Rodríguez-Buritica, S and Armenteras, D}, title = {Author Correction: A policy-driven framework for conserving the best of Earth's remaining moist tropical forests.}, journal = {Nature ecology &amp; evolution}, volume = {8}, number = {12}, pages = {2336}, doi = {10.1038/s41559-024-02557-8}, pmid = {39271937}, issn = {2397-334X}, }
@article {pmid39271747, year = {2024}, author = {Shin, S and Baker, AJ and Enk, J and McKenna, DD and Foquet, B and Vandergast, AG and Weissman, DB and Song, H}, title = {Orthoptera-specific target enrichment (OR-TE) probes resolve relationships over broad phylogenetic scales.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {21377}, pmid = {39271747}, issn = {2045-2322}, support = {DEB-1937815//National Science Foundation/ ; IOS-1253493//National Science Foundation/ ; DEB-1064082//National Science Foundation/ ; Hatch Grant TEX0-2-6584//U.S. Department of Agriculture/ ; }, mesh = {Animals ; *Phylogeny ; *Orthoptera/genetics/classification ; Transcriptome/genetics ; Computational Biology/methods ; DNA Probes/genetics ; Evolution, Molecular ; }, abstract = {Phylogenomic data are revolutionizing the field of insect phylogenetics. One of the most tenable and cost-effective methods of generating phylogenomic data is target enrichment, which has resulted in novel phylogenetic hypotheses and revealed new insights into insect evolution. Orthoptera is the most diverse insect order within polyneoptera and includes many evolutionarily and ecologically interesting species. Still, the order as a whole has lagged behind other major insect orders in terms of transitioning to phylogenomics. In this study, we developed an Orthoptera-specific target enrichment (OR-TE) probe set from 80 transcriptomes across Orthoptera. The probe set targets 1828 loci from genes exhibiting a wide range of evolutionary rates. The utility of this new probe set was validated by generating phylogenomic data from 36 orthopteran species that had not previously been subjected to phylogenomic studies. The OR-TE probe set captured an average of 1037 loci across the tested taxa, resolving relationships across broad phylogenetic scales. Our detailed documentation of the probe design and bioinformatics process is intended to facilitate the widespread adoption of this tool.}, }
@article {pmid39269993, year = {2024}, author = {Golumbeanu, M and Briët, O and Champagne, C and Lemant, J and Winkel, M and Zogo, B and Gerhards, M and Sinka, M and Chitnis, N and Penny, M and Pothin, E and Smith, T}, title = {AnophelesModel: An R package to interface mosquito bionomics, human exposure and intervention effects with models of malaria intervention impact.}, journal = {PLoS computational biology}, volume = {20}, number = {9}, pages = {e1011609}, pmid = {39269993}, issn = {1553-7358}, mesh = {Animals ; Humans ; *Malaria/transmission/prevention &amp; control ; *Anopheles/physiology ; *Mosquito Vectors/physiology ; *Mosquito Control/methods ; *Software ; Computational Biology ; Models, Biological ; }, abstract = {In recent decades, field and semi-field studies of malaria transmission have gathered geographic-specific information about mosquito ecology, behaviour and their sensitivity to interventions. Mathematical models of malaria transmission can incorporate such data to infer the likely impact of vector control interventions and hence guide malaria control strategies in various geographies. To facilitate this process and make model predictions of intervention impact available for different geographical regions, we developed AnophelesModel. AnophelesModel is an online, open-access R package that quantifies the impact of vector control interventions depending on mosquito species and location-specific characteristics. In addition, it includes a previously published, comprehensive, curated database of field entomological data from over 50 Anopheles species, field data on mosquito and human behaviour, and estimates of vector control effectiveness. Using the input data, the package parameterizes a discrete-time, state transition model of the mosquito oviposition cycle and infers species-specific impacts of various interventions on vectorial capacity. In addition, it offers formatted outputs ready to use in downstream analyses and by other models of malaria transmission for accurate representation of the vector-specific components. Using AnophelesModel, we show how the key implications for intervention impact change for various vectors and locations. The package facilitates quantitative comparisons of likely intervention impacts in different geographical settings varying in vector compositions, and can thus guide towards more robust and efficient malaria control recommendations. The AnophelesModel R package is available under a GPL-3.0 license at https://github.com/SwissTPH/AnophelesModel.}, }
@article {pmid39269992, year = {2024}, author = {O'Meara, BC and Beaulieu, JM}, title = {Noise leads to the perceived increase in evolutionary rates over short time scales.}, journal = {PLoS computational biology}, volume = {20}, number = {9}, pages = {e1012458}, pmid = {39269992}, issn = {1553-7358}, mesh = {*Computational Biology/methods ; Models, Genetic ; Biological Evolution ; Evolution, Molecular ; Animals ; Models, Statistical ; Humans ; }, abstract = {Across a variety of biological datasets, from genomes to conservation to the fossil record, evolutionary rates appear to increase toward the present or over short time scales. This has long been seen as an indication of processes operating differently at different time scales, even potentially as an indicator of a need for new theory connecting macroevolution and microevolution. Here we introduce a set of models that assess the relationship between rate and time and demonstrate that these patterns are statistical artifacts of time-independent errors present across ecological and evolutionary datasets, which produce hyperbolic patterns of rates through time. We show that plotting a noisy numerator divided by time versus time leads to the observed hyperbolic pattern; in fact, randomizing the amount of change over time generates patterns functionally identical to observed patterns. Ignoring errors can not only obscure true patterns but create novel patterns that have long misled scientists.}, }
@article {pmid39267994, year = {2024}, author = {Boyes, D and Broad, GR and Holland, PWH and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Oak Nycteoline moth, Nycteola revayana (Scopoli, 1772).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {258}, pmid = {39267994}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Nycteola revayana (the Oak Nycteoline moth; Arthropoda; Insecta; Lepidoptera; Nolidae). The genome sequence is 621.0 megabases in span. Most of the assembly is scaffolded into 26 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.25 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,235 protein-coding genes.}, }
@article {pmid39266599, year = {2024}, author = {He, H and Boehringer, T and Schäfer, B and Heppell, K and Beck, C}, title = {Analyzing spatio-temporal dynamics of dissolved oxygen for the River Thames using superstatistical methods and machine learning.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {21288}, pmid = {39266599}, issn = {2045-2322}, support = {VH-NG-1727//Helmholtz Association and the Networking Fund/ ; }, abstract = {By employing superstatistical methods and machine learning, we analyze time series data of water quality indicators for the River Thames (UK). The indicators analyzed include dissolved oxygen, temperature, electrical conductivity, pH, ammonium, turbidity, and rainfall, with a specific focus on the dynamics of dissolved oxygen. After detrending, the probability density functions of dissolved oxygen fluctuations exhibit heavy tails that are effectively modeled using q-Gaussian distributions. Our findings indicate that the multiplicative Empirical Mode Decomposition method stands out as the most effective detrending technique, yielding the highest log-likelihood in nearly all fittings. We also observe that the optimally fitted width parameter of the q-Gaussian shows a negative correlation with the distance to the sea, highlighting the influence of geographical factors on water quality dynamics. In the context of same-time prediction of dissolved oxygen, regression analysis incorporating various water quality indicators and temporal features identify the Light Gradient Boosting Machine as the best model. SHapley Additive exPlanations reveal that temperature, pH, and time of year play crucial roles in the predictions. Furthermore, we use the Transformer, a state-of-the-art machine learning model, to forecast dissolved oxygen concentrations. For long-term forecasting, the Informer model consistently delivers superior performance, achieving the lowest Mean Absolute Error (0.15) and Symmetric Mean Absolute Percentage Error (21.96%) with the 192 historical time steps that we used. This performance is attributed to the Informer's ProbSparse self-attention mechanism, which allows it to capture long-range dependencies in time-series data more effectively than other machine learning models. It effectively recognizes the half-life cycle of dissolved oxygen, with particular attention to critical periods such as morning to early afternoon, late evening to early morning, and key intervals between the 16th and 26th quarter-hours of the previous half-day. Our findings provide valuable insights for policymakers involved in ecological health assessments, aiding in accurate predictions of river water quality and the maintenance of healthy aquatic ecosystems.}, }
@article {pmid39264951, year = {2024}, author = {Pfennig, T and Kullmann, E and Zavřel, T and Nakielski, A and Ebenhöh, O and Červený, J and Bernát, G and Matuszyńska, AB}, title = {Shedding light on blue-green photosynthesis: A wavelength-dependent mathematical model of photosynthesis in Synechocystis sp. PCC 6803.}, journal = {PLoS computational biology}, volume = {20}, number = {9}, pages = {e1012445}, pmid = {39264951}, issn = {1553-7358}, mesh = {*Photosynthesis/physiology ; *Synechocystis/metabolism/physiology ; *Light ; *Models, Biological ; Computational Biology ; Carbon Dioxide/metabolism ; Carbon Cycle/physiology ; Phycobilisomes/metabolism ; Computer Simulation ; }, abstract = {Cyanobacteria hold great potential to revolutionize conventional industries and farming practices with their light-driven chemical production. To fully exploit their photosynthetic capacity and enhance product yield, it is crucial to investigate their intricate interplay with the environment including the light intensity and spectrum. Mathematical models provide valuable insights for optimizing strategies in this pursuit. In this study, we present an ordinary differential equation-based model for the cyanobacterium Synechocystis sp. PCC 6803 to assess its performance under various light sources, including monochromatic light. Our model can reproduce a variety of physiologically measured quantities, e.g. experimentally reported partitioning of electrons through four main pathways, O2 evolution, and the rate of carbon fixation for ambient and saturated CO2. By capturing the interactions between different components of a photosynthetic system, our model helps in understanding the underlying mechanisms driving system behavior. Our model qualitatively reproduces fluorescence emitted under various light regimes, replicating Pulse-amplitude modulation (PAM) fluorometry experiments with saturating pulses. Using our model, we test four hypothesized mechanisms of cyanobacterial state transitions for ensemble of parameter sets and found no physiological benefit of a model assuming phycobilisome detachment. Moreover, we evaluate metabolic control for biotechnological production under diverse light colors and irradiances. We suggest gene targets for overexpression under different illuminations to increase the yield. By offering a comprehensive computational model of cyanobacterial photosynthesis, our work enhances the basic understanding of light-dependent cyanobacterial behavior and sets the first wavelength-dependent framework to systematically test their producing capacity for biocatalysis.}, }
@article {pmid39264914, year = {2024}, author = {Zhang, K and Cao, Y and Guo, X and Kong, F and Sun, H and Jing, T and Zhan, Y and Qi, F}, title = {Comparative transcriptome analysis of differentially expressed genes and pathways in male and female flowers of Fraxinus mandshurica.}, journal = {PloS one}, volume = {19}, number = {9}, pages = {e0308013}, pmid = {39264914}, issn = {1932-6203}, mesh = {*Flowers/genetics/metabolism/growth &amp; development ; *Gene Expression Regulation, Plant ; *Gene Expression Profiling ; *Fraxinus/genetics ; *Transcriptome ; Signal Transduction/genetics ; Plant Proteins/genetics/metabolism ; Gene Ontology ; Genes, Plant ; }, abstract = {Fraxinus mandshurica Rupr. (F. mandshurica) is a dioecious tree species with important ecological and application values. To delve deeper into the regulatory pathways and genes responsible for male and female flowers in F. mandshurica, we conducted transcriptome sequencing on male and female flowers at four distinct stages. The analysis revealed that the female database generated 38,319,967 reads while the male database generated 43,320,907 reads, resulting in 2930 differentially expressed genes with 1441 were up-regulated and 1489 down-regulated in males compared to females. Following an analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), four distinct pathways (hormone signal transduction, energy metabolism, flavonoid biosynthesis, and photoperiod) linked to female and male flowers were identified. Subsequently, qRT-PCR verification revealed that FmAUX/IAA, FmEIN3, and FmA-ARR genes in hormone signal transduction pathway are related to female flower development. Meanwhile, FmABF genes in hormone signal transduction pathway, FmGS and FmGDH genes in energy metabolism pathway, FmFLS genes in flavonoid biosynthesis pathway, and FmCaM, FmCRY, and FmPKA genes in photoperiod pathway are related to male flower development. This study was the first to analyze the transcriptome of male and female flowers of F. mandshurica, providing a reference for the developmental pathways and gene expression levels of male and female plants.}, }
@article {pmid39264239, year = {2024}, author = {Silva, M and Capps, S and London, JK}, title = {Community-Engaged Research and the Use of Open Access ToxVal/ToxRef In Vivo Databases and New Approach Methodologies (NAM) to Address Human Health Risks From Environmental Contaminants.}, journal = {Birth defects research}, volume = {116}, number = {9}, pages = {e2395}, pmid = {39264239}, issn = {2472-1727}, support = {P30 ES023513/ES/NIEHS NIH HHS/United States ; }, mesh = {Humans ; *Environmental Pollutants ; *Databases, Factual ; Risk Assessment/methods ; Environmental Exposure/adverse effects ; United States ; United States Environmental Protection Agency ; Pesticides/adverse effects/toxicity ; }, abstract = {BACKGROUND: The paper analyzes opportunities for integrating Open access resources (Abstract Sifter, US EPA and NTP Toxicity Value and Toxicity Reference [ToxVal/ToxRefDB]) and New Approach Methodologies (NAM) integration into Community Engaged Research (CEnR).<br><br>METHODS: CompTox Chemicals Dashboard and Integrated Chemical Environment with in vivo ToxVal/ToxRef and NAMs (in vitro) databases are presented in three case studies to show how these resources could be used in Pilot Projects involving Community Engaged Research (CEnR) from the University of California, Davis, Environmental Health Sciences Center.<br><br>RESULTS: Case #1 developed a novel assay methodology for testing pesticide toxicity. Case #2 involved detection of water contaminants from wildfire ash and Case #3 involved contaminants on Tribal Lands. Abstract Sifter/ToxVal/ToxRefDB regulatory data and NAMs could be used to screen/prioritize risks from exposure to metals, PAHs and PFAS from wildfire ash leached into water and to investigate activities of environmental toxins (e.g., pesticides) on Tribal lands. Open access NAMs and computational tools can apply to detection of sensitive biological activities in potential or known adverse outcome pathways to predict points of departure (POD) for comparison with regulatory values for hazard identification. Open access Systematic Empirical Evaluation of Models or biomonitoring exposures are available for human subpopulations and can be used to determine bioactivity (POD) to exposure ratio to facilitate mitigation.<br><br>CONCLUSIONS: These resources help prioritize chemical toxicity and facilitate regulatory decisions and health protective policies that can aid stakeholders in deciding on needed research. Insights into exposure risks can aid environmental justice and health equity advocates.}, }
@article {pmid39263387, year = {2024}, author = {Deeleman-Reinhold, CL and Addink, W and Miller, JA}, title = {The genera Chrysillaand Phintelloidesrevisited with the description of a new species (Araneae, Salticidae) using digital specimen DOIs and nanopublications.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e129438}, pmid = {39263387}, issn = {1314-2828}, abstract = {BACKGROUND: Two Southeast Asian spider collections: that of Frances and John Murphy, now in the Manchester University Museum and the Deeleman collection, now at the Naturalis Biodiversity Center in Leiden constituted the basis of this analysis of Chrysilla Thorell, 1887 and related genera. The latter collection also includes many thousands of spiders obtained by canopy fogging for an ecological project in Borneo by A. Floren.<br><br>NEW INFORMATION: Some incongruences within the genera of the tribe Chrysillini are disentangled. The transfer of C.jesudasi Caleb &amp; Mathai, 2014 from Chrysilla as type species of Phintelloides Kanesharatnam &amp; Benjamin, 2019, based on analysis of molecular data is validated by morphology. An interesting new species known only from the forest canopy in Borneo, Phintelloidesscandens sp. nov, is described based on both male and female specimens. Distinguishing chrysilline genera is mostly based on traditional somatic characters, e.g., habitus, carapace and abdomen patterns, mouthparts, and genital organs. The utility of two character systems for distinguishing chrysilline genera is highlighted: 1) the presence of a flexible, articulating embolic tegular branch (etb) in combination with the conformation of the characteristic construction of the epigyne in Chrysilla and Phintelloides; 2) presence of red colour on carapace and abdomen of live males and females, in combination with abundant blue/violet/white iridescent scales such as inChrysilla and Siler. The red colour usually gets lost in alcohol, hampering species identification of alcohol material. The genera Chrysilla andPhintelloidesare redefined. Specimens of the heretofore unknown female of Chrysilla deelemani Pr&#xf3;szy&#x144;ski &amp; Deeleman-Reinhold, 2010 are described. The male and female ofChrysillalauta and male of C.volupe are redescribed. The genus Chrysilla is diagnosed and discriminated from PhintellaB&#xf6;senberg &amp; Strand, 1906, SilerSimon, 1889, Phintelloides Kanesharatnam &amp; Benjamin, 2019 andProszynskiaKanesharatnam &amp; Benjamin, 2019. The structure of the female genital organ of Phintelloidesflavumi Kanesharatnam &amp; Benjamin, 2019 is scrutinized and the generic placement of Phintelloides is discussed. Males and females of one of the most variable species, Phintelloidesversicolor (C. L. Koch, 1846) are redescribed.Phintelloidesmunita(B&#xf6;senberg &amp; Strand, 1906) is removed from synonymy with P.versicolor. Phintellaleucaspis Simon 1903 (male, Sumatra) is synonymized withP.versicolor.Biodiversity data are increasingly reliant on digital infrastructure. By linking physical specimens to digital representations of their associated data, we can lower barriers to information flow. Here we demonstrate a workflow whereby persistent identifiers (PIDs) in the form of DOIs issued by DataCite are assigned to specimens. Recognized taxa are identified by their catalog of life identifier, or by registration in ZooBank where no catalog of life identifier is available. We demonstrate the use of nanopublications, creating a series of machine readable, scientifically meaningful assertions regarding the provenance and identification of cited specimens. All human agents associated with the specimen data are linked to a persistent identifier issued by either ORCiD or Wikidata.}, }
@article {pmid39262445, year = {2023}, author = {Borry, M and Forsythe, A and Andrades Valtueña, A and Hübner, A and Ibrahim, A and Quagliariello, A and White, AE and Kocher, A and Vågene, &#xc5;J and Bartholdy, BP and Spurīte, D and Ponce-Soto, GY and Neumann, G and Huang, IT and Light, I and Velsko, IM and Jackson, I and Frangenberg, J and Serrano, JG and Fumey, J and Özdoğan, KT and Blevins, KE and Daly, KG and Lopopolo, M and Moraitou, M and Michel, M and van Os, M and Bravo-Lopez, MJ and Sarhan, MS and Dagtas, ND and Oskolkov, N and Smith, OS and Lebrasseur, O and Rozwalak, P and Eisenhofer, R and Wasef, S and Ramachandran, SL and Vanghi, V and Warinner, C and Fellows Yates, JA}, title = {Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT.}, journal = {F1000Research}, volume = {12}, number = {}, pages = {926}, pmid = {39262445}, issn = {2046-1402}, support = {T32 GM139782/GM/NIGMS NIH HHS/United States ; }, mesh = {*Metagenomics/methods ; Humans ; *Metadata ; High-Throughput Nucleotide Sequencing/methods ; Software ; Metagenome ; Computational Biology/methods ; DNA, Ancient/analysis ; }, abstract = {BACKGROUND: Access to sample-level metadata is important when selecting public metagenomic sequencing datasets for reuse in new biological analyses. The Standards, Precautions, and Advances in Ancient Metagenomics community (SPAAM, https://spaam-community.org) has previously published AncientMetagenomeDir, a collection of curated and standardised sample metadata tables for metagenomic and microbial genome datasets generated from ancient samples. However, while sample-level information is useful for identifying relevant samples for inclusion in new projects, Next Generation Sequencing (NGS) library construction and sequencing metadata are also essential for appropriately reprocessing ancient metagenomic data. Currently, recovering information for downloading and preparing such data is difficult when laboratory and bioinformatic metadata is heterogeneously recorded in prose-based publications.<br><br>METHODS: Through a series of community-based hackathon events, AncientMetagenomeDir was updated to provide standardised library-level metadata of existing and new ancient metagenomic samples. In tandem, the companion tool 'AMDirT' was developed to facilitate rapid data filtering and downloading of ancient metagenomic data, as well as improving automated metadata curation and validation for AncientMetagenomeDir.<br><br>RESULTS: AncientMetagenomeDir was extended to include standardised metadata of over 6000 ancient metagenomic libraries. The companion tool 'AMDirT' provides both graphical- and command-line interface based access to such metadata for users from a wide range of computational backgrounds. We also report on errors with metadata reporting that appear to commonly occur during data upload and provide suggestions on how to improve the quality of data sharing by the community.<br><br>CONCLUSIONS: Together, both standardised metadata reporting and tooling will help towards easier incorporation and reuse of public ancient metagenomic datasets into future analyses.}, }
@article {pmid39257810, year = {2024}, author = {Hartley, GA and Okhovat, M and Hoyt, SJ and Fuller, E and Pauloski, N and Alexandre, N and Alexandrov, I and Drennan, R and Dubocanin, D and Gilbert, DM and Mao, Y and McCann, C and Neph, S and Ryabov, F and Sasaki, T and Storer, JM and Svendsen, D and Troy, W and Wells, J and Core, L and Stergachis, A and Carbone, L and O'Neill, RJ}, title = {Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39257810}, issn = {2692-8205}, support = {P51 OD011092/OD/NIH HHS/United States ; R01 GM123312/GM/NIGMS NIH HHS/United States ; R01 HG007352/HG/NHGRI NIH HHS/United States ; R01 HG010333/HG/NHGRI NIH HHS/United States ; }, abstract = {Great apes have maintained a stable karyotype with few large-scale rearrangements; in contrast, gibbons have undergone a high rate of chromosomal rearrangements coincident with rapid centromere turnover. Here we characterize assembled centromeres in the Eastern hoolock gibbon, Hoolock leuconedys (HLE), finding a diverse group of transposable elements (TEs) that differ from the canonical alpha satellites found across centromeres of other apes. We find that HLE centromeres contain a CpG methylation centromere dip region, providing evidence this epigenetic feature is conserved in the absence of satellite arrays; nevertheless, we report a variety of atypical centromeric features, including protein-coding genes and mismatched replication timing. Further, large structural variations define HLE centromeres and distinguish them from other gibbons. Combined with differentially methylated TEs, topologically associated domain boundaries, and segmental duplications at chromosomal breakpoints, we propose that a "perfect storm" of multiple genomic attributes with propensities for chromosome instability shaped gibbon centromere evolution.}, }
@article {pmid39257624, year = {2024}, author = {Lohse, K and Vila, R and Hayward, A and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Lulworth Skipper, Thymelicus acteon (Rottemburg, 1775).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {266}, pmid = {39257624}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Thymelicus acteon (the Lulworth Skipper; Arthropoda; Insecta; Lepidoptera; Hesperiidae). The genome sequence is 537.0 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 17.08 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,813 protein-coding genes.}, }
@article {pmid39257623, year = {2024}, author = {Boyes, D and Januszczak, I and Lees, DC and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the White-pinion Spotted, Lomographa bimaculata (Fabricius, 1775).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {96}, pmid = {39257623}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Lomographa bimaculata (the White-pinion Spotted; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 554.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.66 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,749 protein coding genes.}, }
@article {pmid39257281, year = {2024}, author = {Calabrese, JM and Schüler, L and Fu, X and Gawel, E and Zozmann, H and Bumberger, J and Quaas, M and Wolf, G and Attinger, S}, title = {A novel, scenario-based approach to comparing non-pharmaceutical intervention strategies across nations.}, journal = {Journal of the Royal Society, Interface}, volume = {21}, number = {218}, pages = {20240301}, pmid = {39257281}, issn = {1742-5662}, support = {//Helmholtz-Gemeinschaft/ ; //Bundesministerium f&#xfc;r Bildung und Forschung/ ; //S&#xe4;chsisches Staatsministerium f&#xfc;r Wissenschaft und Kunst/ ; }, mesh = {*COVID-19/epidemiology/prevention &amp; control ; Humans ; New Zealand/epidemiology ; Switzerland/epidemiology ; Germany/epidemiology ; *SARS-CoV-2 ; Pandemics/prevention &amp; control ; }, abstract = {Comparing COVID-19 response strategies across nations is a key step in preparing for future pandemics. Conventional comparisons, which rank individual non-pharmaceutical intervention (NPI) effects, are limited by: (i) a focus on epidemiological outcomes; (ii) NPIs typically being applied as packages of interventions; and (iii) different political, economic and social conditions among nations. Here, we develop a coupled epidemiological-behavioural-macroeconomic model that can transfer NPI effects from a reference nation to a focal nation. This approach quantifies epidemiological, behavioural and economic outcomes while accounting for both packaged NPIs and differing conditions among nations. As a first proof of concept, we take Germany as our focal nation during Spring 2020, and New Zealand and Switzerland as reference nations with contrasting NPI strategies. Our results suggest that, while New Zealand's more aggressive strategy would have yielded modest epidemiological gains in Germany, it would have resulted in substantially higher economic costs while dramatically reducing social contacts. In contrast, Switzerland's more lenient strategy would have prolonged the first wave in Germany, but would also have increased relative costs. More generally, these findings indicate that our approach can provide novel, multifaceted insights on the efficacy of pandemic response strategies, and therefore merits further exploration and development.}, }
@article {pmid39255632, year = {2024}, author = {Amenu, K and Daborn, C and Huntington, B and Knight-Jones, T and Rushton, J and Grace, D}, title = {Prioritization, resource allocation and utilization of decision support tools in animal health: Results of qualitative interviews with experts.}, journal = {Preventive veterinary medicine}, volume = {233}, number = {}, pages = {106333}, doi = {10.1016/j.prevetmed.2024.106333}, pmid = {39255632}, issn = {1873-1716}, mesh = {Animals ; *Resource Allocation ; Decision Support Techniques ; Health Priorities ; Decision Making ; Animal Husbandry/methods ; Surveys and Questionnaires ; }, abstract = {A follow up to an online questionnaire survey (in a kind of a sequential study design), qualitative assessment was made on the views of selected animal health experts on disease prioritization methods, resource allocation and use of decision-support tools. This was done through in-depth interviews with experts working for national or international organizations and sectors. A semi-structured question guide was formulated based on the information generated in the online questionnaire and a systematic content analysis of animal and human health manuals for disease prioritization and resource allocation. In-depth, one-on-one, online interviews on the process of disease prioritization, animal health decision-making, types of prioritization tools and aspects of improvements in the tools were conducted during March and April 2022 with 20 expert informants. Prioritization approaches reported by experts were either single criterion-based or multiple criteria-based. Experts appreciated the single-criterion-based approach (quantitative) for its objectivity in contrast to multicriteria prioritization approaches which were criticized for their subjectivity. Interviews with the experts revealed a perceived lack of quality and reliable data to inform disease prioritization, especially in smallholder livestock production systems. It was found that outputs of disease prioritization exercises do not generally directly influence resource allocation in animal health and highlighted the paucity of funding for animal health compared to other agricultural sectors. The experts considered that the available decision-support tools in animal health need improvement in terms of data visualization for interpretation, management decision making and advocacy. Further recommendations include minimizing subjective biases by increasing the availability and quality of data and improving the translation of disease prioritization outputs into actions and the resources to deliver those actions. DATA AVAILABILITY STATEMENT: The data can be obtained from the corresponding author upon request.}, }
@article {pmid39255272, year = {2024}, author = {Sylla, A and Chevillon, C and Djidjiou-Demasse, R and Seydi, O and Campos, CAV and Dogbe, M and Fast, KM and Pechal, JL and Rakestraw, A and Scott, ME and Sandel, MW and Jordan, H and Benbow, ME and Guégan, JF}, title = {Understanding the transmission of bacterial agents of sapronotic diseases using an ecosystem-based approach: A first spatially realistic metacommunity model.}, journal = {PLoS computational biology}, volume = {20}, number = {9}, pages = {e1012435}, pmid = {39255272}, issn = {1553-7358}, mesh = {Humans ; *Ecosystem ; Mycobacterium ulcerans/pathogenicity ; Buruli Ulcer/transmission/microbiology ; Models, Biological ; Computational Biology ; Animals ; }, abstract = {Pathogens such as bacteria, fungi and viruses are important components of soil and aquatic communities, where they can benefit from decaying and living organic matter, and may opportunistically infect human and animal hosts. One-third of human infectious diseases is constituted by sapronotic disease agents that are natural inhabitants of soil or aquatic ecosystems. They are capable of existing and reproducing in the environment outside of the host for extended periods of time. However, as ecological research on sapronosis is infrequent and epidemiological models are even rarer, very little information is currently available. Their importance is overlooked in medical and veterinary research, as well as the relationships between free environmental forms and those that are pathogenic. Here, using dynamical models in realistic aquatic metacommunity systems, we analyze sapronosis transmission, using the human pathogen Mycobacterium ulcerans that is responsible for Buruli ulcer. We show that the persistence of bacilli in aquatic ecosystems is driven by a seasonal upstream supply, and that the attachment and development of cells to aquatic living forms is essential for such pathogen persistence and population dynamics. Our work constitutes the first set of metacommunity models of sapronotic disease transmission, and is highly flexible for adaptation to other types of sapronosis. The importance of sapronotic agents on animal and human disease burden needs better understanding and new models of sapronosis disease ecology to guide the management and prevention of this important group of pathogens.}, }
@article {pmid39255143, year = {2024}, author = {Jiang, W and Windl, M and Tag, B and Sarsenbayeva, Z and Mayer, S}, title = {An Immersive and Interactive VR Dataset to Elicit Emotions.}, journal = {IEEE transactions on visualization and computer graphics}, volume = {30}, number = {11}, pages = {7343-7353}, doi = {10.1109/TVCG.2024.3456202}, pmid = {39255143}, issn = {1941-0506}, mesh = {Humans ; *Emotions/physiology ; *Virtual Reality ; Female ; Male ; *Computer Graphics ; Adult ; Young Adult ; User-Computer Interface ; Databases, Factual ; Video Recording ; }, abstract = {Images and videos are widely used to elicit emotions; however, their visual appeal differs from real-world experiences. With virtual reality becoming more realistic, immersive, and interactive, we envision virtual environments to elicit emotions effectively, rapidly, and with high ecological validity. This work presents the first interactive virtual reality dataset to elicit emotions. We created five interactive virtual environments based on corresponding validated 360° videos and validated their effectiveness with 160 participants. Our results show that our virtual environments successfully elicit targeted emotions. Compared with the existing methods using images or videos, our dataset allows virtual reality researchers and practitioners to integrate their designs effectively with emotion elicitation settings in an immersive and interactive way.}, }
@article {pmid39253482, year = {2024}, author = {Mortzfeld, BM and Bhattarai, SK and Bucci, V}, title = {Expanding the toolbox: Novel class IIb microcins show activity against Gram-negative ESKAPE and plant pathogens.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.12.05.570296}, pmid = {39253482}, issn = {2692-8205}, abstract = {Interspecies interactions involving direct competition via bacteriocin production play a vital role in shaping ecological dynamics within microbial ecosystems. For instance, the ribosomally-produced siderophore bacteriocins, known as class IIb microcins, affect the colonization of host-associated pathogenic Enterobacteriaceae species. Notably, to date, only five of these antimicrobials have been identified, all derived from specific Escherichia coli and Klebsiella pneumoniae strains. We hypothesized that class IIb microcin production extends beyond these specific compounds and organisms. With a customized informatics-driven approach, screening bacterial genomes in public databases with BLAST and manual curation, we have discovered twelve previously unknown class IIb microcins in seven additional Enterobacteriaceae species, encompassing phytopathogens and environmental isolates. We introduce three novel clades of microcins (MccW, MccX, and MccZ), while also identifying eight new variants of the five known class IIb microcins. To validate their antimicrobial potential, we heterologously expressed these microcins in E. coli and demonstrated efficacy against a variety of bacterial isolates, including plant pathogens from the genera Brenneria, Gibbsiella, and Rahnella . Two newly discovered microcins exhibit activity against Gram-negative ESKAPE pathogens, i.e. Acinetobacter baumannii or Pseudomonas aeruginosa , providing the first evidence that class IIb microcins can target bacteria outside of the Enterobacteriaceae family. This study underscores that class IIb microcin genes are more prevalent in the microbial world than previously recognized and that synthetic hybrid microcins can be a viable tool to target clinically relevant drug-resistant pathogens. Our findings hold significant promise for the development of innovative engineered live biotherapeutic products tailored to combat these resilient bacteria.}, }
@article {pmid39250076, year = {2024}, author = {Zancolli, G and von Reumont, BM and Anderluh, G and Caliskan, F and Chiusano, ML and Fröhlich, J and Hapeshi, E and Hempel, BF and Ikonomopoulou, MP and Jungo, F and Marchot, P and de Farias, TM and Modica, MV and Moran, Y and Nalbantsoy, A and Procházka, J and Tarallo, A and Tonello, F and Vitorino, R and Zammit, ML and Antunes, A}, title = {Web of venom: exploration of big data resources in animal toxin research.}, journal = {GigaScience}, volume = {13}, number = {}, pages = {}, pmid = {39250076}, issn = {2047-217X}, support = {//European Cooperation in Science and Technology/ ; //Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, mesh = {Animals ; *Venoms ; *Internet ; *Computational Biology/methods ; *Big Data ; Databases, Factual ; }, abstract = {Research on animal venoms and their components spans multiple disciplines, including biology, biochemistry, bioinformatics, pharmacology, medicine, and more. Manipulating and analyzing the diverse array of data required for venom research can be challenging, and relevant tools and resources are often dispersed across different online platforms, making them less accessible to nonexperts. In this article, we address the multifaceted needs of the scientific community involved in venom and toxin-related research by identifying and discussing web resources, databases, and tools commonly used in this field. We have compiled these resources into a comprehensive table available on the VenomZone website (https://venomzone.expasy.org/10897). Furthermore, we highlight the challenges currently faced by researchers in accessing and using these resources and emphasize the importance of community-driven interdisciplinary approaches. We conclude by underscoring the significance of enhancing standards, promoting interoperability, and encouraging data and method sharing within the venom research community.}, }
@article {pmid39244927, year = {2024}, author = {Ibrahim, AS and Kuuire, V and Kepe, T}, title = {On mapping urban community resilience: Land use vulnerability, coping and adaptive strategies in Ghana.}, journal = {Journal of environmental management}, volume = {370}, number = {}, pages = {122426}, doi = {10.1016/j.jenvman.2024.122426}, pmid = {39244927}, issn = {1095-8630}, mesh = {Ghana ; *Floods ; Humans ; *Cities ; Climate Change ; Urban Population ; Geographic Information Systems ; }, abstract = {Cities across the globe are prioritizing resilience in the wake of increasing climate change-related disasters. About 44% of these disasters are floods and their manifestation in cities is more pronounced, threatening urban social, ecological, and economic systems. This study draws on community resilience and participatory GIS, to examine land use vulnerability to flooding and local coping and adaptive strategies to achieve resilience. Using Ghana as a case study, the results show that participatory mapping offers community resilience benefits by providing context to community resilience challenges and potentials, enabling a deeper understanding of socio-environmental coupling that contributes to flood vulnerability and builds on community adaptive strategies through harnessing local community knowledge. We identified that topography, poor drainage and road network, rainfall variability, residents' land use practices, and land use planning conundrum drive disparities in land use vulnerability to flooding. Participants underscored the necessity of critical urban infrastructure in facilitating community adaptability to floods. The findings indicate that socio-spatial inequities threaten urban community resilience, especially in increasingly cosmopolitan urban contexts, by putting the marginalized urban population in a more vulnerable position. We recommend the prioritization of recognitional equity in community resilience planning efforts to allow for the targeting of resilient interventions that reflect and respect social differentiation in the urban environment so that outcomes will not exacerbate or generate new urban socio-spatial inequalities.}, }
@article {pmid39242865, year = {2023}, author = {Karakulak, A and Tepe, B and Dimitrova, R and Abdelrahman, M and Akaliyski, P and Alaseel, R and Alkamali, YA and Amin, A and Lizarzaburu Aguinaga, DA and Andres, A and Aruta, JJBR and Assiotis, M and Avanesyan, H and Ayub, N and Bacikova-Sleskova, M and Baikanova, R and Bakkar, B and Bartoluci, S and Benitez, D and Bodnar, I and Bolatov, A and Borchet, J and Bosnar, K and Broche-Pérez, Y and Buzea, C and Cassibba, R and Carbonell, MM and Chen, BB and Dimitrovska, GR and Công Doanh, D and Dominguez Espinosa, ADC and Edine, WG and Ferenczi, N and Fernández-Morales, R and Gaete, J and Gan, Y and Giolo, S and Giordani, RCF and Friehs, MT and Gindi, S and Gjoneska, B and Godoy, JC and Del Pilar Grazioso, M and Hancheva, C and Hapunda, G and Hihara, S and Husain, MS and Islam, MS and Janovská, A and Javakhishvili, N and Jovanović, V and Kabir, RS and Abdul Kadir, NB and Karl, J and Katović, D and Kauyzbay, Z and Kawashima, TD and Kazmierczak, M and Khanna, R and Khosla, M and Klicperová-Baker, M and Kozina, A and Krauss, SE and Landabur, R and Lefringhausen, K and Lewandowska-Walter, A and Liang, YH and Makashvili, A and Malik, S and Manrique-Millones, D and Mastrotheodoros, S and McGrath, B and Mechili, EA and Mejía, M and Mhizha, S and Michalek-Kwiecien, J and Miconi, D and Mohsen, F and Moreta-Herrera, R and Muhl, C and Muradyan, M and Musso, P and Naterer, A and Nemat, A and Neto, F and Neto, J and Palacio, LMA and Okati-Aliabad, H and Orellana, CI and Orellana, LM and Mishra, SK and Park, J and Pavlova, I and Peralta, E and Petrytsa, P and Pišot, S and Prot, F and Rasia, J and Rivera, R and Riyanti, BPD and Samekin, A and Seisembekov, T and Serapinas, D and Silletti, F and Sharma, P and Shukla, S and Skrzypińska, K and Šolcová, IP and Solomontos-Kountouri, O and Stanciu, A and Stefenel, D and Steinmetz, LCL and Stogianni, M and Stuart, J and Sudarnoto, LF and Sugimura, K and Sultana, S and Suryani, AO and Tair, E and Tavitian-Elmadjan, L and Thome, LD and Uka, F and Valickienė, RP and Walter, B and Wendt, GW and Yang, PJ and Yıldırım, E and Yu, Y and Yunes, MAM and Zanoni da Silva, M and Rudnev, M}, title = {Trust in government moderates the association between fear of COVID-19 as well as empathic concern and preventive behaviour.}, journal = {Communications psychology}, volume = {1}, number = {1}, pages = {43}, pmid = {39242865}, issn = {2731-9121}, support = {INV-003092/GATES/Gates Foundation/United States ; }, abstract = {With the COVID-19 pandemic, behavioural scientists aimed to illuminate reasons why people comply with (or not) large-scale cooperative activities. Here we investigated the motives that underlie support for COVID-19 preventive behaviours in a sample of 12,758 individuals from 34 countries. We hypothesized that the associations of empathic prosocial concern and fear of disease with support towards preventive COVID-19 behaviours would be moderated by trust in the government. Results suggest that the association between fear of disease and support for COVID-19 preventive behaviours was strongest when trust in the government was weak (both at individual- and country-level). Conversely, the association with empathic prosocial concern was strongest when trust in the government was high, but this moderation was only found at individual-level scores of governmental trust. We discuss how motivations may be shaped by socio-cultural context, and outline how findings may contribute to a better understanding of collective action during global crises.}, }
@article {pmid39242702, year = {2023}, author = {Santangeli, A and Haukka, A and Morris, W and Arkkila, S and Delhey, K and Kempenaers, B and Valcu, M and Dale, J and Lehikoinen, A and Mammola, S}, title = {What drives our aesthetic attraction to birds?.}, journal = {npj biodiversity}, volume = {2}, number = {1}, pages = {20}, pmid = {39242702}, issn = {2731-4243}, abstract = {In the Anthropocene, the era when the imprint of humans on nature is pervasive across the planet, it is of utmost importance to understand human relationships with other species. The aesthetics of nature, and of species, is one of the values that plays a role in shaping human-nature relationships. Birds are ubiquitous across the world. The beauty of birds exerts a powerful tug on human emotions, and bird-rich areas attract scores of eco-tourists. People naturally find some birds more beautiful or interesting than others, but we currently lack a global understanding of the specifics of what makes a species aesthetically attractive. Here, we used a global citizen-science database on bird attractiveness covering nearly all extant bird species, to show that there are specific visual features that drive our aesthetic appeal for some bird species over others. First, our aesthetic attraction is highest for smaller birds with specific, vivid colors (e.g., blue and red, and departing from brown-grey) and extreme ornaments (a long crest or tail). Second, our aesthetic attraction is highest for species with broad ranges, possibly because such species may be more familiar to us. The features that make us attracted to a particular bird strongly align with broad human visual aesthetic preferences in modern society. Unveiling the visual features underpinning our aesthetic attraction to birds is a critical step towards optimizing conservation (e.g., via conservation marketing) and education campaigns, and leverage the cultural ecosystem service potential of birds.}, }
@article {pmid39240878, year = {2024}, author = {Shipley, ON and Dabrowski, AJ and Bowen, GJ and Hayden, B and Pauli, JN and Jordan, C and Anderson, L and Bailey, A and Bataille, CP and Cicero, C and Close, HG and Cook, C and Cook, JA and Desai, AR and Evaristo, J and Filley, TR and France, CAM and Jackson, AL and Kim, SL and Kopf, S and Loisel, J and Manlick, PJ and McFarlin, JM and McMeans, BC and O'Connell, TC and Pilaar Birch, SE and Putman, AL and Semmens, BX and Stantis, C and Stricker, CA and Szejner, P and Trammell, TLE and Uhen, MD and Weintraub-Leff, S and Wooller, MJ and Williams, JW and Yarnes, CT and Vander Zanden, HB and Newsome, SD}, title = {Design, development, and implementation of IsoBank: A centralized repository for isotopic data.}, journal = {PloS one}, volume = {19}, number = {9}, pages = {e0295662}, pmid = {39240878}, issn = {1932-6203}, mesh = {*Databases, Factual ; *Metadata ; Isotopes ; Internet ; }, abstract = {Stable isotope data have made pivotal contributions to nearly every discipline of the physical and natural sciences. As the generation and application of stable isotope data continues to grow exponentially, so does the need for a unifying data repository to improve accessibility and promote collaborative engagement. This paper provides an overview of the design, development, and implementation of IsoBank (www.isobank.org), a community-driven initiative to create an open-access repository for stable isotope data implemented online in 2021. A central goal of IsoBank is to provide a web-accessible database supporting interdisciplinary stable isotope research and educational opportunities. To achieve this goal, we convened a multi-disciplinary group of over 40 analytical experts, stable isotope researchers, database managers, and web developers to collaboratively design the database. This paper outlines the main features of IsoBank and provides a focused description of the core metadata structure. We present plans for future database and tool development and engagement across the scientific community. These efforts will help facilitate interdisciplinary collaboration among the many users of stable isotopic data while also offering useful data resources and standardization of metadata reporting across eco-geoinformatics landscapes.}, }
@article {pmid39240386, year = {2025}, author = {Han, S and Hogue, W}, title = {Assessing Human Influence and Vegetative Dune Dynamics on Barrier Islands via Satellite Raster Classification.}, journal = {Environmental management}, volume = {75}, number = {3}, pages = {524-537}, pmid = {39240386}, issn = {1432-1009}, mesh = {Alabama ; Humans ; *Conservation of Natural Resources ; *Ecosystem ; Mississippi ; Climate Change ; Islands ; Satellite Imagery ; *Environmental Monitoring/methods ; Geographic Information Systems ; }, abstract = {Barrier islands support ecological diversity and offshore ecosystems and provide critical protection to coastal communities. Climate change has intensified the frequency and severity of hurricanes affecting these islands, leading to ongoing erosion. The primary goal of this study was to explore the relationship between human intervention such as development and construction and the vegetative dune systems on Gulf Coast barrier islands in Alabama and Mississippi, USA. This research employed two decades of satellite images of three neighboring barrier islands and employed GIS raster classification to track changes in the vegetative dune system in terms of: (1) dune coverage (surface area of the vegetation), (2) vegetative maturity (vegetation type), and (3) stability (fluctuations in the vegetative coverage over time). Time series and trend analyses were used to compare the results for three neighboring islands. The findings show that Dauphin Island, which features both commercial facilities and vacation homes, exhibited a decrease in total area over time, and had the lowest percentage of vegetative dune coverage and highest level of vegetative fluctuation. In contrast, Petit Bois and Horn Islands, which remain untouched by human activity, displayed significantly higher levels of vegetative maturity and coverage and comparatively less fluctuation. This research provides a foundation for those advocating for dune restoration strategies, development limitations, and conservation regulations as nature-based infrastructure solutions to combat erosion on barrier islands and serves as a point of entry for future inquiries in the field of environmental management.}, }
@article {pmid39239169, year = {2024}, author = {Boyes, D and Holland, PWH and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Elephant Hawk-moth, Deilephila elpenor (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {104}, pmid = {39239169}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Deilephila elpenor (the Elephant Hawk-moth; Arthropoda; Insecta; Lepidoptera; Sphingidae). The genome sequence is 414.1 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.37 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,748 protein coding genes.}, }
@article {pmid39235751, year = {2025}, author = {Lemée, P and Bridier, A}, title = {Bioinformatic Pipeline for Profiling Foodborne Bacterial Ecology and Resistome from Short-Read Metagenomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2852}, number = {}, pages = {289-309}, pmid = {39235751}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; *Computational Biology/methods ; *Food Microbiology/methods ; *Bacteria/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Microbiota/genetics ; }, abstract = {Next-generation sequencing revolutionized food safety management these last years providing access to a huge quantity of valuable data to identify, characterize, and monitor bacterial pathogens on the food chain. Shotgun metagenomics emerged as a particularly promising approach as it enables in-depth taxonomic profiling and functional investigation of food microbial communities. In this chapter, we provide a comprehensive step-by-step bioinformatical workflow to characterize bacterial ecology and resistome composition from metagenomic short-reads obtained by shotgun sequencing.}, }
@article {pmid39233902, year = {2024}, author = {Boyes, D and Holland, PWH and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Green Silver-lines, Pseudoips prasinana (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {117}, pmid = {39233902}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Pseudoips prasinana (the Green Silver-lines; Arthropoda; Insecta; Lepidoptera; Nolidae). The genome sequence is 1,125.7 megabases in span. Most of the assembly is scaffolded into 33 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.23 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,065 protein coding genes.}, }
@article {pmid39233899, year = {2024}, author = {Boyes, D and Holland, PWH and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Scarlet Tiger moth, Callimorpha dominula (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {31}, pmid = {39233899}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Callimorpha dominula (the Scarlet Tiger moth; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 658.1 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.45 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,234 protein coding genes.}, }
@article {pmid39233418, year = {2024}, author = {Li, X and Zhang, LY and Wu, C}, title = {Vegetation changes and influencing factors in different watersheds of Henan Province based on GEE and geographic detectors.}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {35}, number = {7}, pages = {1887-1896}, doi = {10.13287/j.1001-9332.202407.021}, pmid = {39233418}, issn = {1001-9332}, mesh = {China ; *Rivers ; *Ecosystem ; *Environmental Monitoring/methods ; Conservation of Natural Resources ; Plant Development ; Geographic Information Systems ; Plants ; }, abstract = {Clarifying vegetation changes and the driving factors can provide references for ecological restoration and sustainable social development. We analyzed vegetation distribution and trend changes in Henan Province and its basin zoning (Haihe River basin zoning, Yellow River basin zoning, Huaihe River basin zoning, Yangtze River basin zoning), with fractional vegetation cover data from 2000 to 2020 based on the Google Earth Engine platform, and by combining Theil-Sen Median trend analysis, Mann-Kendall test, and Hurst index. We also utilized factor detection and factor interaction to explore the individual and mutual influences of natural and anthropogenic factors on vegetation at different scales. The results showed that the fractional vegetation cover (FVC) in Henan Province exhibited a distribution pattern of higher coverage in the south and lower in the north during the study period, predominantly characterized by moderate to high vegetation coverage. The Yangtze River basin zoning had the highest coverage. FVC in Henan Province and its zoning exhibited a consistent pattern of fluctuating upward trends, with all areas showing significant improvement. Particularly, the Yangtze River basin zoning had the largest area of improvement. According to the Hurst index, apart from the possibility of continued improvement in the Huaihe River basin zoning, other zoning would be likely to shift from improvement to degradation in the future. Vegetation changes in Henan Province and its zoning were the result of combined effects of anthropogenic and natural factors, with the influence of these factors changing over time and the dominant factors varying by region. Anthropogenic factors such as land use/cover type and nighttime lighting had a stronger impact on vegetation than natural factors like elevation, slope, and annual mean low temperature. The interaction between factors, particularly between anthropogenic and natural factors, exhibited a nonlinear enhancing pattern.}, }
@article {pmid39233286, year = {2024}, author = {Long, XB and Yao, CR and Li, SY and Zhang, JG and Lu, ZJ and Ma, DD and Jiang, YX and Ying, GG and Shi, WJ}, title = {Multiomics analysis reveal the impact of 17α-Ethinylestradiol on mortality in juvenile zebrafish.}, journal = {Comparative biochemistry and physiology. Toxicology &amp; pharmacology : CBP}, volume = {286}, number = {}, pages = {110027}, doi = {10.1016/j.cbpc.2024.110027}, pmid = {39233286}, issn = {1532-0456}, mesh = {Animals ; *Zebrafish ; *Ethinyl Estradiol/toxicity ; *Water Pollutants, Chemical/toxicity ; Endocrine Disruptors/toxicity ; Transcriptome/drug effects ; Multiomics ; }, abstract = {17α-Ethinylestradiol (EE2) is known for its endocrine-disrupting effects on embryonic and adult fish. However, its impact on juvenile zebrafish has not been well established. In this study, juvenile zebrafish were exposed to EE2 at concentrations of 5 ng/L (low dose, L), 10 ng/L (medium dose, M), and 50 ng/L (high dose, H) from 21 days post-fertilization (dpf) to 49 dpf. We assessed their growth, development, behavior, transcriptome, and metabolome. The findings showed that the survival rate in the EE2-H group was 66.8 %, with all surviving fish displaying stunted growth and swollen, transparent abdomens by 49 dpf. Moreover, severe organ deformities were observed in the gills, kidneys, intestines, and heart of fish in both the EE2-H and EE2-M groups. Co-expression analysis of mRNA and lncRNA revealed that EE2 downregulated the transcription of key genes involved in the cell cycle, DNA replication, and Fanconi anemia signaling pathways. Additionally, metabolomic analysis indicated that EE2 influenced metabolism and development-related signaling pathways. These pathways were also significantly identified based on the genes regulated by lncRNA. Consequently, EE2 induced organ deformities and mortality in juvenile zebrafish by disrupting signaling pathways associated with development and metabolism. The results of this study offer new mechanistic insights into the adverse effects of EE2 on juvenile zebrafish based on multiomics analysis. The juvenile zebrafish are highly sensitive to EE2 exposure, which is not limited to adult and embryonic stages. It is a potential model for studying developmental toxicity.}, }
@article {pmid39233066, year = {2024}, author = {Wen, J and Chuai, X and Xiang, A and Liu, Y and Wang, T and Luo, Y and Miao, L and Zhang, L and Li, J and Zhao, R}, title = {Re-identifying farmland carbon neutrality gap under a new carbon counting and the framework of regional interactions in China.}, journal = {The Science of the total environment}, volume = {952}, number = {}, pages = {175996}, doi = {10.1016/j.scitotenv.2024.175996}, pmid = {39233066}, issn = {1879-1026}, abstract = {The farmland ecosystem, with its numerous material cycles and energy flows, is an important part of the carbon cycle in terrestrial ecosystems. Focusing on the carbon neutrality of farmland is meaningful for mitigating global warming and serving national low-carbon strategies. This study enriches the carbon accounting items of farmland and establishes a new research framework to check the carbon neutrality of farmland from the aspect of regional interactions and, subsequently, the inequality among China's provinces. The results revealed that there is still a great gap in the capability of China[']s farmland to reach carbon neutrality, with a gap value of up to 10,503 × 10[4] t C. All of the provinces presented net carbon emissions, and the per unit area carbon neutrality gaps showed spatial regularity decreasing from the coastal regions to the inland areas. Anthropogenic carbon emissions on farmland played a dominant role compared with soil organic carbon. Five provinces had reduced interior-regional carbon emissions through grain trade, and the amounts were especially high for developed regions, such as Guangdong, Zhejiang, Beijing, Shanghai and Jiangsu. Sixteen provinces gained external carbon emissions through trade; these were the less developed regions located mainly in the north, such as Inner Mongolia, Hebei, Jilin, Heilongjiang and Xinjiang. Under regional inequality, 15 provinces added to the net amount of the carbon emissions generated in external regions, with China's megacities adding the highest percentage, especially Beijing, with 389.95 % compared with its original emissions. Inequality showed that most provinces had a moderate status. Sichuan and Hunan experienced weak advantages, and six provinces had disadvantages. Therefore, constructing compensation and trade-based rights and responsibilities traceability mechanisms is important.}, }
@article {pmid39230451, year = {2024}, author = {Hendrix, JG and Robitaille, AL and Kusch, JM and Webber, QMR and Vander Wal, E}, title = {Faithful pals and familiar locales: differentiating social and spatial site fidelity during reproduction.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {379}, number = {1912}, pages = {20220525}, pmid = {39230451}, issn = {1471-2970}, support = {//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Animals ; Female ; *Reproduction ; *Reindeer/physiology ; Newfoundland and Labrador ; Social Behavior ; Geographic Information Systems ; }, abstract = {Site fidelity-the tendency to reuse familiar spaces-is expected to improve fitness. Familiarity with the local environment is particularly crucial when resource demands or predation risk are high. Consequently, site fidelity often peaks during reproduction when energetic costs are high and offspring are vulnerable. For many species, the environment they experience is not solely a function of geography but also of the social environment. Social fidelity, the selection for familiar social environments, could constitute an independent or parallel strategy to spatial fidelity when considering behaviour at the spatial-social interface. Using global positioning system locations from caribou across Newfoundland, we tested whether females selected calving sites based on proximity to familiar conspecifics, in addition to geographical (spatial) fidelity. These strategies were synergistic, not alternative, and correlated across the population but more variable within individuals. We also tested whether either form of fidelity affected reproductive success. We failed to detect an effect of spatial or social fidelity on reproductive success in this population. Nevertheless, given the association between social and spatial fidelity and the demonstrated fitness consequences of site fidelity in other systems, familiar conspecifics and the potential benefits these social partners provide may be an underappreciated component driving site fidelity.This article is part of the theme issue 'The spatial-social interface: a theoretical and empirical integration'.}, }
@article {pmid39229001, year = {2024}, author = {Obbard, DJ and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of a drosophilid fruit fly, Drosophila limbata von Roser 1840.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {365}, pmid = {39229001}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Drosophila limbata (drosophilid fruit fly; Arthropoda; Insecta; Diptera; Drosophilidae). The genome sequence is 233.5 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.09 kilobases in length.}, }
@article {pmid39226337, year = {2024}, author = {Rahman, AU and Tikhonov, G and Oksanen, J and Rossi, T and Ovaskainen, O}, title = {Accelerating joint species distribution modelling with Hmsc-HPC by GPU porting.}, journal = {PLoS computational biology}, volume = {20}, number = {9}, pages = {e1011914}, pmid = {39226337}, issn = {1553-7358}, mesh = {*Algorithms ; *Computational Biology/methods ; *Software ; Models, Biological ; Machine Learning ; Computer Graphics ; Models, Statistical ; Humans ; }, abstract = {Joint species distribution modelling (JSDM) is a widely used statistical method that analyzes combined patterns of all species in a community, linking empirical data to ecological theory and enhancing community-wide prediction tasks. However, fitting JSDMs to large datasets is often computationally demanding and time-consuming. Recent studies have introduced new statistical and machine learning techniques to provide more scalable fitting algorithms, but extending these to complex JSDM structures that account for spatial dependencies or multi-level sampling designs remains challenging. In this study, we aim to enhance JSDM scalability by leveraging high-performance computing (HPC) resources for an existing fitting method. Our work focuses on the Hmsc R-package, a widely used JSDM framework that supports the integration of various dataset types into a single comprehensive model. We developed a GPU-compatible implementation of its model-fitting algorithm using Python and the TensorFlow library. Despite these changes, our enhanced framework retains the original user interface of the Hmsc R-package. We evaluated the performance of the proposed implementation across various model configurations and dataset sizes. Our results show a significant increase in model fitting speed for most models compared to the baseline Hmsc R-package. For the largest datasets, we achieved speed-ups of over 1000 times, demonstrating the substantial potential of GPU porting for previously CPU-bound JSDM software. This advancement opens promising opportunities for better utilizing the rapidly accumulating new biodiversity data resources for inference and prediction.}, }
@article {pmid39225619, year = {2024}, author = {Liu, Z and Sun, Y and Li, Y and Ma, A and Willaims, NF and Jahanbahkshi, S and Hoyd, R and Wang, X and Zhang, S and Zhu, J and Xu, D and Spakowicz, D and Ma, Q and Liu, B}, title = {An Explainable Graph Neural Framework to Identify Cancer-Associated Intratumoral Microbial Communities.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {11}, number = {41}, pages = {e2403393}, pmid = {39225619}, issn = {2198-3844}, support = {2020YFA0712400//National Key Research and Development Program of China/ ; 62272270//National Nature Science Foundation of China/ ; 11931008//National Nature Science Foundation of China/ ; ZR2023JQ002//Shandong Provincial Natural Science Foundation for Distinguished Young Scholars/ ; }, mesh = {Mice ; *Microbiota ; Animals ; *Neoplasms/microbiology ; *Neural Networks, Computer ; Humans ; Reproducibility of Results ; Disease Models, Animal ; }, abstract = {Microbes are extensively present among various cancer tissues and play critical roles in carcinogenesis and treatment responses. However, the underlying relationships between intratumoral microbes and tumors remain poorly understood. Here, a MIcrobial Cancer-association Analysis using a Heterogeneous graph transformer (MICAH) to identify intratumoral cancer-associated microbial communities is presented. MICAH integrates metabolic and phylogenetic relationships among microbes into a heterogeneous graph representation. It uses a graph transformer to holistically capture relationships between intratumoral microbes and cancer tissues, which improves the explainability of the associations between identified microbial communities and cancers. MICAH is applied to intratumoral bacterial data across 5 cancer types and 5 fungi datasets, and its generalizability and reproducibility are demonstrated. After experimentally testing a representative observation using a mouse model of tumor-microbe-immune interactions, a result consistent with MICAH's identified relationship is observed. Source tracking analysis reveals that the primary known contributor to a cancer-associated microbial community is the organs affected by the type of cancer. Overall, this graph neural network framework refines the number of microbes that can be used for follow-up experimental validation from thousands to tens, thereby helping to accelerate the understanding of the relationship between tumors and intratumoral microbiomes.}, }
@article {pmid39224879, year = {2023}, author = {Boyes, D and Mulley, JF and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Small Emerald, Hemistola chrysoprasaria (Esper, 1795).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {441}, pmid = {39224879}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Hemistola chrysoprasaria (the Small Emerald; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 438.2 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.63 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,512 protein coding genes.}, }
@article {pmid39224768, year = {2024}, author = {Jentoft, S and Tørresen, OK and Tooming-Klunderud, A and Skage, M and Kollias, S and Jakobsen, KS and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Atlantic cod, Gadus morhua (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {189}, pmid = {39224768}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Gadus morhua (the Atlantic cod; Chordata; Actinopteri; Gadiformes; Gadidae). The genome sequence is 669.9 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomolecules. Gene annotation of this assembly on Ensembl identified 23,515 protein coding genes.}, }
@article {pmid39224703, year = {2024}, author = {Shi, Y and Zhang, W and Li, L and Wu, W and Li, M and Xiao, K and Wang, K and Sheng, Z and Xie, F and Wang, X and Shi, X and Tong, Y and Xie, L}, title = {Evaluation of phage-based decontamination in respiratory intensive care unit environments using ddPCR and 16S rRNA targeted sequencing techniques.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1442062}, pmid = {39224703}, issn = {2235-2988}, mesh = {*RNA, Ribosomal, 16S/genetics ; *Klebsiella pneumoniae/virology/genetics ; *Intensive Care Units ; *Decontamination/methods ; *Bacteriophages/genetics ; Humans ; Polymerase Chain Reaction/methods ; Cross Infection/prevention &amp; control/microbiology ; Disinfectants/pharmacology ; Klebsiella Infections/prevention &amp; control/microbiology ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Klebsiella pneumoniae is a major cause of hospital-acquired infections (HAIs), primarily spread through environmental contamination in hospitals. The effectiveness of current chemical disinfectants is waning due to emerging resistance, which poses environmental hazards and fosters new resistance in pathogens. Developing environmentally friendly and effective disinfectants against multidrug-resistant organisms is increasingly important.<br><br>METHODS: This study developed a bacteriophage cocktail targeting two common carbapenem-resistant Klebsiella pneumoniae (CRKP) strains, ST11 KL47 and ST11 KL64. The cocktail was used as an adjunctive disinfectant in a hospital's respiratory intensive care unit (RICU) via ultrasonic nebulization. Digital PCR was used to quantify CRKP levels post-intervention. The microbial community composition was analyzed via 16S rRNA sequencing to assess the intervention's impact on overall diversity.<br><br>RESULTS: The phage cocktail significantly reduced CRKP levels within the first 24 hours post-treatment. While a slight increase in pathogen levels was observed after 24 hours, they remained significantly lower than those treated with conventional disinfectants. 16S rRNA sequencing showed a decrease in the target pathogens' relative abundance, while overall species diversity remained stable, confirming that phages selectively target CRKP without disrupting ecological balance.<br><br>DISCUSSION: The findings highlight the efficacy and safety of phage-based biocleaners as a sustainable alternative to conventional disinfectants. Phages selectively reduce multidrug-resistant pathogens while preserving microbial diversity, making them a promising tool for infection control.}, }
@article {pmid39222768, year = {2024}, author = {Yushin, N and Jakhu, R and Chaligava, O and Grozdov, D and Zinicovscaia, I}, title = {Evaluation of the potentially toxic elements and radionuclides in the soil sample of Novaya Zemlya in the Arctic Circle.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {361}, number = {}, pages = {124871}, doi = {10.1016/j.envpol.2024.124871}, pmid = {39222768}, issn = {1873-6424}, mesh = {Arctic Regions ; *Soil/chemistry ; Russia ; Environmental Monitoring/methods ; Soil Pollutants/analysis ; Thorium/analysis ; Cesium Radioisotopes/analysis ; Soil Pollutants, Radioactive/analysis ; Radiation Monitoring/methods ; Animals ; Birds ; Radioisotopes/analysis ; Radium ; }, abstract = {The study presented here elucidate the concentrations of radionuclides and potentially toxic elements in the soil samples around the Novaya Zemlya in the Russian Arctic zone, determined using HPGe gamma spectrometry, inductively coupled plasma optical emission spectrometry and direct mercury analyzer. The average detected concentrations for [226]Ra, [232]Th, [40]K, [235]U and [137]Cs were 36.40, 46.06, 768, 2.06 and 4.71 Bq/kg, respectively. At many sampling sites, the concentrations of potentially toxic elements (Zn, Cu, Pb, Cd, Ni, and Cr) were higher than the natural levels. Positive Matrix Factorization analysis revealed the contribution of oil dumps (32%), natural sources (16%), bird colonies (32%) and atmospheric deposition (20%) for elevated elements content. In the case of radionuclides, the natural occurring contamination (38%) was primary source followed by dumped material (32%) and bird colonies (30%). The radiological risk from radionuclides was relatively high, yet still under permissible levels. For potentially toxic elements, Fe was predominant non-carcinogenic pollutant and Ni emerged as major carcinogenic contaminant. Keeping in view the high content of some elements, future studies are required to keep the human and ecological risk low, and to establish scientific grounds for the contribution of settled bird species. The findings of the study advance the present knowledge about the contamination of the study area and lays the path for further effort.}, }
@article {pmid39222062, year = {2024}, author = {Acheampong, DA and Jenjaroenpun, P and Wongsurawat, T and Kurilung, A and Pomyen, Y and Kandel, S and Kunadirek, P and Chuaypen, N and Kusonmano, K and Nookaew, I}, title = {CAIM: coverage-based analysis for identification of microbiome.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {5}, pages = {}, pmid = {39222062}, issn = {1477-4054}, support = {P20 GM125503/GM/NIGMS NIH HHS/United States ; R01 CA143130/CA/NCI NIH HHS/United States ; P20GM125503//National Institute of General Medical Sciences of the National Institutes of Health/ ; R01CA143130/NH/NIH HHS/United States ; }, mesh = {Humans ; *Microbiota/genetics ; *Metagenomics/methods ; Computational Biology/methods ; Metagenome ; High-Throughput Nucleotide Sequencing/methods ; Software ; Algorithms ; Sequence Analysis, DNA/methods ; }, abstract = {Accurate taxonomic profiling of microbial taxa in a metagenomic sample is vital to gain insights into microbial ecology. Recent advancements in sequencing technologies have contributed tremendously toward understanding these microbes at species resolution through a whole shotgun metagenomic approach. In this study, we developed a new bioinformatics tool, coverage-based analysis for identification of microbiome (CAIM), for accurate taxonomic classification and quantification within both long- and short-read metagenomic samples using an alignment-based method. CAIM depends on two different containment techniques to identify species in metagenomic samples using their genome coverage information to filter out false positives rather than the traditional approach of relative abundance. In addition, we propose a nucleotide-count-based abundance estimation, which yield lesser root mean square error than the traditional read-count approach. We evaluated the performance of CAIM on 28 metagenomic mock communities and 2 synthetic datasets by comparing it with other top-performing tools. CAIM maintained a consistently good performance across datasets in identifying microbial taxa and in estimating relative abundances than other tools. CAIM was then applied to a real dataset sequenced on both Nanopore (with and without amplification) and Illumina sequencing platforms and found high similarity of taxonomic profiles between the sequencing platforms. Lastly, CAIM was applied to fecal shotgun metagenomic datasets of 232 colorectal cancer patients and 229 controls obtained from 4 different countries and 44 primary liver cancer patients and 76 controls. The predictive performance of models using the genome-coverage cutoff was better than those using the relative-abundance cutoffs in discriminating colorectal cancer and primary liver cancer patients from healthy controls with a highly confident species markers.}, }
@article {pmid39222055, year = {2024}, author = {Xu, C and Wang, JC and Sun, L and Zhuang, LH and Guo, ZJ and Ding, QS and Ma, DN and Song, LY and Li, J and Tang, HC and Zhu, XY and Zheng, HL}, title = {Genome-Wide Identification of Pentatricopeptide Repeat (PPR) Gene Family and Multi-Omics Analysis Provide New Insights Into the Albinism Mechanism of Kandelia obovata Propagule Leaves.}, journal = {Plant, cell &amp; environment}, volume = {47}, number = {12}, pages = {5498-5510}, doi = {10.1111/pce.15132}, pmid = {39222055}, issn = {1365-3040}, support = {//This study was supported by the Natural Science Foundation of China (NSFC) (32171740, 31870581) and&#xa0;the National Key Research and Development Program of China (2017YFC0506102)./ ; }, mesh = {*Plant Leaves/genetics/metabolism ; *Genome-Wide Association Study ; *Plant Proteins/genetics/metabolism ; Multigene Family ; RNA Editing/genetics ; Rhizophoraceae/genetics/physiology ; Phylogeny ; Gene Expression Regulation, Plant ; Gene Expression Profiling ; Genes, Plant ; Genome, Plant ; Multiomics ; }, abstract = {Pentatricopeptide repeat (PPR) gene family constitutes one of the largest gene families in plants, which mainly participate in RNA editing and RNA splicing of organellar RNAs, thereby affecting the organellar development. Recently, some evidence elucidated the important roles of PPR proteins in the albino process of plant leaves. However, the functions of PPR genes in the woody mangrove species have not been investigated. In this study, using a typical true mangrove Kandelia obovata, we systematically identified 298 PPR genes and characterized their general features and physicochemical properties, including evolutionary relationships, the subcellular localization, PPR motif type, the number of introns and PPR motifs, and isoelectric point, and so forth. Furthermore, we combined genome-wide association studies (GWAS) and transcriptome analysis to identify the genetic architecture and potential PPR genes associated with propagule leaves colour variations of K. obovata. As a result, we prioritized 16 PPR genes related to the albino phenotype using different strategies, including differentially expressed genes analysis and genetic diversity analysis. Further analysis discovered two genes of interest, namely Maker00002998 (PLS-type) and Maker00003187 (P-type), which were differentially expressed genes and causal genes detected by GWAS analysis. Moreover, we successfully predicted downstream target chloroplast genes (rps14, rpoC1 and rpoC2) bound by Maker00002998 PPR proteins. The experimental verification of RNA editing sites of rps14, rpoC1, and rpoC2 in our previous study and the verification of interaction between Maker00002998 and rps14 transcript using in vitro RNA pull-down assays revealed that Maker00002998 PPR protein might be involved in the post-transcriptional process of chloroplast genes. Our result provides new insights into the roles of PPR genes in the albinism mechanism of K. obovata propagule leaves.}, }
@article {pmid39221663, year = {2024}, author = {Crawford, AD and Slavin, R and Tabar, M and Radhakrishnan, K and Wang, M and Estrada, A and McGrath, JM}, title = {Methodological approaches in developing and implementing digital health interventions amongst underserved women.}, journal = {Public health nursing (Boston, Mass.)}, volume = {41}, number = {6}, pages = {1612-1621}, doi = {10.1111/phn.13410}, pmid = {39221663}, issn = {1525-1446}, mesh = {Humans ; Female ; *Telemedicine ; Texas ; Vulnerable Populations ; Women's Health ; Medically Underserved Area ; Artificial Intelligence ; Adult ; Mobile Applications ; Digital Health ; }, abstract = {BACKGROUND: Minority populations are utilizing mobile health applications more frequently to access health information. One group that may benefit from using mHealth technology is underserved women, specifically those on community supervision.<br><br>OBJECTIVE: Discuss methodological approaches for navigating digital health strategies to address underserved women's health disparities.<br><br>Using an intersectional lens, we identified strategies for conducting research using digital health technology and artificial intelligence amongst the underserved, particularly those with community supervision.<br><br>We explore (1) methodological approaches that combine traditional research methods with precision medicine, digital phenotyping, and ecological momentary assessment; (2) implications for artificial intelligence; and (3) ethical considerations with data collection, storage, and engagement.<br><br>DISCUSSION: Researchers must address gendered differences related to health, social, and economic disparities concurrently with an unwavering focus on the protection of human subjects when addressing the unique needs of underserved women while utilizing digital health methodologies.<br><br>PUBLIC CONTRIBUTION: Women on community supervision in South Central Texas helped inform the design of JUN, the mHealth app we reported in the case exemplar. JUN is named after the Junonia shell, a native shell to South Texas, which means strength, power, and self-sufficiency, like the participants in our preliminary studies.}, }
@article {pmid39221442, year = {2024}, author = {Morales, HE and Norris, K and Henshaw, S and Tatayah, V and Ruhomaun, K and van Oosterhout, C and Groombridge, JJ and Gilbert, MTP and ,  and ,  and ,  and , }, title = {The genome sequence of the Mauritius kestrel, Falco punctatus (Temminck, 1821).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {312}, pmid = {39221442}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Falco punctatus (the Mauritius kestrel; Chordata; Aves; Falconiformes; Falconidae). The genome sequence is 1,279.3 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 17.34 kilobases in length.}, }
@article {pmid39219129, year = {2024}, author = {Xie, Z and Hu, D and Jiang, F and Fu, X and Li, R and Zheng, D and Zhao, L and Xu, J and Yuan, X and Bao, Y and Zhou, H and Wang, B and Wang, Q}, title = {Assessment of urban flood resilience based on the socio-ecological composite index model: a case study in Wuhua District, Kunming City, China.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {89}, number = {2}, pages = {252-270}, doi = {10.2166/wst.2023.413}, pmid = {39219129}, issn = {0273-1223}, mesh = {China ; *Floods ; *Cities ; Models, Theoretical ; Geographic Information Systems ; Socioeconomic Factors ; }, abstract = {Global climate change and rapid urbanization have increased the frequency of flooding, making urban flood resilience a critical objective. This article introduces a methodology for assessing urban flood resilience, utilizing a social-ecological synthesis index that integrates geographical and temporal data with Geographic Information System (GIS). The study focuses on ten administrative subdistricts in Wuhua District, Kunming City, China, and selects 18 social-ecological indicators. These indicators, chosen from social and ecological perspectives, are weighted using the entropy weight method to determine their significance in the assessment system. By combining scores for each subdistrict, the study quantifies flood resilience and creates a spatial distribution map using ArcGIS. Key findings reveal that out of the ten administrative subdistricts, five in Wuhua District, particularly in the core urban area of Kunming, demonstrate strong overall flood resilience. Influenced by social-ecological indicators, there is significant spatial differentiation in flood resilience within Wuhua District, with a decreasing trend radiating from the city center to areas farther from the urban core. The research indicates that regions with well-established transportation infrastructure, a wide distribution of government institutions, improved water management facilities, and a substantial population with higher education levels contribute significantly to enhancing urban flood resilience.}, }
@article {pmid39218423, year = {2025}, author = {Morris, JS}, title = {Tracking vaccine effectiveness in an evolving pandemic, countering misleading hot takes and epidemiologic fallacies.}, journal = {American journal of epidemiology}, volume = {194}, number = {4}, pages = {898-907}, pmid = {39218423}, issn = {1476-6256}, support = {UL1 TR001878/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; Bias ; *COVID-19/prevention &amp; control/epidemiology ; *COVID-19 Vaccines/immunology ; *Pandemics/prevention &amp; control ; SARS-CoV-2/immunology ; Social Media ; *Vaccine Efficacy ; }, abstract = {With the emergence of Omicron during the pandemic and the establishment of antibody waning over time, vaccine effectiveness, especially against infection, declined sharply from the original levels seen after the initial rollout. However, studies have demonstrated that they still provided substantial protection vs severe/fatal disease even with Omicron and after waning. Social media has been rife with reports claiming vaccines provided no benefit and some even claiming they made things worse, often driven by simple presentations of raw observational data using erroneous arguments involving epidemiologic fallacies including the base rate fallacy, Simpson's paradox, and the ecological fallacy and ignoring the extensive bias especially from confounding that is an inherent feature of these data. Similar fallacious arguments have been made by some in promoting vaccination policies, as well. Generally, vaccine effectiveness cannot be accurately estimated from raw population summaries but instead require rigorous, careful studies using epidemiologic designs and statistical analysis tools attempting to adjust for key confounders and sources of bias. This article summarizes what aggregated evidence across studies reveals about effectiveness of the mRNA vaccines as the pandemic has evolved, chronologically summarized with emerging variants and highlighting some of the fallacies and flawed arguments feeding social media-based claims that have obscured society's collective understanding.}, }
@article {pmid39209912, year = {2024}, author = {Yuan, R and Qu, Q and Lu, Z and Geng, X and Tian, S and Jin, Y and Gong, J and Ye, X and Tang, P and Chen, X}, title = {A chromosome-level genome assembly of the gall maker pest inquiline, Diomorus aiolomorphi Kamijo (Hymenoptera: Torymidae).}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {944}, pmid = {39209912}, issn = {2052-4463}, support = {32070467//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31920103005//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; Chromosomes, Insect ; Genome Size ; *Genome, Insect ; *Hymenoptera/genetics ; Wasps/parasitology ; Datasets as Topic ; }, abstract = {Diomorus aiolomorphi Kamijo (Hymenoptera: Torymidae) is an inquiline of gall maker Aiolomorphus rhopaloides Walker (Hymenoptera: Eurytomidae). They are of significant economic significance and predominantly inhabit bamboo forest. So far, only four scaffold-level genomes have been published for the family Torymidae. In this study, we present a high-quality genome assembly of D. aiolomorphi at the chromosome level, achieved through the integration of Nanopore (ONT) long-read, Illumina pair-end DNA short-read, and High-through Chromosome Conformation Capture (Hi-C) sequencing methods. The final assembly was 1,084.56 Mb in genome size, with 1,083.41 Mb (99.89%) assigned to five pseudochromosomes. The scaffold N50 length reached 224.87 Mb, and the complete Benchmarking Universal Single-Copy Orthologs (BUSCO) score was 97.3%. The genome contained 762.12 Mb of repetitive elements, accounting for 70.27% of the total genome size. A total of 18,011 protein-coding genes were predicted, with 17,829 genes being functionally annotated. The high-quality genome assembly of D. aiolomorphi presented in this study will serve as a valuable genomic resource for future research on parasitoid wasps. The results of this study may also contribute to the development of biological control strategies for pest management in bamboo forests, enhancing ecological balance and economic sustainability.}, }
@article {pmid39209853, year = {2024}, author = {Mi, J and Jing, X and Ma, C and Yang, Y and Li, Y and Zhang, Y and Long, R and Zheng, H}, title = {Massive expansion of the pig gut virome based on global metagenomic mining.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {76}, pmid = {39209853}, issn = {2055-5008}, mesh = {Animals ; Swine ; *Virome/genetics ; *Metagenomics/methods ; *Gastrointestinal Microbiome ; *Viruses/genetics/classification/isolation &amp; purification ; *Genome, Viral ; Data Mining ; Metagenome ; Phylogeny ; }, abstract = {The pig gut virome plays a vital role in the gut microbial ecosystem of pigs. However, a comprehensive understanding of their diversity and a reference database for the virome are currently lacking. To address this gap, we established a Pig Virome Database (PVD) that comprised of 5,566,804 viral contig sequences from 4650 publicly available gut metagenomic samples using a pipeline designated "metav". By clustering sequences, we identified 48,299 viral operational taxonomic units (vOTUs) genomes of at least medium quality, of which 92.83% of which were not found in existing major databases. The majority of vOTUs were identified as Caudoviricetes (72.21%). The PVD database contained a total of 2,362,631 protein-coding genes across the above medium-quality vOTUs genomes that can be used to explore the functional potential of the pig gut virome. These findings highlight the extensive diversity of viruses in the pig gut and provide a pivotal reference dataset for forthcoming research concerning the pig gut virome.}, }
@article {pmid39213392, year = {2024}, author = {Du, Q and Zhang, Z and Yang, W and Zhou, X and Zhou, N and Wu, C and Bao, J}, title = {CBGDA: a manually curated resource for gene-disease associations based on genome-wide CRISPR.}, journal = {Database : the journal of biological databases and curation}, volume = {2024}, number = {}, pages = {}, pmid = {39213392}, issn = {1758-0463}, support = {31971162 32071275 U20A20410//National Nature Science Foundation of China/ ; 31971162 32071275 U20A20410//National Nature Science Foundation of China/ ; }, mesh = {Humans ; *Databases, Genetic ; *Data Curation/methods ; Genome-Wide Association Study/methods ; Genetic Predisposition to Disease ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; CRISPR-Cas Systems ; Disease/genetics ; }, abstract = {The field of understanding the association between genes and diseases is rapidly expanding, making it challenging for researchers to keep up with the influx of new publications and genetic datasets. Fortunately, there are now several regularly updated databases available that focus on cataloging gene-disease relationships. The development of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 system has revolutionized the field of gene editing, providing a highly efficient, accurate, and reliable method for exploring gene-disease associations. However, currently, there is no resource specifically dedicated to collecting and integrating the latest experimentally supported gene-disease association data derived from genome-wide CRISPR screening. To address this gap, we have developed the CRISPR-Based Gene-Disease Associations (CBGDA) database, which includes over 200 manually curated gene-disease association data derived from genome-wide CRISPR screening studies. Through CBGDA, users can explore gene-disease association data derived from genome-wide CRISPR screening, gaining insights into the expression patterns of genes in different diseases, associated chemical data, and variant information. This provides a novel perspective on understanding the associations between genes and diseases. What is more, CBGDA integrates data from several other databases and resources, enhancing its comprehensiveness and utility. In summary, CBGDA offers a fresh perspective and comprehensive insights into the research on gene-disease associations. It fills the gap by providing a dedicated resource for accessing up-to-date, experimentally supported gene-disease association data derived from genome-wide CRISPR screening. Database URL: http://cbgda.zhounan.org/main.}, }
@article {pmid39213378, year = {2024}, author = {Wang, M and Li, Z and Wang, H and Zhao, J and Zhang, Y and Lin, K and Zheng, S and Feng, Y and Zhang, Y and Teng, W and Tong, Y and Zhang, W and Xue, Y and Mao, H and Li, H and Zhang, B and Rasheed, A and Bhavani, S and Liu, C and Ling, HQ and Hu, YQ and Zhang, Y}, title = {A Quantitative Computational Framework for Allopolyploid Single-Cell Data Integration and Core Gene Ranking in Development.}, journal = {Molecular biology and evolution}, volume = {41}, number = {9}, pages = {}, pmid = {39213378}, issn = {1537-1719}, support = {//National Natural Science Foundation of China/ ; //National Key R&amp;D Program of China/ ; //Yangfan Project of Shanghai Science and Technology Commission/ ; //State Key Laboratory of Genetic Engineering/ ; //State Key Laboratory of Crop Gene Exploration and Utilization in Southwest/ ; //State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology/ ; //Shanghai Key Laboratory of Agricultural Genetics and Breeding/ ; }, mesh = {*Single-Cell Analysis/methods ; *Polyploidy ; Animals ; Computational Biology/methods ; }, abstract = {Polyploidization drives regulatory and phenotypic innovation. How the merger of different genomes contributes to polyploid development is a fundamental issue in evolutionary developmental biology and breeding research. Clarifying this issue is challenging because of genome complexity and the difficulty in tracking stochastic subgenome divergence during development. Recent single-cell sequencing techniques enabled probing subgenome-divergent regulation in the context of cellular differentiation. However, analyzing single-cell data suffers from high error rates due to high dimensionality, noise, and sparsity, and the errors stack up in polyploid analysis due to the increased dimensionality of comparisons between subgenomes of each cell, hindering deeper mechanistic understandings. In this study, we develop a quantitative computational framework, called "pseudo-genome divergence quantification" (pgDQ), for quantifying and tracking subgenome divergence directly at the cellular level. Further comparing with cellular differentiation trajectories derived from single-cell RNA sequencing data allows for an examination of the relationship between subgenome divergence and the progression of development. pgDQ produces robust results and is insensitive to data dropout and noise, avoiding high error rates due to multiple comparisons of genes, cells, and subgenomes. A statistical diagnostic approach is proposed to identify genes that are central to subgenome divergence during development, which facilitates the integration of different data modalities, enabling the identification of factors and pathways that mediate subgenome-divergent activity during development. Case studies have demonstrated that applying pgDQ to single-cell and bulk tissue transcriptomic data promotes a systematic and deeper understanding of how dynamic subgenome divergence contributes to developmental trajectories in polyploid evolution.}, }
@article {pmid39209112, year = {2024}, author = {Ji, N and Kumar, A and Joe, W and Kuriyan, R and Sethi, V and Finkelstein, JL and Mehta, S}, title = {Prevalence and Correlates of Double and Triple Burden of Malnutrition Among Children and Adolescents in India: The Comprehensive National Nutrition Survey.}, journal = {The Journal of nutrition}, volume = {154}, number = {10}, pages = {2932-2947}, doi = {10.1016/j.tjnut.2024.08.021}, pmid = {39209112}, issn = {1541-6100}, mesh = {Humans ; India/epidemiology ; Adolescent ; Child ; Female ; Male ; Prevalence ; *Nutrition Surveys ; Child, Preschool ; *Malnutrition/epidemiology ; Nutritional Status ; Young Adult ; Overnutrition/epidemiology ; Socioeconomic Factors ; Child Nutrition Disorders/epidemiology ; }, abstract = {BACKGROUND: Limited information on the co-prevalence of undernutrition, micronutrient deficiencies, overnutrition, and abnormal levels of noncommunicable disease biomarkers at the same time in children and adolescents in India hinders efforts to comprehensively address their health.<br><br>OBJECTIVES: This study aimed to examine the prevalence and correlates of double burden of malnutrition (DBM) and triple burden of malnutrition (TBM) among children and adolescents (5-19 y) to inform policies and programs.<br><br>METHODS: A total of 17,599 children (5-9 y) and 16,184 adolescents (10-19 y) with available biomarker data from the Comprehensive National Nutrition Survey were included. Malnutrition was defined based on either undernutrition based on anthropometry, overnutrition/abnormal metabolic markers, and anemia/micronutrient deficiency. DBM was defined as the coexistence of any 2 forms of malnutrition. DBM+ was defined as the coexistence of undernutrition and/or micronutrient deficiency along with overnutrition. TBM was defined as having the coexistence of all 3 forms of malnutrition. The prevalence of DBM, DBM+, and TBM was estimated accounting for probabilistic selection. We used mixed-effect binomial regression to determine correlates of DBM/TBM in children and adolescents separately.<br><br>RESULTS: The prevalence of DBM, DBM+, and TBM was 50.8%, 37.2%, and 14.4%, respectively, in children and 53.4%, 36.1%, and 12.7%, respectively, in adolescents. The prevalence of DBM+ was significantly higher in girls compared to in boys in the 5-9 y age group. In children, being in a disadvantaged caste group, having a lower wealth index, having inadequate diet diversity, having no maternal schooling, and having a recent history of acute illness were associated with DBM. In adolescents, being in a disadvantaged caste group, maternal occupation, and lower paternal age were correlated with DBM. A similar set of variables was associated with TBM in both age groups.<br><br>CONCLUSIONS: The prevalence of DBM and TBM is substantial in children and adolescents in India and varies across states. Socioeconomic factors and acute illness were the main correlates for DBM and TBM.}, }
@article {pmid39208288, year = {2024}, author = {Ishigohoka, J and Bascón-Cardozo, K and Bours, A and Fuß, J and Rhie, A and Mountcastle, J and Haase, B and Chow, W and Collins, J and Howe, K and Uliano-Silva, M and Fedrigo, O and Jarvis, ED and Pérez-Tris, J and Illera, JC and Liedvogel, M}, title = {Distinct patterns of genetic variation at low-recombining genomic regions represent haplotype structure.}, journal = {Evolution; international journal of organic evolution}, volume = {78}, number = {12}, pages = {1916-1935}, doi = {10.1093/evolut/qpae117}, pmid = {39208288}, issn = {1558-5646}, support = {MFFALIMN0001//The Max Planck Society/ ; 395940726//Magnetoreception and Navigation in Vertebrates/ ; 407495230//DFG Research Infrastructure/ ; 423957469//Next Generation Sequencing Competence Network/ ; 1ZIAHG200398//Intramural Research Program of the NHGRI/ ; //Spanish Ministry of Science/ ; //Innovation and Universities/ ; PGC2018-097575-B-I00//The European Regional Development Fund/ ; }, mesh = {Animals ; *Haplotypes ; *Recombination, Genetic ; *Genetic Variation ; *Songbirds/genetics ; Selection, Genetic ; Genome ; }, abstract = {Genomic regions sometimes show patterns of genetic variation distinct from the genome-wide population structure. Such deviations have often been interpreted to represent effects of selection. However, systematic investigation of whether and how non-selective factors, such as recombination rates, can affect distinct patterns has been limited. Here, we associate distinct patterns of genetic variation with reduced recombination rates in a songbird, the Eurasian blackcap (Sylvia atricapilla), using a new reference genome assembly, whole-genome resequencing data and recombination maps. We find that distinct patterns of genetic variation reflect haplotype structure at genomic regions with different prevalence of reduced recombination rate across populations. At low-recombining regions shared in most populations, distinct patterns reflect conspicuous haplotypes segregating in multiple populations. At low-recombining regions found only in a few populations, distinct patterns represent variance among cryptic haplotypes within the low-recombining populations. With simulations, we confirm that these distinct patterns evolve neutrally by reduced recombination rate, on which the effects of selection can be overlaid. Our results highlight that distinct patterns of genetic variation can emerge through evolutionary reduction of local recombination rate. The recombination landscape as an evolvable trait therefore plays an important role determining the heterogeneous distribution of genetic variation along the genome.}, }
@article {pmid39208193, year = {2024}, author = {Naser, AY}, title = {Insights into hospitalization pattern for drug, medicament, and biological substance poisoning, adverse effect, and underdosing in Australia: An ecological study between 1998 and 2019.}, journal = {PloS one}, volume = {19}, number = {8}, pages = {e0309362}, pmid = {39208193}, issn = {1932-6203}, mesh = {Humans ; *Hospitalization/statistics &amp; numerical data/trends ; Australia/epidemiology ; Female ; Male ; Adult ; Middle Aged ; Adolescent ; Aged ; Child ; Young Adult ; Poisoning/epidemiology ; Child, Preschool ; Infant ; Drug-Related Side Effects and Adverse Reactions/epidemiology ; Aged, 80 and over ; Databases, Factual ; }, abstract = {BACKGROUND: Drug, medicament, and biological substance poisoning, adverse effects, and underdosing are significant public health concerns. Gaining insight into the patterns and trends in hospitalizations caused by these occurrences is essential for the development of preventative initiatives, optimization of treatment regimens, and improvement of patient safety. The aim of this study is to examine the trend of hospitalisation related to poisoning by, adverse effect of and underdosing of drugs, medicaments and biological substances in Australia between 1998 and 2019.<br><br>METHODS: This is an ecological descriptive study that examined hospitalisation related to poisoning by, adverse effect of and underdosing of drugs, medicaments and biological substances in Australia between 1998 and 2019. A nationwide hospital admissions database was used for this study.<br><br>RESULTS: Between 1998 and 2019, a total of 683,869 hospital admission episodes were recorded in Australia. The overall annual number of hospital admissions for various reasons increased by 20.5% from 29,854 in 1998 to 35,960 in 2019, representing a decrease in hospital admission rate of 10.6% [from 158.69 (95% CI 156.90-160.49) in 1998 to 141.91 (95% CI 140.44-143.37) in 2019 per 100,000 persons, trend test, p<0.05]. Overnight-stay admissions accounted for 69.2% of the total number of hospital admissions, and 30.8% were same-day admissions. Rates of same-day hospital admission decreased by 13.3% [from 50.55 (95%CI 49.54-51.57) in 1998 to 43.81 (95%CI 43.00-44.63) in 2019 per 100,000 persons]. Rates of overnight-stay hospital admission decreased by 11.1% [from 108.14 (95%CI 106.66-109.63) in 1998 to 96.17 (95%CI 94.96-97.38) in 2019 per 100,000 persons]. Admissions related to antiepileptic, sedative-hypnotic and antiparkinsonism drugs was the most prevalent hospital admissions type accounting for 26.8%. Females were responsible for 418,751 hospital admission episodes, representing 61.5% of the total number of hospital admission.<br><br>CONCLUSION: This study found that while the overall annual number of admissions increased, the rate of admission decreased over the same period. The most common reasons for admissions were antiepileptic, sedative-hypnotic, and anti-parkinsonism drugs. The study also noted increases in admissions related to anaesthetics, therapeutic gases, hormones, and their synthetic substitutes. These findings suggest a concerning rise in the suboptimal use of these medications. In order to combat the increasing incidence of this type of admissions, it is imperative to strengthen public awareness initiatives on medicine safety and abuse.}, }
@article {pmid39205176, year = {2024}, author = {Vanslembrouck, A and Jansen, S and De Witte, J and Janssens, C and Vereecken, S and Helms, M and Lange, U and Lühken, R and Schmidt-Chanasit, J and Heitmann, A and Müller, R}, title = {Larval Competition between Aedes and Culex Mosquitoes Carries over to Higher Arboviral Infection during Their Adult Stage.}, journal = {Viruses}, volume = {16}, number = {8}, pages = {}, pmid = {39205176}, issn = {1999-4915}, support = {G0G2319N//BiodivERsA/ ; CA17108//European Cooperation in Science and Technology/ ; 653316//European Union's Horizon 2020 research and innovation program/ ; Dubois-Brigu&#xe9; scholarship//Doctor Albert Dubois Foundation for tropical pathology/ ; }, mesh = {Animals ; *Culex/virology/growth &amp; development ; *Aedes/virology/growth &amp; development/physiology ; *Larva/virology ; *Mosquito Vectors/virology/growth &amp; development ; Arbovirus Infections/transmission/virology ; Arboviruses/physiology ; West Nile virus/physiology ; Female ; Chikungunya virus/physiology ; Encephalitis Virus, Japanese/physiology ; }, abstract = {The common house mosquito (Culex pipiens) is a native vector for West Nile virus (WNV). Invasive species like the tiger mosquito (Aedes albopictus) and Asian bush mosquito (Aedes japonicus) are rapidly spreading through Europe, posing a major threat as vectors for dengue, chikungunya (CHIKV), and Japanese encephalitis virus (JEV). These mosquitoes share a similar ecological niche as larvae, but the carry-over effects of aquatic larval interactions to the terrestrial adult stage remain largely unknown and their medical relevance requires further investigation. This study examines the context dependency of larval interactions among Aedes albopictus, Aedes japonicus, and Culex pipiens. The survival, development time, growth, and energetic storage were measured in different European populations within density-response (intraspecific) experiments and replacement (interspecific) experiments at 20 °C and 26 °C. Overall, Ae. japonicus was the weakest competitor, while competition between Ae. albopictus and Cx. pipiens varied with temperature. Adults emerging from this larval competition were infected as follows: Culex pipiens with WNV, Ae. albopictus with CHIKV, and Ae. japonicus with JEV. While no JEV infection was observed, mosquitoes experiencing interspecific interactions during their larval stages exhibited higher infection rates and viral RNA titers for CHIKV and WNV. This increased susceptibility to viral infection after larval competition suggests a higher risk of arbovirus transmission in co-occurring populations.}, }
@article {pmid39202353, year = {2024}, author = {Maltseva, PY and Plotnitskaya, NA and Krivoruchko, AV and Beletskiy, AV and Rakitin, AL and Mardanov, AV and Ivshina, IB}, title = {Bioinformatics Analysis of the Genome of Rhodococcus rhodochrous IEGM 1362, an (-)-Isopulegol Biotransformer.}, journal = {Genes}, volume = {15}, number = {8}, pages = {}, pmid = {39202353}, issn = {2073-4425}, support = {24-14-20015//the Russian Science Foundation/ ; }, mesh = {*Rhodococcus/genetics/metabolism ; *Genome, Bacterial ; *Computational Biology/methods ; *Biotransformation/genetics ; Cytochrome P-450 Enzyme System/genetics/metabolism ; Monoterpenes/metabolism ; }, abstract = {A genome of Rhodococcus rhodochrous IEGM 1362 was sequenced and annotated. This strain can transform monoterpene alcohol (-)-isopulegol with the formation of two novel pharmacologically promising metabolites. Nine genes encoding cytochrome P450, presumably involved in (-)-isopulegol transformation, were found in the genome of R. rhodochrous IEGM 1362. Primers and PCR conditions for their detection were selected. The obtained data can be used for the further investigation of genes encoding enzymes involved in monoterpene biotransformation.}, }
@article {pmid39202178, year = {2024}, author = {de Llanza Varona, M and Martínez, M}, title = {Synergy Makes Direct Perception Inefficient.}, journal = {Entropy (Basel, Switzerland)}, volume = {26}, number = {8}, pages = {}, pmid = {39202178}, issn = {1099-4300}, support = {PID2021-127046NA-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; CEX2021-001169-M MCIN/AEI/10.13039/501100011033)//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; 2021-SGR-00276//Government of Catalonia/ ; }, abstract = {A typical claim in anti-representationalist approaches to cognition such as ecological psychology or radical embodied cognitive science is that ecological information is sufficient for guiding behavior. According to this view, affordances are immediately perceptually available to the agent (in the so-called "ambient energy array"), so sensory data does not require much further inner processing. As a consequence, mental representations are explanatorily idle: perception is immediate and direct. Here we offer one way to formalize this direct-perception claim and identify some important limits to it. We argue that the claim should be read as saying that successful behavior just implies picking out affordance-related information from the ambient energy array. By relying on the Partial Information Decomposition framework, and more concretely on its development of the notion of synergy, we show that in multimodal perception, where various energy arrays carry affordance-related information, the "just pick out affordance-related information" approach is very inefficient, as it is bound to miss all synergistic components. Efficient multimodal information combination requires transmitting sensory-specific (and not affordance-specific) information to wherever it is that the various information streams are combined. The upshot is that some amount of computation is necessary for efficient affordance reconstruction.}, }
@article {pmid39198944, year = {2024}, author = {Wang, HT and Li, HY and Lu, QW and He, SL}, title = {[Determination of eight neonicotinoid pesticides in wastewater by solid phase extraction combined with liquid chromatography-tandem mass spectrometry].}, journal = {Se pu = Chinese journal of chromatography}, volume = {42}, number = {9}, pages = {856-865}, pmid = {39198944}, issn = {1872-2059}, mesh = {*Tandem Mass Spectrometry/methods ; *Solid Phase Extraction/methods ; *Wastewater/chemistry/analysis ; *Neonicotinoids/analysis ; *Water Pollutants, Chemical/analysis ; Chromatography, Liquid/methods ; *Nitro Compounds/analysis ; Thiamethoxam/analysis ; Guanidines/analysis ; Thiazoles/analysis ; Pesticides/analysis ; Thiazines/analysis ; Oxazines/analysis ; }, abstract = {Neonicotinoid pesticides are a relatively new class of pesticides that have garnered significant attention owing to their potential ecological risks to nontarget organisms. A method combining solid phase extraction with liquid chromatography-tandem mass spectrometry (SPE-LC-MS/MS) was developed for the rapid and accurate detection of eight neonicotinoid pesticides (dinotefuran, E-nitenpyram, thiamethoxam, clothianidin, imidacloprid, imidaclothiz, acetamiprid, and thiacloprid) in wastewater. The chromatographic mobile phase and MS parameters were selected, and a single-factor method was used to determine the optimal column type, extraction volume, sample loading speed, and pH for SPE. The optimal parameters were as follows: column type, HLB column (500 mg/6 mL); sample extraction volume, 500 mL; sample loading speed, 10 mL/min; and sample pH, 6-8. The matrix effects of the wastewater samples were reduced by optimizing the chromatographic gradient-elution program, examining the dilution factor of the samples, and using the isotope internal standard calibration method. Prior to analysis, the wastewater samples were diluted 5-fold with ultrapure water for pretreatment. Subsequently, 2 mmol/L ammonium acetate aqueous solution containing 0.1% (v/v) formic acid and methanol was used as mobile phases for gradient elution on a ZORBAX Eclipse Plus C18 column (100 mm×2.1 mm, 1.8 μm). The samples were quantified using positive-ion multiple reaction monitoring (MRM) mode for 10 min. Imidacloprid-d4 was used as the isotope internal standard. The SPE process was further optimized by applying response surface methodology to select the type and mass of rinsing and elution solvents. The optimal pretreatment of the SPE column included rinsing with 10% methanol aqueous solution and elution with methanol-acetonitrile (1∶1, v/v) mixture (7 mL). The eight neonicotinoid pesticides showed satisfactory linearity within the relevant range, with linear correlation coefficients (r) all greater than 0.9990. The method detection limits (MDLs) ranged from 0.2 to 1.2 ng/L, and the method quantification limits (MQLs) ranged from 0.8 to 4.8 ng/L. The average recoveries of the eight neonicotinoid pesticides were in the range of 82.6%-94.2% at three spiked levels, with relative standard deviations (RSDs) ranging from 3.9% to 9.4%. Finally, the optimized method was successfully applied to analyze wastewater samples collected from four sewage treatment plants. The results indicated that the eight neonicotinoid pesticides could be generally detected at concentrations ranging from not detected (ND) to 256 ng/L. The developed method has a low MDL and high accuracy, rendering it a suitable choice for the trace detection of the eight neonicotinoid pesticides in wastewater when compared with other similar methods. The proposed method can be utilized to monitor the environmental impact and assess the potential risks of neonicotinoid pesticides in wastewater, thus promoting the protection of nontarget organisms and the sustainable use of these pesticides in agriculture.}, }
@article {pmid39198489, year = {2024}, author = {Chanda, MM and Campbell, L and Walke, H and Salzer, JS and Hemadri, D and Patil, SS and Purse, BV and Shivachandra, SB}, title = {A thirty-year time series analyses identifies coherence between oscillations in Anthrax outbreaks and El Niño in Karnataka, India.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {19928}, pmid = {39198489}, issn = {2045-2322}, mesh = {*Anthrax/epidemiology ; India/epidemiology ; *Disease Outbreaks ; Animals ; *El Nino-Southern Oscillation ; Bayes Theorem ; Bacillus anthracis/isolation &amp; purification/pathogenicity ; Humans ; Livestock/microbiology ; }, abstract = {Anthrax is an economically important zoonotic disease affecting both livestock and humans. The disease is caused by a spore forming bacterium, Bacillus anthracis, and is considered endemic to the state of Karnataka, India. It is critical to quantify the role of climatic factors in determining the temporal pattern of anthrax outbreaks, so that reliable forecasting models can be developed. These models will aid in establishing public health surveillance and guide strategic vaccination programs, which will reduce the economic loss to farmers, and prevent the spill-over of anthrax from livestock to humans. In this study, correlation and coherence between time series of anthrax outbreaks in livestock (1987-2016) and meteorological variables and Sea Surface Temperature anomalies (SST) were identified using a combination of cross-correlation analyses, spectral analyses (wavelets and empirical mode decomposition) and further quantified using a Bayesian time series regression model accounting for temporal autocorrelation. Monthly numbers of anthrax outbreaks were positively associated with a lagged effect of rainfall and wet day frequency. Long-term periodicity in anthrax outbreaks (approximately 6-8 years) was coherent with the periodicity in SST anomalies and outbreak numbers increased with decrease in SST anomalies. These findings will be useful in planning long-term anthrax prevention and control strategies in Karnataka state of India.}, }
@article {pmid39198479, year = {2024}, author = {Zhu, J and Li, Z and Yang, J and Yu, K and Zhang, D and Zhong, J}, title = {Ecological space management and control zoning of Giant Panda National Park from the perspective of ecosystem services and land use.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {19951}, pmid = {39198479}, issn = {2045-2322}, support = {GJGY2020-ZD002//Key Project of National Park Research Center, Key Social Science Research Base of Sichuan Province, "National Park Natural Ecosystem Service Function Importance Evaluation and Protection Policy Research"/ ; ZDJS202303//Chengdu University of Technology "Double First-Class" initiative Construction Philosophy and Social Sciences Key Construction Project/ ; }, mesh = {Animals ; Bayes Theorem ; Carbon Sequestration ; China ; Computer Simulation ; *Conservation of Natural Resources/legislation &amp; jurisprudence/methods ; Conservation of Water Resources ; Datasets as Topic ; *Ecosystem ; *Parks, Recreational/legislation &amp; jurisprudence/organization &amp; administration/standards ; Probability ; Soil ; *Ursidae ; Ecology/legislation &amp; jurisprudence/methods/organization &amp; administration ; }, abstract = {Since China proposed building a national park system in 2017, the establishment of a planning system for nature reserves, with national parks as the main body, is being actively promoted around the country. Among them, scientific ecological space management and control zoning (ESMCZ) is an important link in maintaining the ecological stability of national parks. How to zone national parks and how to improve the precision of zoning has become a new task for national parks. Therefore, this study takes the Giant Panda National Park as the study area, takes ecosystem services and land use/cover change as the research perspective, integrates the InVEST model, PLUS model and bayes belief network (BBN) model, and builds a set of ecological space management and control zoning (ESMCZ) spatial zoning framework based on raster scale, dividing the study area into strictly protected zone, ecological buffer zone, ecological control zone and controlled development zone. The results showed that: (1) The study area showed an increasing trend in water conservation, soil conservation and carbon storage from 2005 to 2020, and the habitat quality index was generally high. The spatial heterogeneity of ecosystem services in the study area was significant, and the effect of a single factor on ecosystem services was most pronounced. (2) Large variation in area for different land uses under natural development scenarios and ecological protection scenarios. In both scenarios, the area of cultivated land, the area of grassland and the area of unused land decrease relative to 2020, and the area of forested land, the area of water and the area of constructed land increase relative to 2020. (3) The Giant Panda National Park is divided into strictly protected zone, ecological buffer zone, ecological control zone and control development zone, of which the strictly protected zone have the largest area and the best ecosystem background condition, and the control development zone have the smallest area and the worst ecosystem background condition. (4) The ecological space management and control zoning (ESMCZ) framework provides a more refined method for the secondary zoning of nature reserves such as the Giant Panda National Park, which is valuable for the implementation of zoning and categorization management for ecological conservation in the Giant Panda National Park.}, }
@article {pmid39196880, year = {2024}, author = {Tsigeman, E and Zemliak, V and Likhanov, M and Papageorgiou, KA and Kovas, Y}, title = {AI can see you: Machiavellianism and extraversion are reflected in eye-movements.}, journal = {PloS one}, volume = {19}, number = {8}, pages = {e0308631}, pmid = {39196880}, issn = {1932-6203}, mesh = {Humans ; *Eye Movements/physiology ; Male ; Female ; Adolescent ; *Extraversion, Psychological ; *Machine Learning ; *Machiavellianism ; Surveys and Questionnaires ; Algorithms ; Personality/physiology ; Eye-Tracking Technology ; }, abstract = {INTRODUCTION: Recent studies showed an association between personality traits and individual patterns of visual behaviour in laboratory and other settings. The current study extends previous research by measuring multiple personality traits in natural settings; and by comparing accuracy of prediction of multiple machine learning algorithms.<br><br>METHODS: Adolescent participants (N = 35) completed personality questionnaires (Big Five Inventory and Short Dark Triad Questionnaire) and visited an interactive museum while their eye movements were recorded with head-mounted eye tracking. To predict personality traits the eye-movement data was analysed using eight machine-learning methods: Random Forest, Adaboost, Naive Bayes, Support Vector Machine, Logistic Regression, k Nearest Neighbours, Decision Tree and a three-layer Perceptron.<br><br>RESULTS AND DISCUSSION: Extracted eye movement features introduced to machine learning algorithms predicted personality traits with above 33% chance accuracy (34%-48%). This result is comparable to previous ecologically valid studies, but lower than in laboratory-based research. Better prediction was achieved for Machiavellianism and Extraversion compared to other traits (10 and 9 predictions above the chance level by different algorithms from different parts of the recording). Conscientiousness, Narcissism and Psychopathy were not reliably predicted from eye movements. These differences in predictability across traits might be explained by differential activation of different traits in different situations, such as new vs. familiar, exciting vs. boring, and complex vs. simple settings. In turn, different machine learning approaches seem to be better at capturing specific gaze patterns (e.g. saccades), associated with specific traits evoked by the situation. Further research is needed to gain better insights into trait-situation-algorithm interactions.}, }
@article {pmid39193916, year = {2024}, author = {Spöri, Y and Flot, JF}, title = {Haxe as a Swiss knife for bioinformatic applications: the SeqPHASE case story.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {5}, pages = {}, pmid = {39193916}, issn = {1477-4054}, support = {T.0078.23//Fonds de la Recherche Scientifique - FNRS/ ; }, mesh = {*Computational Biology/methods ; *Programming Languages ; *Software ; }, abstract = {Haxe is a general purpose, object-oriented programming language supporting syntactic macros. The Haxe compiler is well known for its ability to translate the source code of Haxe programs into the source code of a variety of other programming languages including Java, C++, JavaScript, and Python. Although Haxe is more and more used for a variety of purposes, including games, it has not yet attracted much attention from bioinformaticians. This is surprising, as Haxe allows generating different versions of the same program (e.g. a graphical user interface version in JavaScript running in a web browser for beginners and a command-line version in C++ or Python for increased performance) while maintaining a single code, a feature that should be of interest for many bioinformatic applications. To demonstrate the usefulness of Haxe in bioinformatics, we present here the case story of the program SeqPHASE, written originally in Perl (with a CGI version running on a server) and published in 2010. As Perl+CGI is not desirable anymore for security purposes, we decided to rewrite the SeqPHASE program in Haxe and to host it at Github Pages (https://eeg-ebe.github.io/SeqPHASE), thereby alleviating the need to configure and maintain a dedicated server. Using SeqPHASE as an example, we discuss the advantages and disadvantages of Haxe's source code conversion functionality when it comes to implementing bioinformatic software.}, }
@article {pmid39193399, year = {2024}, author = {Boyes, D and Crowley, LM and Hutchinson, F and Wawman, DC and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Lesser Yellow Underwing, Noctua comes Hübner, 1813.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {200}, pmid = {39193399}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Noctua comes (the Lesser Yellow Underwing; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 540.7 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.37 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,001 protein coding genes.}, }
@article {pmid39193313, year = {2024}, author = {Kang, B and Ma, J and Jeong, I and Yoon, S and Kim, JI and Heo, SJ and Oh, SS}, title = {Behavioral marker-based predictive modeling of functional status for older adults with subjective cognitive decline and mild cognitive impairment: Study protocol.}, journal = {Digital health}, volume = {10}, number = {}, pages = {20552076241269555}, pmid = {39193313}, issn = {2055-2076}, abstract = {OBJECTIVE: This study describes a research protocol for a behavioral marker-based predictive model that examines the functional status of older adults with subjective cognitive decline and mild cognitive impairment.<br><br>METHODS: A total of 130 older adults aged &#x2265;65 years with subjective cognitive decline or mild cognitive impairment will be recruited from the Dementia Relief Centers or the Community Service Centers. Data on behavioral and psychosocial markers (e.g. physical activity, mobility, sleep/wake patterns, social interaction, and mild behavioral impairment) will be collected using passive wearable actigraphy, in-person questionnaires, and smartphone-based ecological momentary assessments. Two follow-up assessments will be performed at 12 and 24 months after baseline. Mixed-effect machine learning models: MErf, MEgbm, MEmod, and MEctree, and standard machine learning models without random effects [random forest, gradient boosting machine] will be employed in our analyses to predict functional status over time.<br><br>RESULTS: The results of this study will be fundamental for developing tailored digital interventions that apply deep learning techniques to behavioral data to predict, identify, and aid in the management of functional decline in older adults with subjective cognitive decline and mild cognitive impairment. These older adults are considered the optimal target population for preventive interventions and will benefit from such tailored strategies.<br><br>CONCLUSIONS: Our study will contribute to the development of self-care interventions that utilize behavioral data and machine learning techniques to provide automated analyses of the functional decline of older adults who are at risk for dementia.}, }
@article {pmid39193090, year = {2023}, author = {Boyes, D and Lewis, OT and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Small Angle Shades, Euplexia lucipara (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {509}, pmid = {39193090}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Euplexia lucipara (the Small Angle Shades; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 661.8 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.37 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,395 protein coding genes.}, }
@article {pmid39192185, year = {2024}, author = {Donthu, R and Marcelino, JAP and Giordano, R and Tao, Y and Weber, E and Avalos, A and Band, M and Akraiko, T and Chen, SC and Reyes, MP and Hao, H and Ortiz-Alvarado, Y and Cuff, CA and Claudio, EP and Soto-Adames, F and Smith-Pardo, AH and Meikle, WG and Evans, JD and Giray, T and Abdelkader, FB and Allsopp, M and Ball, D and Morgado, SB and Barjadze, S and Correa-Benitez, A and Chakir, A and Báez, DR and Chavez, NHM and Dalmon, A and Douglas, AB and Fraccica, C and Fernández-Marín, H and Galindo-Cardona, A and Guzman-Novoa, E and Horsburgh, R and Kence, M and Kilonzo, J and Kükrer, M and Le Conte, Y and Mazzeo, G and Mota, F and Muli, E and Oskay, D and Ruiz-Martínez, JA and Oliveri, E and Pichkhaia, I and Romane, A and Sanchez, CG and Sikombwa, E and Satta, A and Scannapieco, AA and Stanford, B and Soroker, V and Velarde, RA and Vercelli, M and Huang, Z}, title = {HBeeID: a molecular tool that identifies honey bee subspecies from different geographic populations.}, journal = {BMC bioinformatics}, volume = {25}, number = {1}, pages = {278}, pmid = {39192185}, issn = {1471-2105}, support = {PRSTRT # 2020-00081//Puerto Rico Science, Technology and Research Trust, United States of America/ ; PRSTRT # 2020-00081//Puerto Rico Science, Technology and Research Trust, United States of America/ ; USDA-APHIS #AP20PPQS &amp; T00C009//United States Dept. of Agriculture - Animal and Plant Health Inspection Service (APHIS), United States of America/ ; USDA-APHIS #AP20PPQS &amp; T00C009//United States Dept. of Agriculture - Animal and Plant Health Inspection Service (APHIS), United States of America/ ; NSF-OISE #1545803//National Science Foundation, United States of America/ ; }, mesh = {Bees/genetics/classification ; Animals ; *Polymorphism, Single Nucleotide/genetics ; Genomics/methods ; }, abstract = {BACKGROUND: Honey bees are the principal commercial pollinators. Along with other arthropods, they are increasingly under threat from anthropogenic factors such as the incursion of invasive honey bee subspecies, pathogens and parasites. Better tools are needed to identify bee subspecies. Genomic data for economic and ecologically important organisms is increasing, but in its basic form its practical application to address ecological problems is limited.<br><br>RESULTS: We introduce HBeeID a means to identify honey bees. The tool utilizes a knowledge-based network and diagnostic SNPs identified by discriminant analysis of principle components and hierarchical agglomerative clustering. Tests of HBeeID showed that it identifies African, Americas-Africanized, Asian, and European honey bees with a high degree of certainty even when samples lack the full 272 SNPs of HBeeID. Its prediction capacity decreases with highly admixed samples.<br><br>CONCLUSION: HBeeID is a high-resolution genomic, SNP based tool, that can be used to identify honey bees and screen species that are invasive. Its flexible design allows for future improvements via sample data additions from other localities.}, }
@article {pmid39188222, year = {2024}, author = {Koracevic, G and Stojanovic, M and Zdravkovic, M and Lovic, D and Simic, D and Mladenovic, K}, title = {Proposal of a Modified Classification of Hypertensive Crises: Urgency, Impending Emergency, and Emergency.}, journal = {Current vascular pharmacology}, volume = {22}, number = {3}, pages = {180-186}, pmid = {39188222}, issn = {1875-6212}, mesh = {Humans ; *Hypertension/diagnosis/physiopathology/drug therapy/classification ; *Antihypertensive Agents/therapeutic use/adverse effects ; Risk Assessment ; Risk Factors ; *Blood Pressure/drug effects ; *Emergencies ; Prognosis ; Predictive Value of Tests ; Decision Support Techniques ; Clinical Decision-Making ; Hypertensive Crisis ; }, abstract = {Systemic arterial hypertension (HTN) is the main cause of morbidity and mortality, and HTN crises contribute significantly to an unfavourable clinical course. For decades, HTN crises have been dichotomized into hypertensive emergency (HTN-E) and hypertensive urgency (HTN-U). The main difference between the two is the presence of acute hypertension-mediated organ damage (HMOD) - if HMOD is present, HTN crisis is HTN-E; if not, it is HTN-U. Patients with HTN-E are in a life-threatening situation. They are hospitalized and receive antihypertensive drugs intravenously (IV). On the other hand, patients with HTN-U are usually not hospitalized and receive their antihypertensives orally. We suggest a modification of the current risk stratification scheme for patients with HTN crises. The new category would be the intermediate risk group, more precisely the 'impending HTN-E' group, with a higher risk in comparison to HTN-U and a lower risk than HTN-E. 'Impending HMOD' means that HMOD has not occurred (yet), and the prognosis is, therefore, better than in patients with ongoing HMOD. There are three main reasons to classify patients as having impending HTN-E: excessively elevated BP, high-risk comorbidities, and ongoing bleeding/high bleeding risk. Their combinations are probable. This approach may enable us to prevent some HTNEs by avoiding acute HMOD using a timely blood pressure treatment. This treatment should be prompt but controlled.}, }
@article {pmid39186487, year = {2024}, author = {Raj, U and Banerjee, A and Ray, S and Bhattacharya, S}, title = {Structure of higher-order interactions in social-ecological networks through Q-analysis of their neighbourhood and clique complex.}, journal = {PloS one}, volume = {19}, number = {8}, pages = {e0306409}, pmid = {39186487}, issn = {1932-6203}, mesh = {Madagascar ; *Agriculture ; Rural Population ; *Forests ; *Ecology/methods ; *Sociology/methods ; *Models, Theoretical ; Humans ; Algorithms ; }, abstract = {This paper studies higher-order interactions in social-ecological networks, which formally represent interactions within the social and ecological units of an ecosystem. Many real-world social ecosystems exhibit not only pairwise interactions but also higher-order interactions among their units. Therefore, the conventional graph-theoretic description of networks falls short of capturing these higher-order interactions due to the inherent limitations of the graph definition. In this work, a mathematical framework for capturing the higher-order interactions of a social-ecological system has been given by incorporating notions from combinatorial algebraic topology. In order to achieve this, two different simplicial complexes, the clique and the neighbourhood complex, have been constructed from a pairwise social-ecological network. As a case study, the Q-analysis and a structural study of the interactions in the rural agricultural system of southern Madagascar have been done at various structural levels denoted by q. The results obtained by calculating all the structural vectors for both simplicial complexes, along with exciting results about the participation of facets of the clique complex at different q-levels, have been discussed. This work also establishes significant theorems concerning the dimension of the neighbourhood complex and clique complex obtained from the parent pairwise network.}, }
@article {pmid39185327, year = {2024}, author = {Panyushkina, IP and Jull, AJT and Molnár, M and Varga, T and Kontul', I and Hantemirov, R and Kukarskih, V and Sljusarenko, I and Myglan, V and Livina, V}, title = {The timing of the ca-660 BCE Miyake solar-proton event constrained to between 664 and 663 BCE.}, journal = {Communications earth &amp; environment}, volume = {5}, number = {1}, pages = {454}, pmid = {39185327}, issn = {2662-4435}, abstract = {Extreme solar energetic particle events, known as Miyake events, are rare phenomena observed by cosmogenic isotopes, with only six documented. The timing of the ca. 660 BCE Miyake event remains undefined until now. Here, we assign its occurrence to 664-663 BCE through new radiocarbon measurements in gymnosperm larch tree rings from arctic-alpine biomes (Yamal and Altai). Using a 22-box carbon cycle model and Bayesian statistics, we calculate the radiocarbon production rate during the event that is 3.2-4.8 times higher than the average solar modulation, and comparable to the 774-775 CE solar-proton event. The prolonged radiocarbon signature manifests a 12‰ rise over two years. The non-uniform signal in the tree rings is likely driven by the low rate of CO2 gas exchange between the trees and the ambient atmosphere, and the high residence time of radiocarbon in the post-event stratosphere. We caution about using the event's pronounced signature for precise single-year-dating.}, }
@article {pmid39184546, year = {2024}, author = {Yuan, H and Mancuso, CA and Johnson, K and Braasch, I and Krishnan, A}, title = {Computational strategies for cross-species knowledge transfer and translational biomedicine.}, journal = {ArXiv}, volume = {}, number = {}, pages = {}, pmid = {39184546}, issn = {2331-8422}, support = {R01 OD011116/OD/NIH HHS/United States ; R35 GM128765/GM/NIGMS NIH HHS/United States ; }, abstract = {Research organisms provide invaluable insights into human biology and diseases, serving as essential tools for functional experiments, disease modeling, and drug testing. However, evolutionary divergence between humans and research organisms hinders effective knowledge transfer across species. Here, we review state-of-the-art methods for computationally transferring knowledge across species, primarily focusing on methods that utilize transcriptome data and/or molecular networks. We introduce the term "agnology" to describe the functional equivalence of molecular components regardless of evolutionary origin, as this concept is becoming pervasive in integrative data-driven models where the role of evolutionary origin can become unclear. Our review addresses four key areas of information and knowledge transfer across species: (1) transferring disease and gene annotation knowledge, (2) identifying agnologous molecular components, (3) inferring equivalent perturbed genes or gene sets, and (4) identifying agnologous cell types. We conclude with an outlook on future directions and several key challenges that remain in cross-species knowledge transfer.}, }
@article {pmid39181462, year = {2024}, author = {de Vries, P}, title = {ECOTOXr: An R package for reproducible and transparent retrieval of data from EPA's ECOTOX database.}, journal = {Chemosphere}, volume = {364}, number = {}, pages = {143078}, doi = {10.1016/j.chemosphere.2024.143078}, pmid = {39181462}, issn = {1879-1298}, mesh = {*United States Environmental Protection Agency ; *Databases, Factual ; *Software ; United States ; Ecotoxicology/methods ; Risk Assessment/methods ; Reproducibility of Results ; }, abstract = {The US EPA ECOTOX database provides key ecotoxicological data that are crucial in environmental risk assessment. It can be used for computational predictions of toxicity or indications of hazard in a wide range of situations. There is no standardised or formalised method for extracting and subsetting data from the database for these purposes. Consequently, results in such meta-analyses are difficult to reproduce. The present study introduces the software package ECOTOXr, which provides the means to formalise data retrieval from the ECOTOX database in the R scripting language. Three cases are presented to evaluate the performance of the package in relation to earlier data extractions and searches on the website. These cases demonstrate that the package can reproduce data sets relatively well. Furthermore, they illustrate how future studies can further improve traceability and reproducibility by applying the package and adhering to some simple guidelines. This contributes to the FAIR principles, credibility and acceptance of research that uses data from the ECOTOX database.}, }
@article {pmid39181078, year = {2024}, author = {Wei, Q and Yin, Y and Tong, Q and Gong, Z and Shi, Y}, title = {Multi-omics analysis of excessive nitrogen fertilizer application: Assessing environmental damage and solutions in potato farming.}, journal = {Ecotoxicology and environmental safety}, volume = {284}, number = {}, pages = {116916}, doi = {10.1016/j.ecoenv.2024.116916}, pmid = {39181078}, issn = {1090-2414}, mesh = {*Solanum tuberosum/microbiology ; *Fertilizers ; *Nitrogen/analysis ; *Soil Microbiology ; Transcriptome ; Metabolome/drug effects ; Agriculture/methods ; Metagenomics ; Soil/chemistry ; Multiomics ; }, abstract = {Potatoes (Solanum tuberosum L.) are the third largest food crop globally and are pivotal for global food security. Widespread N fertilizer waste in potato cultivation has caused diverse environmental issues. This study employed microbial metagenomic sequencing to analyze the causes behind the declining N use efficiency (NUE) and escalating greenhouse gas emissions resulting from excessive N fertilizer application. Addressing N fertilizer inefficiency through breeding has emerged as a viable solution for mitigating overuse in potato cultivation. In this study, transcriptome and metabolome analyses were applied to identify N fertilizer-responsive genes. Metagenomic sequencing revealed that excessive N fertilizer application triggered alterations in the population dynamics of 11 major bacterial phyla, consequently affecting soil microbial functions, particularly N metabolism pathways and bacterial secretion systems. Notably, the enzyme levels associated with NO3[-] increased, and those associated with NO and N2O increased. Furthermore, excessive N fertilizer application enhanced soil virulence factors and increased potato susceptibility to diseases. Transcriptome and metabolome sequencing revealed significant impacts of excessive N fertilizer use on lipid and amino acid metabolism pathways. Weighted gene co‑expression network analysis (WGCNA) was adopted to identify two genes associated with N fertilizer response: PGSC0003DMG400021157 and PGSC0003DMG400009544.}, }
@article {pmid39180071, year = {2024}, author = {Zhuang, M and Qiao, C and Han, L and Bi, Y and Cao, M and Wang, S and Guo, L and Pang, R and Xie, H}, title = {Multi-omics analyses reveal the responses of wheat (Triticum aestivum L.) and rhizosphere bacterial community to nano(micro)plastics stress.}, journal = {Journal of nanobiotechnology}, volume = {22}, number = {1}, pages = {507}, pmid = {39180071}, issn = {1477-3155}, support = {2023YFD1400902//National Key Research and Development Program of China/ ; J210019//Beijing Municipal Natural Science Foundation/ ; C2021204190//Natural Science Foundation of Hebei Province/ ; 21JCZXJC00110//Natural Science Foundation of Tianjin Municipality/ ; }, mesh = {*Triticum ; *Rhizosphere ; *Bacteria/genetics/metabolism/drug effects ; *Microplastics ; *Soil Microbiology ; Nanoparticles/chemistry ; Stress, Physiological ; Microbiota ; Soil Pollutants ; Particle Size ; Polystyrenes/chemistry ; Multiomics ; }, abstract = {The pervasive existence of nanoplastics (NPs) and microplastics (MPs) in soil has become a worldwide environmental concern. N/MPs exist in the environment in a variety of forms, sizes, and concentrations, while multi-omics studies on the comprehensive impact of N/MPs with different properties (e.g. type and size) on plants remain limited. Therefore, this study utilized multi-omics analysis methods to investigate the effects of three common polymers [polyethylene-NPs (PE-NPs, 50 nm), PE-MPs (PE-MPs, 10 μm), and polystyrene-MPs (PS-MPs, 10 μm)] on the growth and stress response of wheat, as well as the rhizosphere microbial community at two concentrations (0.05 and 0.5 g/kg). PS and PE exhibited different effects for the same particle size and concentration. PE-NPs had the most severe stress effects, resulting in reduced rhizosphere bacteria diversity, plant biomass, and antioxidant enzyme activity while increasing beneficial bacteria richness. N/MPs altered the expression of nitrogen-, phosphorus-, and sulfur-related functional genes in rhizosphere bacteria, thereby affecting photosynthesis, as well as metabolite and gene levels in wheat leaves. Partial least squares pathway models (PLSPMs) indicated that concentration, size, and type play important roles in the impact of N/MPs on the plant ecological environment, which could have essential implications for assessing the environmental risk of N/MPs.}, }
@article {pmid39178805, year = {2024}, author = {Bravo-Ortiz, MA and Guevara-Navarro, E and Holguín-García, SA and Rivera-Garcia, M and Cardona-Morales, O and Ruz, GA and Tabares-Soto, R}, title = {SpectroCVT-Net: A convolutional vision transformer architecture and channel attention for classifying Alzheimer's disease using spectrograms.}, journal = {Computers in biology and medicine}, volume = {181}, number = {}, pages = {109022}, doi = {10.1016/j.compbiomed.2024.109022}, pmid = {39178805}, issn = {1879-0534}, mesh = {*Alzheimer Disease/classification/physiopathology/diagnosis ; Humans ; *Electroencephalography/methods ; *Signal Processing, Computer-Assisted ; Male ; Female ; Databases, Factual ; Aged ; }, abstract = {Dementia arises from various brain-affecting diseases and injuries, with Alzheimer's disease being the most prevalent, impacting around 55 million people globally. Current clinical diagnosis often relies on biomarkers indicative of Alzheimer's distinctive features. Electroencephalography (EEG) serves as a cost-effective, user-friendly, and safe biomarker for early Alzheimer's detection. This study utilizes EEG signals processed with Short-Time Fourier Transform (STFT) to generate spectrograms, facilitating visualization of EEG signal properties. Leveraging the Brainlat database, we propose SpectroCVT-Net, a novel convolutional vision transformer architecture incorporating channel attention mechanisms. SpectroCVT-Net integrates convolutional and attention mechanisms to capture local and global dependencies within spectrograms. Comprising feature extraction and classification stages, the model enhances Alzheimer's disease classification accuracy compared to transfer learning methods, achieving 92.59 ± 2.3% accuracy across Alzheimer's, healthy controls, and behavioral variant frontotemporal dementia (bvFTD). This article introduces a new architecture and evaluates its efficacy with unconventional data for Alzheimer's diagnosis, contributing: SpectroCVT-Net, tailored for EEG spectrogram classification without reliance on transfer learning; a convolutional vision transformer (CVT) module in the classification stage, integrating local feature extraction with attention heads for global context analysis; Grad-CAM analysis for network decision insight, identifying critical layers, frequencies, and electrodes influencing classification; and enhanced interpretability through spectrograms, illuminating key brain wave contributions to Alzheimer's, frontotemporal dementia, and healthy control classifications, potentially aiding clinical diagnosis and management.}, }
@article {pmid39178313, year = {2024}, author = {Du, J and Liu, W and Li, M and Li, Z and Li, X and Dai, Y and Liu, G and Wang, X and Zhu, P and Gladyshev, VN and Zhou, X}, title = {Comparative time-series multi-omics analyses suggest H1.2 involvement in anoxic adaptation and cancer resistance.}, journal = {PLoS biology}, volume = {22}, number = {8}, pages = {e3002778}, pmid = {39178313}, issn = {1545-7885}, support = {P01 AG047200/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Mice ; *Histones/metabolism ; Humans ; Neoplasms/genetics/metabolism/pathology ; Mole Rats/genetics ; Hypoxia-Inducible Factor 1, alpha Subunit/metabolism/genetics ; Proteomics/methods ; Fibroblasts/metabolism ; Autophagy/genetics ; Adaptation, Physiological/genetics ; Transcriptome/genetics ; Cell Hypoxia/genetics ; Cell Line, Tumor ; Signal Transduction ; Multiomics ; }, abstract = {The naked mole rat (NMR), Heterocephalus glaber, is known as the longest-lived rodent and is extraordinarily resistant to hypoxia and cancer. Here, both NMR embryonic fibroblasts (NEFs) and their mouse counterparts (MEFs) were subjected to anoxic conditions (0% O2, 5% CO2). A combination of comparative transcriptomics and proteomics was then employed to identify differentially expressed genes (DEGs). Notably, we observed distinct levels of histone H1.2 (encoded by HIST1H1C) accumulation between NEFs and MEFs. Subsequent mechanistic analyses showed that higher H1.2 expression in NEFs was associated with the lower expression of its inhibitor, PARP1. Additionally, we discovered that H1.2 can directly interact with HIF-1α PAS domains, thereby promoting the expression of HIF-1α through facilitating the dimerization with HIF-1β. The overexpression of H1.2 was also found to trigger autophagy and to suppress the migration of cancer cells, as well as the formation of xenograft tumors, via the NRF2/P62 signaling pathway. Moreover, an engineered H1.2 knock-in mouse model exhibited significantly extended survival in hypoxic conditions (4% O2) and showed a reduced rate of tumor formation. Collectively, our results indicate a potential mechanistic link between H1.2 and the dual phenomena of anoxic adaptation and cancer resistance.}, }
@article {pmid39176874, year = {2024}, author = {Knak, AK and Roheger, M and Wulff, A}, title = {Challenges in Daily Computerized Assessment of Cognitive Functions of Post-COVID Patients.}, journal = {Studies in health technology and informatics}, volume = {316}, number = {}, pages = {1950-1954}, doi = {10.3233/SHTI240815}, pmid = {39176874}, issn = {1879-8365}, mesh = {Humans ; *COVID-19 ; Cognitive Dysfunction ; Diagnosis, Computer-Assisted/methods ; SARS-CoV-2 ; Fatigue ; Post-Acute COVID-19 Syndrome ; Cognition ; }, abstract = {While it would be quite helpful to learn more about the daily fluctuations of fatigue and cognitive impairments of post-COVID patients, their condition can make investigating these especially challenging. By discussing these issues with post-COVID patients and clinical practitioners, we identified six challenges that specifically apply to daily computerized assessment of cognitive functions of post-COVID patients. We proposed solutions for each of the challenges which can be summarized as offering a carefully planned and flexible study design to participants and monitoring their well-being throughout the assessments. We argue that when the proposed precautions are taken, it is feasible to conduct a study that will generate valuable insights into the trajectories of (cognitive) post-COVID symptoms.}, }
@article {pmid39176504, year = {2024}, author = {Kokolakis, S and Kokinou, E and Chronaki, C and Moen, A and Datta, G}, title = {Earth Observation and Geoinformatics to Monitoring the Environmental Status of Urban Streams Inextricably Linked to People's Mental Health.}, journal = {Studies in health technology and informatics}, volume = {316}, number = {}, pages = {1560-1564}, doi = {10.3233/SHTI240716}, pmid = {39176504}, issn = {1879-8365}, mesh = {*Environmental Monitoring/methods ; Humans ; *Mental Health ; Rivers ; Geographic Information Systems ; Cities ; }, abstract = {The general condition of urban watercourses is inextricably linked to ecological balance and public health (physical and mental well-being). Given the vulnerability of these systems to climate change and human pollution, this work aims to demonstrate the effective use of environmental indicators to: a) rapidly assess soil and water conditions near urban streams and b) highlight the importance of geoinformatics and earth observation supported by ground-based techniques. There is a great need for new technology and methods for spatial and temporal monitoring and further quantification of environmental quality in urban streams and the land surrounding them to sensitize policymakers and the public to the environmental degradation of these exceptional habitats and to further protect people's mental health.}, }
@article {pmid39173171, year = {2024}, author = {Barahona, M and Alegría, A and Amstein, C and Cárcamo, M and Barahona, M}, title = {Epidemiology of high-energy trauma in Chile: An ecological analysis using public registries.}, journal = {Medwave}, volume = {24}, number = {7}, pages = {e2929}, doi = {10.5867/medwave.2024.07.2929}, pmid = {39173171}, issn = {0717-6384}, mesh = {Chile/epidemiology ; Humans ; *Accidents, Traffic/statistics &amp; numerical data/mortality ; Male ; Adult ; *Databases, Factual ; *Registries ; Female ; Young Adult ; Middle Aged ; *Multiple Trauma/epidemiology/mortality ; Wounds and Injuries/epidemiology/mortality ; Public Health ; Sex Distribution ; Adolescent ; Age Distribution ; World Health Organization ; Aged ; }, abstract = {High-energy trauma is defined as severe organic injuries resulting from events that generate a large amount of kinetic, electrical, or thermal energy. It represents a significant public health concern, accounting for 10% of global mortality. This article aims to describe the epidemiology of high-energy trauma in Chile. Specifically, it seeks to compare the mortality rate per 100 000 inhabitants among member countries of the World Health Organization (WHO), provide a descriptive analysis of notifications under the Explicit Health Guarantees (GES) for the health issue of polytraumatized patients, and analyze the trend in the mortality rate due to external causes in Chile. This study employs an ecological design using three open-access databases. First, the WHO database on deaths from traffic accidents in 2019 was used. Then, the GES database was consulted for the "Polytraumatized" issue between 2018 and 2022. Finally, the Chilean Department of Health Statistics database on causes of death between 1997 and 2020 was utilized. In 2019, Chile ranked in the middle regarding the mortality rate per 100 000 inhabitants due to traffic accidents. GES notifications for polytrauma predominantly involved men aged 20 to 40 years and those affiliated with the public health system, highlighting a primary focus for prevention efforts. Mortality from accidents showed a decreasing trend, with significant structural changes identified in 2000 and 2007.}, }
@article {pmid39170344, year = {2024}, author = {D, S and Vellaturi, G and Shaik Ibrahim, SH and Molugu, S and Desanamukula, VS and Kocherla, R and Vatambeti, R}, title = {Enhanced deep learning models for automatic fish species identification in underwater imagery.}, journal = {Heliyon}, volume = {10}, number = {15}, pages = {e35217}, pmid = {39170344}, issn = {2405-8440}, abstract = {Underwater cameras are crucial in marine ecology, but their data management needs automatic species identification. This study proposes a two-stage deep learning approach. First, the Unsharp Mask Filter (UMF) preprocesses images. Then, an enhanced region-based fully convolutional network (R-FCN) detects fish using two-order integrals for position-sensitive score maps and precise region of interest (PS-Pr-RoI) pooling for accuracy. The second stage integrates ShuffleNetV2 with the Squeeze and Excitation (SE) module, forming the Improved ShuffleNetV2 model, enhancing classification focus. Hyperparameters are optimized with the Enhanced Northern Goshawk Optimization Algorithm (ENGO). The improved R-FCN model achieves 99.94 % accuracy, 99.58 % precision and recall, and a 99.27 % F-measure on the Fish4knowledge dataset. Similarly, the ENGO-based ShuffleNetV2 model, evaluated on the same dataset, shows 99.93 % accuracy, 99.19 % precision, 98.29 % recall, and a 98.71 % F-measure, highlighting its superior classification accuracy.}, }
@article {pmid39169276, year = {2024}, author = {Arcioni, L and Arcieri, M and Martino, JD and Liberati, F and Bottoni, P and Castrignanò, T}, title = {HPC-T-Annotator: an HPC tool for de novo transcriptome assembly annotation.}, journal = {BMC bioinformatics}, volume = {25}, number = {1}, pages = {272}, pmid = {39169276}, issn = {1471-2105}, support = {B87G22000450001//Ministry of University and Research, Italy/ ; }, mesh = {*Software ; *Transcriptome/genetics ; *Molecular Sequence Annotation/methods ; Gene Expression Profiling/methods ; Computational Biology/methods ; Databases, Genetic ; }, abstract = {BACKGROUND: The availability of transcriptomic data for species without a reference genome enables the construction of de novo transcriptome assemblies as alternative reference resources from RNA-Seq data. A transcriptome provides direct information about a species' protein-coding genes under specific experimental conditions. The de novo assembly process produces a unigenes file in FASTA format, subsequently targeted for the annotation. Homology-based annotation, a method to infer the function of sequences by estimating similarity with other sequences in a reference database, is a computationally demanding procedure.<br><br>RESULTS: To mitigate the computational burden, we introduce HPC-T-Annotator, a tool for de novo transcriptome homology annotation on high performance computing (HPC) infrastructures, designed for straightforward configuration via a Web interface. Once the configuration data are given, the entire parallel computing software for annotation is automatically generated and can be launched on a supercomputer using a simple command line. The output data can then be easily viewed using post-processing utilities in the form of Python notebooks integrated in the proposed software.<br><br>CONCLUSIONS: HPC-T-Annotator expedites homology-based annotation in de novo transcriptome assemblies. Its efficient parallelization strategy on HPC infrastructures significantly reduces computational load and execution times, enabling large-scale transcriptome analysis and comparison projects, while its intuitive graphical interface extends accessibility to users without IT skills.}, }
@article {pmid39167718, year = {2024}, author = {Zass, L and Mwapagha, LM and Louis-Jacques, AF and Allali, I and Mulindwa, J and Kiran, A and Hanachi, M and Souiai, O and Mulder, N and Oduaran, OH}, title = {Advancing microbiome research through standardized data and metadata collection: introducing the Microbiome Research Data Toolkit.}, journal = {Database : the journal of biological databases and curation}, volume = {2024}, number = {}, pages = {}, pmid = {39167718}, issn = {1758-0463}, support = {U24 HG009780/HG/NHGRI NIH HHS/United States ; 1U24HG009780/NH/NIH HHS/United States ; }, mesh = {*Metadata ; *Microbiota ; Humans ; Databases, Factual ; }, abstract = {Microbiome research has made significant gains with the evolution of sequencing technologies. Ensuring comparability between studies and enhancing the findability, accessibility, interoperability and reproducibility of microbiome data are crucial for maximizing the value of this growing body of research. Addressing the challenges of standardized metadata reporting, collection and curation, the Microbiome Working Group of the Human Hereditary and Health in Africa (H3Africa) consortium aimed to develop a comprehensive solution. In this paper, we present the Microbiome Research Data Toolkit, a versatile tool designed to standardize microbiome research metadata, facilitate MIxS-MIMS and PhenX reporting, standardize prospective collection of participant biological and lifestyle data, and retrospectively harmonize such data. This toolkit enables past, present and future microbiome research endeavors to collaborate effectively, fostering novel collaborations and accelerating knowledge discovery in the field. Database URL: https://doi.org/10.25375/uct.24218999.v2.}, }
@article {pmid39162518, year = {2024}, author = {Hu, D and Zhang, T and He, S and Pu, T and Yin, Y and Hu, Y}, title = {Mining metagenomic data to gain a new insight into the gut microbial biosynthetic potential in placental mammals.}, journal = {Microbiology spectrum}, volume = {12}, number = {10}, pages = {e0086424}, pmid = {39162518}, issn = {2165-0497}, support = {32370552//MOST | National Natural Science Foundation of China (NSFC)/ ; 32070414,32325010//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Metagenomics ; *Mammals/microbiology ; *Metagenome ; *Multigene Family ; Bacteria/genetics/classification/metabolism ; Polyketides/metabolism ; Data Mining ; Biological Products/metabolism ; Female ; Biosynthetic Pathways/genetics ; }, abstract = {Mammals host a remarkable diversity and abundance of gut microbes. Biosynthetic gene clusters (BGCs) in microbial genomes encode biologically active chemical products and play an important role in microbe-host interactions. Traditionally, the exploration of gut microbial metabolic functions has relied on the pure culture method. However, given the limited amounts of microbes being cultivated, insights into the metabolism of gut microbes in mammals continued to be very limited. In this study, we adopted a computational pipeline for mining the metagenomic data (named taxonomy-guided identification of biosynthetic gene clusters, TaxiBGC) to identify experimentally verified BGCs in 373 metagenomes across 53 mammalian species in an unbiased manner. We demonstrated that polyketides (PKs) and nonribosomal peptides (NRPs) are representative of mammals, and the products derived from them were associated with cell-cell communication and resistance to inflammation. Large carnivores had the highest number of BGCs, followed by large herbivores and small mammals. We also observed that the large mammals had more common BGCs that aid in the biosynthesis of a variety of natural products. However, small mammals not only had fewer BGCs but were also unique to each species. Our results provide novel insights into the mining of metagenomic data sets to identify active BGCs and their products across mammals.IMPORTANCEThe gut microbes host numerous biosynthetic gene clusters (BGCs) that biosynthesize natural products and impact the host's physiology. Historically, our understanding of BGCs in mammalian gut microbes was largely based on studies on cultured isolates; however, only a small fraction of mammal-associated microbes have been investigated. The biochemical diversity of the mammalian gut microbiota is poorly understood. Metagenomic sequencing contains data from a vast number of organisms and provides information on the total gene content of communities. Unfortunately, the existing BGC prediction tools are designed for individual microbial genomes. Recently, a BGC prediction tool called the taxonomy-guided identification of biosynthetic gene clusters (TaxiBGC) that directly mine the metagenome was developed. To gain new insights into the microbial metabolism, we used TaxiBGC to predict BGCs from 373 metagenomes across 53 mammalian species representing seven orders. Our findings elucidate the functional activities of complex microbial communities in the gut.}, }
@article {pmid39161242, year = {2024}, author = {Setyawati, I and Husaini, AF and Setiawan, AG and Artika, IM and Ambarsari, L and Nurcholis, W and Vidilaseris, K and Kurniatin, PA}, title = {Structural Classification Insights Into the Plant Defensive Peptides.}, journal = {Proteins}, volume = {92}, number = {12}, pages = {1413-1427}, doi = {10.1002/prot.26736}, pmid = {39161242}, issn = {1097-0134}, support = {102/E5/PG.02.00.PL/2023//Ministry of Education, Culture, Research, and Technology, Republic of Indonesia/ ; }, mesh = {*Phylogeny ; *Plant Proteins/chemistry/genetics/metabolism ; *Plants/metabolism/chemistry ; *Databases, Protein ; Evolution, Molecular ; Amino Acid Sequence ; Models, Molecular ; }, abstract = {This study presents a structural phylogenetic analysis of plant defensive peptides, revealing their evolutionary relationships, structural diversification, and functional adaptations. Utilizing a robust dataset comprising both experimental and predicted structures sourced from the RCSB Protein Data Bank and AlphaFold DB, we constructed a detailed phylogenetic tree to elucidate the distinct evolutionary paths of plant defensive peptide families. Our findings showcase the evolutionary intricacies of defensive peptides, highlighting their diversity and the conservation of key structural motifs critical to their antimicrobial or defensive functions. The results also underscore the adaptive significance of defensive peptides in plant evolution, highlighting their roles in responding to ecological pressures and pathogen interactions.}, }
@article {pmid39155119, year = {2024}, author = {Reitz, ZL}, title = {Predicting metallophore structure and function through genome mining.}, journal = {Methods in enzymology}, volume = {702}, number = {}, pages = {371-401}, doi = {10.1016/bs.mie.2024.06.007}, pmid = {39155119}, issn = {1557-7988}, mesh = {*Genomics/methods ; Genome, Bacterial ; Computational Biology/methods ; Siderophores/metabolism/chemistry/genetics ; Data Mining/methods ; }, abstract = {Metallophores are small molecule chelators that many microbes use to obtain trace metals from their environment. Through genome mining, where genomes are scanned for metallophore biosynthesis genes, one can not only identify which organisms are likely to produce a metallophore, but also predict the metallophore structure, thus preventing undesired reisolation of known compounds and accelerating characterization. Furthermore, the presence of accessory genes for the transport, utilization, and regulation can suggest the biological function and fate of a metallophore. Modern, user-friendly tools have made powerful genomic analyses accessible to scientists with no bioinformatics experience, but these tools are often not utilized to their full potential. This chapter provides an introduction to metallophore genomics and demonstrates how to use the free, publicly available antiSMASH platform to infer metallophore function and structure.}, }
@article {pmid39154763, year = {2024}, author = {Lin, X and Sun, B and Wang, P and Zhao, M and Liu, D and Zhang, Q and Wu, B and Liu, D}, title = {Enhanced low-concentration phosphate adsorption using magnetic UiO-66@Fe3O4 composite with potential linker exchange.}, journal = {Chemosphere}, volume = {364}, number = {}, pages = {143126}, doi = {10.1016/j.chemosphere.2024.143126}, pmid = {39154763}, issn = {1879-1298}, mesh = {Adsorption ; *Phosphates/chemistry ; *Water Pollutants, Chemical/chemistry ; Water Purification/methods ; Metal-Organic Frameworks/chemistry ; Ferric Compounds/chemistry ; Magnetics ; Phthalic Acids ; }, abstract = {A magnetic FenUiO-66 adsorbent was created to achieve high phosphate adsorption capacity. The incorporation of Fe3O4 facilitated the precipitation and growth of UiO-66 during crystallization, resulting in a shift towards a multilayer heterogeneous distribution of adsorption sites. The increased Fe3O4 content notably enhanced the magnetic properties of FenUiO-66, while negligibly affecting its adsorption performance. The Fe1.5UiO-66 demonstrated exceptional phosphate adsorption capacity (136.54 mg/g), outstanding selectivity, and sustained reusability, with an 80% removal efficiency after nine cycles of treating actual water. The mechanism of phosphate adsorption by FenUiO-66 involved electrostatic attraction, ligand exchange, and linker exchange. Notably, while linker exchange significantly contributed to high adsorption capacity, it resulted in irreversible damage to the FenUiO-66 crystal. These unequivocal findings will serve as a solid foundation for further research and underline the critical role of linkers in the process of phosphate adsorption.}, }
@article {pmid39154477, year = {2024}, author = {Bai, Z and He, Y and Hu, G and Cheng, L and Wang, M}, title = {Microplastics at an environmentally relevant dose enhance mercury toxicity in a marine copepod under multigenerational exposure: Multi-omics perspective.}, journal = {Journal of hazardous materials}, volume = {478}, number = {}, pages = {135529}, doi = {10.1016/j.jhazmat.2024.135529}, pmid = {39154477}, issn = {1873-3336}, mesh = {Animals ; *Copepoda/drug effects ; *Mercury/toxicity ; *Water Pollutants, Chemical/toxicity ; *Microplastics/toxicity ; Reproduction/drug effects ; Apoptosis/drug effects ; Proteomics ; Multiomics ; }, abstract = {Here, we subjected the marine copepod Tigriopus japonicus to environmentally-relevant concentrations of microplastics (MPs) and mercury (Hg) for three generations (F0-F2) to investigate their physiological and molecular responses. Hg accumulation and phenotypic traits were measured in each generation, with multi-omics analysis conducted in F2. The results showed that MPs insignificantly impacted the copepod's development and reproduction, however, which were significantly compromised by Hg exposure. Interestingly, MPs significantly increased Hg accumulation and consequently aggravated this metal toxicity in T. japonicus, demonstrating their carrier role. Multi-omics analysis indicated that Hg pollution produced numerous toxic events, e.g., induction of apoptosis, damage to cell/organ morphogenesis, and disordered energy metabolism, ultimately resulting in retarded development and decreased fecundity. Importantly, MPs enhanced Hg toxicity mainly via increased oxidative apoptosis, compromised cell/organ morphogenesis, and energy depletion. Additionally, phosphoproteomic analysis revealed extensive regulation of the above processes, and also impaired neuron activity under combined MPs and Hg exposure. These alterations adversely affected development and reproduction of T. japonicus. Overall, our findings should offer novel molecular insights into the response of T. japonicus to long-term exposure to MPs and Hg, with a particular emphasis on the carrier role of MPs on Hg toxicity.}, }
@article {pmid39151562, year = {2024}, author = {Rahimian, M and Panahi, B}, title = {Metagenome sequence data mining for viral interaction studies: Review on progress and prospects.}, journal = {Virus research}, volume = {349}, number = {}, pages = {199450}, pmid = {39151562}, issn = {1872-7492}, mesh = {*Metagenomics/methods ; *Metagenome ; *Viruses/genetics/classification ; *Computational Biology/methods ; *Data Mining ; *High-Throughput Nucleotide Sequencing ; Humans ; Animals ; }, abstract = {Metagenomics has been greatly accelerated by the development of next-generation sequencing (NGS) technologies, which allow scientists to discover and describe novel microorganisms without the need for conventional culture techniques. Examining integrative bioinformatics methods used in viral interaction research, this study highlights metagenomic data from various contexts. Accurate viral identification depends on high-purity genetic material extraction, appropriate NGS platform selection, and sophisticated bioinformatics tools like VirPipe and VirFinder. The efficiency and precision of metagenomic analysis are further improved with the advent of AI-based techniques. The diversity and dynamics of viral communities are demonstrated by case studies from a variety of environments, emphasizing the seasonal and geographical variations that influence viral populations. In addition to speeding up the discovery of new viruses, metagenomics offers thorough understanding of virus-host interactions and their ecological effects. This review provides a promising framework for comprehending the complexity of viral communities and their interactions with hosts, highlighting the transformational potential of metagenomics and bioinformatics in viral research.}, }
@article {pmid39147186, year = {2024}, author = {Song, J and Zhou, S and Zou, D and Kwan, MP and Cai, J and Lu, J}, title = {Non-linear associations between noise level and people's short-term noise annoyance in different activity contexts.}, journal = {Environmental research}, volume = {260}, number = {}, pages = {119772}, doi = {10.1016/j.envres.2024.119772}, pmid = {39147186}, issn = {1096-0953}, mesh = {Humans ; Male ; Female ; Adult ; *Noise/adverse effects ; Young Adult ; Ecological Momentary Assessment ; Environmental Exposure ; Middle Aged ; Noise, Transportation/adverse effects ; Geographic Information Systems ; Nonlinear Dynamics ; }, abstract = {Recent research has become increasingly interested in the on-linear associations between noise levels and people's short-term noise annoyance. However, there has been limited investigation into measuring short-term noise annoyance and how different activity contexts may affect these non-linear associations. To address this research gap, this study measured people's short-term noise annoyance using real-time Ecological Momentary Assessment (EMA) data and the Day Reconstruction Method's (DRM) recalled data. Corresponding noise levels were captured using Global Positioning Systems and portable noise sensors. Employing the Shapley additive explanations method, we examined the non-linear associations between noise level and people's real-time and recalled noise annoyance across different activity contexts. The results indicated that 1) People had greater sensitivity to noise levels in real-time annoyance (non-linear association threshold: 60 dB) compared to recalled annoyance, which had a higher non-linear association threshold of 70 dB. 2) The non-linear associations between noise level and people's real-time/recalled noise annoyance varied between different activity contexts. People tended to be more sensitive to noise in real-time annoyance than recalled annoyance on travel routes and at workplaces. 3) Among the factors examined, the contribution of noise level varied across activity contexts. Noise level contributed more significantly to people's real-time noise annoyance in outdoor recreational sites and on travel routes. These findings enhance our understanding of the non-linear association between noise level and people's short-term noise annoyance, moving beyond the linear paradigm. Policymakers should consider the non-linear relationships and different activity contexts when implementing noise control measures.}, }
@article {pmid39146704, year = {2024}, author = {Li, G and Wu, M and Xiao, Y and Tong, Y and Li, S and Qian, H and Zhao, T}, title = {Multi-omics reveals the ecological and biological functions of Enterococcus mundtii in the intestine of lepidopteran insects.}, journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics}, volume = {52}, number = {}, pages = {101309}, doi = {10.1016/j.cbd.2024.101309}, pmid = {39146704}, issn = {1878-0407}, mesh = {Animals ; *Bombyx/microbiology/genetics ; *Enterococcus/genetics ; *Gastrointestinal Microbiome ; *Intestines/microbiology ; Proteomics ; Symbiosis ; Multiomics ; }, abstract = {Insect guts offer unique habitats for microbial colonization, with gut bacteria potentially offering numerous benefits to their hosts. Although Enterococcus has emerged as one of the predominant gut commensal bacteria in insects, its establishment in various niches within the gut has not been characterized well. In this study, Enterococcus mundtii was inoculated into the silkworm (Bombyx mori L.) to investigate its biological functions. Genome-based analysis revealed that its successful colonization is related to adherence genes (ebpA, ebpC, efaA, srtC, and scm). This bacterium did not alter the activities of related metabolic enzymes or the intestinal barrier function. However, significant changes in the gene expressions levels of Att2, CecA, and Lys suggest potential adaptive mechanisms of host immunity to symbiotic E. mundtii. Moreover, 16S metagenomics analysis revealed a significant increase in the relative abundance of E. mundtii in the intestines of silkworms following inoculation. The intestinal microbiome displayed marked heterogeneity, an elevated gut microbiome health index, a reduced microbial dysbiosis index, and low potential pathogenicity in the treatment group. Additionally, E. mundtii enhanced the breakdown of carbohydrates in host intestines. Overall, E. mundtii serves as a beneficial microbe for insects, promoting intestinal homeostasis by providing competitive advantage. This characteristic helps E. mundtii dominate complex microbial environments and remain prevalent across Lepidoptera, likely fostering long-term symbiosis between the both parties. The present study contributes to clarifying the niche of E. mundtii in the intestine of lepidopteran insects and further reveals its potential roles in their insect hosts.}, }
@article {pmid39146377, year = {2024}, author = {Nuismer, SL and Basinski, AJ and Schreiner, CL and Eskew, EA and Fichet-Calvet, E and Remien, CH}, title = {Quantifying the risk of spillover reduction programs for human health.}, journal = {PLoS computational biology}, volume = {20}, number = {8}, pages = {e1012358}, pmid = {39146377}, issn = {1553-7358}, support = {R01 GM122079/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Animals ; *Computer Simulation ; *Zoonoses/transmission/epidemiology/prevention &amp; control/virology ; Computational Biology ; Public Health ; Lassa Fever/epidemiology/prevention &amp; control/transmission ; Disease Outbreaks/prevention &amp; control/statistics &amp; numerical data ; Risk Assessment ; Africa, Western/epidemiology ; }, abstract = {Reducing spillover of zoonotic pathogens is an appealing approach to preventing human disease and minimizing the risk of future epidemics and pandemics. Although the immediate human health benefit of reducing spillover is clear, over time, spillover reduction could lead to counterintuitive negative consequences for human health. Here, we use mathematical models and computer simulations to explore the conditions under which unanticipated consequences of spillover reduction can occur in systems where the severity of disease increases with age at infection. Our results demonstrate that, because the average age at infection increases as spillover is reduced, programs that reduce spillover can actually increase population-level disease burden if the clinical severity of infection increases sufficiently rapidly with age. If, however, immunity wanes over time and reinfection is possible, our results reveal that negative health impacts of spillover reduction become substantially less likely. When our model is parameterized using published data on Lassa virus in West Africa, it predicts that negative health outcomes are possible, but likely to be restricted to a small subset of populations where spillover is unusually intense. Together, our results suggest that adverse consequences of spillover reduction programs are unlikely but that the public health gains observed immediately after spillover reduction may fade over time as the age structure of immunity gradually re-equilibrates to a reduced force of infection.}, }
@article {pmid39146316, year = {2024}, author = {He, YJ and Liao, H and Yang, G and Qiu, W and Xuan, R and Zheng, G and Xu, B and Yang, X and Magnuson, JT and Schlenk, D and Zheng, C}, title = {Perfluorohexanesulfonic Acid (PFHxS) Impairs Lipid Homeostasis in Zebrafish Larvae through Activation of PPARα.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {37}, pages = {16258-16268}, doi = {10.1021/acs.est.4c03053}, pmid = {39146316}, issn = {1520-5851}, mesh = {Animals ; *Zebrafish ; *Larva/drug effects/metabolism ; *Homeostasis ; *PPAR alpha/metabolism ; Lipid Metabolism/drug effects ; Fluorocarbons ; Sulfonic Acids ; }, abstract = {Perfluorohexanesulfonic acid (PFHxS), an emerging short-chain per- and polyfluoroalkyl substance, has been frequently detected in aquatic environments. Adverse outcome pathway studies have shown that perfluorinated compounds impair lipid homeostasis through peroxisome proliferator activated receptors (PPARs). However, many of these studies were performed at high concentrations and may thus be a result of overt toxicity. To better characterize the molecular and key events of PFHxS to biota, early life-stage zebrafish (Danio rerio) were exposed to concentrations detected in the environment (0.01, 0.1, 1, and 10 μg/L). Lipidomic and transcriptomic evaluations were integrated to predict potential molecular targets. PFHxS significantly impaired lipid homeostasis by the dysregulation of glycerophospholipids, fatty acyls, glycerolipids, sphingolipids, prenol lipids, and sterol lipids. Informatic analyses of the lipidome and transcriptome indicated alterations of the PPAR signaling pathway, with downstream changes to retinol, linoleic acid, and glycerophospholipid metabolism. To assess the role of PPARs, potential binding of PFHxS to PPARs was predicted and animals were coexposed to a PPAR antagonist (GW6471). Molecular simulation indicated PFHxS had a 27.1% better binding affinity than oleic acid, an endogenous agonist of PPARα. Antagonist coexposures rescued impaired glycerophosphocholine concentrations altered by PFHxS. These data indicate PPARα activation may be an important molecular initiating event for PFHxS.}, }
@article {pmid39145536, year = {2024}, author = {Pipes, L and Nielsen, R}, title = {A rapid phylogeny-based method for accurate community profiling of large-scale metabarcoding datasets.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {39145536}, issn = {2050-084X}, support = {BIO180028//Pittsburgh Supercomputing Center/ ; 1R01GM138634-01/GM/NIGMS NIH HHS/United States ; 1K99GM144747-01/GM/NIGMS NIH HHS/United States ; BIO180028//Advanced Cyberinfrastructure Coordination Ecosystem: Services &amp; Support/ ; R01 GM138634/GM/NIGMS NIH HHS/United States ; K99 GM144747/GM/NIGMS NIH HHS/United States ; }, mesh = {*Phylogeny ; *DNA Barcoding, Taxonomic/methods ; Computational Biology/methods ; DNA, Environmental/genetics ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Environmental DNA (eDNA) is becoming an increasingly important tool in diverse scientific fields from ecological biomonitoring to wastewater surveillance of viruses. The fundamental challenge in eDNA analyses has been the bioinformatical assignment of reads to taxonomic groups. It has long been known that full probabilistic methods for phylogenetic assignment are preferable, but unfortunately, such methods are computationally intensive and are typically inapplicable to modern next-generation sequencing data. We present a fast approximate likelihood method for phylogenetic assignment of DNA sequences. Applying the new method to several mock communities and simulated datasets, we show that it identifies more reads at both high and low taxonomic levels more accurately than other leading methods. The advantage of the method is particularly apparent in the presence of polymorphisms and/or sequencing errors and when the true species is not represented in the reference database.}, }
@article {pmid39145283, year = {2023}, author = {Boyes, D and Skojec, C and Kawahara, AY and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Buff Footman, Eilema depressum (Esper, 1787).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {342}, pmid = {39145283}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Eilema depressum (the Buff Footman; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 622.0 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.46 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,038 protein coding genes.}, }
@article {pmid39143756, year = {2024}, author = {Bauer, IE and Davies, MA and Bona, KA and Hararuk, O and Shaw, CH and Thompson, DK and Kurz, WA and Webster, KL and Garneau, M and McLaughlin, JW and Packalen, MS and Prystupa, E and Sanderson, NK and Tarnocai, C}, title = {Peat profile database from peatlands in Canada.}, journal = {Ecology}, volume = {105}, number = {10}, pages = {e4398}, doi = {10.1002/ecy.4398}, pmid = {39143756}, issn = {1939-9170}, support = {//Government of Canada (Expanding Market Opportunities Program)/ ; }, mesh = {Canada ; *Soil/chemistry ; Databases, Factual ; Ecosystem ; }, abstract = {Peatlands cover approximately 12% of the Canadian landscape and play an important role in the carbon cycle through their centennial- to millennial-scale storage of carbon under waterlogged and anoxic conditions. In recognizing the potential of these ecosystems as natural climate solutions and therefore the need to include them in national greenhouse gas inventories, the Canadian Model for Peatlands module (CaMP v. 2.0) was developed by the Canadian Forest Service. Model parameterization included compiling peat profiles across Canada to calibrate peat decomposition rates from different peatland types, to define typical bulk density profiles, and to describe the hydrological (i.e., water table) response of peatlands to climatic changes. A total of 1217 sites were included in the dataset from published and unpublished sources. The CORESITES table contains site location and summary data for each profile, as well as an estimate of total carbon mass per unit area (in megagrams of C per hectare). Total carbon mass per unit area at each location was calculated using bulk density and carbon content through each profile. The PROFILES table contains data for depth (in centimeters), bulk density (in grams per cubic meter), ash and carbon content (in percentage), and material descriptions for contiguous samples through each peat profile. Data gaps for bulk density and C content were filled using interpolation, regression trees, and assigned values based on material description and/or soil classification to allow for the estimation of total carbon mass per unit area. A subset of the sites (N = 374) also have pH and pore water trace-elemental geochemistry data and are found in the WATER table. The REFERENCES table contains the full citation of each source of the data and is linked to each core location through the SOURCEDATA table. The LOOKUP table defines codes in the database that required more space that what was sufficient in the metadata tables. The data can be accessed on Open Government Canada and will be useful for future work on carbon stock mapping and ecosystem modeling. All metadata and data are provided © Her Majesty the Queen in Right of Canada, 2023 and information contained in this publication may be reproduced for personal or public noncommercial purposes with attribution, whereas commercial reproduction and distribution are prohibited except with written permission from NRCan; complete details are noted in the Supporting Information file Metadata S1 (see Class III.B.3: Copyright restrictions).}, }
@article {pmid39140146, year = {2024}, author = {Yang, F and Han, QL and Zhao, WD and Zhao, Y}, title = {EC number prediction of protein sequences based on combination of hierarchical and global features.}, journal = {Yi chuan = Hereditas}, volume = {46}, number = {8}, pages = {661-669}, doi = {10.16288/j.yczz.24-102}, pmid = {39140146}, issn = {0253-9772}, mesh = {*Computational Biology/methods ; Amino Acid Sequence ; Proteins/chemistry ; Algorithms ; Sequence Analysis, Protein/methods ; Enzymes/chemistry/metabolism ; }, abstract = {The identification of enzyme functions plays a crucial role in understanding the mechanisms of biological activities and advancing the development of life sciences. However, existing enzyme EC number prediction methods did not fully utilize protein sequence information and still had shortcomings in identification accuracy. To address this issue, we proposed an EC number prediction network using hierarchical features and global features (ECPN-HFGF). This method first utilized residual networks to extract generic features from protein sequences, and then employed hierarchical feature extraction modules and global feature extraction modules to further extract hierarchical and global features of protein sequences. Subsequently, the prediction results of both feature types were combined, and a multitask learning framework was utilized to achieve accurate prediction of enzyme EC numbers. Experimental results indicated that the ECPN-HFGF method performed best in the task of predicting EC numbers for protein sequences, achieving macro F1 and micro F1 scores of 95.5% and 99.0%, respectively. The ECPN-HFGF method effectively combined hierarchical and global features of protein sequences, allowing for rapid and accurate EC number prediction. Compared to current commonly used methods, this method offers significantly higher prediction accuracy, providing an efficient approach for the advancement of enzymology research and enzyme engineering applications.}, }
@article {pmid39139763, year = {2023}, author = {Boyes, D and Boyes, C and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Acer Sober, Anarsia innoxiella (Gregersen &amp; Karsholt, 2017).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {357}, pmid = {39139763}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Anarsia innoxiella (the Acer Sober; Arthropoda; Insecta; Lepidoptera; Gelechiidae). The genome sequence is 302.9 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.25 kilobases in length.}, }
@article {pmid39139615, year = {2024}, author = {Boyes, D and Boyes, C and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Crescent Groundling, Teleiodes luculella (Hübner, 1813).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {143}, pmid = {39139615}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Teleiodes luculella (the Crescent Groundling; Arthropoda; Insecta; Lepidoptera; Gelechiidae). The genome sequence is 454.5 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.32 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,943 protein coding genes.}, }
@article {pmid39139614, year = {2024}, author = {Boyes, D and Crowley, LM and McCulloch, J and Boyes, C and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Elm Groundling moth, Carpatolechia fugitivella (Zeller, 1839).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {211}, pmid = {39139614}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Carpatolechia fugitivella (the Elm Groundling; Arthropoda; Insecta; Lepidoptera; Gelechiidae). The genome sequence is 493.1 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.26 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,721 protein coding genes.}, }
@article {pmid39137474, year = {2024}, author = {Tanaka, S and Uraguchi, K and Suzuki, E and Matsumoto, N and Tsumura, M and Fujimoto, S and Miyamoto, S and Yorifuji, T and Ando, M}, title = {Survey of pharyngeal foreign bodies in Japan: An ecological study using the nationwide claims data.}, journal = {International journal of pediatric otorhinolaryngology}, volume = {184}, number = {}, pages = {112055}, doi = {10.1016/j.ijporl.2024.112055}, pmid = {39137474}, issn = {1872-8464}, mesh = {Humans ; *Foreign Bodies/epidemiology ; Japan/epidemiology ; Female ; Male ; Child ; Child, Preschool ; Adolescent ; Infant ; Adult ; *Pharynx ; Young Adult ; Feeding Behavior ; Middle Aged ; Incidence ; Databases, Factual ; Seasons ; Aged ; Sex Distribution ; Age Distribution ; }, abstract = {OBJECTIVE: Pharyngeal foreign bodies (PFBs) are a prevalent disease affected by food culture and dietary habits, with fish bones as the leading cause. Most studies were limited to specific regions, and a nationwide survey was not conducted in Japan. In this ecological study, we aimed to conduct a nationwide analysis of outpatient PFB cases in Japan over three years, focusing on seasonal trends, sex- and age-stratified cases, and regional differences.<br><br>METHODS: We used the National Database of Health Insurance Claims and Specific Health Checkups of Japan open data from April 2019 to March 2022. The case data were analyzed by month, age, sex, and prefecture. Additionally, we calculated the standardized claim ratios (SCRs) for each prefecture and investigated the association between dietary habits, food culture, and SCR of PFBs using a two-level linear regression model.<br><br>RESULTS: We analyzed a total of 164,337 outpatient PFB cases in Japan, revealing an average incidence rate of 45.6 per 100,000 persons. The seasonal trend revealed a peak in July each year from 2019 to 2021, confirming seasonality in PFB incidents. Children reported a higher incidence rate. Living west of Japan and expenditure on fish and shellfish had a strongly positive association with the SCR of PFBs.<br><br>CONCLUSION: Our nationwide survey reveals that, even within Japan, there were regional variations influenced by food culture and dietary habits. The data showed that PFB incidence was higher among children, highlighting the need for preventive education.<br><br>LEVEL OF EVIDENCE: Level 3.}, }
@article {pmid39133313, year = {2024}, author = {Kuchař, M and Kotěrová, AP and Morávek, A and Santos, F and Harnádková, K and Henyš, P and Cunha, E and Brůžek, J}, title = {Correction to: Automatic variable extraction from 3D coxal bone models for sex estimation using the DSP2 method.}, journal = {International journal of legal medicine}, volume = {138}, number = {6}, pages = {2739}, doi = {10.1007/s00414-024-03311-2}, pmid = {39133313}, issn = {1437-1596}, }
@article {pmid39132840, year = {2024}, author = {Vale, FF and Roberts, RJ and Kobayashi, I and Camargo, MC and Rabkin, CS and , }, title = {Gene content, phage cycle regulation model and prophage inactivation disclosed by prophage genomics in the Helicobacter pylori Genome Project.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2379440}, pmid = {39132840}, issn = {1949-0984}, support = {R01 CA281732/CA/NCI NIH HHS/United States ; P30 DK058404/DK/NIDDK NIH HHS/United States ; R03 CA167773/CA/NCI NIH HHS/United States ; K22 CA226395/CA/NCI NIH HHS/United States ; P01 CA116087/CA/NCI NIH HHS/United States ; R01 DK062813/DK/NIDDK NIH HHS/United States ; K07 CA125588/CA/NCI NIH HHS/United States ; P01 CA028842/CA/NCI NIH HHS/United States ; K08 CA252635/CA/NCI NIH HHS/United States ; R01 CA077955/CA/NCI NIH HHS/United States ; R01 CA190612/CA/NCI NIH HHS/United States ; U54 GM133807/GM/NIGMS NIH HHS/United States ; P30 CA068485/CA/NCI NIH HHS/United States ; I01 CX002171/CX/CSRD VA/United States ; R01 ES010178/ES/NIEHS NIH HHS/United States ; R01 DK058587/DK/NIDDK NIH HHS/United States ; }, mesh = {*Helicobacter pylori/genetics/virology ; *Prophages/genetics/physiology ; *Genome, Bacterial ; Humans ; *Phylogeny ; *Genomics ; Helicobacter Infections/microbiology ; }, abstract = {Prophages can have major clinical implications through their ability to change pathogenic bacterial traits. There is limited understanding of the prophage role in ecological, evolutionary, adaptive processes and pathogenicity of Helicobacter pylori, a widespread bacterium causally associated with gastric cancer. Inferring the exact prophage genomic location and completeness requires complete genomes. The international Helicobacter pylori Genome Project (HpGP) dataset comprises 1011 H. pylori complete clinical genomes enriched with epigenetic data. We thoroughly evaluated the H. pylori prophage genomic content in the HpGP dataset. We investigated population evolutionary dynamics through phylogenetic and pangenome analyses. Additionally, we identified genome rearrangements and assessed the impact of prophage presence on bacterial gene disruption and methylome. We found that 29.5% (298) of the HpGP genomes contain prophages, of which only 32.2% (96) were complete, minimizing the burden of prophage carriage. The prevalence of H. pylori prophage sequences was variable by geography and ancestry, but not by disease status of the human host. Prophage insertion occasionally results in gene disruption that can change the global bacterial epigenome. Gene function prediction allowed the development of the first model for lysogenic-lytic cycle regulation in H. pylori. We have disclosed new prophage inactivation mechanisms that appear to occur by genome rearrangement, merger with other mobile elements, and pseudogene accumulation. Our analysis provides a comprehensive framework for H. pylori prophage biological and genomics, offering insights into lysogeny regulation and bacterial adaptation to prophages.}, }
@article {pmid39131439, year = {2024}, author = {Menger, J and Magagna, B and Henle, K and Harpke, A and Frenzel, M and Rick, J and Wiltshire, K and Grimm-Seyfarth, A}, title = {FAIR-EuMon: a FAIR-enabling resource for biodiversity monitoring schemes.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e125132}, pmid = {39131439}, issn = {1314-2828}, abstract = {BACKGROUND: Within the scope of the Helmholtz Metadata Collaboration (HMC), the ADVANCE project - Advanced metadata standards for biodiversity survey and monitoring data: supporting of research and conservation - aimed at supporting rich metadata generation with interoperable metadata standards and semantic artefacts that facilitate data access, integration and reuse across terrestrial, freshwater and marine realms. HMC's mission is to facilitate the discovery, access, machine-readability, and reuse of research data across and beyond the Helmholtz Association.<br><br>NEW INFORMATION: We revised, adapted and expanded existing metadata schemas, vocabularies and thesauri to build a FAIR metadata schema and a metadata entry form built on it for users to provide their metadata instances focused on biodiversity monitoring data. The schema is FAIR because it is both machine-interpretable and follows domain-relevant community standards. This report provides a general overview of the project results and instructions on how to access, re-use and complete the metadata form.}, }
@article {pmid39131363, year = {2025}, author = {Martin, C and Gitter, A and Anantharaman, K}, title = {Protein Set Transformer: A protein-based genome language model to power high diversity viromics.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39131363}, issn = {2692-8205}, support = {R35 GM143024/GM/NIGMS NIH HHS/United States ; }, abstract = {Exponential increases in microbial and viral genomic data demand transformational advances in scalable, generalizable frameworks for their interpretation. Standard homology-based functional analyses are hindered by the rapid divergence of microbial and especially viral genomes and proteins that significantly decreases the volume of usable data. Here, we present Protein Set Transformer (PST), a protein-based genome language model that models genomes as sets of proteins without considering sparsely available functional labels. Trained on >100k viruses, PST outperformed other homology- and language model-based approaches for relating viral genomes based on shared protein content. Further, PST demonstrated protein structural and functional awareness by clustering capsid-fold-containing proteins with known capsid proteins and uniquely clustering late gene proteins within related viruses. Our data establish PST as a valuable method for diverse viral genomics, ecology, and evolutionary applications. We posit that the PST framework can be a foundation model for microbial genomics when trained on suitable data.}, }
@article {pmid39131277, year = {2024}, author = {Yoo, D and Rhie, A and Hebbar, P and Antonacci, F and Logsdon, GA and Solar, SJ and Antipov, D and Pickett, BD and Safonova, Y and Montinaro, F and Luo, Y and Malukiewicz, J and Storer, JM and Lin, J and Sequeira, AN and Mangan, RJ and Hickey, G and Anez, GM and Balachandran, P and Bankevich, A and Beck, CR and Biddanda, A and Borchers, M and Bouffard, GG and Brannan, E and Brooks, SY and Carbone, L and Carrel, L and Chan, AP and Crawford, J and Diekhans, M and Engelbrecht, E and Feschotte, C and Formenti, G and Garcia, GH and de Gennaro, L and Gilbert, D and Green, RE and Guarracino, A and Gupta, I and Haddad, D and Han, J and Harris, RS and Hartley, GA and Harvey, WT and Hiller, M and Hoekzema, K and Houck, ML and Jeong, H and Kamali, K and Kellis, M and Kille, B and Lee, C and Lee, Y and Lees, W and Lewis, AP and Li, Q and Loftus, M and Loh, YHE and Loucks, H and Ma, J and Mao, Y and Martinez, JFI and Masterson, P and McCoy, RC and McGrath, B and McKinney, S and Meyer, BS and Miga, KH and Mohanty, SK and Munson, KM and Pal, K and Pennell, M and Pevzner, PA and Porubsky, D and Potapova, T and Ringeling, FR and Roha, JL and Ryder, OA and Sacco, S and Saha, S and Sasaki, T and Schatz, MC and Schork, NJ and Shanks, C and Smeds, L and Son, DR and Steiner, C and Sweeten, AP and Tassia, MG and Thibaud-Nissen, F and Torres-González, E and Trivedi, M and Wei, W and Wertz, J and Yang, M and Zhang, P and Zhang, S and Zhang, Y and Zhang, Z and Zhao, SA and Zhu, Y and Jarvis, ED and Gerton, JL and Rivas-González, I and Paten, B and Szpiech, ZA and Huber, CD and Lenz, TL and Konkel, MK and Yi, SV and Canzar, S and Watson, CT and Sudmant, PH and Molloy, E and Garrison, E and Lowe, CB and Ventura, M and O'Neill, RJ and Koren, S and Makova, KD and Phillippy, AM and Eichler, EE}, title = {Complete sequencing of ape genomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39131277}, issn = {2692-8205}, support = {R35 GM122550/GM/NIGMS NIH HHS/United States ; R01 MH120295/MH/NIMH NIH HHS/United States ; UH3 AG064706/AG/NIA NIH HHS/United States ; R35 GM146886/GM/NIGMS NIH HHS/United States ; R01 HG010329/HG/NHGRI NIH HHS/United States ; R01 AG056169/AG/NIA NIH HHS/United States ; R01 GM123312/GM/NIGMS NIH HHS/United States ; T15 LM007093/LM/NLM NIH HHS/United States ; U24 HG007497/HG/NHGRI NIH HHS/United States ; R01 HG002385/HG/NHGRI NIH HHS/United States ; P20 GM139769/GM/NIGMS NIH HHS/United States ; U24 HG010263/HG/NHGRI NIH HHS/United States ; R35 GM133747/GM/NIGMS NIH HHS/United States ; P51 OD011092/OD/NIH HHS/United States ; R56 AG056169/AG/NIA NIH HHS/United States ; P01 AI152999/AI/NIAID NIH HHS/United States ; R35 HG011332/HG/NHGRI NIH HHS/United States ; R01 HG013017/HG/NHGRI NIH HHS/United States ; R35 GM133600/GM/NIGMS NIH HHS/United States ; U19 AG023122/AG/NIA NIH HHS/United States ; R01 HG007352/HG/NHGRI NIH HHS/United States ; R35 GM142916/GM/NIGMS NIH HHS/United States ; R01 HG010169/HG/NHGRI NIH HHS/United States ; U41 HG007234/HG/NHGRI NIH HHS/United States ; R35 GM146926/GM/NIGMS NIH HHS/United States ; R35 GM151945/GM/NIGMS NIH HHS/United States ; }, abstract = {We present haplotype-resolved reference genomes and comparative analyses of six ape species, namely: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan, and siamang. We achieve chromosome-level contiguity with unparalleled sequence accuracy (<1 error in 500,000 base pairs), completely sequencing 215 gapless chromosomes telomere-to-telomere. We resolve challenging regions, such as the major histocompatibility complex and immunoglobulin loci, providing more in-depth evolutionary insights. Comparative analyses, including human, allow us to investigate the evolution and diversity of regions previously uncharacterized or incompletely studied without bias from mapping to the human reference. This includes newly minted gene families within lineage-specific segmental duplications, centromeric DNA, acrocentric chromosomes, and subterminal heterochromatin. This resource should serve as a definitive baseline for all future evolutionary studies of humans and our closest living ape relatives.}, }
@article {pmid39129912, year = {2023}, author = {Boyes, D and Hutchinson, F and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Brown Rustic, Charanyca ferruginea (Esper, 1785).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {547}, pmid = {39129912}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Charanyca ferruginea (the Brown Rustic; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 854.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.36 kilobases in length. Gene annotation of this assembly on Ensembl identified 23,126 protein coding genes.}, }
@article {pmid39127755, year = {2024}, author = {Pekár, S}, title = {Datasets of traits of zodariid spiders (Araneae: Zodariidae).}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {862}, pmid = {39127755}, issn = {2052-4463}, mesh = {*Spiders/classification/anatomy &amp; histology/physiology ; Animals ; Ecosystem ; Databases, Factual ; Australia ; }, abstract = {Species traits are essential for inferences on ecology and the evolution of organisms. Spiders are the most abundant and diversified terrestrial predators, playing an important role in a range of ecosystem services. Here, I present datasetse on all traits of zodariid spiders, which are known to be free-living ground-dwellers occurring on all continents (except Antarctica) with the highest species diversity in Australia. I collated the data from published resources. The datasets includes nearly 100 000 trait records on all (90) genera and almost all species (1249) of the family. The majority of the 88 traits collected are morphometric, followed by those relating to ecology, reproduction, and physiology. Morphometric traits were available for the majority of species. Other trait classes were only available for some species. I provide a standardized classification of selected categorical traits (habitat, microhabitat, retreat type, circadian activity, prey, primary defensive, and predators). This is the first complete database of traits of a whole spider family, which is available through the World Spider Trait database.}, }
@article {pmid39122728, year = {2024}, author = {Hixon, SW and Fernandes, R and Andriamahaihavana, A and Baden, AL and Blanco, MB and Caulier, G and Dammhahn, M and Eeckhaut, I and Eppley, TM and Frédérich, B and Ganzhorn, JU and Garbaras, A and Gibson, D and Goodman, SM and Irwin, M and Kelley, EA and Michel, LN and Lepoint, G and Loudon, JE and Mittelheiser, L and Rakotondranary, J and Rasamisoa, DC and Rasolofonirina, R and Ratovonamana, Y and Razafindramanana, J and Reisdorff, C and Sponheimer, M and Terrana, L and Vasey, N and Crowley, BE}, title = {Introducing IsoMad, a compilation of isotopic datasets for Madagascar.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {857}, pmid = {39122728}, issn = {2052-4463}, mesh = {Madagascar ; *Databases, Factual ; Animals ; Carbon Isotopes/analysis ; Nitrogen Isotopes/analysis ; }, abstract = {We present the first open-access, island-wide isotopic database (IsoMad) for modern biologically relevant materials collected on Madagascar within the past 150 years from both terrestrial and nearshore marine environments. Isotopic research on the island has increasingly helped with biological studies of endemic organisms, including evaluating foraging niches and investigating factors that affect the spatial distribution and abundance of species. The IsoMad database should facilitate future work by making it easy for researchers to access existing data (even for those who are relatively unfamiliar with the literature) and identify both research gaps and opportunities for using various isotope systems to answer research questions. We also hope that this database will encourage full data reporting in future publications.}, }
@article {pmid39122322, year = {2024}, author = {Martín, G and Erinjery, JJ and Ediriweera, D and Goldstein, E and Somaweera, R and de Silva, HJ and Lalloo, DG and Iwamura, T and Murray, KA}, title = {Effects of global change on snakebite envenoming incidence up to 2050: a modelling assessment.}, journal = {The Lancet. Planetary health}, volume = {8}, number = {8}, pages = {e533-e544}, pmid = {39122322}, issn = {2542-5196}, support = {MR/P024513/1/MRC_/Medical Research Council/United Kingdom ; MR/R015600/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Snake Bites/epidemiology ; Incidence ; Sri Lanka/epidemiology ; Humans ; *Climate Change ; Models, Theoretical ; Forecasting ; Animals ; Snakes ; }, abstract = {BACKGROUND: Human activities are driving climate, land cover, and population change (global change), and shifting the baseline geographical distribution of snakebite. The interacting effects of global change on snakes and communities at risk of snakebite are poorly understood, limiting capacity to anticipate and manage future changes in snakebite risk.<br><br>METHODS: In this modelling study, we projected how global change will affect snakebite envenoming incidence in Sri Lanka, as a model system that has a high incidence of snakebite. We used the shared socioeconomic pathway (SSP) scenario analysis framework to integrate forecasts across the domains of: climate change (historical trend from WorldClim plus three underlying regional circulation models [RCMs] in the Coordinated Regional Downscaling Experiment-South Asia repository, with two emissions pathways [representative concentration pathways RCP4.5 and RCP8.5]); land cover change (Dyna-CLUE model); and human population density change (based on Gridded Population of the World data) from Jan 1, 2010 to Dec 31, 2050. Forecasts were integrated under three different development scenarios: a sustainability pathway (SSP1 and no further emissions), a middle-of-the-road pathway (SSP2 and RCP4.5), and a fossil-fuelled pathway (SSP5 and RCP8.5). For SSP2 and SSP5, we nested three different RCMs (CNRM-CM5, GFDL-CCM3, and MPI-ESM-LR; mean averaged to represent consensus) to account for variability in climate predictions. Data were used as inputs to a mechanistic model that predicted snakebite envenoming incidence based on human-snake contact patterns.<br><br>FINDINGS: From 2010 to 2050, at the national level, envenoming incidence in Sri Lanka was projected to decrease by 12&#xb7;0-23&#xb7;0%, depending on the scenario. The rate of decrease in envenoming incidence was higher in SSP5-RCP8.5 than in SSP1 and SSP2-RCP4.5. Change in envenoming incidence was heterogenous across the country. In SSP1, incidence decreased in urban areas expected to have population growth, and with land cover changes towards anthropised classes. In SSP2-RCP4.5 and SSP5-RCP8.5, most areas were projected to have decreases in incidence (SSP5-RCP8.5 showing the largest area with incidence reductions), while areas such as the central highlands and the north of the country showed localised increases. In the model, decreases occurred with human population growth, land use change towards anthropised classes (potentially shifting occupational risk factors), and decreasing abundance of some snake species, potentially due to global warming and reduced climatic and habitat suitability, with displacement of some snake species.<br><br>INTERPRETATION: Snakebite envenoming incidence was projected to decrease overall in the coming decades in Sri Lanka, but with an apparent emerging conflict with sustainability objectives. Therefore, efforts to mitigate snakebite envenoming incidence will need to consider the potential impacts of sustainability interventions, particularly related to climate and land use change and in areas where increases in incidence are projected. In view of global change, neglected tropical diseases and public health issues related to biodiversity, such as snakebite, should be managed collaboratively by both environment and health stakeholders.<br><br>FUNDING: UK Medical Research Council.}, }
@article {pmid39116194, year = {2024}, author = {Guseva, K and Mohrlok, M and Alteio, L and Schmidt, H and Pollak, S and Kaiser, C}, title = {Bacteria face trade-offs in the decomposition of complex biopolymers.}, journal = {PLoS computational biology}, volume = {20}, number = {8}, pages = {e1012320}, pmid = {39116194}, issn = {1553-7358}, mesh = {Biopolymers/metabolism/chemistry ; *Bacteria/metabolism/enzymology ; Models, Biological ; Computational Biology ; }, abstract = {Although depolymerization of complex carbohydrates is a growth-limiting bottleneck for microbial decomposers, we still lack understanding about how the production of different types of extracellular enzymes affect individual microbes and in turn the performance of whole decomposer communities. In this work we use a theoretical model to evaluate the potential trade-offs faced by microorganisms in biopolymer decomposition which arise due to the varied biochemistry of different depolymerizing enzyme classes. We specifically consider two broad classes of depolymerizing extracellular enzymes, which are widespread across microbial taxa: exo-enzymes that cleave small units from the ends of polymer chains and endo-enzymes that act at random positions generating degradation products of varied sizes. Our results demonstrate a fundamental trade-off in the production of these enzymes, which is independent of system's complexity and which appears solely from the intrinsically different temporal depolymerization dynamics. As a consequence, specialists that produce either exo- or only endo-enzymes limit their growth to high or low substrate conditions, respectively. Conversely, generalists that produce both enzymes in an optimal ratio expand their niche and benefit from the synergy between the two enzymes. Finally, our results show that, in spatially-explicit environments, consortia composed of endo- and exo-specialists can only exist under oligotrophic conditions. In summary, our analysis demonstrates that the (evolutionary or ecological) selection of a depolymerization pathway will affect microbial fitness under low or high substrate conditions, with impacts on the ecological dynamics of microbial communities. It provides a possible explanation why many polysaccharide degraders in nature show the genetic potential to produce both of these enzyme classes.}, }
@article {pmid39114815, year = {2023}, author = {Lohse, K and Ebdon, S and Mackintosh, A and Martin, S and Saccheri, IJ and Bourn, NAD and Vila, R and ,  and ,  and ,  and , }, title = {The genome sequence of the Arctic Skipper, Carterocephalus palaemon (Pallas, 1771).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {369}, pmid = {39114815}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Carterocephalus palaemon (the Arctic Skipper; Arthropoda; Insecta; Lepidoptera; Hesperiidae). The genome sequence is 394.5 megabases in span. The whole assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.78 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,032 protein coding genes.}, }
@article {pmid39114490, year = {2024}, author = {Butlin, R and Mérot, C and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of a kelp fly, Coelopa pilipes Haliday, 1838.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {197}, pmid = {39114490}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Coelopa pilipes (kelp fly; Arthropoda; Insecta; Diptera; Coelopidae). The genome sequence is 263.0 megabases in span. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.86 kilobases in length.}, }
@article {pmid39112823, year = {2024}, author = {Darabi, H and Bazhdar, Y and Ehsani, AH}, title = {Modeling the spatial relationship between landscape services and vulnerability assessment.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {9}, pages = {797}, pmid = {39112823}, issn = {1573-2959}, mesh = {*Geographic Information Systems ; *Environmental Monitoring/methods ; *Conservation of Natural Resources ; *Ecosystem ; Iran ; Remote Sensing Technology ; Models, Theoretical ; Spatial Analysis ; }, abstract = {Even though many studies have been thus far devoted to landscape services (LS) or vulnerability assessment (VA) alone, the relationship between these two concepts has been less investigated. The current study attempts to model the spatial relationship between LS and VA in the Tarhan area (west of Iran). For this purpose, a combination of the analytic hierarchy process (AHP), remote sensing (RS), and geographic information system (GIS) techniques are applied to assess vulnerability. Variogram models and geostatistical simulations are used for mapping and evaluating landscape services. Moreover, the geographically weighted regression (GWR) is operated to predict the relationship between LS and VA. The results indicate that landform and socioeconomic variables are also two main factors shaping variations in VA. As well, the levels of services provided in the possible landscape are affected by the vulnerability. The assessment accordingly establishes that natural and cultural values have significant effects on services, in terms of their spatial distribution and nature. Exploring the relationship between LS and VA correspondingly depicts that VA has a direct influence on the capacity and entity of LS provision (adjusted R[2] = 0.67). The outcomes of the study provide a foundation for nature management and conservation, although it is less able to analyze the trade-off between ecosystem degradation and future development trends. The nexus of LS and future ecological processes in an integrated system can be thus the subject of further research.}, }
@article {pmid39109333, year = {2024}, author = {Boyes, D and Mulhair, PO and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Beautiful China-mark moth Nymphula nitidulata (Hufnagel, 1767).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {135}, pmid = {39109333}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Nymphula nitidulata (the Beautiful China-mark moth; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 635.8 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.36 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,031 protein coding genes.}, }
@article {pmid39109332, year = {2024}, author = {Boyes, D and Boyes, C and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Brown Ash Ermine moth, Zelleria hepariella Stainton, 1849.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {242}, pmid = {39109332}, issn = {2398-502X}, abstract = {We present a genome assembly from a male Zelleria hepariella (the Brown Ash Ermine; Arthropoda; Insecta; Lepidoptera; Yponomeutidae). The genome sequence is 428.8 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.31 kilobases in length. Gene annotation of this assembly on Ensembl identified 15,718 protein coding genes.}, }
@article {pmid39108663, year = {2023}, author = {Taylor, SC and Crowley, LM and Luker, S and Harvey, M and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Downland Villa bee-fly, Villa cingulata (Meigen, 1804).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {526}, pmid = {39108663}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Villa cingulata (the Downland Villa bee-fly; Arthropoda; Insecta; Diptera; Bombyliidae). The genome sequence is 412.6 megabases in span. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 22.43 kilobases in length.}, }
@article {pmid39103962, year = {2024}, author = {Prakofjewa, J and Sartori, M and Kalle, R and Łuczaj, &#x141; and Karbarz, M and Mattalia, G and Šarka, P and Prūse, B and Stryamets, N and Anegg, M and Kuznetsova, N and Kolosova, V and Belichenko, O and Aziz, MA and Pieroni, A and Sõukand, R}, title = {"But how true that is, I do not know": the influence of written sources on the medicinal use of fungi across the western borderlands of the former Soviet Union.}, journal = {IMA fungus}, volume = {15}, number = {1}, pages = {22}, pmid = {39103962}, issn = {2210-6340}, support = {714874//HORIZON EUROPE European Research Council/ ; }, abstract = {Fungi have been used for medicinal purposes for many centuries. This study, based on 35 historical written sources and 581 in-depth semi-structured interviews from eight countries in the western borderlands of the former Soviet Union, investigates the medicinal use of fungi by local communities. We compared the taxa and uses obtained from fieldwork and historical sources with works that advocated fungi use within Soviet herbals, representing the centralised medical system. During fieldwork, we identified eight locally used fungi and one lichen. The highest numbers of medicinal uses were documented in Russia, Estonia and Ukraine. Studies published before the Soviet era listed 21 fungal taxa and one lichen species used in the study region. However, only six of these taxa were mentioned as used by people in our field studies (Amanita muscaria, Boletus edulis, Lycoperdon, Morchella, Phallus impudicus and Cetraria islandica). Notably, these same six taxa were consistently endorsed in Soviet herbals. Of the remaining three taxa recorded in the fieldwork, none were mentioned in historical written sources. However, they were promoted either in Soviet herbals (Inonotus obliquus, Kombucha) or later popular publications (Cantharellus cibarius). This highlights the significant influence of written sources on the use of fungi for medicinal purposes within the studied local communities.}, }
@article {pmid39103035, year = {2024}, author = {Shi, C and Cheng, L and Yu, Y and Chen, S and Dai, Y and Yang, J and Zhang, H and Chen, J and Geng, N}, title = {Multi-omics integration analysis: Tools and applications in environmental toxicology.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {360}, number = {}, pages = {124675}, doi = {10.1016/j.envpol.2024.124675}, pmid = {39103035}, issn = {1873-6424}, mesh = {*Environmental Pollutants/toxicity ; *Ecotoxicology/methods ; *Proteomics ; Genomics ; Metabolomics ; Animals ; Humans ; Multiomics ; }, abstract = {Nowadays, traditional single-omics study is not enough to explain the causality between molecular alterations and toxicity endpoints for environmental pollutants. With the development of high-throughput sequencing technology and high-resolution mass spectrometry technology, the integrative analysis of multi-omics has become an efficient strategy to understand holistic biological mechanisms and to uncover the regulation network in specific biological processes. This review summarized sample preparation methods, integration analysis tools and the application of multi-omics integration analyses in environmental toxicology field. Currently, omics methods have been widely applied being as the sensitivity of early biological response, especially for low-dose and long-term exposure to environmental pollutants. Integrative omics can reveal the overall changes of genes, proteins, and/or metabolites in the cells, tissues or organisms, which provide new insights into revealing the overall toxicity effects, screening the toxic targets, and exploring the underlying molecular mechanism of pollutants.}, }
@article {pmid39102402, year = {2024}, author = {Saad-Roy, CM and Morris, SE and Boots, M and Baker, RE and Lewis, BL and Farrar, J and Marathe, MV and Graham, AL and Levin, SA and Wagner, CE and Metcalf, CJE and Grenfell, BT}, title = {Impact of waning immunity against SARS-CoV-2 severity exacerbated by vaccine hesitancy.}, journal = {PLoS computational biology}, volume = {20}, number = {8}, pages = {e1012211}, pmid = {39102402}, issn = {1553-7358}, support = {U01 CK000555/CK/NCEZID CDC HHS/United States ; }, mesh = {Humans ; *COVID-19/immunology/prevention &amp; control/epidemiology ; *SARS-CoV-2/immunology ; *COVID-19 Vaccines/immunology ; Vaccination Hesitancy/statistics &amp; numerical data ; Severity of Illness Index ; Vaccination/statistics &amp; numerical data ; Pandemics/prevention &amp; control ; Computational Biology ; }, abstract = {The SARS-CoV-2 pandemic has generated a considerable number of infections and associated morbidity and mortality across the world. Recovery from these infections, combined with the onset of large-scale vaccination, have led to rapidly-changing population-level immunological landscapes. In turn, these complexities have highlighted a number of important unknowns related to the breadth and strength of immunity following recovery or vaccination. Using simple mathematical models, we investigate the medium-term impacts of waning immunity against severe disease on immuno-epidemiological dynamics. We find that uncertainties in the duration of severity-blocking immunity (imparted by either infection or vaccination) can lead to a large range of medium-term population-level outcomes (i.e. infection characteristics and immune landscapes). Furthermore, we show that epidemiological dynamics are sensitive to the strength and duration of underlying host immune responses; this implies that determining infection levels from hospitalizations requires accurate estimates of these immune parameters. More durable vaccines both reduce these uncertainties and alleviate the burden of SARS-CoV-2 in pessimistic outcomes. However, heterogeneity in vaccine uptake drastically changes immune landscapes toward larger fractions of individuals with waned severity-blocking immunity. In particular, if hesitancy is substantial, more robust vaccines have almost no effects on population-level immuno-epidemiology, even if vaccination rates are compensatorily high among vaccine-adopters. This pessimistic scenario for vaccination heterogeneity arises because those few individuals that are vaccine-adopters are so readily re-vaccinated that the duration of vaccinal immunity has no appreciable consequences on their immune status. Furthermore, we find that this effect is heightened if vaccine-hesitants have increased transmissibility (e.g. due to riskier behavior). Overall, our results illustrate the necessity to characterize both transmission-blocking and severity-blocking immune time scales. Our findings also underline the importance of developing robust next-generation vaccines with equitable mass vaccine deployment.}, }
@article {pmid39102091, year = {2024}, author = {Kuchař, M and Pilmann Kotěrová, A and Morávek, A and Santos, F and Harnádková, K and Henyš, P and Cunha, E and Brůžek, J}, title = {Automatic variable extraction from 3D coxal bone models for sex estimation using the DSP2 method.}, journal = {International journal of legal medicine}, volume = {138}, number = {6}, pages = {2647-2658}, pmid = {39102091}, issn = {1437-1596}, mesh = {Humans ; *Sex Determination by Skeleton/methods ; Male ; Female ; *Pelvic Bones/diagnostic imaging ; *Algorithms ; *Imaging, Three-Dimensional ; *Forensic Anthropology/methods ; Adult ; Middle Aged ; Aged ; Young Adult ; Portugal ; Aged, 80 and over ; }, abstract = {Thanks to technical progress and the availability of virtual data, sex estimation methods as part of a biological profile are undergoing an inevitable evolution. Further reductions in subjectivity, but potentially also in measurement errors, can be brought by approaches that automate the extraction of variables. Such automatization also significantly accelerates and facilitates the specialist's work. The aim of this study is (1) to apply a previously proposed algorithm (Kuchař et al. 2021) to automatically extract 10 variables used for the DSP2 sex estimation method, and (2) to test the robustness of the new automatic approach in a current heterogeneous population. For the first aim, we used a sample of 240 3D scans of pelvic bones from the same individuals, which were measured manually for the DSP database. For the second aim a sample of 108 pelvic bones from the New Mexico Decedent Image Database was used. The results showed high agreement between automatic and manual measurements with rTEM below 5% for all dimensions except two. The accuracy of final sex estimates based on all 10 variables was excellent (error rate 0.3%). However, we observed a higher number of undetermined individuals in the Portuguese sample (25% of males) and the New Mexican sample (36.5% of females). In conclusion, the procedure for automatic dimension extraction was successfully applied both to a different type of data and to a heterogeneous population.}, }
@article {pmid39101049, year = {2024}, author = {Boyes, D and Lees, DC and Holland, PWH and ,  and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Oak Beauty, Biston strataria (Hufnagel, 1767).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {35}, pmid = {39101049}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Biston strataria (the Oak Beauty; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 424.0 megabases in span. Most of the assembly is scaffolded into 16 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.61 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,406 protein coding genes.}, }
@article {pmid39100235, year = {2024}, author = {Ciach, MA and Pawłowska, J and Górecki, P and Muszewska, A}, title = {The interkingdom horizontal gene transfer in 44 early diverging fungi boosted their metabolic, adaptive, and immune capabilities.}, journal = {Evolution letters}, volume = {8}, number = {4}, pages = {526-538}, pmid = {39100235}, issn = {2056-3744}, abstract = {Numerous studies have been devoted to individual cases of horizontally acquired genes in fungi. It has been shown that such genes expand the hosts' metabolic capabilities and contribute to their adaptations as parasites or symbionts. Some studies have provided an extensive characterization of the horizontal gene transfer (HGT) in Dikarya. However, in the early diverging fungi (EDF), a similar characterization is still missing. In order to fill this gap, we have designed a computational pipeline to obtain a statistical sample of reliable HGT events with a low false discovery rate. We have analyzed 44 EDF proteomes and identified 829 xenologs in fungi ranging from Chytridiomycota to Mucoromycota. We have identified several patterns and statistical properties of EDF HGT. We show that HGT is driven by bursts of gene exchange and duplication, resulting in highly divergent numbers and molecular properties of xenologs between fungal lineages. Ancestrally aquatic fungi are generally more likely to acquire foreign genetic material than terrestrial ones. Endosymbiotic bacteria can be a source of useful xenologs, as exemplified by NOD-like receptors transferred to Mortierellomycota. Closely related fungi have similar rates of intronization of xenologs. Posttransfer gene fusions and losses of protein domains are common and may influence the encoded proteins' functions. We argue that there is no universal approach for HGT identification and inter- and intra-kingdom transfers require tailored identification methods. Our results help to better understand how and to what extent HGT has shaped the metabolic, adaptive, and immune capabilities of fungi.}, }
@article {pmid39099847, year = {2024}, author = {Kapsetaki, SE and Compton, ZT and Dolan, J and Harris, V&#x39a; and Mellon, W and Rupp, SM and Duke, EG and Harrison, TM and Aksoy, S and Giraudeau, M and Vincze, O and McGraw, KJ and Aktipis, A and Tollis, M and Boddy, A&#x39c; and Maley, CC}, title = {Life history traits and cancer prevalence in birds.}, journal = {Evolution, medicine, and public health}, volume = {12}, number = {1}, pages = {105-116}, pmid = {39099847}, issn = {2050-6201}, support = {R01 CA140657/CA/NCI NIH HHS/United States ; }, abstract = {BACKGROUND AND OBJECTIVES: Cancer is a disease that affects nearly all multicellular life, including the broad and diverse taxa of Aves. While little is known about the factors that contribute to cancer risk across Aves, life history trade-offs may explain some of this variability in cancer prevalence. We predict birds with high investment in reproduction may have a higher likelihood of developing cancer. In this study, we tested whether life history traits are associated with cancer prevalence in 108 species of birds.<br><br>METHODOLOGY: We obtained life history data from published databases and cancer data from 5,729 necropsies from 108 species of birds across 24 taxonomic orders from 25 different zoological facilities. We performed phylogenetically controlled regression analyses between adult body mass, lifespan, incubation length, clutch size, sexually dimorphic traits, and both neoplasia and malignancy prevalence. We also compared the neoplasia and malignancy prevalence of female and male birds.<br><br>RESULTS: Providing support for a life history trade-off between somatic maintenance and reproduction, we found a positive relationship between clutch size and cancer prevalence across Aves. There was no significant association with body mass, lifespan, incubation length, sexual dimorphism, and cancer.<br><br>CONCLUSIONS AND IMPLICATIONS: Life history theory presents an important framework for understanding differences in cancer defenses across various species. These results suggest a trade-off between reproduction and somatic maintenance, where Aves with small clutch sizes get less cancer.}, }
@article {pmid39099645, year = {2023}, author = {Obbard, DJ and ,  and ,  and ,  and , }, title = {The genome sequence of a drosophilid fruit fly, Chymomyza fuscimana (Drosophilidae) (Zetterstedt, 1838).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {477}, pmid = {39099645}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Chymomyza fuscimana (drosophilid fruit fly; Arthropoda; Insecta; Diptera; Drosophilidae). The genome sequence is 338.0 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.47 kilobases in length.}, }
@article {pmid39092794, year = {2024}, author = {Ma, X and Huete, A and Liu, Y and Zhu, X and Nguyen, H and Miura, T and Chen, M and Li, X and Asrar, G}, title = {A holistic big data approach to understand and manage increasing pollen-induced respiratory allergies under global change.}, journal = {Global change biology}, volume = {30}, number = {8}, pages = {e17451}, doi = {10.1111/gcb.17451}, pmid = {39092794}, issn = {1365-2486}, support = {1027576//National Institute of Food and Agriculture/ ; DP210100347//Australian Research Council/ ; 42171305//National Natural Science Foundation of China/ ; }, mesh = {*Pollen/immunology ; *Big Data ; *Climate Change ; Humans ; Respiratory Hypersensitivity/etiology ; }, }
@article {pmid39092001, year = {2024}, author = {Boyes, D and Holland, PWH and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Orange-tailed Clearwing, Synanthedon andrenaeformis (Laspeyres, 1801).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {160}, pmid = {39092001}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Synanthedon andrenaeformis (the Orange-tailed Clearwing; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 348.4 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.65 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,867 protein coding genes.}, }
@article {pmid39090383, year = {2024}, author = {Manubens-Gil, L and Zhou, Z and Chen, H and Ramanathan, A and Liu, X and Liu, Y and Bria, A and Gillette, T and Ruan, Z and Yang, J and Radojević, M and Zhao, T and Cheng, L and Qu, L and Liu, S and Bouchard, KE and Gu, L and Cai, W and Ji, S and Roysam, B and Wang, CW and Yu, H and Sironi, A and Iascone, DM and Zhou, J and Bas, E and Conde-Sousa, E and Aguiar, P and Li, X and Li, Y and Nanda, S and Wang, Y and Muresan, L and Fua, P and Ye, B and He, HY and Staiger, JF and Peter, M and Cox, DN and Simonneau, M and Oberlaender, M and Jefferis, G and Ito, K and Gonzalez-Bellido, P and Kim, J and Rubel, E and Cline, HT and Zeng, H and Nern, A and Chiang, AS and Yao, J and Roskams, J and Livesey, R and Stevens, J and Liu, T and Dang, C and Guo, Y and Zhong, N and Tourassi, G and Hill, S and Hawrylycz, M and Koch, C and Meijering, E and Ascoli, GA and Peng, H}, title = {Author Correction: BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets.}, journal = {Nature methods}, volume = {21}, number = {10}, pages = {1959}, doi = {10.1038/s41592-024-02395-3}, pmid = {39090383}, issn = {1548-7105}, }
@article {pmid39089617, year = {2025}, author = {Chen, SH and Chen, CH and Lin, HC and Yeh, SA and Hwang, TL and Chen, PJ}, title = {Drug repurposing of cyclin-dependent kinase inhibitors for neutrophilic acute respiratory distress syndrome and psoriasis.}, journal = {Journal of advanced research}, volume = {72}, number = {}, pages = {485-500}, pmid = {39089617}, issn = {2090-1224}, mesh = {Humans ; *Drug Repositioning/methods ; *Respiratory Distress Syndrome/drug therapy ; *Cyclin-Dependent Kinases/antagonists &amp; inhibitors/metabolism ; *Psoriasis/drug therapy ; *Neutrophils/drug effects/metabolism/immunology ; *Protein Kinase Inhibitors/therapeutic use/pharmacology ; Animals ; Neutrophil Activation/drug effects ; }, abstract = {BACKGROUND: Neutrophilic inflammation, characterized by dysregulated neutrophil activation, triggers a variety of inflammatory responses such as chemotactic infiltration, oxidative bursts, degranulation, neutrophil extracellular traps (NETs) formation, and delayed turnover. This type of inflammation is pivotal in the pathogenesis of acute respiratory distress syndrome (ARDS) and psoriasis. Despite current treatments, managing neutrophil-associated inflammatory symptoms remains a significant challenge.<br><br>AIM OF REVIEW: This review emphasizes the role of cyclin-dependent kinases (CDKs) in neutrophil activation and inflammation. It aims to highlight the therapeutic potential of repurposing CDK inhibitors to manage neutrophilic inflammation, particularly in ARDS and psoriasis. Additionally, it discusses the necessary precautions for the clinical application of these inhibitors due to potential off-target effects and the need for dose optimization.<br><br>CDKs regulate key neutrophilic functions, including chemotactic responses, degranulation, NET formation, and apoptosis. Repurposing CDK inhibitors, originally developed for cancer treatment, shows promise in controlling neutrophilic inflammation. Clinical anticancer drugs, palbociclib and ribociclib, have demonstrated efficacy in treating neutrophilic ARDS and psoriasis by targeting off-label pathways, phosphoinositide 3-kinase (PI3K) and phosphodiesterase 4 (PDE4), respectively. While CDK inhibitors offer promising therapeutic benefits, their clinical repurposing requires careful consideration of off-target effects and dose optimization. Further exploration and clinical trials are necessary to ensure their safety and efficacy in treating inflammatory conditions.}, }
@article {pmid39086664, year = {2023}, author = {Boyes, D and Eljounaidi, K and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Rose-flounced Tabby, Endotricha flammealis (Denis &amp; Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {516}, pmid = {39086664}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Endotricha flammealis (the Rose-flounced Tabby; Arthropoda; Insecta; Lepidoptera; Pyralidae). The genome sequence is 473.9 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.23 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,578 protein coding genes.}, }
@article {pmid39083325, year = {2024}, author = {Webb, EK and Stevens, JS and Ely, TD and Lebois, LAM and van Rooij, SJH and Bruce, SE and House, SL and Beaudoin, FL and An, X and Neylan, TC and Clifford, GD and Linnstaedt, SD and Germine, LT and Bollen, KA and Rauch, SL and Haran, JP and Storrow, AB and Lewandowski, C and Musey, PI and Hendry, PL and Sheikh, S and Jones, CW and Punches, BE and Swor, RA and Murty, VP and Hudak, LA and Pascual, JL and Seamon, MJ and Datner, EM and Pearson, C and Peak, DA and Domeier, RM and Rathlev, NK and O'Neil, BJ and Sergot, P and Sanchez, LD and Joormann, J and Pizzagalli, DA and Harte, SE and Kessler, RC and Koenen, KC and Ressler, KJ and McLean, SA and Harnett, NG}, title = {Neighborhood Resources Associated With Psychological Trajectories and Neural Reactivity to Reward After Trauma.}, journal = {JAMA psychiatry}, volume = {81}, number = {11}, pages = {1090-1100}, pmid = {39083325}, issn = {2168-6238}, support = {K01 MH129828/MH/NIMH NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; *Stress Disorders, Post-Traumatic/physiopathology/diagnostic imaging ; Female ; Male ; *Reward ; Adult ; *Magnetic Resonance Imaging ; *Resilience, Psychological ; Longitudinal Studies ; *Residence Characteristics ; Middle Aged ; Young Adult ; Brain/physiopathology/diagnostic imaging ; Survivors/psychology ; }, abstract = {IMPORTANCE: Research on resilience after trauma has often focused on individual-level factors (eg, ability to cope with adversity) and overlooked influential neighborhood-level factors that may help mitigate the development of posttraumatic stress disorder (PTSD).<br><br>OBJECTIVE: To investigate whether an interaction between residential greenspace and self-reported individual resources was associated with a resilient PTSD trajectory (ie, low/no symptoms) and to test if the association between greenspace and PTSD trajectory was mediated by neural reactivity to reward.<br><br>As part of a longitudinal cohort study, trauma survivors were recruited from emergency departments across the US. Two weeks after trauma, a subset of participants underwent functional magnetic resonance imaging during a monetary reward task. Study data were analyzed from January to November 2023.<br><br>EXPOSURES: Residential greenspace within a 100-m buffer of each participant's home address was derived from satellite imagery and quantified using the Normalized Difference Vegetation Index and perceived individual resources measured by the Connor-Davidson Resilience Scale (CD-RISC).<br><br>MAIN OUTCOME AND MEASURES: PTSD symptom severity measured at 2 weeks, 8 weeks, 3 months, and 6 months after trauma. Neural responses to monetary reward in reward-related regions (ie, amygdala, nucleus accumbens, orbitofrontal cortex) was a secondary outcome. Covariates included both geocoded (eg, area deprivation index) and self-reported characteristics (eg, childhood maltreatment, income).<br><br>RESULTS: In 2597 trauma survivors (mean [SD] age, 36.5 [13.4] years; 1637 female [63%]; 1304 non-Hispanic Black [50.2%], 289 Hispanic [11.1%], 901 non-Hispanic White [34.7%], 93 non-Hispanic other race [3.6%], and 10 missing/unreported [0.4%]), 6 PTSD trajectories (resilient, nonremitting high, nonremitting moderate, slow recovery, rapid recovery, delayed) were identified through latent-class mixed-effect modeling. Multinominal logistic regressions revealed that for individuals with higher CD-RISC scores, greenspace was associated with a greater likelihood of assignment in a resilient trajectory compared with nonremitting high (Wald z test&#x2009;=&#x2009;-3.92; P&#x2009;<&#x2009;.001), nonremitting moderate (Wald z test&#x2009;=&#x2009;-2.24; P&#x2009;=&#x2009;.03), or slow recovery (Wald z test&#x2009;=&#x2009;-2.27; P&#x2009;=&#x2009;.02) classes. Greenspace was also associated with greater neural reactivity to reward in the amygdala (n&#x2009;=&#x2009;288; t277&#x2009;=&#x2009;2.83; adjusted P value&#x2009;=&#x2009;0.02); however, reward reactivity did not differ by PTSD trajectory.<br><br>CONCLUSIONS AND RELEVANCE: In this cohort study, greenspace and self-reported individual resources were significantly associated with PTSD trajectories. These findings suggest that factors at multiple ecological levels may contribute to the likelihood of resiliency to PTSD after trauma.}, }
@article {pmid39082646, year = {2024}, author = {Mallawaarachchi, V and Wickramarachchi, A and Xue, H and Papudeshi, B and Grigson, SR and Bouras, G and Prahl, RE and Kaphle, A and Verich, A and Talamantes-Becerra, B and Dinsdale, EA and Edwards, RA}, title = {Solving genomic puzzles: computational methods for metagenomic binning.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {5}, pages = {}, pmid = {39082646}, issn = {1477-4054}, support = {RC2 DK116713/DK/NIDDK NIH HHS/United States ; /NH/NIH HHS/United States ; DP220102915//Australian Research Council/ ; RC2DK116713/DK/NIDDK NIH HHS/United States ; }, mesh = {*Metagenomics/methods ; Computational Biology/methods ; Metagenome ; Algorithms ; Genomics/methods ; }, abstract = {Metagenomics involves the study of genetic material obtained directly from communities of microorganisms living in natural environments. The field of metagenomics has provided valuable insights into the structure, diversity and ecology of microbial communities. Once an environmental sample is sequenced and processed, metagenomic binning clusters the sequences into bins representing different taxonomic groups such as species, genera, or higher levels. Several computational tools have been developed to automate the process of metagenomic binning. These tools have enabled the recovery of novel draft genomes of microorganisms allowing us to study their behaviors and functions within microbial communities. This review classifies and analyzes different approaches of metagenomic binning and different refinement, visualization, and evaluation techniques used by these methods. Furthermore, the review highlights the current challenges and areas of improvement present within the field of research.}, }
@article {pmid39082518, year = {2024}, author = {Cabral, BVB and Sousa, GJB and Cordeiro, LI and Maranhão, TA and Pereira, MLD}, title = {Temporal Pattern and Spatial Distribution of Tuberculosis Prevalence Associated with Multimorbidity in Brazil.}, journal = {Revista da Sociedade Brasileira de Medicina Tropical}, volume = {57}, number = {}, pages = {e00408}, pmid = {39082518}, issn = {1678-9849}, mesh = {Humans ; Brazil/epidemiology ; Prevalence ; *Tuberculosis/epidemiology ; *Spatio-Temporal Analysis ; Male ; *Multimorbidity ; Female ; Adult ; Middle Aged ; Chronic Disease/epidemiology ; Socioeconomic Factors ; }, abstract = {BACKGROUND: Four main chronic conditions may be involved in the tuberculosis pathogenic process and/or clinical evolution: HIV/AIDS, diabetes mellitus, mental illness, and Chronic Obstructive Pulmonary Disease. This study aimed to determine the spatiotemporal pattern of tuberculosis (TB) associated with multimorbidity in Brazil.<br><br>METHODS: Ecological study use data from the Notifiable Diseases Information System (SINAN), collected from the electronic portal of the Department of Informatics of the SUS (DATASUS). These data included TB cases that were reported between 2007 and 2021 and were associated with two or more chronic clinical health conditions (multimorbidity).<br><br>RESULTS: A total of 7,795 cases of TB associated with multimorbidity were recorded, with an average growth trend of 4.6% per year (95% Confidence Interval (CI): 3.3-5.9; p<0.001) and higher growth in the first temporal segment (2007 to 2011) (8.9%; 95%CI: 4.2-13.9; p=0.002). The spatial analysis, after Bayesian smoothing, highlighted the main municipalities states of the study, namely: S&#xe3;o Paulo (19.8%; n = 297), Porto Alegre (23.6%; n = 354), and Rio de Janeiro (44.8%; n = 672). The proportion of extremely poor (&#x3b2;=-0.002), the bolsa fam&#xed;lia program (&#x3b2;=0.002), the average per-person income (&#x3b2;=0.001), and the percentage of the population living in households with a density of more than 2 people per bedroom (&#x3b2;=0.001) were related to chronic health conditions.<br><br>CONCLUSIONS: These findings will stimulate public action to manage this situation. However, as this is still a recent topic in the literature, we encourage the development of studies on the synergistic characteristics of TB and other clinical conditions.}, }
@article {pmid39082244, year = {2024}, author = {Farrell, MJ and Le Guillarme, N and Brierley, L and Hunter, B and Scheepens, D and Willoughby, A and Yates, A and Mideo, N}, title = {The changing landscape of text mining: a review of approaches for ecology and evolution.}, journal = {Proceedings. Biological sciences}, volume = {291}, number = {2027}, pages = {20240423}, pmid = {39082244}, issn = {1471-2954}, support = {//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {*Data Mining ; *Ecology/methods ; *Biological Evolution ; *Natural Language Processing ; Machine Learning ; }, abstract = {In ecology and evolutionary biology, the synthesis and modelling of data from published literature are commonly used to generate insights and test theories across systems. However, the tasks of searching, screening, and extracting data from literature are often arduous. Researchers may manually process hundreds to thousands of articles for systematic reviews, meta-analyses, and compiling synthetic datasets. As relevant articles expand to tens or hundreds of thousands, computer-based approaches can increase the efficiency, transparency and reproducibility of literature-based research. Methods available for text mining are rapidly changing owing to developments in machine learning-based language models. We review the growing landscape of approaches, mapping them onto three broad paradigms (frequency-based approaches, traditional Natural Language Processing and deep learning-based language models). This serves as an entry point to learn foundational and cutting-edge concepts, vocabularies, and methods to foster integration of these tools into ecological and evolutionary research. We cover approaches for modelling ecological texts, generating training data, developing custom models and interacting with large language models and discuss challenges and possible solutions to implementing these methods in ecology and evolution.}, }
@article {pmid39081076, year = {2024}, author = {Levy, O and Shahar, S}, title = {Artificial Intelligence for Climate Change Biology: From Data Collection to Predictions.}, journal = {Integrative and comparative biology}, volume = {64}, number = {3}, pages = {953-974}, doi = {10.1093/icb/icae127}, pmid = {39081076}, issn = {1557-7023}, support = {300/22//Israeli Science Foundation/ ; NGS-84241T-21//National Geographic Society/ ; IOS-1754949//National Science Foundation/ ; }, mesh = {*Climate Change ; *Artificial Intelligence ; Animals ; Big Data ; Microclimate ; Data Collection/methods ; }, abstract = {In the era of big data, ecological research is experiencing a transformative shift, yet big-data advancements in thermal ecology and the study of animal responses to climate conditions remain limited. This review discusses how big data analytics and artificial intelligence (AI) can significantly enhance our understanding of microclimates and animal behaviors under changing climatic conditions. We explore AI's potential to refine microclimate models and analyze data from advanced sensors and camera technologies, which capture detailed, high-resolution information. This integration can allow researchers to dissect complex ecological and physiological processes with unprecedented precision. We describe how AI can enhance microclimate modeling through improved bias correction and downscaling techniques, providing more accurate estimates of the conditions that animals face under various climate scenarios. Additionally, we explore AI's capabilities in tracking animal responses to these conditions, particularly through innovative classification models that utilize sensors such as accelerometers and acoustic loggers. For example, the widespread usage of camera traps can benefit from AI-driven image classification models to accurately identify thermoregulatory responses, such as shade usage and panting. AI is therefore instrumental in monitoring how animals interact with their environments, offering vital insights into their adaptive behaviors. Finally, we discuss how these advanced data-driven approaches can inform and enhance conservation strategies. In particular, detailed mapping of microhabitats essential for species survival under adverse conditions can guide the design of climate-resilient conservation and restoration programs that prioritize habitat features crucial for biodiversity resilience. In conclusion, the convergence of AI, big data, and ecological science heralds a new era of precision conservation, essential for addressing the global environmental challenges of the 21st century.}, }
@article {pmid39080706, year = {2024}, author = {Hamamoto, K and Mizuyama, M and Nishijima, M and Maeda, A and Gibu, K and Poliseno, A and Iguchi, A and Reimer, JD}, title = {Diversity, composition and potential roles of sedimentary microbial communities in different coastal substrates around subtropical Okinawa Island, Japan.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {54}, pmid = {39080706}, issn = {2524-6372}, support = {20H00653//Japan Society for the Promotion of Science/ ; }, abstract = {BACKGROUND: Marine benthic prokaryotic communities play crucial roles in material recycling within coastal environments, including coral reefs. Coastal sedimentary microbiomes are particularly important as potential reservoirs of symbiotic, beneficial, and pathogenic bacteria in coral reef environments, and therefore presumably play a core role in local ecosystem functioning. However, there is a lack of studies comparing different environments with multiple sites on the island scale, particularly studies focusing on prokaryotic communities, as previous investigations have focused mainly on a single site or on specific environmental conditions. In our study, we collected coastal sediments from seven sites around Okinawa Island, Japan, including three different benthic types; sandy bottoms, seagrass meadows, and hard substratum with living scleractinian corals. We then used metabarcoding to identify prokaryotic compositions and estimate enzymes encoded by genes to infer their functions.<br><br>RESULTS: The results showed that the three substrata had significantly different prokaryotic compositions. Seagrass meadow sites exhibited significantly higher prokaryotic alpha-diversity compared to sandy bottom sites. ANCOM analysis revealed that multiple bacterial orders were differentially abundant within each substratum. At coral reef sites, putative disease- and thermal stress-related opportunistic bacteria such as Rhodobacterales, Verrucomicrobiales, and Cytophagales were comparatively abundant, while seagrass meadow sites abundantly harbored Desulfobacterales, Steroidobacterales and Chromatiales, which are common bacterial orders in seagrass meadows. According to our gene-coded enzyme analyses the numbers of differentially abundant enzymes were highest in coral reef sites. Notably, superoxide dismutase, an important enzyme for anti-oxidative stress in coral tissue, was abundant at coral sites. Our results provide a list of prokaryotes to look into in each substrate, and further emphasize the importance of considering the microbiome, especially when focusing on environmental conservation.<br><br>CONCLUSION: Our findings prove that prokaryotic metabarcoding is capable of capturing compositional differences and the diversity of microbial communities in three different environments. Furthermore, several taxa were suggested to be differentially more abundant in specific environments, and gene-coded enzymic compositions also showed possible differences in ecological functions. Further study, in combination with field observations and temporal sampling, is key to achieving a better understanding of the interactions between the local microbiome and the surrounding benthic community.}, }
@article {pmid39079269, year = {2024}, author = {Tian, Y and Liu, Y and Yue, L and Zhao, X and Zhou, Q and Uwaremwe, C and Wang, Y and Chen, G and Sha, Y and Zhang, Y and Wang, R}, title = {Multi-omics analysis reveals the effects of three application modes of plant growth promoting microbes biofertilizer on potato (Solanum tuberosum L.) growth under alkaline loess conditions.}, journal = {Microbiological research}, volume = {287}, number = {}, pages = {127855}, doi = {10.1016/j.micres.2024.127855}, pmid = {39079269}, issn = {1618-0623}, mesh = {*Solanum tuberosum/microbiology/growth &amp; development ; *Fertilizers/analysis ; *Soil Microbiology ; Bacillus amyloliquefaciens/growth &amp; development ; Transcriptome ; Plant Tubers/microbiology/growth &amp; development ; Microbiota ; Soil/chemistry ; Metabolome ; Rhizosphere ; Sucrose/metabolism ; Plant Development ; Metabolomics/methods ; Multiomics ; }, abstract = {Potato is an important crop due to its high contents of starch, protein, and various vitamins and minerals. Biofertilizers are composed of plant growth promoting microbes (PGPMs) which are essential for improving the growth and resistance of potato. However, little information has focused on the modes of inoculation of biofertilizers on plant growth and microecology. This study aims to reveal the response mechanism of the potato to three modes of inoculation of biofertilizers all containing PGPM Bacillus amyloliquefaciens EZ99, i.e. scattered mode of 5 kg/ha biofertilizer (M5), soaking seed tubers with dissolved 5 kg/ha biofertilizer (MZG), and scattered mode of 3 kg/ha biofertilizer + 2 kg/ha sucrose (MY34) in alkaline loess field through multi-omics analysis of transcriptome, metabolome and microbiome. The physiological result revealed that two application modes of equal amount of biofertilizer M5 and MZG significantly improved the growth and yield of potatoes. Furthermore, the transcriptome of potato exhibited sets of differentially expressed genes enriched in photosynthesis, sugar metabolism, and phenylpropanoid biosynthesis among the three modes, with the M5 mode exhibiting overall up-regulation of 828 genes. Based on the untargeted metabolomic analysis of potato tuber, M5 mode significantly accumulated sucrose, while MZG and MY34 mode significantly accumulated the stress metabolites euchrenone b6 and mannobiose, respectively. Besides, the microbial structure of potato rhizosphere showed that the diversity of bacteria and fungi was similar in all soils, but their abundances varied significantly. Specifically, beneficial Penicillium was enriched in M5 and MZG soils, whereas MY34 soil accumulated potential pathogens Plectosphaerella and saccharophilic Mortierella. Collectively, these e findings highlight that MZG is the most effective mode to promote potato growth and stimulate rhizosphere effect. The present study not only encourages sustainable agriculture through agroecological practices, but also provides broad prospects for the application of PGPM biofertilizer in staple foods.}, }
@article {pmid39075558, year = {2024}, author = {Pinheiro-Junior, EL and Alirahimi, E and Peigneur, S and Isensee, J and Schiffmann, S and Erkoc, P and Fürst, R and Vilcinskas, A and Sennoner, T and Koludarov, I and Hempel, BF and Tytgat, J and Hucho, T and von Reumont, BM}, title = {Diversely evolved xibalbin variants from remipede venom inhibit potassium channels and activate PKA-II and Erk1/2 signaling.}, journal = {BMC biology}, volume = {22}, number = {1}, pages = {164}, pmid = {39075558}, issn = {1741-7007}, support = {2016/04761-4//S&#xe3;o Paulo Research Foundation/ ; GOC2319 N//F.W.O.-Vlaanderen/ ; GOA4919 N//F.W.O.-Vlaanderen/ ; G0E7120N//F.W.O.-Vlaanderen/ ; PDM/19/164//KU Leuven funding/ ; CA19144 EUVEN//EU COST Action/ ; }, mesh = {Animals ; *Potassium Channels/metabolism/genetics ; MAP Kinase Signaling System/drug effects ; Phylogeny ; Mice ; Cyclic AMP-Dependent Protein Kinases/metabolism/genetics ; Evolution, Molecular ; Humans ; Arthropod Venoms/chemistry ; }, abstract = {BACKGROUND: The identification of novel toxins from overlooked and taxonomically exceptional species bears potential for various pharmacological applications. The remipede Xibalbanus tulumensis, an underwater cave-dwelling crustacean, is the only crustacean for which a venom system has been described. Its venom contains several xibalbin peptides that have an inhibitor cysteine knot (ICK) scaffold.<br><br>RESULTS: Our screenings revealed that all tested xibalbin variants particularly inhibit potassium channels. Xib1 and xib13 with their eight-cysteine domain similar to spider knottins also inhibit voltage-gated sodium channels. No activity was noted on calcium channels. Expanding the functional testing, we demonstrate that xib1 and xib13 increase PKA-II and Erk1/2 sensitization signaling in nociceptive neurons, which may initiate pain sensitization. Our phylogenetic analysis suggests that xib13 either originates from the common ancestor of pancrustaceans or earlier while xib1 is more restricted to remipedes. The ten-cysteine scaffolded xib2 emerged from xib1, a result that is supported by our phylogenetic and machine learning-based analyses.<br><br>CONCLUSIONS: Our functional characterization of synthesized variants of xib1, xib2, and xib13 elucidates their potential as inhibitors of potassium channels in mammalian systems. The specific interaction of xib2 with Kv1.6 channels, which are relevant to treating variants of epilepsy, shows potential for further studies. At higher concentrations, xib1 and xib13 activate the kinases PKA-II and ERK1/2 in mammalian sensory neurons, suggesting pain sensitization and potential applications related to pain research and therapy. While tested insect channels suggest that all probably act as neurotoxins, the biological function of xib1, xib2, and xib13 requires further elucidation. A novel finding on their evolutionary origin is the apparent emergence of X. tulumensis-specific xib2 from xib1. Our study is an important cornerstone for future studies to untangle the origin and function of these enigmatic proteins as important components of remipede but also other pancrustacean and arthropod venoms.}, }
@article {pmid39074140, year = {2024}, author = {Melo, D and Pallares, LF and Ayroles, JF}, title = {Reassessing the modularity of gene co-expression networks using the Stochastic Block Model.}, journal = {PLoS computational biology}, volume = {20}, number = {7}, pages = {e1012300}, pmid = {39074140}, issn = {1553-7358}, support = {R01 ES029929/ES/NIEHS NIH HHS/United States ; R35 GM124881/GM/NIGMS NIH HHS/United States ; }, mesh = {*Drosophila melanogaster/genetics ; Animals ; *Gene Regulatory Networks/genetics ; *Stochastic Processes ; *Algorithms ; *Computational Biology/methods ; Models, Genetic ; Gene Expression Profiling/methods ; }, abstract = {Finding communities in gene co-expression networks is a common first step toward extracting biological insight from these complex datasets. Most community detection algorithms expect genes to be organized into assortative modules, that is, groups of genes that are more associated with each other than with genes in other groups. While it is reasonable to expect that these modules exist, using methods that assume they exist a priori is risky, as it guarantees that alternative organizations of gene interactions will be ignored. Here, we ask: can we find meaningful communities without imposing a modular organization on gene co-expression networks, and how modular are these communities? For this, we use a recently developed community detection method, the weighted degree corrected stochastic block model (SBM), that does not assume that assortative modules exist. Instead, the SBM attempts to efficiently use all information contained in the co-expression network to separate the genes into hierarchically organized blocks of genes. Using RNAseq gene expression data measured in two tissues derived from an outbred population of Drosophila melanogaster, we show that (a) the SBM is able to find ten times as many groups as competing methods, that (b) several of those gene groups are not modular, and that (c) the functional enrichment for non-modular groups is as strong as for modular communities. These results show that the transcriptome is structured in more complex ways than traditionally thought and that we should revisit the long-standing assumption that modularity is the main driver of the structuring of gene co-expression networks.}, }
@article {pmid39071792, year = {2023}, author = {Falk, S and Gorše, I and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the hawkweed Cheilosia, Cheilosia urbana (Meigen, 1822).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {311}, pmid = {39071792}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Cheilosia urbana (the hawkweed Cheilosia; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 546.9 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 17.08 kilobases in length.}, }
@article {pmid39069513, year = {2024}, author = {Xu, R and Xu, C and Li, Z and Zheng, T and Yu, W and Yang, C}, title = {Boundary guidance network for medical image segmentation.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {17345}, pmid = {39069513}, issn = {2045-2322}, support = {2019YFC0117800//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Urinary Bladder Neoplasms/diagnostic imaging/pathology ; Image Processing, Computer-Assisted/methods ; Deep Learning ; Magnetic Resonance Imaging/methods ; Tomography, X-Ray Computed/methods ; Neural Networks, Computer ; Algorithms ; Cystoscopy/methods ; Image Interpretation, Computer-Assisted/methods ; }, abstract = {Accurate segmentation of the tumor area is crucial for the treatment and prognosis of patients with bladder cancer. Cystoscopy is the gold standard for diagnosing bladder tumors. However, The vast majority of current work uses deep learning to identify and segment tumors from CT and MRI findings, and rarely involves cystoscopy findings. Accurately segmenting bladder tumors remains a great challenge due to their diverse morphology and fuzzy boundaries. In order to solve the above problems, this paper proposes a medical image segmentation network with boundary guidance called boundary guidance network. This network combines local features extracted by CNNs and long-range dependencies between different levels inscribed by Parallel ViT, which can capture tumor features more effectively. The Boundary extracted module is designed to extract boundary features and utilize the boundary features to guide the decoding process. Foreground-background dual-channel decoding is performed by boundary integrated module. Experimental results on our proposed new cystoscopic bladder tumor dataset (BTD) show that our method can efficiently perform accurate segmentation of tumors and retain more boundary information, achieving an IoU score of 91.3%, a Hausdorff Distance of 10.43, an mAP score of 85.3%, and a F1 score of 94.8%. On BTD and three other public datasets, our model achieves the best scores compared to state-of-the-art methods, which proves the effectiveness of our model for common medical image segmentation.}, }
@article {pmid39068884, year = {2024}, author = {Fan, Q and Huang, S and Guo, J and Xie, Y and Chen, M and Chen, Y and Qi, W and Liu, H and Jia, Z and Hu, H and Qu, J}, title = {Spatiotemporal distribution and transport flux of organophosphate esters in the sediment of the Yangtze River.}, journal = {Journal of hazardous materials}, volume = {477}, number = {}, pages = {135312}, doi = {10.1016/j.jhazmat.2024.135312}, pmid = {39068884}, issn = {1873-3336}, abstract = {The Yangtze River Basin is an important area for organophosphate esters (OPEs) consumption and emission. Studies proved high OPE detection in Yangtze River water, but there is limited information about the spatiotemporal distribution and transport flux of OPEs in sediment. The present study investigated 16 OPEs in sediment from upstream to mid-downstream of the Yangtze River. The mean concentration of OPEs was 84.30 ng/g, and alkyl-OPEs was the primary component. Great specific surface area and high content of organic carbon significantly increased OPE concentration in Three Gorges Reservoir (TGR) by physical adsorption and chemical bonds (p < 0.05), making TGR the most contaminated area in mainstream. No significant differences in OPE constituents were found in seasonal distribution. Four potential sources of OPEs were identified by principal component analysis and self-organizing maps, and traffic emissions were the dominant source for OPEs. The hazard quotient model results indicated that aryl-OPEs showed moderate risks in the mainstream of Yangtze River, alkyl-OPEs and Cl-OPEs showed low risks. TGR was a significant sink of OPEs in Yangtze River and buried 7.41 tons of OPEs in 2020, a total of 14.87 tons of OPE were transported into the sea by sediment.}, }
@article {pmid39066964, year = {2025}, author = {Árvay, J and Hauptvogl, M and Demková, L and Jančo, I and Jakabová, S and Mleczek, M}, title = {GIS-based Visualization of Elemental Distribution in Neoboletus Luridiformis Fruiting Body.}, journal = {Biological trace element research}, volume = {203}, number = {4}, pages = {2271-2283}, pmid = {39066964}, issn = {1559-0720}, support = {1/0602/22//Vedeck&#xe1; Grantov&#xe1; Agent&#xfa;ra M&#x160;VVa&#x160; SR a SAV/ ; }, mesh = {*Fruiting Bodies, Fungal/chemistry/metabolism ; *Geographic Information Systems ; *Trace Elements/analysis/metabolism ; *Agaricales/chemistry/metabolism ; *Basidiomycota/chemistry/metabolism ; }, abstract = {The fruiting body of Neoboletus luridiformis (Scarletina bolete) mushroom was used to determine the level of bioconcentration and subsequent distribution of seventeen elements (Ag, Al, Ba, Ca, Cd, Cr, Cu, Fe, K, Mg, Mn, Na, Ni, Pb, Se, Sr, and Zn). A two-centimeter-thick vertical section of the entire fruit body was divided into 101 partial sub-samples where the contents of the studied elements were determined using ICP OES. The actual distribution of the elements in the fruiting body profile was visualized using a GIS interpolation method resulting in distribution maps. The study provides valuable insights into the distribution patterns of 17 elements within the fruiting body of N. luridiformis. Based on the visualization of the elemental content, the determined elements can be divided into three categories. Elements accumulated primarily (i) in the cap (Al, Ag, Ca, Cd, Cu, Fe, K, Mg, Ni, and Zn), (ii) in the stipe (Ba, Mn, Na, Pb, and Se), and (iii) elements with non-specific distribution (Cr and Sr). Since such detailed information supported by graphical visualization has not been published to date, the information in this study will help to better understand the accumulation and distribution of elements within the fruiting bodies of wild as well as cultivated mushroom species.}, }
@article {pmid39066932, year = {2024}, author = {Seldeslachts, A and Maurstad, MF and Øyen, JP and Undheim, EAB and Peigneur, S and Tytgat, J}, title = {Exploring oak processionary caterpillar induced lepidopterism (Part 1): unveiling molecular insights through transcriptomics and proteomics.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {81}, number = {1}, pages = {311}, pmid = {39066932}, issn = {1420-9071}, support = {GOC2319N, GOA4919N, and G0E7120N//Fonds Wetenschappelijk Onderzoek/ ; 12W7822N//Fonds Wetenschappelijk Onderzoek/ ; 1S51521N and 1S51523N//Fonds Wetenschappelijk Onderzoek/ ; CA19144 EUVEN//European Cooperation in Science and Technology/ ; FRIPRO-YRT Fellowship no. 287462//Norwegian Research Council/ ; 101039862//H2020 European Research Council/ ; }, mesh = {Animals ; Allergens/immunology ; Arthropod Venoms ; Computational Biology/methods ; Gene Expression Profiling ; Insect Proteins/genetics/metabolism ; Larva/metabolism ; *Moths/genetics ; Proteome/metabolism ; *Proteomics/methods ; *Transcriptome ; }, abstract = {Lepidopterism, a skin inflammation condition caused by direct or airborne exposure to irritating hairs (setae) from processionary caterpillars, is becoming a significant public health concern. Recent outbreaks of the oak processionary caterpillar (Thaumetopoea processionea) have caused noteworthy health and economic consequences, with a rising frequency expected in the future, exacerbated by global warming promoting the survival of the caterpillar. Current medical treatments focus on symptom relief due to the lack of an effective therapy. While the source is known, understanding the precise causes of symptoms remain incomplete understood. In this study, we employed an advanced method to extract venom from the setae and identify the venom components through high-quality de novo transcriptomics, venom proteomics, and bioinformatic analysis. A total of 171 venom components were identified, including allergens, odorant binding proteins, small peptides, enzymes, enzyme inhibitors, and chitin biosynthesis products, potentially responsible for inflammatory and allergic reactions. This work presents the first comprehensive proteotranscriptomic database of T. processionea, contributing to understanding the complexity of lepidopterism. Furthermore, these findings hold promise for advancing therapeutic approaches to mitigate the global health impact of T. processionea and related caterpillars.}, }
@article {pmid39060281, year = {2024}, author = {Khaki, JJ and Meiring, JE and Thindwa, D and Henrion, MYR and Jere, TM and Msuku, H and ,  and Heyderman, RS and Gordon, MA and Giorgi, E}, title = {Modelling Salmonella Typhi in high-density urban Blantyre neighbourhood, Malawi, using point pattern methods.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {17164}, pmid = {39060281}, issn = {2045-2322}, support = {106158/Z/14/Z/WT_/Wellcome Trust/United Kingdom ; 617 OPP1141321//Bill and Melinda Gates Foundation/ ; }, mesh = {Humans ; *Typhoid Fever/epidemiology/microbiology ; *Salmonella typhi/isolation &amp; purification ; Adolescent ; Child ; Malawi/epidemiology ; Adult ; Child, Preschool ; Male ; Female ; Young Adult ; Incidence ; Infant ; Risk Factors ; Sanitation ; Urban Population ; }, abstract = {Salmonella Typhi is a human-restricted pathogen that is transmitted by the faecal-oral route and causative organism of typhoid fever. Using health facility data from 2016 to 2020, this study focuses on modelling the spatial variation in typhoid risk in Ndirande township in Blantyre. To pursue this objective, we developed a marked inhomogeneous Poisson process model that allows us to incorporate both individual-level and environmental risk factors. The results from our analysis indicate that typhoid cases are spatially clustered, with the incidence decreasing by 54% for a unit increase in the water, sanitation, and hygiene (WASH) score. Typhoid intensity was also higher in children aged below 18 years than in adults. However, our results did not show evidence of a strong temporal variation in typhoid incidence. We also discuss the inferential benefits of using point pattern models to characterise the spatial variation in typhoid risk and outline possible extensions of the proposed modelling framework.}, }
@article {pmid39060268, year = {2024}, author = {Tagliaferro, S and Maio, S and Pirona, F and Stanisci, I and Sarno, G and Silvi, P and Kermenidou, M and Papaioannou, N and Perchard, R and Prpic, I and Polanska, K and Jerzynska, J and Ramos, E and Rovira, J and Belmonte, J and Snoj Tratnik, JS and Horvat, M and Kocman, D and Spiric, Z and Zickella, J and Fasola, S and La Grutta, S and Malizia, V and Montalbano, L and ,  and ,  and Baldacci, S and Annesi-Maesano, I}, title = {Assessing external exposome by implementing an Environmental Data Management System using Open Data.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {17142}, pmid = {39060268}, issn = {2045-2322}, support = {603946//European Commission/ ; }, mesh = {Humans ; Male ; Female ; *Exposome ; Environmental Exposure ; Data Management ; Environmental Monitoring/methods ; Europe ; Aged, 80 and over ; Cities ; Aged ; }, abstract = {Due to the increasing importance of exposome in environmental epidemiology, feasibility and usefulness of an Environmental Data Management System (EDMS) using Open Data was evaluated. The EDMS includes data from 10 European cities (Celje (Slovenia), Łódź (Poland), Manchester (UK), Palermo (Italy), Paris (France), Porto (Portugal), Regensburg (Germany), Reus (Spain), Rijeka (Croatia), Thessaloniki (Greece)) about external non-specific and specific exposome factors at the city or country level (2017-2020). Findings showed that the highest values of life expectancy were in Reus females (86 years) and Palermo males (81 years). UK had the highest obesity rate (28%), Croatia the highest prescribed drug consumption (62%), Greece and Portugal the highest smoking rates (37%, 42%) and daily alcohol consumption (21%), respectively. The most polluted cities were Thessaloniki for PM10 (38 µg/m[3]), Łódź for PM2.5 (25 µg/m[3]), Porto for NO2 (62 µg/m[3]) and Rijeka for O3 (92 µg/m[3]). Thessaloniki had the highest grey space (98%) and Łódź the highest cumulative amount of pollen (39,041 p/m[3]). The highest daily noise levels ≥ 55 dB was in Reus (81% to traffic) and Regensburg (21% to railway). In drinking water, arsenic had the highest value in Thessaloniki (6.4 µg/L), boron in Celje (24 mg/L) and lead in Paris (46.7 µg/L). Portugal and Greece showed the highest pesticide residues in food (7%). In conclusion, utilizing open-access databases enables the translation of research findings into actionable strategies for public health interventions.}, }
@article {pmid39059890, year = {2024}, author = {Tikhomirov, L and Semmler, C and McCradden, M and Searston, R and Ghassemi, M and Oakden-Rayner, L}, title = {Medical artificial intelligence for clinicians: the lost cognitive perspective.}, journal = {The Lancet. Digital health}, volume = {6}, number = {8}, pages = {e589-e594}, doi = {10.1016/S2589-7500(24)00095-5}, pmid = {39059890}, issn = {2589-7500}, mesh = {*Artificial Intelligence ; Humans ; *Clinical Decision-Making/methods ; Cognition ; Decision Support Systems, Clinical ; Radiology ; }, abstract = {The development and commercialisation of medical decision systems based on artificial intelligence (AI) far outpaces our understanding of their value for clinicians. Although applicable across many forms of medicine, we focus on characterising the diagnostic decisions of radiologists through the concept of ecologically bounded reasoning, review the differences between clinician decision making and medical AI model decision making, and reveal how these differences pose fundamental challenges for integrating AI into radiology. We argue that clinicians are contextually motivated, mentally resourceful decision makers, whereas AI models are contextually stripped, correlational decision makers, and discuss misconceptions about clinician-AI interaction stemming from this misalignment of capabilities. We outline how future research on clinician-AI interaction could better address the cognitive considerations of decision making and be used to enhance the safety and usability of AI models in high-risk medical decision-making contexts.}, }
@article {pmid39057817, year = {2024}, author = {Chanda, MM and Purse, BV and Sedda, L and Benz, D and Prasad, M and Reddy, YN and Yarabolu, KR and Byregowda, SM and Carpenter, S and Prasad, G and Rogers, DJ}, title = {Bluetongue Risk Map for Vaccination and Surveillance Strategies in India.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {7}, pages = {}, pmid = {39057817}, issn = {2076-0817}, support = {BB/H009167/1//BBSRC, DFID, Scottish government/ ; }, mesh = {India/epidemiology ; *Bluetongue/epidemiology/prevention &amp; control/transmission ; Animals ; *Bluetongue virus/immunology ; Sheep ; *Vaccination/veterinary ; Ceratopogonidae/virology ; Viral Vaccines/immunology ; Epidemiological Monitoring/veterinary ; }, abstract = {Bluetongue virus (BTV, Sedoreoviridae: Orbivirus) causes an economically important disease, namely, bluetongue (BT), in domestic and wild ruminants worldwide. BTV is endemic to South India and has occurred with varying severity every year since the virus was first reported in 1963. BT can cause high morbidity and mortality to sheep flocks in this region, resulting in serious economic losses to subsistence farmers, with impacts on food security. The epidemiology of BTV in South India is complex, characterized by an unusually wide diversity of susceptible ruminant hosts, multiple vector species biting midges (Culicoides spp., Diptera: Ceratopogonidae), which have been implicated in the transmission of BTV and numerous co-circulating virus serotypes and strains. BT presence data (1997-2011) for South India were obtained from multiple sources to develop a presence/absence model for the disease. A non-linear discriminant analysis (NLDA) was carried out using temporal Fourier transformed variables that were remotely sensed as potential predictors of BT distribution. Predictive performance was then characterized using a range of different accuracy statistics (sensitivity, specificity, and Kappa). The top ten variables selected to explain BT distribution were primarily thermal metrics (land surface temperature, i.e., LST, and middle infrared, i.e., MIR) and a measure of plant photosynthetic activity (the Normalized Difference Vegetation Index, i.e., NDVI). A model that used pseudo-absence points, with three presence and absence clusters each, outperformed the model that used only the recorded absence points and showed high correspondence with past BTV outbreaks. The resulting risk maps may be suitable for informing disease managers concerned with vaccination, prevention, and control of BT in high-risk areas and for planning future state-wide vector and virus surveillance activities.}, }
@article {pmid39056317, year = {2024}, author = {Stulberg, EL and Lisabeth, L and Schneider, ALC and Skolarus, L and Kershaw, KN and Zheutlin, AR and Harris, BRE and Sarpong, D and Wong, KH and Sheth, KN and de Havenon, A}, title = {Correlations of Socioeconomic and Clinical Determinants with United States County-Level Stroke Prevalence.}, journal = {Annals of neurology}, volume = {96}, number = {4}, pages = {739-744}, pmid = {39056317}, issn = {1531-8249}, support = {R01 NS107463/NH/NIH HHS/United States ; R01MD016178/NS/NINDS NIH HHS/United States ; R01 NS038916/NS/NINDS NIH HHS/United States ; HT9425-23-1-0981//Department of Defense/ ; R38 HL143605/HL/NHLBI NIH HHS/United States ; R01 HL152741/NH/NIH HHS/United States ; R01 HL156906/NH/NIH HHS/United States ; U24 NS107215/NS/NINDS NIH HHS/United States ; U01 NS106513/NS/NINDS NIH HHS/United States ; //American Heart Association/American Stroke Association/ ; R01 NS110721/NS/NINDS NIH HHS/United States ; U24NS107136/NS/NINDS NIH HHS/United States ; R01 MD016178/MD/NIMHD NIH HHS/United States ; R01EB301114/NS/NINDS NIH HHS/United States ; R01 NR018335/NR/NINR NIH HHS/United States ; K23 NS123340/NS/NINDS NIH HHS/United States ; UG3 NS130228/NS/NINDS NIH HHS/United States ; R01NR018335/NS/NINDS NIH HHS/United States ; /AG/NIA NIH HHS/United States ; U24 NS107136/NS/NINDS NIH HHS/United States ; 1R38HL167282-01/HI/NHLBI NIH HHS/United States ; R01NS130189/NS/NINDS NIH HHS/United States ; U24NS129500/NS/NINDS NIH HHS/United States ; R01NS110721/NS/NINDS NIH HHS/United States ; R01 NS130189/NS/NINDS NIH HHS/United States ; K23NS123340/NS/NINDS NIH HHS/United States ; R01 HL152741/HL/NHLBI NIH HHS/United States ; W81XWH-21-1-0590//Department of Defense/ ; R38 HL167282/HL/NHLBI NIH HHS/United States ; U24NS107215/NS/NINDS NIH HHS/United States ; R01 NS038916/NH/NIH HHS/United States ; U01NS106513/NS/NINDS NIH HHS/United States ; UG3NS130228/NS/NINDS NIH HHS/United States ; K23NS105924/NS/NINDS NIH HHS/United States ; U24 NS129500/NS/NINDS NIH HHS/United States ; K23 NS105924/NS/NINDS NIH HHS/United States ; R01 NS107463/NS/NINDS NIH HHS/United States ; }, mesh = {Humans ; *Stroke/epidemiology ; United States/epidemiology ; Prevalence ; Socioeconomic Factors ; Risk Factors ; Social Class ; Male ; Female ; Adult ; Middle Aged ; Health Services Accessibility ; Aged ; }, abstract = {Socioeconomic status (SES) is a multi-faceted theoretical construct associated with stroke risk and outcomes. Knowing which SES measures best correlate with population stroke metrics would improve its accounting in observational research and inform interventions. Using the Centers for Disease Control and Prevention's (CDC) Population Level Analysis and Community Estimates (PLACES) and other publicly available databases, we conducted an ecological study comparing correlations of different United States county-level SES, health care access and clinical risk factor measures with age-adjusted stroke prevalence. The prevalence of adults living below 150% of the federal poverty level most strongly correlated with stroke prevalence compared to other SES and non-SES measures (correlation coefficient = 0.908, R[2] = 0.825; adjusted partial correlation coefficient: 0.589, R[2] = 0.347). ANN NEUROL 2024;96:739-744.}, }
@article {pmid39056051, year = {2024}, author = {Navarro-Farfán, MDM and García-Romero, L and Martínez-Cinco, MA and Domínguez-Sánchez, C and Sánchez-Quispe, ST}, title = {Methodology for the assessment of poor-data water resources.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e17755}, pmid = {39056051}, issn = {2167-8359}, mesh = {*Water Resources ; Models, Theoretical ; Hydrology/methods ; Environmental Monitoring/methods ; }, abstract = {Surface hydrologic modeling becomes a problem when insufficient spatial and temporal information is available. It is common to have useful modeling periods of less than 15 years. The purpose of this work is to develop a methodology that allows the selection of meteorological and hydrometric stations that are suitable for modeling when information is scarce in the area. Based on the scarcity of data, a series of statistical tests are proposed to eliminate stations according to a decision-making process. Although the number of stations decreases drastically, the information used is reliable and of adequate quality, ensuring less uncertainty in the surface simulation models. Individual basin modeling can be carried out considering the poor data. The transfer of parameters can be applied through the nesting of basins to have information distributed over an extensive area. Therefore, temporally and spatially extended modeling can be achieved with information that preserves statistical parameters over time. If data management and validation is performed, the modeled watersheds are well represented; if this is not done, only 26% to 50% of the runoff is represented.}, }
@article {pmid39053536, year = {2024}, author = {He, M and Cui, J and Yi, Y and Chen, HW and Zhang, Q and Li, L and Huang, L and Hong, S}, title = {Vegetation increases global climate vulnerability risk by shifting climate zones in response to rising atmospheric CO2.}, journal = {The Science of the total environment}, volume = {949}, number = {}, pages = {174810}, doi = {10.1016/j.scitotenv.2024.174810}, pmid = {39053536}, issn = {1879-1026}, mesh = {*Carbon Dioxide/analysis ; *Climate Change ; *Ecosystem ; Atmosphere/chemistry ; }, abstract = {Global climate zones are experiencing widespread shifts with ongoing rise in atmospheric CO2, influencing vegetation growth and shifting its distributions to challenge ecosystem structure and function, posing threats on ecological and societal safety. However, how rising atmospheric CO2 affects the pace of global climate zone shifts is highly uncertain. More attentions are urgently required to understand the underlying mechanisms and quantifications of regional climate vulnerability in response to rising CO2. In this study, we employ nine Earth system models from CMIP6 to investigate global climate zone shifts with rising CO2, unravel the effects of vegetation physiological response (PHY), and categorize climate vulnerable regions depending on the extent of climate zone shifts. We find that climate zone shifts over half of the global land area, 16.8% of which is contributed by PHY at 4 × CO2. Intriguingly, besides warming, PHY-induced precipitation changes and their interactions with warming dominate about two-fifths of PHY-forced shifts, providing potential direction for model improvement in future predictions of climate zone shifts. Aided with PHY effects, 4 × CO2 imposes substantial climate zone shifts over about one-fifth of the global land area, suggesting substantial changes in local climate and ecosystem structure and functions. Hence, those regions would experience strong climate vulnerability, and face high risk of climate extremes, water scarcity and food production. Our results quantitatively identify the vulnerable regions and unravel the underlying drivers, providing scientific insights to prioritize conservation and restoration efforts to ensure ecological and social safety globally.}, }
@article {pmid39051209, year = {2024}, author = {de Souza, OF and Araújo, ACB and Vieira, LB and Bachur, JA and Lopez, AGP and Gonçalves, TG and de Abreu, LC}, title = {Sex Disparity in Stroke Mortality among Adults: A Time Series Analysis in the Greater Vitoria Region, Brazil (2000-2021).}, journal = {Epidemiologia (Basel, Switzerland)}, volume = {5}, number = {3}, pages = {402-410}, pmid = {39051209}, issn = {2673-3986}, abstract = {The disparity between the sexes in stroke mortality has been demonstrated in people from different locations. The objective of this study was to analyze the disparity between sexes in stroke mortality in adults in the metropolitan area of Greater Vitoria between 2000 and 2021. Ecological time series design was conducted with a database of the Brazilian Health System Informatics Department. The annual percentage change and average annual percentage change were calculated through joinpoint regression. Pairwise comparisons using parallelism and coincidence tests were applied to compare temporal trends between men and women. Men had higher mortality rates in most years between 2000 and 2021. In contrast, women had higher proportional mortality values in all years evaluated from 2000 to 2021. The paired comparison revealed a disparity between the sexes in the proportional mortality time series (parallelism test: p = 0.003; coincidence test: p < 0.001). However, the time series of the mortality rates showed no disparity between the sexes (parallelism test: p = 0.114; coincidence test: p = 0.093). From 2000 to 2021, there was a disparity in proportional mortality from stroke between the sexes of the population in the metropolitan area of Greater Vitoria, Brazil. However, the time series of mortality rates between the sexes did not reveal any disparity in the study period.}, }
@article {pmid39050029, year = {2024}, author = {Kryukov, K and Nakahama, N and Kuraku, S}, title = {Genome assembly catalog for species in the Japanese Red List: unlocking endangered biodiversity through genomic inventory.}, journal = {F1000Research}, volume = {13}, number = {}, pages = {583}, pmid = {39050029}, issn = {2046-1402}, mesh = {Animals ; *Biodiversity ; *Endangered Species ; Genome ; *Genomics/methods ; Japan ; }, abstract = {Improvements in DNA sequencing technology are allowing the dramatic increase of whole genome data for a wide variety of species. Such genome sequence data can assist the monitoring of intraspecific genetic diversity, but is often lacking for threatened species. In this project, we focused on the national Red List, a catalog of extinct and threatened species, issued by the Japanese government. We combined the data included in it with the record of genome assembly in NCBI and tabulated the assembly availability of the species in the list. The combined data shows a low percentage (2.1%) of the availability of whole genome sequence data for the taxa ranked on the Japanese Red List as well as a strong bias towards mammals and birds in Animalia and vascular plants in Plantae. Our data presentation highlights potential systematic limitations in genome sequencing (e.g., budget for sequencing large genomes of amphibians) and instructs future policies including which taxon needs more effort for genome sequencing. The resultant tables are available in the original website https://treethinkers.nig.ac.jp/redlist/ and are regularly updated.}, }
@article {pmid39049113, year = {2024}, author = {Yurkov, A and Visagie, CM and Crous, PW and Hashimoto, A and Baschien, C and Begerow, D and Kemler, M and Schoutteten, N and Stadler, M and Wijayawardene, NN and Hyde, KD and Zhang, N and Boekhout, T and ,  and May, TW and Thines, M and Hawksworth, DL}, title = {Cultures as types and the utility of viable specimens for fungal nomenclature.}, journal = {IMA fungus}, volume = {15}, number = {1}, pages = {20}, pmid = {39049113}, issn = {2210-6340}, abstract = {The debates over the requirement of the International Code of Nomenclature for algae, fungi, and plants (ICNafp) for a viable specimen to represent the name-bearing type material for a species or infraspecific taxon have a long history. Taxonomy of fungi commonly studied as living cultures exemplified by yeasts and moulds, strongly depend on viable reference material. The availability of viable cultures is also particularly useful for several groups of filamentous and dimorphic fungi. While the preservation of metabolically inactive cultures is permitted and recommended by the ICNafp, there is room for improvement. Below, we review the history and current status of cultures as the name-bearing type material under the Code. We also present a roadmap with tasks to be achieved in order to establish a stable nomenclatural system that properly manages taxa typified by viable specimens. Furthermore, we propose setting up rules and defining the nomenclatural status of ex-type cultures under Chapter F, the section of the ICNafp that includes provisions specific to names of fungi.}, }
@article {pmid39048683, year = {2024}, author = {Gauci, V and Pangala, SR and Shenkin, A and Barba, J and Bastviken, D and Figueiredo, V and Gomez, C and Enrich-Prast, A and Sayer, E and Stauffer, T and Welch, B and Elias, D and McNamara, N and Allen, M and Malhi, Y}, title = {Global atmospheric methane uptake by upland tree woody surfaces.}, journal = {Nature}, volume = {631}, number = {8022}, pages = {796-800}, pmid = {39048683}, issn = {1476-4687}, mesh = {*Atmosphere/chemistry ; *Forests ; *Methane/metabolism/analysis ; Taiga ; *Trees/chemistry/metabolism/microbiology ; Tropical Climate ; *Wood/chemistry/metabolism/microbiology ; Greenhouse Gases/analysis/metabolism ; Carbon Isotopes ; Forestry ; Global Warming/prevention &amp; control/statistics &amp; numerical data ; Greenhouse Effect/prevention &amp; control/statistics &amp; numerical data ; }, abstract = {Methane is an important greenhouse gas[1], but the role of trees in the methane budget remains uncertain[2]. Although it has been shown that wetland and some upland trees can emit soil-derived methane at the stem base[3,4], it has also been suggested that upland trees can serve as a net sink for atmospheric methane[5,6]. Here we examine in situ woody surface methane exchange of upland tropical, temperate and boreal forest trees. We find that methane uptake on woody surfaces, in particular at and above about 2 m above the forest floor, can dominate the net ecosystem contribution of trees, resulting in a net tree methane sink. Stable carbon isotope measurement of methane in woody surface chamber air and process-level investigations on extracted wood cores are consistent with methanotrophy, suggesting a microbially mediated drawdown of methane on and in tree woody surfaces and tissues. By applying terrestrial laser scanning-derived allometry to quantify global forest tree woody surface area, a preliminary first estimate suggests that trees may contribute 24.6-49.9 Tg of atmospheric methane uptake globally. Our findings indicate that the climate benefits of tropical and temperate forest protection and reforestation may be greater than previously assumed.}, }
@article {pmid39048062, year = {2024}, author = {Kondak, S and Kondak, D and Kabadayi, O and Erdei, L and Rónavári, A and Kónya, Z and Galbács, G and Kolbert, Z}, title = {Current insights into the green synthesis, in planta characterization and phytoeffects of nickel nanoparticles and their agricultural implications.}, journal = {Environmental research}, volume = {260}, number = {}, pages = {119665}, doi = {10.1016/j.envres.2024.119665}, pmid = {39048062}, issn = {1096-0953}, mesh = {*Nickel/toxicity ; *Metal Nanoparticles/toxicity ; Plants/drug effects ; Agriculture ; Green Chemistry Technology ; }, abstract = {The intensifying production and release into the environment as well as the increasing potential in agricultural applications make the relationship between plants and nickel nanoparticles (Ni NPs) a relevant and timely topic. The aim of this review is to give an overview and discuss the latest findings about the relationship of Ni NPs and plants. Ni NPs can be synthesized using phytochemicals derived from plant parts in an environmentally friendly manner. There are several ways for these nanoparticles to enter plant cells and tissues. This can be demonstrated through various imaging and chemical mapping approaches (e.g., transmission electron microscopy, X-ray fluorescence spectroscopy etc.). NiO NPs affect plants at multiple levels, including subcellular, cellular, tissue, organ, and whole-plant levels. However, the effects of Ni NPs on plants' ecological partners (e.g., rhizobiome, pollinators) remain largely unknown despite their ecotoxicological significance. The main cause of the Ni NPs-triggered damages is the reactive oxygen species imbalance as a consequence of the modulation of antioxidants. In non-tolerant plants, the toxicity of NiO NPs can be mitigated by exogenous treatments such as the application of silicon, salicylic acid, or jasmonic acid, which induce defense mechanisms whereas Ni-hypertolerant plant species possess endogenous defense systems, such as cell wall modifications and nitrosative signaling against NiO NP stress. Research highlights the role of Ni NPs in managing fungal diseases, showcasing their antifungal properties against specific pathogens. Due to the essentiality of Ni, the application of Ni NPs as nanofertilizers might be promising and has recently started to come into view.}, }
@article {pmid39047578, year = {2024}, author = {Maxion, A and Gaebler, AJ and Röhrig, R and Mathiak, K and Zweerings, J and Kutafina, E}, title = {Spectral changes in electroencephalography linked to neuroactive medications: A computational pipeline for data mining and analysis.}, journal = {Computer methods and programs in biomedicine}, volume = {255}, number = {}, pages = {108319}, doi = {10.1016/j.cmpb.2024.108319}, pmid = {39047578}, issn = {1872-7565}, mesh = {Humans ; *Electroencephalography/methods ; *Data Mining/methods ; Carbamazepine/therapeutic use/pharmacology ; Risperidone ; Antipsychotic Agents/pharmacology ; Anticonvulsants/pharmacology/therapeutic use ; Brain/drug effects ; }, abstract = {BACKGROUND AND OBJECTIVES: The increasing amount of open-access medical data provides new opportunities to gain clinically relevant information without recruiting new patients. We developed an open-source computational pipeline, that utilizes the publicly available electroencephalographic (EEG) data of the Temple University Hospital to identify EEG profiles associated with the usage of neuroactive medications. It facilitates access to the data and ensures consistency in data processing and analysis, thus reducing the risk of errors and creating comparable and reproducible results. Using this pipeline, we analyze the influence of common neuroactive medications on brain activity.<br><br>METHODS: The pipeline is constructed using easily controlled modules. The user defines the medications of interest and comparison groups. The data is downloaded and preprocessed, spectral features are extracted, and statistical group comparison with visualization through a topographic EEG map is performed. The pipeline is adjustable to answer a variety of research questions. Here, the effects of carbamazepine and risperidone were statistically compared with control data and with other medications from the same classes (anticonvulsants and antipsychotics).<br><br>RESULTS: The comparison between carbamazepine and the control group showed an increase in absolute and relative power for delta and theta, and a decrease in relative power for alpha, beta, and gamma. Compared to antiseizure medications, carbamazepine showed an increase in alpha and theta for absolute powers, and for relative powers an increase in alpha and theta, and a decrease in gamma and delta. Risperidone compared with the control group showed a decrease in absolute and relative power for alpha and beta and an increase in theta for relative power. Compared to antipsychotic medications, risperidone showed a decrease in delta for absolute powers. These results show good agreement with state-of-the-art research. The database allows to create large groups for many different medications. Additionally, it provides a collection of records labeled as "normal" after expert assessment, which is convenient for the creation of control groups.<br><br>CONCLUSIONS: The pipeline allows fast testing of different hypotheses regarding links between medications and EEG spectrum through ecological usage of readily available data. It can be utilized to make informed decisions about the design of new clinical studies.}, }
@article {pmid39045996, year = {2024}, author = {Lima, AGCF and Ribeiro, CJN and Lima, SVMA and Barbosa, YM and Oliveira, IM and Araújo, KCGM}, title = {Space-time analysis of work-related musculoskeletal disorders in Brazil: an ecological study.}, journal = {Cadernos de saude publica}, volume = {40}, number = {7}, pages = {e00141823}, pmid = {39045996}, issn = {1678-4464}, mesh = {Humans ; Brazil/epidemiology ; *Musculoskeletal Diseases/epidemiology ; *Occupational Diseases/epidemiology ; *Spatio-Temporal Analysis ; Incidence ; Male ; Female ; Bayes Theorem ; Risk Factors ; Adult ; }, abstract = {This study aimed to analyze the incidence of work-related musculoskeletal disorders (WMSD) in Brazil from 2007 to 2019, examining the spatial, temporal, and spatiotemporal patterns of their occurrence. An ecological time series study was conducted using spatial analysis techniques. WMSD morbidity data from 2007 to 2019 were collected from the Brazilian Information System for Notificable Diseases of the Brazilian Health Informatics Department. Incidence rates were standardized and smoothed using the local empirical Bayes' theorem. Time trends were analyzed by segmented linear regression. Spatial analysis was performed using Moran's univariate global (I) and local (LISA) indexes. The spatiotemporal scan statistic was used to identify high-risk spatiotemporal clusters for WMSD. A total of 93,387 cases of WMSD were recorded in Brazil. Temporal trends showed an increase in all regions except the Northeast, which remained stable. The incidence of WMSD showed a spatial dependence, with spatial and space-time clusters identified, especially in the Southeast region, overlapping the largest economic-industrial center of the country. The spatiotemporal clustering observed in one region suggests the highest level of industrial and economic development. Our findings highlight the need to implement intersectoral surveillance policies, inspect working conditions, and invest in the prevention and promotion of workers' health.}, }
@article {pmid39045504, year = {2024}, author = {Heeres, J and Tallian, A and Wikenros, C and Heeres, RW}, title = {"ClusterApp": A Shiny R application to guide cluster studies based on GPS data.}, journal = {Ecology and evolution}, volume = {14}, number = {7}, pages = {e11695}, pmid = {39045504}, issn = {2045-7758}, abstract = {The rapid evolution of GPS devices, and therefore, collection of GPS data can be used to investigate a wide variety of topics in wildlife research. The combination of remotely collected GPS data with on-the-ground field investigations is a powerful tool for exploring behavioral ecology. "GPS cluster studies" are aimed at pinpointing and investigating identified clusters in the field. Activity clusters can be based on various parameters (e.g., distance between GPS locations and the number of locations needed to establish a cluster), which are closely related to the set research questions. Variation in methods across years within the same study may result in data collection biases. Therefore, a streamlined method to parametrize, generate interactive maps, and extract activity cluster data using a predefined approach will limit biases, and make field work and data management straightforward for field technicians. We developed the "ClusterApp" Shiny application in the R software to facilitate a step-by-step guide to execute cluster analyses and data management of cluster studies on any species using GPS data. We illustrate the use of the "ClusterApp" with two location datasets constructed by data collected on brown bears (Ursus arctos) and gray wolves (Canis lupus).}, }
@article {pmid39032255, year = {2024}, author = {Hossain, M and Wiegand, B and Reza, A and Chaudhuri, H and Mukhopadhyay, A and Yadav, A and Patra, PK}, title = {A machine learning approach to investigate the impact of land use land cover (LULC) changes on groundwater quality, health risks and ecological risks through GIS and response surface methodology (RSM).}, journal = {Journal of environmental management}, volume = {366}, number = {}, pages = {121911}, doi = {10.1016/j.jenvman.2024.121911}, pmid = {39032255}, issn = {1095-8630}, mesh = {*Groundwater/analysis ; *Machine Learning ; *Water Quality ; *Geographic Information Systems ; India ; Environmental Monitoring/methods ; Bayes Theorem ; Humans ; Agriculture ; }, abstract = {Groundwater resources are enormously affected by land use land cover (LULC) dynamics caused by increasing urbanisation, agricultural and household discharge as a result of global population growth. This study investigates the impact of decadal LULC changes in groundwater quality, human and ecological health from 2009 to 2021 in a diverse landscape, West Bengal, India. Using groundwater quality data from 479 wells in 2009 and 734 well in 2021, a recently proposed Water Pollution Index (WPI) was computed, and its geospatial distribution by a machine learning-based 'Empirical Bayesian Kriging' (EBK) tool manifested a decline in water quality since the number of excellent water category decreased from 30.5% to 28% and polluted water increased from 44% to 45%. ANOVA and Friedman tests revealed statistically significant differences (p < 0.0001) in year-wise water quality parameters as well as group comparisons for both years. Landsat 7 and 8 satellite images were used to classify the LULC types applying machine learning tools for both years, and were coupled with response surface methodology (RSM) for the first time, which revealed that the alteration of groundwater quality were attributed to LULC changes, e.g. WPI showed a positive correlation with built-up areas, village-vegetation cover, agricultural lands, and a negative correlation with surface water, barren lands, and forest cover. Expansion in built-up areas by 0.7%, and village-vegetation orchards by 2.3%, accompanied by a reduction in surface water coverage by 0.6%, and 2.4% in croplands caused a 1.5% drop in excellent water and 1% increase in polluted water category. However, ecological risks through the ecological risk index (ERI) exhibited a lower risk in 2021 attributed to reduced high-risk potential zones. This study highlights the potentiality in linking LULC and water quality changes using some advanced statistical tools like GIS and RSM for better management of water quality and landscape ecology.}, }
@article {pmid39032150, year = {2024}, author = {Kim, J and Foo, JC and Murata, T and Togo, F}, title = {Reduced heart rate variability is related to fluctuations in psychological stress levels in daily life.}, journal = {Stress and health : journal of the International Society for the Investigation of Stress}, volume = {40}, number = {5}, pages = {e3447}, doi = {10.1002/smi.3447}, pmid = {39032150}, issn = {1532-2998}, support = {19K24283//Japan Society for the Promotion of Science/ ; 21K17681//Japan Society for the Promotion of Science/ ; 031L0190A//Bundesministerium f&#xfc;r Bildung und Forschung/ ; }, mesh = {Humans ; *Heart Rate/physiology ; *Stress, Psychological/physiopathology/psychology ; Male ; Female ; Adult ; *Ecological Momentary Assessment ; Young Adult ; Affect/physiology ; Exercise/psychology/physiology ; }, abstract = {Laboratory-based studies have shown that psychological stress caused by response to various stressors triggers acute changes in the cardiovascular system. A better understanding is needed of the emerging evidence on temporal associations between psychological stress and cardiovascular responses in natural settings. This study examined the association of psychological stress and heart rate variability (HRV) in daily life, at high resolution over 2 weeks, taking the effect of physical activity into account. Participants (n = 34) completed ecological momentary assessments (EMA) 6 times per day, reporting levels of perceived stress, low-arousal negative affect (LNA), and high-arousal negative affect. Chest-mounted heart-rate monitors were worn to assess HRV. Multilevel models were used to examine the association between psychological stress levels and preceding/subsequent HRV. Reduced time domain HRV measures (mean and standard deviation of R-wave to R-wave intervals) during the prior hour predicted higher levels of perceived stress. Frequency domain HRV measures higher low to high frequency (LF/HF) and lower HF to total power (HF nu) ratios during the preceding 10 min predicted higher perceived stress levels, suggesting the dominance of sympathetic nervous system activity. EMA reports of higher perceived stress levels were associated with reduced time domain HRV measures during the following 10 min. On the other hand, higher LNA were related to increased HRV measures, such as lower LF/HF and higher HF nu during the following hour. The dynamic associations observed may have therapeutic implications for 'just-in-time' interventions in the management of daily stress and cardiovascular health.}, }
@article {pmid39031697, year = {2024}, author = {Zembere, K and Jones, CM and Mthawanji, R and Nkolokosa, C and Kamwezi, R and Kalonde, PK and Stanton, MC}, title = {Small dams drive Anopheles abundance during the dry season in a high malaria burden area of Malawi.}, journal = {Medical and veterinary entomology}, volume = {38}, number = {4}, pages = {375-392}, doi = {10.1111/mve.12733}, pmid = {39031697}, issn = {1365-2915}, support = {215184/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Anopheles/physiology ; Malawi ; *Seasons ; *Mosquito Vectors/physiology ; *Malaria/transmission ; *Population Density ; Larva/physiology/growth &amp; development ; Female ; }, abstract = {This study explores the influence of small dams on the exposure to malaria vectors during the dry season in Kasungu district, Malawi, an area recently identified as high priority for malaria interventions by the National Malaria Control Programme. Small dam impoundments provide communities with a continuous supply of water for domestic and agricultural activities across sub-Saharan Africa and are considered vital to food security and climate change resilience. However, these permanent water bodies also create ideal breeding sites for mosquitoes in typically arid landscapes. The study focuses on a specific dam impoundment and its vicinity, aiming to assess its spatial and temporal influence on indoor vector densities. From May to August 2021, CDC light traps were used to measure indoor mosquito densities for two consecutive nights per month in three communities located at increasing distances from the dam (0, ~1 and ~2 km). Simultaneously, drone imagery was captured for each community, enabling the identification of additional standing water within approximately 400 m of selected households. Larval sampling was carried out within the impoundment periphery and in additional water bodies identified in the drone imagery. Generalised linear mixed models (GLMMs) were employed to analyse the indoor Anopheles abundance data, estimating the effects of household structure (open/closed eaves), month, temperature and water proximity on malaria vector exposure. Throughout 685 trapping nights, a total of 1256 mosquitoes were captured, with 33% (412) being female Anopheles. Among these, 91% were morphologically identified as Anopheles funestus s.l., and 5% as Anopheles gambiae s.l. Catches progressively decline in each consecutive trapping month as the environment became drier. This decline was much slower in Malangano, the community next to the dam, with abundance being notably higher in June and July. Further, the majority of An. gambiae s.l. were caught in May, with none identified in July and August. Anopheles larvae were found both in the impoundment and other smaller water bodies such as irrigation wells in each survey month; however, the presence of these smaller water bodies did not have a significant impact on adult female mosquito catches in the GLMM. The study concludes that proximity to the dam impoundment was the primary driver of differences between survey communities with the abundance in Chikhombwe (~1 km away) and Chiponde (~2 km away) being 0.35 (95% confidence interval [CI], 0.19-0.66) and 0.28 (95% CI, 0.16-0.47) lower than Malangano, respectively, after adjusting for other factors. These findings underscore the importance of targeted interventions, such as larval source management or housing improvements, near small dams to mitigate malaria transmission risks during the dry season. Further research is needed to develop cost-effective strategies for vector control within and around these impoundments.}, }
@article {pmid39031316, year = {2025}, author = {Chakraborty, K and Saha, S and Mandal, D}, title = {Hydrological modelling using SWAT for the assessment of streamflow dynamics in the Ganga River basin.}, journal = {Environmental science and pollution research international}, volume = {32}, number = {16}, pages = {10258-10278}, doi = {10.1007/s11356-024-34385-5}, pmid = {39031316}, issn = {1614-7499}, mesh = {*Rivers ; Hydrology ; *Models, Theoretical ; *Environmental Monitoring/methods ; Geographic Information Systems ; *Water Movements ; Rain ; }, abstract = {Growing concerns over water availability arise from the problems of population growth, rapid industrialization, and human interferences, necessitating accurate streamflow estimation at the river basin scale. It is extremely challenging to access stream flow data of a transboundary river at a spatio-temporal scale due to data unavailability caused by water conflicts for assessing the water availability.Primarily, this estimation is done using rainfall-runoff models. The present study addresses this challenge by applying the soil and water assessment tool (SWAT) for hydrological modelling, utilizing high-resolution geospatial inputs. Hydrological modelling using remote sensing and GIS (Geographic Information System) through this model is initiated to assess the water availability in the Ganga River basin at different locations. The outputs are calibrated and validated using the observed station data from Global Runoff Data Centre (GRDC). To check the performance of the model, Nash-Sutcliffe efficiency (NSE), percent bias (PBIAS), coefficient of determination (R[2]), and RSR efficacy measures are initiated in ten stations using the observed and simulated stream flow data. The R[2] values of eight stations range from 0.82 to 0.93, reflecting the efficacy of the model in rainfall-runoff modelling. Moreover, the results obtained from this hydrological modelling can serve as valuable resources for water resource planners and geographers for future reference.}, }
@article {pmid39029911, year = {2024}, author = {Tyagi, S and Katara, P}, title = {Metatranscriptomics: A Tool for Clinical Metagenomics.}, journal = {Omics : a journal of integrative biology}, volume = {28}, number = {8}, pages = {394-407}, doi = {10.1089/omi.2024.0130}, pmid = {39029911}, issn = {1557-8100}, mesh = {*Metagenomics/methods ; *Microbiota/genetics ; Humans ; *Computational Biology/methods ; *Transcriptome/genetics ; Gene Expression Profiling/methods ; RNA, Ribosomal, 16S/genetics ; Metagenome/genetics ; }, abstract = {In the field of bioinformatics, amplicon sequencing of 16S rRNA genes has long been used to investigate community membership and taxonomic abundance in microbiome studies. As we can observe, shotgun metagenomics has become the dominant method in this field. This is largely owing to advancements in sequencing technology, which now allow for random sequencing of the entire genetic content of a microbiome. Furthermore, this method allows profiling both genes and the microbiome's membership. Although these methods have provided extensive insights into various microbiomes, they solely assess the existence of organisms or genes, without determining their active role within the microbiome. Microbiome scholarship now includes metatranscriptomics to decipher how a community of microorganisms responds to changing environmental conditions over a period of time. Metagenomic studies identify the microbes that make up a community but metatranscriptomics explores the diversity of active genes within that community, understanding their expression profile and observing how these genes respond to changes in environmental conditions. This expert review article offers a critical examination of the computational metatranscriptomics tools for studying the transcriptomes of microbial communities. First, we unpack the reasons behind the need for community transcriptomics. Second, we explore the prospects and challenges of metatranscriptomic workflows, starting with isolation and sequencing of the RNA community, then moving on to bioinformatics approaches for quantifying RNA features, and statistical techniques for detecting differential expression in a community. Finally, we discuss strengths and shortcomings in relation to other microbiome analysis approaches, pipelines, use cases and limitations, and contextualize metatranscriptomics as a tool for clinical metagenomics.}, }
@article {pmid39027808, year = {2024}, author = {Falk, S and Poole, O and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of a hoverfly, Cheilosia impressa (Loew, 1840).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {74}, pmid = {39027808}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Cheilosia impressa (hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 395.0 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.87 kilobases in length.}, }
@article {pmid39026607, year = {2023}, author = {Boyes, D and Holland, PWH and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Brindled Beauty, Lycia hirtaria (Clerck, 1759).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {303}, pmid = {39026607}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Lycia hirtaria (the Brindled Beauty; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 552.0 megabases in span. Most of the assembly is scaffolded into 14 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.58 kilobases in length.}, }
@article {pmid39026606, year = {2023}, author = {Boyes, D and Crowley, LM and Boyes, C and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Little Grey, Eudonia lacustrata (Panzer, 1804).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {302}, pmid = {39026606}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Eudonia lacustrata (the Little Grey; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 699.5 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.29 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,652 protein coding genes.}, }
@article {pmid39026203, year = {2024}, author = {Piacenza, F and Di Rosa, M and Soraci, L and Montesanto, A and Corsonello, A and Cherubini, A and Fabbietti, P and Provinciali, M and Lisa, R and Bonfigli, AR and Filicetti, E and Greco, GI and Muglia, L and Lattanzio, F and Volpentesta, M and Biscetti, L}, title = {Interactions between patterns of multimorbidity and functional status among hospitalized older patients: a novel approach using cluster analysis and association rule mining.}, journal = {Journal of translational medicine}, volume = {22}, number = {1}, pages = {669}, pmid = {39026203}, issn = {1479-5876}, support = {RF-2013-02358848//Ministero della Salute/ ; }, mesh = {Humans ; Male ; Female ; *Multimorbidity ; Aged ; Cluster Analysis ; *Hospitalization ; Aged, 80 and over ; *Activities of Daily Living ; Functional Status ; Data Mining ; Retrospective Studies ; }, abstract = {BACKGROUND: Multimorbidity (MM) is generally defined as the presence of 2 or more chronic diseases in the same patient and seems to be frequently associated with frailty and poor quality of life. However, the complex interplay between MM and functional status in hospitalized older patients has not been fully elucidated so far. Here, we implemented a 2-step approach, combining cluster analysis and association rule mining to explore how patterns of MM and disease associations change as a function of disability.<br><br>METHODS: This retrospective cohort study included 3366 hospitalized older patients discharged from acute care units of Ancona and Cosenza sites of Italian National Institute on Aging (INRCA-IRCCS) between 2011 and 2017. Cluster analysis and association rule mining (ARM) were used to explore patterns of MM and disease associations in the whole population and after stratifying by dependency in activities of daily living (ADL) at discharge. Sensitivity analyses in men and women were conducted to test for robustness of study findings.<br><br>RESULTS: Out of 3366 included patients, 78% were multimorbid. According to functional status, 22.2% of patients had no disability in ADL (functionally independent group), 22.7% had 1 ADL dependency (mildly dependent group), and 57.4% 2 or more ADL impaired (moderately-severely dependent group). Two main MM clusters were identified in the whole general population and in single ADL groups. ARM revealed interesting within-cluster disease associations, characterized by high lift and confidence. Specifically, in the functionally independent group, the most significant ones involved atrial fibrillation (AF)-anemia and chronic kidney disease (CKD) (lift&#x2009;=&#x2009;2.32), followed by coronary artery disease (CAD)-AF and heart failure (HF) (lift&#x2009;=&#x2009;2.29); in patients with moderate-severe ADL disability, the most significant ARM involved CAD-HF and AF (lift&#x2009;=&#x2009;1.97), thyroid dysfunction and AF (lift&#x2009;=&#x2009;1.75), cerebrovascular disease (CVD)-CAD and AF (lift&#x2009;=&#x2009;1.55), and hypertension-anemia and CKD (lift&#x2009;=&#x2009;1.43).<br><br>CONCLUSIONS: Hospitalized older patients have high rates of MM and functional impairment. Combining cluster analysis to ARM may assist physicians in discovering unexpected disease associations in patients with different ADL status. This could be relevant in the view of individuating personalized diagnostic and therapeutic approaches, according to the modern principles of precision medicine.}, }
@article {pmid39024004, year = {2024}, author = {Hernandez, R and Hoogendoorn, C and Gonzalez, JS and Pyatak, EA and Crespo-Ramos, G and Schneider, S}, title = {Reliability and Validity of Ecological Momentary Assessment Response Time-Based Measures of Emotional Clarity: Secondary Data Analysis.}, journal = {JMIR mental health}, volume = {11}, number = {}, pages = {e58352}, pmid = {39024004}, issn = {2368-7959}, support = {R01 DK121298/DK/NIDDK NIH HHS/United States ; P30 DK111022/DK/NIDDK NIH HHS/United States ; UL1 TR001855/TR/NCATS NIH HHS/United States ; UL1 TR000130/TR/NCATS NIH HHS/United States ; R01 AG068190/AG/NIA NIH HHS/United States ; U2C AG060408/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; *Ecological Momentary Assessment ; Female ; Male ; Reproducibility of Results ; Adult ; *Emotions ; Middle Aged ; Diabetes Mellitus, Type 1/psychology ; Reaction Time/physiology ; Emotional Regulation/physiology ; Data Analysis ; Personal Satisfaction ; Surveys and Questionnaires ; Secondary Data Analysis ; }, abstract = {BACKGROUND: Emotional clarity has often been assessed with self-report measures, but efforts have also been made to measure it passively, which has advantages such as avoiding potential inaccuracy in responses stemming from social desirability bias or poor insight into emotional clarity. Response times (RTs) to emotion items administered in ecological momentary assessments (EMAs) may be an indirect indicator of emotional clarity. Another proposed indicator is the drift rate parameter, which assumes that, aside from how fast a person responds to emotion items, the measurement of emotional clarity also requires the consideration of how careful participants were in providing responses.<br><br>OBJECTIVE: This paper aims to examine the reliability and validity of RTs and drift rate parameters from EMA emotion items as indicators of individual differences in emotional clarity.<br><br>METHODS: Secondary data analysis was conducted on data from 196 adults with type 1 diabetes who completed a 2-week EMA study involving the completion of 5 to 6 surveys daily. If lower RTs and higher drift rates (from EMA emotion items) were indicators of emotional clarity, we hypothesized that greater levels (ie, higher clarity) should be associated with greater life satisfaction; lower levels of neuroticism, depression, anxiety, and diabetes distress; and fewer difficulties with emotion regulation. Because prior literature suggested emotional clarity could be valence specific, EMA items for negative affect (NA) and positive affect were examined separately.<br><br>RESULTS: Reliability of the proposed indicators of emotional clarity was acceptable with a small number of EMA prompts (ie, 4 to 7 prompts in total or 1 to 2 days of EMA surveys). Consistent with expectations, the average drift rate of NA items across multiple EMAs had expected associations with other measures, such as correlations of r=-0.27 (P<.001) with depression symptoms, r=-0.27 (P=.001) with anxiety symptoms, r=-0.15 (P=.03) with emotion regulation difficulties, and r=0.63 (P<.001) with RTs to NA items. People with a higher NA drift rate responded faster to NA emotion items, had greater subjective well-being (eg, fewer depression symptoms), and had fewer difficulties with overall emotion regulation, which are all aligned with the expectation for an emotional clarity measure. Contrary to expectations, the validities of average RTs to NA items, the drift rate of positive affect items, and RTs to positive affect items were not strongly supported by our results.<br><br>CONCLUSIONS: Study findings provided initial support for the validity of NA drift rate as an indicator of emotional clarity but not for that of other RT-based clarity measures. Evidence was preliminary because the sample size was not sufficient to detect small but potentially meaningful correlations, as the sample size of the diabetes EMA study was chosen for other more primary research questions. Further research on passive emotional clarity measures is needed.}, }
@article {pmid39023004, year = {2024}, author = {Rillig, MC and Li, C and Rodríguez Del Río, &#xc1; and Zhu, YG and Jin, L}, title = {Elevated levels of antibiotic resistance genes as a factor of human-caused global environmental change.}, journal = {Global change biology}, volume = {30}, number = {7}, pages = {e17419}, doi = {10.1111/gcb.17419}, pmid = {39023004}, issn = {1365-2486}, support = {C5063-22G//Research Grants Council of Hong Kong/ ; 2021-DST-004//Ningbo S&amp;T/ ; P0044024//Hong Kong Polytechnic University/ ; P0040336//Hong Kong Polytechnic University/ ; //Alexander-von-Humboldt Foundation/ ; }, mesh = {Humans ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Climate Change ; Ecosystem ; Human Activities ; }, abstract = {Antibiotic resistance genes (ARGs) have moved into focus as a critically important response variable in global change biology, given the increasing environmental and human health threat posed by these genes. However, we propose that elevated levels of ARGs should also be considered a factor of global change, not just a response. We provide evidence that elevated levels of ARGs are a global change factor, since this phenomenon is linked to human activity, occurs globally, and affects biota. We explain why ARGs could be considered the global change factor, rather than the organisms containing them; and we highlight the difference between ARGs and the presence of antibiotics, which are not necessarily linked since elevated levels of ARGs are caused by multiple factors. Importantly, shifting the perspective to elevated levels of ARGs as a factor of global change opens new avenues of research, where ARGs can be the experimental treatment. This includes asking questions about how elevated ARG levels interact with other global change factors, or how ARGs influence ecosystem processes, biodiversity or trophic relationships. Global change biology stands to profit from this new framing in terms of capturing more completely the real extent of human impacts on this planet.}, }
@article {pmid39018100, year = {2024}, author = {Corponi, F and Li, BM and Anmella, G and Valenzuela-Pascual, C and Mas, A and Pacchiarotti, I and Valentí, M and Grande, I and Benabarre, A and Garriga, M and Vieta, E and Young, AH and Lawrie, SM and Whalley, HC and Hidalgo-Mazzei, D and Vergari, A}, title = {Wearable Data From Subjects Playing Super Mario, Taking University Exams, or Performing Physical Exercise Help Detect Acute Mood Disorder Episodes via Self-Supervised Learning: Prospective, Exploratory, Observational Study.}, journal = {JMIR mHealth and uHealth}, volume = {12}, number = {}, pages = {e55094}, pmid = {39018100}, issn = {2291-5222}, mesh = {Humans ; *Supervised Machine Learning ; Prospective Studies ; *Wearable Electronic Devices/statistics &amp; numerical data/standards ; Male ; Female ; *Mood Disorders/diagnosis/psychology ; Adult ; Exercise/psychology/physiology ; Universities/statistics &amp; numerical data/organization &amp; administration ; }, abstract = {BACKGROUND: Personal sensing, leveraging data passively and near-continuously collected with wearables from patients in their ecological environment, is a promising paradigm to monitor mood disorders (MDs), a major determinant of the worldwide disease burden. However, collecting and annotating wearable data is resource intensive. Studies of this kind can thus typically afford to recruit only a few dozen patients. This constitutes one of the major obstacles to applying modern supervised machine learning techniques to MD detection.<br><br>OBJECTIVE: In this paper, we overcame this data bottleneck and advanced the detection of acute MD episodes from wearables' data on the back of recent advances in self-supervised learning (SSL). This approach leverages unlabeled data to learn representations during pretraining, subsequently exploited for a supervised task.<br><br>METHODS: We collected open access data sets recording with the Empatica E4 wristband spanning different, unrelated to MD monitoring, personal sensing tasks-from emotion recognition in Super Mario players to stress detection in undergraduates-and devised a preprocessing pipeline performing on-/off-body detection, sleep/wake detection, segmentation, and (optionally) feature extraction. With 161 E4-recorded subjects, we introduced E4SelfLearning, the largest-to-date open access collection, and its preprocessing pipeline. We developed a novel E4-tailored transformer (E4mer) architecture, serving as the blueprint for both SSL and fully supervised learning; we assessed whether and under which conditions self-supervised pretraining led to an improvement over fully supervised baselines (ie, the fully supervised E4mer and pre-deep learning algorithms) in detecting acute MD episodes from recording segments taken in 64 (n=32, 50%, acute, n=32, 50%, stable) patients.<br><br>RESULTS: SSL significantly outperformed fully supervised pipelines using either our novel E4mer or extreme gradient boosting (XGBoost): n=3353 (81.23%) against n=3110 (75.35%; E4mer) and n=2973 (72.02%; XGBoost) correctly classified recording segments from a total of 4128 segments. SSL performance was strongly associated with the specific surrogate task used for pretraining, as well as with unlabeled data availability.<br><br>CONCLUSIONS: We showed that SSL, a paradigm where a model is pretrained on unlabeled data with no need for human annotations before deployment on the supervised target task of interest, helps overcome the annotation bottleneck; the choice of the pretraining surrogate task and the size of unlabeled data for pretraining are key determinants of SSL success. We introduced E4mer, which can be used for SSL, and shared the E4SelfLearning collection, along with its preprocessing pipeline, which can foster and expedite future research into SSL for personal sensing.}, }
@article {pmid39015757, year = {2023}, author = {Boyes, D and Boyes, C and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Wainscot Smudge, Ypsolopha scabrella (Linnaeus, 1761).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {341}, pmid = {39015757}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Ypsolopha scabrella (the Wainscot Smudge; Arthropoda; Insecta; Lepidoptera; Ypsolophidae). The genome sequence is 853.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.7 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,594 protein coding genes.}, }
@article {pmid39015615, year = {2024}, author = {Boyes, D and Lewis, OT and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Mottled Pug, Eupithecia exiguata (Hübner, 1813).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {65}, pmid = {39015615}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Eupithecia exiguata (the Mottled Pug; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 372.9 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.39 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,194 protein coding genes.}, }
@article {pmid39015613, year = {2024}, author = {Obbard, DJ and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of a drosophilid fruit fly, Drosophila histrio (Meigen, 1830).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {56}, pmid = {39015613}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Drosophila histrio (the drosophilid fruit fly; Arthropoda; Insecta; Diptera; Drosophilidae). The genome sequence is 189.2 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.02 kilobases in length.}, }
@article {pmid39015611, year = {2024}, author = {Boyes, D and Boyes, C and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Dotted Grey Groundling, Athrips mouffetella (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {42}, pmid = {39015611}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Athrips mouffetella (the Dotted Grey Groundling; Arthropoda; Insecta; Lepidoptera; Gelechiidae). The genome sequence is 869.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.23 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,889 protein coding genes.}, }
@article {pmid39014019, year = {2024}, author = {Cavaliere, M and Yang, G and De Dreu, CKW and Gross, J}, title = {Cooperation and social organization depend on weighing private and public reputations.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {16443}, pmid = {39014019}, issn = {2045-2322}, mesh = {Humans ; *Cooperative Behavior ; Social Networking ; Game Theory ; Interpersonal Relations ; }, abstract = {To avoid exploitation by defectors, people can use past experiences with others when deciding to cooperate or not ('private information'). Alternatively, people can derive others' reputation from 'public' information provided by individuals within the social network. However, public information may be aligned or misaligned with one's own private experiences and different individuals, such as 'friends' and 'enemies', may have different opinions about the reputation of others. Using evolutionary agent-based simulations, we examine how cooperation and social organization is shaped when agents (1) prioritize private or public information about others' reputation, and (2) integrate others' opinions using a friend-focused or a friend-and-enemy focused heuristic (relying on reputation information from only friends or also enemies, respectively). When agents prioritize public information and rely on friend-and-enemy heuristics, we observe polarization cycles marked by high cooperation, invasion by defectors, and subsequent population fragmentation. Prioritizing private information diminishes polarization and defector invasions, but also results in limited cooperation. Only when using friend-focused heuristics and following past experiences or the recommendation of friends create prosperous and stable populations based on cooperation. These results show how combining one's own experiences and the opinions of friends can lead to stable and large-scale cooperation and highlight the important role of following the advice of friends in the evolution of group cooperation.}, }
@article {pmid39008135, year = {2024}, author = {Urbano, F and Viterbi, R and Pedrotti, L and Vettorazzo, E and Movalli, C and Corlatti, L}, title = {Correction to: Enhancing biodiversity conservation and monitoring in protected areas through efficient data management.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {8}, pages = {733}, doi = {10.1007/s10661-024-12886-7}, pmid = {39008135}, issn = {1573-2959}, }
@article {pmid39007251, year = {2024}, author = {Pili, AN and Leroy, B and Measey, JG and Farquhar, JE and Toomes, A and Cassey, P and Chekunov, S and Grenié, M and van Winkel, D and Maria, L and Diesmos, MLL and Diesmos, AC and Zurell, D and Courchamp, F and Chapple, DG}, title = {Forecasting potential invaders to prevent future biological invasions worldwide.}, journal = {Global change biology}, volume = {30}, number = {7}, pages = {e17399}, doi = {10.1111/gcb.17399}, pmid = {39007251}, issn = {1365-2486}, support = {DP210103050//Australian Research Council/ ; FT200100108//Australian Research Council/ ; IL230100175//Australian Research Council/ ; //Monash University Faculty of Science's Dean's Postgraduate Research Scholarship and Dean's International Postgraduate Research Scholarship, and by Monash University Graduate Research Office's Graduate Research Completion Award and Post-Graduate Publication Award/ ; BIFA3_026//the Philippine Department of Environment and Natural Resources FORIS project and the Global Biodiversity Information Facility Biodiversity Fund for Asia Project/ ; }, mesh = {*Introduced Species ; Animals ; *Forecasting ; *Reptiles/physiology ; *Amphibians/physiology ; Risk Assessment/methods ; Models, Theoretical ; Models, Biological ; }, abstract = {The ever-increasing and expanding globalisation of trade and transport underpins the escalating global problem of biological invasions. Developing biosecurity infrastructures is crucial to anticipate and prevent the transport and introduction of invasive alien species. Still, robust and defensible forecasts of potential invaders are rare, especially for species without known invasion history. Here, we aim to support decision-making by developing a quantitative invasion risk assessment tool based on invasion syndromes (i.e., generalising typical attributes of invasive alien species). We implemented a workflow based on 'Multiple Imputation with Chain Equation' to estimate invasion syndromes from imputed datasets of species' life-history and ecological traits and macroecological patterns. Importantly, our models disentangle the factors explaining (i) transport and introduction and (ii) establishment. We showcase our tool by modelling the invasion syndromes of 466 amphibians and reptile species with invasion history. Then, we project these models to amphibians and reptiles worldwide (16,236 species [c.76% global coverage]) to identify species with a risk of being unintentionally transported and introduced, and risk of establishing alien populations. Our invasion syndrome models showed high predictive accuracy with a good balance between specificity and generality. Unintentionally transported and introduced species tend to be common and thrive well in human-disturbed habitats. In contrast, those with established alien populations tend to be large-sized, are habitat generalists, thrive well in human-disturbed habitats, and have large native geographic ranges. We forecast that 160 amphibians and reptiles without known invasion history could be unintentionally transported and introduced in the future. Among them, 57 species have a high risk of establishing alien populations. Our reliable, reproducible, transferable, statistically robust and scientifically defensible quantitative invasion risk assessment tool is a significant new addition to the suite of decision-support tools needed for developing a future-proof preventative biosecurity globally.}, }
@article {pmid39004905, year = {2024}, author = {Herraiz, C and Triguero-Ocaña, R and Laguna, E and Jiménez-Ruiz, S and Peralbo-Moreno, A and Martínez-López, B and García-Bocanegra, I and Risalde, M&#xc1; and Vicente, J and Acevedo, P}, title = {Movement-driven modelling reveals new patterns in disease transmission networks.}, journal = {The Journal of animal ecology}, volume = {93}, number = {9}, pages = {1275-1287}, doi = {10.1111/1365-2656.14142}, pmid = {39004905}, issn = {1365-2656}, support = {PID2019-111699RB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; AGL2013-48523-C3-1-R//Ministerio de Econom&#xed;a y Competitividad/ ; AGL2016-76358-R//Ministerio de Econom&#xed;a y Competitividad/ ; //European Social Fund/ ; //Government of Castilla-La Mancha/ ; //University of Castilla-La Mancha/ ; }, mesh = {Animals ; Cattle ; Swine ; *Models, Biological ; Spain ; Geographic Information Systems ; Tuberculosis, Bovine/transmission/microbiology ; Swine Diseases/transmission/microbiology ; Movement ; }, abstract = {Interspecific interactions are highly relevant in the potential transmission of shared pathogens in multi-host systems. In recent decades, several technologies have been developed to study pathogen transmission, such as proximity loggers, GPS tracking devices and/or camera traps. Despite the diversity of methods aimed at detecting contacts, the analysis of transmission risk is often reduced to contact rates and the probability of transmission given the contact. However, the latter process is continuous over time and unique for each contact, and is influenced by the characteristics of the contact and the pathogen's relationship with both the host and the environment. Our objective was to assess whether a more comprehensive approach, using a movement-based model which assigns a unique transmission risk to each contact by decomposing transmission into contact formation, contact duration and host characteristics, could reveal disease transmission dynamics that are not detected with more traditional approaches. The model was built from GPS-collar data from two management systems in Spain where animal tuberculosis (TB) circulates: a national park with extensively reared endemic cattle, and an area with extensive free-range pigs and cattle farms. In addition, we evaluated the effect of the GPS device fix rate on the performance of the model. Different transmission dynamics were identified between both management systems. Considering the specific conditions under which each contact occurs (i.e. whether the contact is direct or indirect, its duration, the hosts characteristics, the environmental conditions, etc.) resulted in the identification of different transmission dynamics compared to using only contact rates. We found that fix intervals greater than 30 min in the GPS tracking data resulted in missed interactions, and intervals greater than 2 h may be insufficient for epidemiological purposes. Our study shows that neglecting the conditions under which each contact occurs may result in a misidentification of the real role of each species in disease transmission. This study describes a clear and repeatable framework to study pathogen transmission from GPS data and provides further insights to understand how TB is maintained in multi-host systems in Mediterranean environments.}, }
@article {pmid39004875, year = {2024}, author = {Taylor, A and Sigona, A and Kelly, M}, title = {Centering Amah Mutsun voices in the analysis of a culturally important, fire-managed coastal grassland.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {34}, number = {6}, pages = {e3014}, doi = {10.1002/eap.3014}, pmid = {39004875}, issn = {1051-0761}, support = {//Critical Mission Studies Grant program of the University of California/ ; //Joseph A. Myers Center for Research on Native American Issues, UC Berkeley/ ; //California Native Plant Society (both statewide and from the Santa Clara Valley chapter)/ ; //UC Berkeley Chapter of Sigma Xi/ ; //California Native Grasslands Association/ ; //Department of Environmental Science, Policy, and Management at UC Berkeley/ ; //University of California Graduate Division Fellowship/ ; //Phi Beta Kappa Fellowship, UC Berkeley/ ; //Inter-institutional Network for Food, Agriculture and Sustainability and Intertribal Agriculture Council Tribal Fellowship/ ; //UC Berkeley Graduate Fellowship in Climate Equity/ ; //Ford Foundation Predoctoral Fellowship Program/ ; //Wilderness Society Scholarship/ ; //UC Berkeley Chancellor's Fellowship/ ; }, mesh = {*Grassland ; California ; *Fires ; *Conservation of Natural Resources ; Humans ; Wildfires ; Indigenous Peoples ; }, abstract = {Indigenous communities throughout California, USA, are increasingly advocating for and practicing cultural fire stewardship, leading to a host of social, cultural, and ecological benefits. Simultaneously, state agencies are recognizing the importance of controlled burning and cultural fire as a means of reducing the risk of severe wildfire while benefiting fire-adapted ecosystems. However, much of the current research on the impacts of controlled burning ignores the cultural importance of these ecosystems, and risks further marginalizing Indigenous knowledge systems. Our work adds a critical Indigenous perspective to the study of controlled burning in California's unique coastal grasslands, one of the most biodiverse and endangered ecosystems in the country. In this study, we partnered with the Amah Mutsun Tribal Band to investigate how the abundance and occurrence of shrubs, cultural plants, and invasive plants differed among three adjacent coastal grasslands with varying fire histories. These three sites are emblematic of the state's diverging approaches to grassland management: fire suppression, fire suppression followed by wildfire, and an exceedingly rare example of a grassland that has been repeatedly burned approximately every 2 years for more than 30 years. We found that Danthonia californica was significantly more abundant on the burned sites, whereas all included shrub species (Baccharis pilularis, Frangula californica, and Rubus ursinus) were significantly more abundant on the site with no recorded fire, results that have important implications for future cultural revitalization efforts and the loss of coastal grasslands to shrub encroachment. In addition to conducting a culturally relevant vegetation survey, we used Sentinel-2 satellite imagery to compare the relative severities of the two most recent fire events within the study area. Critically, we used interviews with Amah Mutsun tribal members to contextualize the results of our vegetation survey and remote sensing analysis, and to investigate how cultural burning contrasts from typical Western fire management approaches in this region. Our study is a novel example of how interviews, field data, and satellite imagery can be combined to gain a deeper ecological and cultural understanding of fire in California's endangered coastal grasslands.}, }
@article {pmid39004446, year = {2024}, author = {Fummey, E and Navarro, P and Plazzer, JP and Frayling, IM and Knott, S and Tenesa, A}, title = {Estimating cancer risk in carriers of Lynch syndrome variants in UK Biobank.}, journal = {Journal of medical genetics}, volume = {61}, number = {9}, pages = {861-869}, pmid = {39004446}, issn = {1468-6244}, mesh = {Humans ; *Colorectal Neoplasms, Hereditary Nonpolyposis/genetics/epidemiology ; Female ; United Kingdom/epidemiology ; *Biological Specimen Banks ; Middle Aged ; *DNA Mismatch Repair/genetics ; *Genetic Predisposition to Disease ; Aged ; Heterozygote ; Exome Sequencing ; Incidence ; Adult ; Breast Neoplasms/genetics/epidemiology ; Endometrial Neoplasms/genetics/epidemiology ; DNA-Binding Proteins/genetics ; MutL Protein Homolog 1/genetics ; UK Biobank ; MutS Homolog 2 Protein ; }, abstract = {UNLABELLED: BackgroundLynch syndrome (LS) is an inherited cancer predisposition syndrome caused by genetic variants affecting DNA mismatch repair (MMR) genes MLH1, MSH2, MSH6 and PMS2 Cancer risk in LS is estimated from cohorts of individuals ascertained by individual or family history of cancer, which may upwardly bias estimates.<br><br>METHODS: 830 carriers of pathogenic or likely pathogenic (path_MMR) MMR gene variants classified by InSiGHT were identified in 454&#x2009;756 UK Biobank (UKB) participants using whole-exome sequence. Nelson-Aalen survival analysis was used to estimate cumulative incidence of colorectal, endometrial and breast cancer (BC).<br><br>RESULTS: Cumulative incidence of colorectal and endometrial cancer (EC) by age 70 years was elevated in path_MMR carriers compared with non-carriers (colorectal: 11.8% (95% confidence interval (CI): 9.5% to 14.6%) vs 1.7% (95% CI: 1.6% to 1.7%), endometrial: 13.4% (95% CI: 10.2% to 17.6%) vs 1.0% (95% CI: 0.9% to 1.0%)), but the magnitude of this increase differed between genes. Cumulative BC incidence by age 70 years was not elevated in path_MMR carriers compared with non-carriers (8.9% (95% CI: 6.3% to 12.4%) vs 7.5% (95% CI: 7.4% to 7.6%)). Cumulative cancer incidence estimates in UKB were similar to estimates from the Prospective Lynch Syndrome Database for all genes and cancers, except there was no evidence for elevated EC risk in carriers of pathogenic PMS2 variants in UKB.<br><br>CONCLUSION: These results support offering incidentally identified carriers of any path_MMR surveillance to manage colorectal cancer risk. Incidentally identified carriers of pathogenic variants in MLH1, MSH2 and MSH6 would also benefit from interventions to reduce EC risk. The results suggest that BC is not an LS-related cancer.}, }
@article {pmid39004058, year = {2024}, author = {Guo, J and Jin, Y and Liu, S and Li, T and Ji, D and Hou, C and Tang, H}, title = {Investigation of the causes and mechanisms of hypoxia in the central Bohai Sea in the summer of 2022.}, journal = {Marine pollution bulletin}, volume = {206}, number = {}, pages = {116710}, doi = {10.1016/j.marpolbul.2024.116710}, pmid = {39004058}, issn = {1879-3363}, mesh = {*Seasons ; China ; *Eutrophication ; *Environmental Monitoring ; *Oceans and Seas ; Seawater/chemistry ; Animals ; Temperature ; }, abstract = {The deep-water area in the central Bohai Sea (BS) serves as a spawning ground and nursery for fish, shrimp, and crabs. Frequent hypoxia will affect the ecological environment in the central BS. Data from an on-site investigation of the central BS in the spring and summer of 2022 were used to analyze the relevant factors generating the occurrence of hypoxia in the central BS through the eutrophication index E, apparent oxygen consumption (AOU), and Spearman correlation. The hypoxia area was largely distributed in the study area's deep water section, and stratification was the main cause of hypoxia at the bottom. Organic matter mineralization, degradation, and biological respiration further exacerbated the hypoxia. In the summer of 2022, temperature stratification was the dominant factor influencing hypoxia.}, }
@article {pmid39001963, year = {2024}, author = {Lu, Y and Xiao, X and Liang, Y and Li, J and Guo, C and Xu, L and Liu, Q and Xiao, Y and Zhou, S}, title = {Distribution and transformation of potentially toxic elements in cracks under coal mining disturbance in farmland.}, journal = {Environmental geochemistry and health}, volume = {46}, number = {9}, pages = {312}, pmid = {39001963}, issn = {1573-2983}, support = {52130402//State Key Program of National Natural Science Foundation of China/ ; }, mesh = {*Soil Pollutants/analysis/toxicity ; *Coal Mining ; *Environmental Monitoring ; *Metals, Heavy/analysis/toxicity ; Soil/chemistry ; Farms ; Risk Assessment ; }, abstract = {The ground cracks resulting from coal mining activities induce alterations in the physical and chemical characteristics of soil. However, limited knowledge exists regarding the impact of subsidence caused by coal mining on the distribution of potentially toxic elements (PTEs) fractions in farmland soil. In this study, we collected 19 soil profiles at varying depths from the soil surface and at horizontal distances of 0, 1, 2, and 5 m from the vertical crack. Using BCR extraction fractionation, we determined the geochemical fractions and total concentrations of Chromium (Cr), nickel (Ni), copper (Cu), zinc (Zn), arsenic (As), cadmium (Cd) and lead (Pb) to investigate their ecological risk, spatial fraction distribution, and main influencing factors. Results showed that the E r i values of Cd appearing in 68.7% of the samples were higher than 40 and less than 80, presented a moderate ecological risk. Chromium (Cr), nickel (Ni), copper (Cu), zinc (Zn), arsenic (As), and lead (Pb) were mainly bound to residual fractions (> 60%) with lower mobility and Cd was dominated by F1 (acid-soluble fractions, 50%) and F2 (reducible fractions, 29%) in surface soil (0-20 cm). The geochemical fractionation revealed that the mobile fractions (F1-acid-soluble and F2-reducible) of PTEs were primarily located near the crack, influenced by available potassium. In contrast, the less mobile fractions (F3-oxidizable and F4-residual) exhibited higher concentrations at distances of 2 and 5 m from the crack, except for arsenic, influenced by the presence of clay particles and available phosphorus.}, }
@article {pmid39001714, year = {2024}, author = {Williams, TA and Davin, AA and Szánthó, LL and Stamatakis, A and Wahl, NA and Woodcroft, BJ and Soo, RM and Eme, L and Sheridan, PO and Gubry-Rangin, C and Spang, A and Hugenholtz, P and Szöllősi, GJ}, title = {Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39001714}, issn = {1751-7370}, support = {GBMF9741//Gordon and Betty Moore Foundation/ ; 714774//European Union's Horizon 2020 Research and Innovation Programme/ ; /ERC_/European Research Council/International ; 947317//European Union's Horizon 2020 Research and Innovation Programme/ ; 735929LPI//Simons Foundation/ ; FL150100038//Australian Research Council Laureate Fellowship/ ; 812811//Simons Foundation/ ; 101087081//European Union's Horizon Europe ERA Chair Program/ ; URF150571//Royal Society University Research Fellowship/ ; }, mesh = {*Phylogeny ; *Archaea/genetics/classification ; Bacteria/genetics/classification ; Evolution, Molecular ; Genome, Bacterial ; Symbiosis ; Ecology ; }, abstract = {In recent years, phylogenetic reconciliation has emerged as a promising approach for studying microbial ecology and evolution. The core idea is to model how gene trees evolve along a species tree and to explain differences between them via evolutionary events including gene duplications, transfers, and losses. Here, we describe how phylogenetic reconciliation provides a natural framework for studying genome evolution and highlight recent applications including ancestral gene content inference, the rooting of species trees, and the insights into metabolic evolution and ecological transitions they yield. Reconciliation analyses have elucidated the evolution of diverse microbial lineages, from Chlamydiae to Asgard archaea, shedding light on ecological adaptation, host-microbe interactions, and symbiotic relationships. However, there are many opportunities for broader application of the approach in microbiology. Continuing improvements to make reconciliation models more realistic and scalable, and integration of ecological metadata such as habitat, pH, temperature, and oxygen use offer enormous potential for understanding the rich tapestry of microbial life.}, }
@article {pmid39000743, year = {2024}, author = {Macchia, A and Marinelli, L and Barbaccia, FI and de Caro, T and Hansen, A and Schuberthan, LM and Izzo, FC and Pintus, V and Testa Chiari, K and La Russa, MF}, title = {Mattel's ©Barbie: Preventing Plasticizers Leakage in PVC Artworks and Design Objects through Film-Forming Solutions.}, journal = {Polymers}, volume = {16}, number = {13}, pages = {}, pmid = {39000743}, issn = {2073-4360}, abstract = {The main conservation problem of p-PVC artworks is phthalate-based plasticizer migration. Phthalate migration from the bulk to the surface of the materials leads to the formation of a glossy and oily film on the outer layers, ultimately reducing the flexibility of the material. This study aimed to develop a removable coating for the preservation of contemporary artworks and design objects made of plasticized polyvinyl chloride (p-PVC). Several coatings incorporating chitosan, collagen, and cellulose ethers were assessed as potential barriers to inhibiting plasticizer migration. Analytical techniques including optical microscopy (OM), ultraviolet/visible/near-infrared spectroscopy (UV/Vis/NIR), Fourier transform infrared spectroscopy with attenuated total reflection (FTIR-ATR), and scanning electron microscopy (SEM) were utilized to evaluate the optical and chemical stability of selected coating formulations applied to laboratory p-PVC sheet specimens. Subsequently, formulations were tested on a real tangible example of a design object, ©Barbie doll, characterized by the prevalent issue of plasticizer migration. Furthermore, the results obtained with the tested formulations were evaluated by a group of conservators using a tailored survey. Finally, a suitable coating formulation capable of safeguarding plastic substrates was suggested.}, }
@article {pmid39000053, year = {2024}, author = {Wang, XY and Ren, CX and Fan, QW and Xu, YP and Wang, LW and Mao, ZL and Cai, XZ}, title = {Integrated Assays of Genome-Wide Association Study, Multi-Omics Co-Localization, and Machine Learning Associated Calcium Signaling Genes with Oilseed Rape Resistance to Sclerotinia sclerotiorum.}, journal = {International journal of molecular sciences}, volume = {25}, number = {13}, pages = {}, pmid = {39000053}, issn = {1422-0067}, support = {2021C02064//Zhejiang Science and Technology Major Program on Agricultural New Variety Breeding/ ; LZ18C140002//Zhejiang Provincial Natural Science Foundation of China/ ; 324CXTD430//Hainan Provincial Natural Science Foundation of China/ ; }, mesh = {*Ascomycota/pathogenicity ; *Machine Learning ; *Disease Resistance/genetics ; *Genome-Wide Association Study ; *Plant Diseases/microbiology/genetics ; *Brassica napus/genetics/microbiology/immunology ; *Calcium Signaling/genetics ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; Genomics/methods ; Multiomics ; }, abstract = {Sclerotinia sclerotiorum (Ss) is one of the most devastating fungal pathogens, causing huge yield loss in multiple economically important crops including oilseed rape. Plant resistance to Ss pertains to quantitative disease resistance (QDR) controlled by multiple minor genes. Genome-wide identification of genes involved in QDR to Ss is yet to be conducted. In this study, we integrated several assays including genome-wide association study (GWAS), multi-omics co-localization, and machine learning prediction to identify, on a genome-wide scale, genes involved in the oilseed rape QDR to Ss. Employing GWAS and multi-omics co-localization, we identified seven resistance-associated loci (RALs) associated with oilseed rape resistance to Ss. Furthermore, we developed a machine learning algorithm and named it Integrative Multi-Omics Analysis and Machine Learning for Target Gene Prediction (iMAP), which integrates multi-omics data to rapidly predict disease resistance-related genes within a broad chromosomal region. Through iMAP based on the identified RALs, we revealed multiple calcium signaling genes related to the QDR to Ss. Population-level analysis of selective sweeps and haplotypes of variants confirmed the positive selection of the predicted calcium signaling genes during evolution. Overall, this study has developed an algorithm that integrates multi-omics data and machine learning methods, providing a powerful tool for predicting target genes associated with specific traits. Furthermore, it makes a basis for further understanding the role and mechanisms of calcium signaling genes in the QDR to Ss.}, }
@article {pmid38997687, year = {2024}, author = {Prakofjewa, J and Sartori, M and Šarka, P and Kalle, R and Pieroni, A and Sõukand, R}, title = {Knowledge in motion: temporal dynamics of wild food plant use in the Polish-Lithuanian-Belarusian border region.}, journal = {Journal of ethnobiology and ethnomedicine}, volume = {20}, number = {1}, pages = {65}, pmid = {38997687}, issn = {1746-4269}, support = {grant agreement No 714874//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme/ ; grant agreement No 714874//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme/ ; grant agreement No 714874//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme/ ; grant agreement No 714874//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme/ ; grant agreement No 714874//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme/ ; grant agreement No 714874//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme/ ; }, mesh = {Lithuania ; Poland ; *Plants, Edible/classification ; Republic of Belarus ; Humans ; Knowledge ; Ethnobotany ; }, abstract = {BACKGROUND: Understanding how Local Ecological Knowledge (LEK) evolves over time is crucial for fostering social and environmental responsibility. This study aims to develop a conceptual model of plant knowledge circulation, providing insights into the temporal dynamics of LEK in the Polish-Lithuanian-Belarusian border region. It explores the key patterns and driving forces behind changes in the use of wild plants for food.<br><br>METHODS: Field research was conducted in 60 rural settlements across Podlasie Voivodeship (Poland), Vilnius Region (Lithuania), and Hrodna Region (Belarus). This included 200 semi-structured interviews and participant observation among two local communities, Lithuanians and Poles. To assess the temporal dynamics of wild food use, we performed a cross-ethnic, cross-border analysis over time, dividing the data into three major temporal dimensions: past, continuous, and recently acquired uses.<br><br>RESULTS: Of the 72 wild plant taxa reported by Poles or Lithuanians in the Polish-Lithuanian-Belarusian borderland, 47 were continuously used for food, 58 were utilised in the past, and 41 were recently acquired. Cross-country trends were similar, with Poland showing more past uses. Diachronic comparisons between Poles and Lithuanians in each studied country revealed no significant differences. Recently acquired taxa overlapped considerably with those used continuously and in the past. The most diversely utilised taxa showed the greatest overlaps. By observing the movement of specific plant taxa within various time dimensions, we distinguished overlapping flow variations: retention (3 taxa), decay (11), invention (8), stagnation (17), revitalisation (6), re-invention (3), and knowledge in motion (24). Shifts in the use of wild food plants were influenced by changes in environmental conditions, governmental policies, cultural practices, and economic factors.<br><br>CONCLUSION: The findings of this study have important implications for improving methods of tracking changes in LEK and enhancing our understanding of the relationship between people and nature. Our results underscore the importance of considering knowledge circulation over time in different directions. Recognising the various stages of knowledge circulation might help in pursuing sustainable solutions that balance the needs of human communities with environmental protection.}, }
@article {pmid38995977, year = {2024}, author = {Rosenblatt, E and Cook, JD and DiRenzo, GV and Grant, EHC and Arce, F and Pepin, KM and Rudolph, FJ and Runge, MC and Shriner, S and Walsh, DP and Mosher, BA}, title = {Epidemiological modeling of SARS-CoV-2 in white-tailed deer (Odocoileus virginianus) reveals conditions for introduction and widespread transmission.}, journal = {PLoS computational biology}, volume = {20}, number = {7}, pages = {e1012263}, pmid = {38995977}, issn = {1553-7358}, mesh = {Animals ; *Deer/virology ; *COVID-19/transmission/epidemiology/veterinary/virology ; *SARS-CoV-2 ; Humans ; Epidemiological Models ; Animals, Wild/virology ; Computational Biology ; Disease Outbreaks/veterinary/statistics &amp; numerical data ; Zoonoses/transmission/epidemiology/virology ; }, abstract = {Emerging infectious diseases with zoonotic potential often have complex socioecological dynamics and limited ecological data, requiring integration of epidemiological modeling with surveillance. Although our understanding of SARS-CoV-2 has advanced considerably since its detection in late 2019, the factors influencing its introduction and transmission in wildlife hosts, particularly white-tailed deer (Odocoileus virginianus), remain poorly understood. We use a Susceptible-Infected-Recovered-Susceptible epidemiological model to investigate the spillover risk and transmission dynamics of SARS-CoV-2 in wild and captive white-tailed deer populations across various simulated scenarios. We found that captive scenarios pose a higher risk of SARS-CoV-2 introduction from humans into deer herds and subsequent transmission among deer, compared to wild herds. However, even in wild herds, the transmission risk is often substantial enough to sustain infections. Furthermore, we demonstrate that the strength of introduction from humans influences outbreak characteristics only to a certain extent. Transmission among deer was frequently sufficient for widespread outbreaks in deer populations, regardless of the initial level of introduction. We also explore the potential for fence line interactions between captive and wild deer to elevate outbreak metrics in wild herds that have the lowest risk of introduction and sustained transmission. Our results indicate that SARS-CoV-2 could be introduced and maintained in deer herds across a range of circumstances based on testing a range of introduction and transmission risks in various captive and wild scenarios. Our approach and findings will aid One Health strategies that mitigate persistent SARS-CoV-2 outbreaks in white-tailed deer populations and potential spillback to humans.}, }
@article {pmid38995706, year = {2024}, author = {Dietrich, SW and Ma, W and Ding, Y and Watanabe, KH and Zelinski, MB and Sluka, JP}, title = {MOTHER-DB: A Database for Sharing Nonhuman Ovarian Histology Images.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {21}, number = {6}, pages = {2598-2603}, pmid = {38995706}, issn = {1557-9964}, support = {P51 OD011092/OD/NIH HHS/United States ; }, mesh = {Female ; *Ovary/cytology/diagnostic imaging ; Animals ; *Databases, Factual ; Metadata ; *Computational Biology/methods ; *Image Processing, Computer-Assisted/methods ; }, abstract = {The goal of the Multispecies Ovary Tissue Histology Electronic Repository (MOTHER) project is to establish a collection of nonhuman ovary histology images for multiple species as a resource for researchers and educators. An important component of sharing scientific data is the inclusion of the contextual metadata that describes the data. MOTHER extends the Ecological Metadata Language (EML) for documenting research data, leveraging its data provenance and usage license with the inclusion of metadata for ovary histology images. The design of the MOTHER metadata includes information on the donor animal, including reproductive cycle status, the slide and its preparation. MOTHER also extends the ezEML tool, called ezEML+MOTHER, for the specification of the metadata. The design of the MOTHER database (MOTHER-DB) captures the metadata about the histology images, providing a searchable resource for discovering relevant images. MOTHER also defines a curation process for the ingestion of a collection of images and its metadata, verifying the validity of the metadata before its inclusion in the MOTHER collection. A Web search provides the ability to identify relevant images based on various characteristics in the metadata itself, such as genus and species, using filters.}, }
@article {pmid38994633, year = {2024}, author = {Gómez-García, A and Prinz, AK and Jiménez, DAA and Zamora, WJ and Barazorda-Ccahuana, HL and Chávez-Fumagalli, M&#xc1; and Valli, M and Andricopulo, AD and da S Bolzani, V and Olmedo, DA and Solís, PN and Núñez, MJ and Rodríguez Pérez, JR and Sánchez, HAV and Cortés Hernández, HF and Mosquera Martinez, OM and Koch, O and Medina-Franco, JL}, title = {Updating and profiling the natural product-likeness of Latin American compound libraries.}, journal = {Molecular informatics}, volume = {43}, number = {7}, pages = {e202400052}, doi = {10.1002/minf.202400052}, pmid = {38994633}, issn = {1868-1751}, mesh = {*Biological Products/chemistry/pharmacology ; Latin America ; Small Molecule Libraries/pharmacology/chemistry ; Drug Discovery ; Cheminformatics ; Databases, Chemical ; }, abstract = {Compound databases of natural products play a crucial role in drug discovery and development projects and have implications in other areas, such as food chemical research, ecology and metabolomics. Recently, we put together the first version of the Latin American Natural Product database (LANaPDB) as a collective effort of researchers from six countries to ensemble a public and representative library of natural products in a geographical region with a large biodiversity. The present work aims to conduct a comparative and extensive profiling of the natural product-likeness of an updated version of LANaPDB and the individual ten compound databases that form part of LANaPDB. The natural product-likeness profile of the Latin American compound databases is contrasted with the profile of other major natural product databases in the public domain and a set of small-molecule drugs approved for clinical use. As part of the extensive characterization, we employed several chemoinformatics metrics of natural product likeness. The results of this study will capture the attention of the global community engaged in natural product databases, not only in Latin America but across the world.}, }
@article {pmid38992177, year = {2025}, author = {Alvarez-Mora, I and Arturi, K and Béen, F and Buchinger, S and El Mais, AER and Gallampois, C and Hahn, M and Hollender, J and Houtman, C and Johann, S and Krauss, M and Lamoree, M and Margalef, M and Massei, R and Brack, W and Muz, M}, title = {Progress, applications, and challenges in high-throughput effect-directed analysis for toxicity driver identification - is it time for HT-EDA?.}, journal = {Analytical and bioanalytical chemistry}, volume = {417}, number = {3}, pages = {451-472}, pmid = {38992177}, issn = {1618-2650}, mesh = {Animals ; Humans ; Chromatography, Thin Layer/methods ; Environmental Pollutants/analysis/toxicity ; *High-Throughput Screening Assays/methods ; Mass Spectrometry/methods ; *Toxicity Tests/methods ; }, abstract = {The rapid increase in the production and global use of chemicals and their mixtures has raised concerns about their potential impact on human and environmental health. With advances in analytical techniques, in particular, high-resolution mass spectrometry (HRMS), thousands of compounds and transformation products with potential adverse effects can now be detected in environmental samples. However, identifying and prioritizing the toxicity drivers among these compounds remain a significant challenge. Effect-directed analysis (EDA) emerged as an important tool to address this challenge, combining biotesting, sample fractionation, and chemical analysis to unravel toxicity drivers in complex mixtures. Traditional EDA workflows are labor-intensive and time-consuming, hindering large-scale applications. The concept of high-throughput (HT) EDA has recently gained traction as a means of accelerating these workflows. Key features of HT-EDA include the combination of microfractionation and downscaled bioassays, automation of sample preparation and biotesting, and efficient data processing workflows supported by novel computational tools. In addition to microplate-based fractionation, high-performance thin-layer chromatography (HPTLC) offers an interesting alternative to HPLC in HT-EDA. This review provides an updated perspective on the state-of-the-art in HT-EDA, and novel methods/tools that can be incorporated into HT-EDA workflows. It also discusses recent studies on HT-EDA, HT bioassays, and computational prioritization tools, along with considerations regarding HPTLC. By identifying current gaps in HT-EDA and proposing new approaches to overcome them, this review aims to bring HT-EDA a step closer to monitoring applications.}, }
@article {pmid38989474, year = {2024}, author = {Li, R and Li, J and Lemer, S and Lopez, JV and Oatley, G and Clayton-Lucey, IA and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of a heart cockle, Fragum fragum (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {129}, pmid = {38989474}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual specimen of Fragum fragum (a heart cockle; Mollusca; Bivalvia; Veneroida; Cardiidae). The genome sequence is 1,153.1 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 22.36 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,262 protein coding genes.}, }
@article {pmid38986397, year = {2024}, author = {Hung, CC and Hsieh, HH and Chou, WC and Liu, EC and Chow, CH and Chang, Y and Lee, TM and Santschi, PH and Ranatunga, RRMKP and Bacosa, HP and Shih, YY}, title = {Assessing CO2 sources and sinks in and around Taiwan: Implication for achieving regional carbon neutrality by 2050.}, journal = {Marine pollution bulletin}, volume = {206}, number = {}, pages = {116664}, doi = {10.1016/j.marpolbul.2024.116664}, pmid = {38986397}, issn = {1879-3363}, mesh = {Taiwan ; *Carbon Dioxide/analysis ; *Carbon Sequestration ; Environmental Monitoring/methods ; Carbon/analysis ; Oceans and Seas ; Forests ; }, abstract = {Taiwan has pledged to achieve net-zero carbon emissions by 2050, but the current extent of carbon sinks in Taiwan remains unclear. Therefore, this study aims to first review the existing nature-based carbon sinks on land and in the oceans around Taiwan. Subsequently, we suggest potential strategies to reduce CO2 emissions and propose carbon dioxide removal methods (CDRs). The natural carbon sinks by forests, sediments, and oceans in and around Taiwan are approximately 21.5, 42.1, and 96.8 Mt-CO2 y[-1], respectively, which is significantly less than Taiwan's CO2 emissions (280 Mt-CO2 y[-1]). Taiwan must consider decarbonization strategies like using electric vehicles, renewable energy, and hydrogen energy by formulating enabling policies. Besides more precisely assessing both terrestrial and marine carbon sinks, Taiwan should develop novel CDRs such as bioenergy with carbon capture and storage, afforestation, reforestation, biochar, seaweed cultivation, and ocean alkalinity enhancement, to reach carbon neutrality by 2050.}, }
@article {pmid38982382, year = {2024}, author = {Blazanin, M}, title = {gcplyr: an R package for microbial growth curve data analysis.}, journal = {BMC bioinformatics}, volume = {25}, number = {1}, pages = {232}, pmid = {38982382}, issn = {1471-2105}, mesh = {*Software ; Computational Biology/methods ; Data Analysis ; }, abstract = {BACKGROUND: Characterization of microbial growth is of both fundamental and applied interest. Modern platforms can automate collection of high-throughput microbial growth curves, necessitating the development of computational tools to handle and analyze these data to produce insights.<br><br>RESULTS: To address this need, here I present a newly-developed R package: gcplyr. gcplyr can flexibly import growth curve data in common tabular formats, and reshapes it under a tidy framework that is flexible and extendable, enabling users to design custom analyses or plot data with popular visualization packages. gcplyr can also incorporate metadata and generate or import experimental designs to merge with data. Finally, gcplyr carries out model-free (non-parametric) analyses. These analyses do not require mathematical assumptions about microbial growth dynamics, and gcplyr is able to extract a broad range of important traits, including growth rate, doubling time, lag time, maximum density and carrying capacity, diauxie, area under the curve, extinction time, and more.<br><br>CONCLUSIONS: gcplyr makes scripted analyses of growth curve data in R straightforward, streamlines common data wrangling and analysis steps, and easily integrates with common visualization and statistical analyses.}, }
@article {pmid38979877, year = {2024}, author = {Overgaard, CK and Jamy, M and Radutoiu, S and Burki, F and Dueholm, MKD}, title = {Benchmarking long-read sequencing strategies for obtaining ASV-resolved rRNA operons from environmental microeukaryotes.}, journal = {Molecular ecology resources}, volume = {24}, number = {7}, pages = {e13991}, doi = {10.1111/1755-0998.13991}, pmid = {38979877}, issn = {1755-0998}, support = {9041-00236B//Danmarks Frie Forskningsfond/ ; 2021-04055//Vetenskapsr&#xe5;det/ ; 101044505/ERC_/European Research Council/International ; }, mesh = {*Eukaryota/genetics/classification ; *Computational Biology/methods ; *High-Throughput Nucleotide Sequencing/methods ; *rRNA Operon/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA/methods ; Phylogeny ; }, abstract = {The use of short-read metabarcoding for classifying microeukaryotes is challenged by the lack of comprehensive 18S rRNA reference databases. While recent advances in high-throughput long-read sequencing provide the potential to greatly increase the phylogenetic coverage of these databases, the performance of different sequencing technologies and subsequent bioinformatics processing remain to be evaluated, primarily because of the absence of well-defined eukaryotic mock communities. To address this challenge, we created a eukaryotic rRNA operon clone-library and turned it into a precisely defined synthetic eukaryotic mock community. This mock community was then used to evaluate the performance of three long-read sequencing strategies (PacBio circular consensus sequencing and two Nanopore approaches using unique molecular identifiers) and three tools for resolving amplicons sequence variants (ASVs) (USEARCH, VSEARCH, and DADA2). We investigated the sensitivity of the sequencing techniques based on the number of detected mock taxa, and the accuracy of the different ASV-calling tools with a specific focus on the presence of chimera among the final rRNA operon ASVs. Based on our findings, we provide recommendations and best practice protocols for how to cost-effectively obtain essentially error-free rRNA operons in high-throughput. An agricultural soil sample was used to demonstrate that the sequencing and bioinformatic results from the mock community also translates to highly diverse natural samples, which enables us to identify previously undescribed microeukaryotic lineages.}, }
@article {pmid38979368, year = {2025}, author = {Xiao, Y and Elmasry, M and Bai, JDK and Chen, A and Chen, Y and Jackson, B and Johnson, JO and Gillies, RJ and Prasanna, P and Chen, C and Damaghi, M}, title = {Eco-evolutionary Guided Pathomics Analysis to Predict DCIS Upstaging.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38979368}, issn = {2692-8205}, support = {P30 CA076292/CA/NCI NIH HHS/United States ; R01 CA249016/CA/NCI NIH HHS/United States ; R01 CA272601/CA/NCI NIH HHS/United States ; U01 CA261841/CA/NCI NIH HHS/United States ; }, abstract = {Cancers evolve in a dynamic ecosystem. Thus, characterizing cancer's ecological dynamics is crucial to understanding cancer evolution and can lead to discovering novel biomarkers to predict disease progression. Ductal carcinoma in situ (DCIS) is an early-stage breast cancer characterized by abnormal epithelial cell growth confined within the milk ducts. In this study, we show that ecological analysis of hypoxia and acidosis biomarkers can significantly improve prediction of DCIS upstaging. First, we developed a novel eco-evolutionary designed approach to define habitats in the tumor intraductal microenvironment based on oxygen diffusion distance. Then, we identified cancer cells with metabolic phenotypes attributed to their habitats, including CA9 for hypoxia responding phenotype, and LAMP2b for acid adapted phenotype. Traditionally these markers have shown limited predictive capabilities for DCIS progression, if any. However, when analyzed from an ecological perspective, their power to differentiate between non-upstaged and upstaged DCIS increased significantly. Second, we discovered distinct niches with spatial patterns of these biomarkers and used the distribution of such niches to predict patient upstaging. The niches were characterized by pattern analysis of both cellular and spatial features. With a 5-fold validation on the biopsy cohort, we trained a random forest classifier to achieve the area under curve (AUC) of 0.74. Our results affirm the importance of tumor ecological features in eco-evolutionary-designed approaches for novel biomarkers discovery.}, }
@article {pmid38977855, year = {2024}, author = {Sharaf, A and Nesengani, LT and Hayah, I and Kuja, JO and Mdyogolo, S and Omotoriogun, TC and Odogwu, BA and Beedessee, G and Smith, RM and Barakat, A and Moila, AM and El Hamouchi, A and Benkahla, A and Boukteb, A and Elmouhtadi, A and Mafwila, AL and Abushady, AM and Elsherif, AK and Ahmed, B and Wairuri, C and Ndiribe, CC and Ebuzome, C and Kinnear, CJ and Ndlovu, DF and Iraqi, D and El Fahime, E and Assefa, E and Ouardi, F and Belharfi, FZ and Tmimi, FZ and Markey, FB and Radouani, F and Zeukeng, F and Mvumbi, GL and Ganesan, H and Hanachi, M and Nigussie, H and Charoute, H and Benamri, I and Mkedder, I and Haddadi, I and Meftah-Kadmiri, I and Mubiru, JF and Domelevo Entfellner, JK and Rokani, JB and Ogwang, J and Daiga, JB and Omumbo, J and Ideozu, JE and Errafii, K and Labuschagne, K and Komi, KK and Tonfack, LB and Hadjeras, L and Ramantswana, M and Chaisi, M and Botes, MW and Kilian, M and Kvas, M and Melloul, M and Chaouch, M and Khyatti, M and Abdo, M and Phasha-Muchemenye, M and Hijri, M and Mediouni, MR and Hassan, MA and Piro, M and Mwale, M and Maaloum, M and Mavhunga, M and Olivier, NA and Aminou, O and Arbani, O and Souiai, O and Djocgoue, PF and Mentag, R and Zipfel, RD and Tata, RB and Megnekou, R and Muzemil, S and Paez, S and Salifu, SP and Kagame, SP and Selka, S and Edwards, S and Gaouar, SBS and Reda, SRA and Fellahi, S and Khayi, S and Ayed, S and Madisha, T and Sahil, T and Udensi, OU and Ras, V and Ezebuiro, V and Duru, VC and David, X and Geberemichael, Y and Tchiechoua, YH and Mungloo-Dilmohamud, Z and Chen, Z and Happi, C and Kariuki, T and Ziyomo, C and Djikeng, A and Badaoui, B and Mapholi, N and Muigai, A and Osuji, JO and Ebenezer, TE}, title = {Establishing African genomics and bioinformatics programs through annual regional workshops.}, journal = {Nature genetics}, volume = {56}, number = {8}, pages = {1556-1565}, pmid = {38977855}, issn = {1546-1718}, mesh = {*Genomics/education ; *Computational Biology/methods/education ; Africa ; Humans ; Biodiversity ; }, abstract = {The African BioGenome Project (AfricaBP) Open Institute for Genomics and Bioinformatics aims to overcome barriers to capacity building through its distributed African regional workshops and prioritizes the exchange of grassroots knowledge and innovation in biodiversity genomics and bioinformatics. In 2023, we implemented 28 workshops on biodiversity genomics and bioinformatics, covering 11 African countries across the 5 African geographical regions. These regional workshops trained 408 African scientists in hands-on molecular biology, genomics and bioinformatics techniques as well as the ethical, legal and social issues associated with acquiring genetic resources. Here, we discuss the implementation of transformative strategies, such as expanding the regional workshop model of AfricaBP to involve multiple countries, institutions and partners, including the proposed creation of an African digital database with sequence information relating to both biodiversity and agriculture. This will ultimately help create a critical mass of skilled genomics and bioinformatics scientists across Africa.}, }
@article {pmid38976642, year = {2024}, author = {Pisarenco, VA and Vizueta, J and Rozas, J}, title = {GALEON: a comprehensive bioinformatic tool to analyse and visualize gene clusters in complete genomes.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {7}, pages = {}, pmid = {38976642}, issn = {1367-4811}, support = {MCIN/AEI/10.13039/501100011033//Ministerio de Ciencia e Innovaci&#xf3;n of Spain/ ; }, mesh = {*Multigene Family ; *Software ; *Computational Biology/methods ; Genome ; Genomics/methods ; Evolution, Molecular ; Humans ; }, abstract = {MOTIVATION: Gene clusters, defined as a set of genes encoding functionally related proteins, are abundant in eukaryotic genomes. Despite the increasing availability of chromosome-level genomes, the comprehensive analysis of gene family evolution remains largely unexplored, particularly for large and highly dynamic gene families or those including very recent family members. These challenges stem from limitations in genome assembly contiguity, particularly in repetitive regions such as large gene clusters. Recent advancements in sequencing technology, such as long reads and chromatin contact mapping, hold promise in addressing these challenges.<br><br>RESULTS: To facilitate the identification, analysis, and visualization of physically clustered gene family members within chromosome-level genomes, we introduce GALEON, a user-friendly bioinformatic tool. GALEON identifies gene clusters by studying the spatial distribution of pairwise physical distances among gene family members along with the genome-wide gene density. The pipeline also enables the simultaneous analysis and comparison of two gene families and allows the exploration of the relationship between physical and evolutionary distances. This tool offers a novel approach for studying the origin and evolution of gene families.<br><br>GALEON is freely available from https://www.ub.edu/softevol/galeon and https://github.com/molevol-ub/galeon.}, }
@article {pmid38974014, year = {2024}, author = {Cassee, FR and Bleeker, EAJ and Durand, C and Exner, T and Falk, A and Friedrichs, S and Heunisch, E and Himly, M and Hofer, S and Hofstätter, N and Hristozov, D and Nymark, P and Pohl, A and Soeteman-Hernández, LG and Suarez-Merino, B and Valsami-Jones, E and Groenewold, M}, title = {Roadmap towards safe and sustainable advanced and innovative materials. (Outlook for 2024-2030).}, journal = {Computational and structural biotechnology journal}, volume = {25}, number = {}, pages = {105-126}, pmid = {38974014}, issn = {2001-0370}, abstract = {The adoption of innovative advanced materials holds vast potential, contingent upon addressing safety and sustainability concerns. The European Commission advocates the integration of Safe and Sustainable by Design (SSbD) principles early in the innovation process to streamline market introduction and mitigate costs. Within this framework, encompassing ecological, social, and economic factors is paramount. The NanoSafety Cluster (NSC) delineates key safety and sustainability areas, pinpointing unresolved issues and research gaps to steer the development of safe(r) materials. Leveraging FAIR data management and integration, alongside the alignment of regulatory aspects, fosters informed decision-making and innovation. Integrating circularity and sustainability mandates clear guidance, ensuring responsible innovation at every stage. Collaboration among stakeholders, anticipation of regulatory demands, and a commitment to sustainability are pivotal for translating SSbD into tangible advancements. Harmonizing standards and test guidelines, along with regulatory preparedness through an exchange platform, is imperative for governance and market readiness. By adhering to these principles, the effective and sustainable deployment of innovative materials can be realized, propelling positive transformation and societal acceptance.}, }
@article {pmid38973368, year = {2024}, author = {Martínez, L and Zattara, EE and Arbetman, MP and Morales, CL and Masonbrink, RE and Severin, AJ and Aizen, MA and Toth, AL}, title = {Chromosome-Level Assembly and Annotation of the Genome of the Endangered Giant Patagonian Bumble Bee Bombus dahlbomii.}, journal = {Genome biology and evolution}, volume = {16}, number = {7}, pages = {}, pmid = {38973368}, issn = {1759-6653}, support = {//Fulbright Science and Technology Award, Argentina Commission/ ; //Iowa State University Faculty Professional Development Leave/ ; NGS-57001R-19//National Geographic Society/ ; }, mesh = {Animals ; Bees/genetics ; *Endangered Species ; *Molecular Sequence Annotation ; *Genome, Insect ; Male ; Chromosomes, Insect/genetics ; }, abstract = {This article describes a genome assembly and annotation for Bombus dahlbomii, the giant Patagonian bumble bee. DNA from a single, haploid male collected in Argentina was used for PacBio (HiFi) sequencing, and Hi-C technology was then used to map chromatin contacts. Using Juicer and manual curation, the genome was scaffolded into 18 main pseudomolecules, representing a high-quality, near chromosome-level assembly. The sequenced genome size is estimated at 265 Mb. The genome was annotated based on RNA sequencing data of another male from Argentina, and BRAKER3 produced 15,767 annotated genes. The genome and annotation show high completeness, with >95% BUSCO scores for both the genome and annotated genes (based on conserved genes from Hymenoptera). This genome provides a valuable resource for studying the biology of this iconic and endangered species, as well as for understanding the impacts of its decline and designing strategies for its preservation.}, }
@article {pmid38972117, year = {2024}, author = {Hyman, S and Zhang, J and Lim, YH and Jovanovic Andersen, Z and Cole-Hunter, T and Li, Y and Møller, P and Daras, K and Williams, R and Thomas, ML and Labib, SM and Topping, D}, title = {Residential greenspace and COVID-19 Severity: A cohort study of 313,657 individuals in Greater Manchester, United Kingdom.}, journal = {Environment international}, volume = {190}, number = {}, pages = {108843}, doi = {10.1016/j.envint.2024.108843}, pmid = {38972117}, issn = {1873-6750}, mesh = {*COVID-19/epidemiology/mortality ; Humans ; Male ; Female ; Middle Aged ; Aged ; United Kingdom/epidemiology ; Retrospective Studies ; *Air Pollution/statistics &amp; numerical data ; *Hospitalization/statistics &amp; numerical data ; SARS-CoV-2 ; Adult ; Cohort Studies ; Severity of Illness Index ; Aged, 80 and over ; }, abstract = {BACKGROUND: Greenspaces contribute positively to mental and physical well-being, promote social cohesion, and alleviate environmental stressors, such as air pollution. Ecological studies suggest that greenspace may affect incidence and severity of Coronavirus Disease 2019 (COVID-19).<br><br>OBJECTIVE: This study examines the association between residential greenspace and COVID-19 related hospitalization and death.<br><br>METHOD: In this retrospective cohort based on patient records from the Greater Manchester Care Records, all first COVID-19 cases diagnosed between March 1, 2020, and May 31, 2022 were followed until COVID-19 related hospitalization or death within 28&#xa0;days. Residential greenspace availability was assessed using the Normalized Difference Vegetation Index per lower super output area in Greater Manchester. The association of greenspace with COVID-19 hospitalization and mortality were estimated using multivariate logistic regression models after adjusting for potential individual, temporal, and spatial confounders. We explored potential effect modifications of the associations with greenspace and COVID-19 severity by age, sex, body mass index, smoking, deprivation, and certain comorbidities. Combined effects of greenspace and air pollution (NO2 and PM2.5) were investigated by mutually adjusting pairs with correlation coefficients&#xa0;&#x2264;&#xa0;0&#xb7;7.<br><br>RESULTS: Significant negative associations were observed between greenspace availability and COVID-19 hospitalization and mortality with odds ratios [OR] (95&#xa0;% Confidence Intervals [CI]) of 0&#xb7;96 (0&#xb7;94-0&#xb7;97) and 0&#xb7;84 (0&#xb7;80-0&#xb7;88) (per interquartile range [IQR]), respectively. These were significantly modified by deprivation (P-value for interaction&#xa0;<&#xa0;0.05), showing that those most deprived obtained largest benefits from greenspace. Inclusion of NO2 and PM2.5 diminished associations to null for COVID-19 hospitalization, but only reduced them slightly for mortality, where inverse associations remained.<br><br>CONCLUSION: In the Greater Manchester area, residential greenspace is associated with reduced risk of hospitalization or death in individuals with COVID-19, with deprived groups obtaining the greatest benefits. Associations were strongest for COVID-19 mortality, which were robust to inclusion of air pollutants in the models.}, }
@article {pmid38972039, year = {2024}, author = {Nurkolis, F and Wiyarta, E and Taslim, NA and Kurniawan, R and Thibault, R and Fernandez, ML and Yang, Y and Han, J and Tsopmo, A and Mayulu, N and Tjandrawinata, RR and Tallei, TE and Hardinsyah, H}, title = {Unraveling diabetes complexity through natural products, miRNAs modulation, and future paradigms in precision medicine and global health.}, journal = {Clinical nutrition ESPEN}, volume = {63}, number = {}, pages = {283-293}, doi = {10.1016/j.clnesp.2024.06.043}, pmid = {38972039}, issn = {2405-4577}, mesh = {Humans ; *Precision Medicine ; *MicroRNAs/genetics ; *Diabetes Mellitus/therapy/genetics ; *Biological Products/therapeutic use ; *Global Health ; Metabolomics ; Computational Biology ; Biomarkers/blood ; Genomics ; }, abstract = {BACKGROUND AND AIMS: The challenge posed by diabetes necessitates a paradigm shift from conventional diagnostic approaches focusing on glucose and lipid levels to the transformative realm of precision medicine. This approach, leveraging advancements in genomics and proteomics, acknowledges the individualistic genetic variations, dietary preferences, and environmental exposures in diabetes management. The study comprehensively analyzes the evolving diabetes landscape, emphasizing the pivotal role of genomics, proteomics, microRNAs (miRNAs), metabolomics, and bioinformatics.<br><br>RESULTS: Precision medicine revolutionizes diabetes research and treatment by diverging from traditional diagnostic methods, recognizing the heterogeneous nature of the condition. MiRNAs, crucial post-transcriptional gene regulators, emerge as promising therapeutic targets, influencing key facets such as insulin signaling and glucose homeostasis. Metabolomics, an integral component of omics sciences, contributes significantly to diabetes research, elucidating metabolic disruptions, and offering potential biomarkers for early diagnosis and personalized therapies. Bioinformatics unveils dynamic connections between natural substances, miRNAs, and cellular pathways, aiding in the exploration of the intricate molecular terrain in diabetes. The study underscores the imperative for experimental validation in natural product-based diabetes therapy, emphasizing the need for in&#xa0;vitro and in&#xa0;vivo studies leading to clinical trials for assessing effectiveness, safety, and tolerability in real-world applications. Global cooperation and ethical considerations play a pivotal role in addressing diabetes challenges worldwide, necessitating a multifaceted approach that integrates traditional knowledge, cultural competence, and environmental awareness.<br><br>CONCLUSIONS: The key components of diabetes treatment, including precision medicine, metabolomics, bioinformatics, and experimental validation, converge in future strategies, embodying a holistic paradigm for diabetes care anchored in cutting-edge research and global healthcare accessibility.}, }
@article {pmid38971026, year = {2024}, author = {Ou, X and Chen, J and Li, B and Yang, Y and Liu, X and Xu, Z and Xiang, X and Wang, Q}, title = {Multiomics reveals the ameliorating effect and underlying mechanism of aqueous extracts of polygonatum sibiricum rhizome on obesity and liver fat accumulation in high-fat diet-fed mice.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {132}, number = {}, pages = {155843}, doi = {10.1016/j.phymed.2024.155843}, pmid = {38971026}, issn = {1618-095X}, mesh = {Animals ; Male ; Mice ; Akkermansia ; Diet, High-Fat/adverse effects ; Gastrointestinal Microbiome/drug effects ; Lipid Metabolism/drug effects ; *Liver/drug effects/metabolism ; Mice, Inbred C57BL ; Multiomics ; *Non-alcoholic Fatty Liver Disease/drug therapy ; *Obesity/drug therapy/etiology ; Orlistat/pharmacology ; *Plant Extracts/pharmacology ; *Polygonatum/chemistry ; Rhizome/chemistry ; Disease Models, Animal ; }, abstract = {BACKGROUND: Polygonatum sibiricum polysaccharides protect against obesity and NAFLD. However, the potential effects of PS rhizome aqueous extracts (PSRwe) on adiposity and hepatic lipid accumulation remains unexplored.<br><br>PURPOSE: Elucidating the impact and underlying mechanism of PSRwe on HFD-induced obesity and liver fat depostition.<br><br>STUDY DESIGN: 56 male mice, aged eight weeks, were divided into seven groups: Positive, four doses of PSRwe, Model, and Control. HFD was fed for eight weeks, followed by alternate-day gavage of orlistat and PSRwe for an additional eight-week period. Integrative analysis encompassing multiomics, physiological and histopathological, and biochemical indexes was employed.<br><br>METHODS: Body weight (BW); liver, fat and Lee's indexes; TC, TG, LDL-C, HDL-C, AST, ALT, FFA, leptin, and adiponectin in the liver and blood; TNF&#x3b1;, IL-6, and LPS in the colon, plasma, and liver; H&amp;E, PAS and oil red O staining on adipose and liver samples were examined. OGTT and ITT were conducted The gut microbiome, microbial metabolome, colonic and liver transcriptome, plasma and liver metabolites were investigated.<br><br>RESULTS: PSRwe at the dosage of 7.5 mg/kg demonstrated significant and consistent reduction in BW and hepatic fat deposition than orlistat. PSRwe significantly decreased TC, TG, LDL-C, LEP, FFA levels in blood and liver. PSRwe significantly enhanced the relative abundance of probiotics including Akkermansia muciniphila, Bifidobacterium pseudolongum, Lactobacillus reuteri, and metabolic pathways including glycolysis and fatty acids &#x3b2;-oxidation. The 70 up-regulated microbial metabolites in PSRwe-treated mice mainly involved in nucleotides and amino acids metabolism, while 40 decreased metabolites primarily associated with lipid metabolism. The up-regulated colonic differentially expressed genes (DEGs) participate in JAK-STAT/PI3K-Akt/FoxO signaling pathway, serotonergic/cholinergic/glutamatergic synapses, while the down-regulated DEGs predominantly focused on fat absorption and transport. The up-regulated liver DEGs mainly concentrated on fatty acid oxidation and metabolism. Liver metabolisms revealed 131 differential metabolites, among which carnitine and oxidized lipids significantly increased in PSRwe-treated mice. In plasma, the 58 up-regulated metabolites mainly participate in co-factors/vitamins metabolism while 154 down-regulated ones in fatty acids biosynthesis. Comprehensive multiomics association analysis revealed significant associations between gut microbiota and colonic/liver gene expression, and suggested exogenous and endogenous betaine may be active compound in alleviating HFD-induced symptoms.<br><br>CONCLUSION: PSRwe effectively mitigate HFD-induced obesity and hepatic steatosis by increasing beneficial bacteria, reducing colonic fat digestion/absorption, increasing hepatic lipid metabolism, and elevating betaine levels.}, }
@article {pmid38970356, year = {2024}, author = {Chan, KO}, title = {Next-generation bioinformatics: An ultrafast and user-friendly tool for phylogenomic data exploration.}, journal = {Molecular ecology resources}, volume = {24}, number = {7}, pages = {e13993}, doi = {10.1111/1755-0998.13993}, pmid = {38970356}, issn = {1755-0998}, mesh = {*Computational Biology/methods ; *Software ; *Phylogeny ; Genomics/methods ; User-Computer Interface ; }, abstract = {With increasingly large genomic datasets, even routine bioinformatic tasks can be arduous, computationally demanding, and time-consuming. Additionally, most bioinformatic programs do not have a graphical user interface (GUI) and thus, require users to be minimally competent in command-line. These impediments present significant economic and technological barriers for practitioners who do not have access to advanced computational resources and support. In this issue of Molecular Ecology Resources, Handika and Esselstyn (2024) developed an ultrafast and memory-efficient bioinformatic tool, SEGUL, that performs common manipulations and calculations of summary statistics on phylogenomic datasets. SEGUL has two main features that distinguish it from other bioinformatic programs: (1) it is based on the recently emergent, high-performance programming language Rust, and (2) it has a GUI written using Flutter, a cross-platform programming framework that also supports mobile operating systems (mobile iOS, iPadOS and Android). By leveraging and combining the power of Rust and Flutter, SEGUL achieves significantly faster computation times and lower memory usage across different platforms and CPU architectures compared to similar programs. The unique and innovative features of SEGUL pave the way for a new era of bioinformatics that can be more energy-efficient, inclusive, and available to a broader swathe of users.}, }
@article {pmid38968897, year = {2024}, author = {Zhu, Y and Chen, F and Jiang, F and Hua, Z and Luo, Z and Ma, J}, title = {Enhanced remediation of PFAS-metal co-contaminated soil by ceramsite supported Fe3O4-MoS2 heterojunction as a high-performance piezocatalyst.}, journal = {Journal of environmental management}, volume = {365}, number = {}, pages = {121716}, doi = {10.1016/j.jenvman.2024.121716}, pmid = {38968897}, issn = {1095-8630}, mesh = {*Soil Pollutants/chemistry/metabolism ; *Soil/chemistry ; *Metals, Heavy/chemistry ; Environmental Restoration and Remediation/methods ; Biodegradation, Environmental ; }, abstract = {In this study, a novel piezoremediation system was developed to remediate an actual soil co-polluted by high contents of per- and polyfluoroalkyl substances (PFAS, 5725 μg/kg soil) and heavy metals (6455 mg/kg soil). Two piezocatalysts, MoS2/ceramsite (MC) and Fe3O4-MoS2/ceramsite (FMC), were synthesized using a facile hydrothermal-coprecipitation method. These two materials were employed to treat the co-contaminated soil in soil slurry environment under sonication. FMC exhibited significantly higher piezoremediation performance than MC, wherein 91.6% of PFAS, 97.8% of Cr[6+] ions and 81% of total metals (Cr, Cu, Zn and Ni) were removed from the soil after 50 min of the FMC piezoremediation process. FMC also exhibited the advantages of easy separation from the slurry phase and excellent reusability. In comparison with MC, the Fe3O4-MoS2 heterojunction in FMC can stabilize MoS2 particles on the surface of ceramsite granules, promote the separation of electron/hole pairs, accelerate charge transfer, therefore enhancing piezocatalytic performance. The electron spin resonance analysis and free radical quenching tests show that [•]OH was the dominant oxidative radical responsible for PFAS degradation. The count of bacteria and the bacterial community structure in the treated soil can be basically restored to the initial states after 30 days of incubation under nutrient stimulation. Overall, this study not only provides a deep insight on soil remediation process, but also offers an efficient and reliable technique for simultaneous decontamination of organic and metal pollutants in soil.}, }
@article {pmid38968305, year = {2024}, author = {Fu, X and Withers, J and Miyamae, JA and Moore, TY}, title = {ArborSim: Articulated, branching, OpenSim routing for constructing models of multi-jointed appendages with complex muscle-tendon architecture.}, journal = {PLoS computational biology}, volume = {20}, number = {7}, pages = {e1012243}, pmid = {38968305}, issn = {1553-7358}, mesh = {*Tendons/physiology/anatomy &amp; histology ; Humans ; Biomechanical Phenomena ; *Software ; *Joints/physiology/anatomy &amp; histology ; *Muscle, Skeletal/physiology/anatomy &amp; histology ; Models, Biological ; Computational Biology ; Computer Simulation ; Animals ; }, abstract = {Computational models of musculoskeletal systems are essential tools for understanding how muscles, tendons, bones, and actuation signals generate motion. In particular, the OpenSim family of models has facilitated a wide range of studies on diverse human motions, clinical studies of gait, and even non-human locomotion. However, biological structures with many joints, such as fingers, necks, tails, and spines, have been a longstanding challenge to the OpenSim modeling community, especially because these structures comprise numerous bones and are frequently actuated by extrinsic muscles that span multiple joints-often more than three-and act through a complex network of branching tendons. Existing model building software, typically optimized for limb structures, makes it difficult to build OpenSim models that accurately reflect these intricacies. Here, we introduce ArborSim, customized software that efficiently creates musculoskeletal models of highly jointed structures and can build branched muscle-tendon architectures. We used ArborSim to construct toy models of articulated structures to determine which morphological features make a structure most sensitive to branching. By comparing the joint kinematics of models constructed with branched and parallel muscle-tendon units, we found that among various parameters-the number of tendon branches, the number of joints between branches, and the ratio of muscle fiber length to muscle tendon unit length-the number of tendon branches and the number of joints between branches are most sensitive to branching modeling method. Notably, the differences between these models showed no predictable pattern with increased complexity. As the proportion of muscle increased, the kinematic differences between branched and parallel models units also increased. Our findings suggest that stress and strain interactions between distal tendon branches and proximal tendon and muscle greatly affect the overall kinematics of a musculoskeletal system. By incorporating complex muscle-tendon branching into OpenSim models using ArborSim, we can gain deeper insight into the interactions between the axial and appendicular skeleton, model the evolution and function of diverse animal tails, and understand the mechanics of more complex motions and tasks.}, }
@article {pmid38968199, year = {2024}, author = {Stratton, CA and Thompson, Y and Zio, K and Morrison, WR and Murrell, EG}, title = {uafR: An R package that automates mass spectrometry data processing.}, journal = {PloS one}, volume = {19}, number = {7}, pages = {e0306202}, pmid = {38968199}, issn = {1932-6203}, support = {U54 MD015959/MD/NIMHD NIH HHS/United States ; }, mesh = {*Gas Chromatography-Mass Spectrometry/methods ; *Algorithms ; *Software ; Cheminformatics/methods ; }, abstract = {Chemical information has become increasingly ubiquitous and has outstripped the pace of analysis and interpretation. We have developed an R package, uafR, that automates a grueling retrieval process for gas -chromatography coupled mass spectrometry (GC -MS) data and allows anyone interested in chemical comparisons to quickly perform advanced structural similarity matches. Our streamlined cheminformatics workflows allow anyone with basic experience in R to pull out component areas for tentative compound identifications using the best published understanding of molecules across samples (pubchem.gov). Interpretations can now be done at a fraction of the time, cost, and effort it would typically take using a standard chemical ecology data analysis pipeline. The package was tested in two experimental contexts: (1) A dataset of purified internal standards, which showed our algorithms correctly identified the known compounds with R2 values ranging from 0.827-0.999 along concentrations ranging from 1 × 10-5 to 1 × 103 ng/μl, (2) A large, previously published dataset, where the number and types of compounds identified were comparable (or identical) to those identified with the traditional manual peak annotation process, and NMDS analysis of the compounds produced the same pattern of significance as in the original study. Both the speed and accuracy of GC -MS data processing are drastically improved with uafR because it allows users to fluidly interact with their experiment following tentative library identifications [i.e. after the m/z spectra have been matched against an installed chemical fragmentation database (e.g. NIST)]. Use of uafR will allow larger datasets to be collected and systematically interpreted quickly. Furthermore, the functions of uafR could allow backlogs of previously collected and annotated data to be processed by new personnel or students as they are being trained. This is critical as we enter the era of exposomics, metabolomics, volatilomes, and landscape level, high-throughput chemotyping. This package was developed to advance collective understanding of chemical data and is applicable to any research that benefits from GC -MS analysis. It can be downloaded for free along with sample datasets from Github at github.org/castratton/uafR or installed directly from R or RStudio using the developer tools: 'devtools::install_github("castratton/uafR")'.}, }
@article {pmid38967613, year = {2024}, author = {Hanners, A and Melnyk, B and Bedell, T and Conroy, S and Volek, J and Brock, G and Kelley, M}, title = {A pilot study of Keto Prescribed+: A healthy thinking and eating educational program for African American women.}, journal = {Journal of the American Association of Nurse Practitioners}, volume = {36}, number = {7}, pages = {377-384}, pmid = {38967613}, issn = {2327-6924}, support = {L30 HL159699/HL/NHLBI NIH HHS/United States ; UL1TR002733//Center for Clinical and Translational Science, Ohio State University/ ; TL1TR002735//Center for Clinical and Translational Science, Ohio State University/ ; }, mesh = {Adult ; Female ; Humans ; Middle Aged ; *Black or African American/psychology/statistics &amp; numerical data ; Pilot Projects ; Patient Education as Topic ; *Health Promotion ; Healthy Lifestyle ; }, abstract = {African American (AA) women have the highest prevalence of obesity in addition to health disparities in preventable diet-related diseases (i.e., diabetes, hypertension), which places them at increased risk for cardiovascular disease. The purpose of this pilot study was to assess the feasibility, acceptability, and preliminary effectiveness of the Keto Prescribed+ (KetoRx+) program on associated physical and psychosocial outcomes among this population. The KetoRx+ program is a healthy eating and thinking educational intervention. The program combined online and in-person community group sessions over 8 weeks. The Keto Prescribed+ was found to be feasible and acceptable with comments on ways to increase acceptability from participants completing program (n = 10). Physical outcomes changed showed an average decrease in weight of 10lbs (SD = 5), baseline average 226lbs. Waist-to-hip ratio and systolic blood pressure also trended down. Psychosocial outcomes showed improvement trends. The KetoRx+ program is feasible and acceptable for overweight or obese AA women. Preliminary efficacy was established for most physical and psychosocial outcomes. However, more research is needed to identify specific program components contributing to healthy lifestyle behavior change and to establish program efficacy and effectiveness. Culturally adapted community-based biopsychosocial interventions using ketogenic nutrition therapy may help improve cardiovascular health of adult AA women.}, }
@article {pmid38966305, year = {2024}, author = {Crowley, LM and Roy, HE and Brown, PMJ and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the ten-spot ladybird, Adalia decempunctata (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {106}, pmid = {38966305}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Adalia decempunctata (the ten-spot ladybird; Arthropoda; Insecta; Coleoptera; Coccinellidae). The genome sequence is 489.4 megabases in span. Most of the assembly is scaffolded into 12 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 19.68 kilobases in length.}, }
@article {pmid38964062, year = {2024}, author = {Jeon, Y and Kwon, YS and Noh, YJ and Lee, SM and Song, JW and Kim, JH and Seo, JS}, title = {Unraveling the mechanisms of benzo[a]pyrene degradation by Pigmentiphaga kullae strain KIT-003 using a multi-omics approach.}, journal = {Ecotoxicology and environmental safety}, volume = {281}, number = {}, pages = {116665}, doi = {10.1016/j.ecoenv.2024.116665}, pmid = {38964062}, issn = {1090-2414}, mesh = {*Benzo(a)pyrene/metabolism/toxicity ; *Biodegradation, Environmental ; Republic of Korea ; Proteomics ; Water Pollutants, Chemical/metabolism/toxicity ; Gas Chromatography-Mass Spectrometry ; Catechols/metabolism ; Rivers/chemistry/microbiology ; Multiomics ; }, abstract = {Polycyclic aromatic hydrocarbons (PAHs), notably benzo[a]pyrene (BaP), are environmental contaminants with multiple adverse ecological implications. Numerous studies have suggested the use of BaP biodegradation using various bacterial strains to remove BaP from the environment. This study investigates the BaP biodegradation capability of Pigmentiphaga kullae strain KIT-003, isolated from the Nak-dong River (South Korea) under specific environmental conditions. The optimum conditions of biodegradation were found to be pH 7.0, 35°C, and a salinity of 0 %. GC-MS analysis suggested alternative pathways by which KIT-003 produced catechol from BaP through several intermediate metabolites, including 4-formylchrysene-5-carboxylic acid, 5,6-dihydro-5,6-dihydroxychrysene-5-carboxylic acid (isomer: 3,4-dihydro-3,4-dihydroxychrysene-4-carboxylic acid), naphthalene-1,2-dicarboxylic acid, and 2-hydroxy-1-naphthoic acid. Proteomic profiles indicated upregulation of enzymes associated with aromatic compound degradation, such as nahAc and nahB, and of those integral to the tricarboxylic acid cycle, reflecting the strain's adaptability to and degradation of BaP. Lipidomic analysis of KIT-003 demonstrated that BaP exposure induced an accumulation of glycerolipids such as diacylglycerol and triacylglycerol, indicating their crucial role in bacterial adaptation mechanisms under BaP stress. This study provides significant scientific knowledge regarding the intricate mechanisms involved in BaP degradation by microorganisms.}, }
@article {pmid38961615, year = {2024}, author = {Papageorgiou, D and Cherono, W and Gall, G and Nyaguthii, B and Farine, DR}, title = {Testing the information centre hypothesis in a multilevel society.}, journal = {The Journal of animal ecology}, volume = {93}, number = {8}, pages = {1147-1159}, doi = {10.1111/1365-2656.14131}, pmid = {38961615}, issn = {1365-2656}, support = {//Max Planck Society/ ; //Wissenschaftskolleg zu Berlin/ ; 422037984//Deutsche Forschungsgemeinschaft/ ; //Deutscher Akademischer Austauschdienst/ ; WW-175ER-17//National Geographic Society/ ; PCEFP3_187058/SNSF_/Swiss National Science Foundation/Switzerland ; 850859/ERC_/European Research Council/International ; }, mesh = {Animals ; *Social Behavior ; *Galliformes/physiology ; Geographic Information Systems ; Female ; Male ; }, abstract = {In various animal species conspecifics aggregate at sleeping sites. Such aggregations can act as information centres where individuals acquire up-to-date knowledge about their environment. In some species, communal sleeping sites comprise individuals from multiple groups, where each group maintains stable membership over time. We used GPS tracking to simultaneously record group movement in a population of wild vulturine guineafowl (Acryllium vulturinum) to investigate whether communal sleeping sites can facilitate the transfer of information among individuals across distinct groups. These birds live in large and stable groups that move both together and apart, often forming communal roosts containing up to five groups. We first test whether roosts provide the opportunity for individuals to acquire information from members of other groups by examining the spatial organization at roosts. The GPS data reveal that groups intermix, thereby providing an opportunity for individuals to acquire out-group information. We next conduct a field experiment to test whether naïve groups can locate novel food patches when co-roosting with knowledgeable groups. We find that co-roosting substantially increases the chances for the members of a naïve group to discover a patch known to individuals from other groups at the shared roost. Further, we find that the discovery of food patches by naïve groups subsequently shapes their space use and inter-group associations. We also draw on our long-term tracking to provide examples that demonstrate natural cases where communal roosting has preceded large-scale multi-group collective movements that extend into areas beyond the groups' normal ranges. Our findings support the extension of the information centre hypothesis to communal sleeping sites that consist of distinct social groups.}, }
@article {pmid38960861, year = {2024}, author = {Dolenz, S and van der Valk, T and Jin, C and Oppenheimer, J and Sharif, MB and Orlando, L and Shapiro, B and Dalén, L and Heintzman, PD}, title = {Unravelling reference bias in ancient DNA datasets.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {7}, pages = {}, pmid = {38960861}, issn = {1367-4811}, support = {2021.0048//Knut and Alice Wallenberg Foundation/ ; }, mesh = {*DNA, Ancient/analysis ; Humans ; *Sequence Analysis, DNA/methods ; Software ; Animals ; Sequence Alignment/methods ; Computational Biology/methods ; Algorithms ; }, abstract = {MOTIVATION: The alignment of sequencing reads is a critical step in the characterization of ancient genomes. However, reference bias and spurious mappings pose a significant challenge, particularly as cutting-edge wet lab methods generate datasets that push the boundaries of alignment tools. Reference bias occurs when reference alleles are favoured over alternative alleles during mapping, whereas spurious mappings stem from either contamination or when endogenous reads fail to align to their correct position. Previous work has shown that these phenomena are correlated with read length but a more thorough investigation of reference bias and spurious mappings for ancient DNA has been lacking. Here, we use a range of empirical and simulated palaeogenomic datasets to investigate the impacts of mapping tools, quality thresholds, and reference genome on mismatch rates across read lengths.<br><br>RESULTS: For these analyses, we introduce AMBER, a new bioinformatics tool for assessing the quality of ancient DNA mapping directly from BAM-files and informing on reference bias, read length cut-offs and reference selection. AMBER rapidly and simultaneously computes the sequence read mapping bias in the form of the mismatch rates per read length, cytosine deamination profiles at both CpG and non-CpG sites, fragment length distributions, and genomic breadth and depth of coverage. Using AMBER, we find that mapping algorithms and quality threshold choices dictate reference bias and rates of spurious alignment at different read lengths in a predictable manner, suggesting that optimized mapping parameters for each read length will be a key step in alleviating reference bias and spurious mappings.<br><br>AMBER is available for noncommercial use on GitHub (https://github.com/tvandervalk/AMBER.git). Scripts used to generate and analyse simulated datasets are available on Github (https://github.com/sdolenz/refbias_scripts).}, }
@article {pmid38959816, year = {2024}, author = {Zhang, Y and Li, D and Li, X and Zhou, X and Newman, G}, title = {The integration of geographic methods and ecological momentary assessment in public health research: A systematic review of methods and applications.}, journal = {Social science &amp; medicine (1982)}, volume = {354}, number = {}, pages = {117075}, pmid = {38959816}, issn = {1873-5347}, support = {P42 ES027704/ES/NIEHS NIH HHS/United States ; R01 MD016587/MD/NIMHD NIH HHS/United States ; }, mesh = {Humans ; *Ecological Momentary Assessment ; *Geographic Information Systems ; *Public Health/methods ; }, abstract = {With the widespread prevalence of mobile devices, ecological momentary assessment (EMA) can be combined with geospatial data acquired through geographic techniques like global positioning system (GPS) and geographic information system. This technique enables the consideration of individuals' health and behavior outcomes of momentary exposures in spatial contexts, mostly referred to as "geographic ecological momentary assessment" or "geographically explicit EMA" (GEMA). However, the definition, scope, methods, and applications of GEMA remain unclear and unconsolidated. To fill this research gap, we conducted a systematic review to synthesize the methodological insights, identify common research interests and applications, and furnish recommendations for future GEMA studies. We followed the Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines to systematically search peer-reviewed studies from six electronic databases in 2022. Screening and eligibility were conducted following inclusion criteria. The risk of bias assessment was performed, and narrative synthesis was presented for all studies. From the initial search of 957 publications, we identified 47 articles included in the review. In public health, GEMA was utilized to measure various outcomes, such as psychological health, physical and physiological health, substance use, social behavior, and physical activity. GEMA serves multiple research purposes: 1) enabling location-based EMA sampling, 2) quantifying participants' mobility patterns, 3) deriving exposure variables, 4) describing spatial patterns of outcome variables, and 5) performing data linkage or triangulation. GEMA has advanced traditional EMA sampling strategies and enabled location-based sampling by detecting location changes and specified geofences. Furthermore, advances in mobile technology have prompted considerations of additional sensor-based data in GEMA. Our results highlight the efficacy and feasibility of GEMA in public health research. Finally, we discuss sampling strategy, data privacy and confidentiality, measurement validity, mobile applications and technologies, and GPS accuracy and missing data in the context of current and future public health research that uses GEMA.}, }
@article {pmid38956468, year = {2024}, author = {Li, X and Cao, T and Liu, H and Fu, L and Wang, Q}, title = {Identification and expression analysis of Sox family genes in echinoderms.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {655}, pmid = {38956468}, issn = {1471-2164}, support = {ZR2021QD158//Natural Science Foundation of Shandong Province, China/ ; ZR2021MC151//Natural Science Foundation of Shandong Province, China/ ; 2023XBZD003//Scientific Research Project of Yantai Vocational College/ ; }, mesh = {Animals ; *SOX Transcription Factors/genetics/metabolism ; *Phylogeny ; *Echinodermata/genetics ; *Multigene Family ; Gene Expression Profiling ; Evolution, Molecular ; Gene Expression Regulation, Developmental ; Computational Biology/methods ; }, abstract = {The Sox gene family, a collection of transcription factors widely distributed throughout the animal kingdom, plays a crucial role in numerous developmental processes. Echinoderms occupy a pivotal position in many research fields, such as neuroscience, sex determination and differentiation, and embryonic development. However, to date, no comprehensive study has been conducted to characterize and analyze Sox genes in echinoderms. In the present study, the evolution and expression of Sox family genes across 11 echinoderms were analyzed using bioinformatics methods. The results revealed a total of 70 Sox genes, with counts ranging from 5 to 8 across different echinoderms. Phylogenetic analysis revealed that the identified Sox genes could be categorized into seven distinct classes: the SoxB1 class, SoxB2 class, SoxC class, SoxD class, SoxE class, SoxF class and SoxH class. Notably, the SoxB1, SoxB2, and SoxF genes were ubiquitously present in all the echinoderms studied, which suggests that these genes may be conserved in echinoderms. The spatiotemporal expression patterns observed for Sox genes in the three echinoderms indicated that various Sox members perform distinct functional roles. Notably, SoxB1 is likely involved in echinoderm ovary development, while SoxH may play a crucial role in testis development in starfish and sea cucumber. In general, the present investigation provides a molecular foundation for exploring the Sox gene in echinoderms, providing a valuable resource for future phylogenetic and genomic studies.}, }
@article {pmid38955825, year = {2024}, author = {Pan, H and Wattiez, R and Gillan, D}, title = {Soil Metaproteomics for Microbial Community Profiling: Methodologies and Challenges.}, journal = {Current microbiology}, volume = {81}, number = {8}, pages = {257}, pmid = {38955825}, issn = {1432-0991}, support = {No.2023-BSBA-024//Joint Funds of the Natural Science Foundation of Liaoning Province of China/ ; }, mesh = {*Soil Microbiology ; *Proteomics/methods ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Microbiota ; Fungi/classification/genetics/metabolism/isolation &amp; purification ; Soil/chemistry ; Computational Biology/methods ; }, abstract = {Soil represents a complex and dynamic ecosystem, hosting a myriad of microorganisms that coexist and play vital roles in nutrient cycling and organic matter transformation. Among these microorganisms, bacteria and fungi are key members of the microbial community, profoundly influencing the fate of nitrogen, sulfur, and carbon in terrestrial environments. Understanding the intricacies of soil ecosystems and the biological processes orchestrated by microbial communities necessitates a deep dive into their composition and metabolic activities. The advent of next-generation sequencing and 'omics' techniques, such as metagenomics and metaproteomics, has revolutionized our understanding of microbial ecology and the functional dynamics of soil microbial communities. Metagenomics enables the identification of microbial community composition in soil, while metaproteomics sheds light on the current biological functions performed by these communities. However, metaproteomics presents several challenges, both technical and computational. Factors such as the presence of humic acids and variations in extraction methods can influence protein yield, while the absence of high-resolution mass spectrometry and comprehensive protein databases limits the depth of protein identification. Notwithstanding these limitations, metaproteomics remains a potent tool for unraveling the intricate biological processes and functions of soil microbial communities. In this review, we delve into the methodologies and challenges of metaproteomics in soil research, covering aspects such as protein extraction, identification, and bioinformatics analysis. Furthermore, we explore the applications of metaproteomics in soil bioremediation, highlighting its potential in addressing environmental challenges.}, }
@article {pmid38954338, year = {2024}, author = {Yao, Z and Zhou, X and Jin, T and Wang, L and Liu, N and Wu, L}, title = {Remediation of phenanthrene contaminated soil by persulphate coupled with Pseudomonas aeruginosa GZ7 based on oxidation prediction model.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {31}, pages = {44415-44430}, pmid = {38954338}, issn = {1614-7499}, support = {52270171//Innovative Research Group Project of the National Natural Science Foundation of China/ ; 51974314//Innovative Research Group Project of the National Natural Science Foundation of China/ ; }, mesh = {*Phenanthrenes/metabolism ; *Pseudomonas aeruginosa ; *Soil Pollutants ; *Oxidation-Reduction ; *Soil/chemistry ; Soil Microbiology ; Environmental Restoration and Remediation/methods ; Biodegradation, Environmental ; Polycyclic Aromatic Hydrocarbons ; Sulfates/chemistry ; }, abstract = {Chemical oxidation coupled with microbial remediation has attracted widespread attention for the removal of polycyclic aromatic hydrocarbons (PAHs). Among them, the precise evaluation of the feasible oxidant concentration of PAH-contaminated soil is the key to achieving the goal of soil functional ecological remediation. In this study, phenanthrene (PHE) was used as the target pollutant, and Fe[2+]-activated persulphate (PS) was used to remediate four types of soils. Linear regression analysis identified the following important factors influencing remediation: PS dosage and soil PHE content for PHE degradation, Fe[2+] dosage, hydrolysable nitrogen (HN), and available phosphorus for PS decomposition. A comprehensive model of "soil characteristics-oxidation conditions-remediation effect" with a high predictive accuracy was constructed. Based on model identification, Pseudomonas aeruginosa GZ7, which had high PAHs degrading ability after domestication, was further applied to coupling repair remediation. The results showed that the optimal PS dose was 0.75% (w/w). The response relationship between soil physical, chemical, and biological indicators at the intermediate interface and oxidation conditions was analysed. Coupled remediation effects were clarified using microbial diversity sequencing. The introduction of Pseudomonas aeruginosa GZ7 stimulated the relative abundance of Cohnella, Enterobacter, Paenibacillus, and Bacillus, which can promote material metabolism and energy transformation during remediation.}, }
@article {pmid38954067, year = {2024}, author = {Bazkiaee, PA and Kamkar, B and Amiri, E and Kazemi, H and Rezaei, M and Araji, HA}, title = {Multi-criteria GIS-based land suitability analysis for rice cultivation: a case study in Guilan Province, Iran.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {7}, pages = {680}, pmid = {38954067}, issn = {1573-2959}, mesh = {*Oryza/growth &amp; development ; Iran ; *Geographic Information Systems ; *Environmental Monitoring/methods ; *Agriculture/methods ; *Soil/chemistry ; Conservation of Natural Resources ; Climate ; }, abstract = {Ensuring food security and sustainable resource management has become a paramount global concern, prompting significant attention to land suitability analysis for enhancing agricultural production. In this study, an AHP-weighted overlay method was employed to delineate rice cultivation suitability in Guilan province, Iran, a central hub for rice production. Sixteen climatic, topographic, and soil variables were integrated, and individual maps were reclassified to align with the specific requisites for rice production. The results revealed three suitability classes: including 'very suitable,' 'suitable,' and 'moderately suitable', covering 91%, 6%, and 3% of the land, respectively. Soil attributes, particularly organic matter, significantly influenced suitability (weight value of 0.745), with topographic and soil factors outweighing climate in assessment. While salinity is generally absent, organic matter deficiency affects 44% of the land. Phosphorus imbalances are prevalent, with potassium toxicity observed in 10%. Microelement deficiencies, especially in iron and zinc, are noted. Additionally, the results indicated that topographic and soil attributes played a more significant role than climate-related factors in assessing land suitability for rice cultivation within the study area. This research provides a comprehensive spatial analysis of all variables in the study region, shedding light on the complexities of land suitability for rice cultivation. These findings contribute to the understanding of agricultural sustainability and resource management strategies in the context of food security.}, }
@article {pmid38951915, year = {2024}, author = {Koci, O and Russell, RK and Shaikh, MG and Edwards, C and Gerasimidis, K and Ijaz, UZ}, title = {CViewer: a Java-based statistical framework for integration of shotgun metagenomics with other omics datasets.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {117}, pmid = {38951915}, issn = {2049-2618}, support = {NE/L011956/1//NERC Environmental Bioinformatics Centre/ ; BB/T010657/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; EP/V030515/1//Engineering and Physical Sciences Research Council/ ; }, mesh = {*Metagenomics/methods ; Humans ; *Software ; Microbiota/genetics ; Gastrointestinal Microbiome/genetics ; Computational Biology/methods ; Metagenome ; Crohn Disease/microbiology/genetics ; }, abstract = {BACKGROUND: Shotgun metagenomics for microbial community survey recovers enormous amount of information for microbial genomes that include their abundances, taxonomic, and phylogenetic information, as well as their genomic makeup, the latter of which then helps retrieve their function based on annotated gene products, mRNA, protein, and metabolites. Within the context of a specific hypothesis, additional modalities are often included, to give host-microbiome interaction. For example, in human-associated microbiome projects, it has become increasingly common to include host immunology through flow cytometry. Whilst there are plenty of software approaches available, some that utilize marker-based and assembly-based approaches, for downstream statistical analyses, there is still a dearth of statistical tools that help consolidate all such information in a single platform. By virtue of stringent computational requirements, the statistical workflow is often passive with limited visual exploration.<br><br>RESULTS: In this study, we have developed a Java-based statistical framework (https://github.com/KociOrges/cviewer) to explore shotgun metagenomics data, which integrates seamlessly with conventional pipelines and offers exploratory as well as hypothesis-driven analyses. The end product is a highly interactive toolkit with a multiple document interface, which makes it easier for a person without specialized knowledge to perform analysis of multiomics datasets and unravel biologically relevant patterns. We have designed algorithms based on frequently used numerical ecology and machine learning principles, with value-driven from integrated omics tools which not only find correlations amongst different datasets but also provide discrimination based on case-control relationships.<br><br>CONCLUSIONS: CViewer was used to analyse two distinct metagenomic datasets with varying complexities. These include a dietary intervention study to understand Crohn's disease changes during a dietary treatment to include remission, as well as a gut microbiome profile for an obesity dataset comparing subjects who suffer from obesity of different aetiologies and against controls who were lean. Complete analyses of both studies in CViewer then provide very powerful mechanistic insights that corroborate with the published literature and demonstrate its full potential. Video Abstract.}, }
@article {pmid38949108, year = {2024}, author = {Bahl, A and Halappanavar, S and Wohlleben, W and Nymark, P and Kohonen, P and Wallin, H and Vogel, U and Haase, A}, title = {Bioinformatics and machine learning to support nanomaterial grouping.}, journal = {Nanotoxicology}, volume = {18}, number = {4}, pages = {373-400}, doi = {10.1080/17435390.2024.2368005}, pmid = {38949108}, issn = {1743-5404}, mesh = {*Machine Learning ; *Nanostructures/chemistry/toxicity ; *Computational Biology/methods ; Humans ; Risk Assessment ; Animals ; }, abstract = {Nanomaterials (NMs) offer plenty of novel functionalities. Moreover, their physicochemical properties can be fine-tuned to meet the needs of specific applications, leading to virtually unlimited numbers of NM variants. Hence, efficient hazard and risk assessment strategies building on New Approach Methodologies (NAMs) become indispensable. Indeed, the design, the development and implementation of NAMs has been a major topic in a substantial number of research projects. One of the promising strategies that can help to deal with the high number of NMs variants is grouping and read-across. Based on demonstrated structural and physicochemical similarity, NMs can be grouped and assessed together. Within an established NM group, read-across may be performed to fill in data gaps for data-poor variants using existing data for NMs within the group. Establishing a group requires a sound justification, usually based on a grouping hypothesis that links specific physicochemical properties to well-defined hazard endpoints. However, for NMs these interrelationships are only beginning to be understood. The aim of this review is to demonstrate the power of bioinformatics with a specific focus on Machine Learning (ML) approaches to unravel the NM Modes-of-Action (MoA) and identify the properties that are relevant to specific hazards, in support of grouping strategies. This review emphasizes the following messages: 1) ML supports identification of the most relevant properties contributing to specific hazards; 2) ML supports analysis of large omics datasets and identification of MoA patterns in support of hypothesis formulation in grouping approaches; 3) omics approaches are useful for shifting away from consideration of single endpoints towards a more mechanistic understanding across multiple endpoints gained from one experiment; and 4) approaches from other fields of Artificial Intelligence (AI) like Natural Language Processing or image analysis may support automated extraction and interlinkage of information related to NM toxicity. Here, existing ML models for predicting NM toxicity and for analyzing omics data in support of NM grouping are reviewed. Various challenges related to building robust models in the field of nanotoxicology exist and are also discussed.}, }
@article {pmid38947430, year = {2024}, author = {Li, S and Mao, Y and Yang, J and Li, Y and Dong, J and Wang, Z and Jiang, L and He, S}, title = {Efficient integration of covalent triazine frameworks (CTFs) for augmented photocatalytic efficacy: A review of synthesis, strategies, and applications.}, journal = {Heliyon}, volume = {10}, number = {11}, pages = {e32202}, pmid = {38947430}, issn = {2405-8440}, abstract = {Heterogeneous photocatalysis emerges as an exceptionally appealing technological avenue for the direct capture, conversion, and storage of renewable solar energy, facilitating the generation of sustainable and ecologically benign solar fuels and a spectrum of other pertinent applications. Heterogeneous nanocomposites, incorporating Covalent Triazine Frameworks (CTFs), exhibit a wide-ranging spectrum of light absorption, well-suited electronic band structures, rapid charge carrier mobility, ample resource availability, commendable chemical robustness, and straightforward synthetic routes. These attributes collectively position them as highly promising photocatalysts with applicability in diverse fields, including but not limited to the production of photocatalytic solar fuels and the decomposition of environmental contaminants. As the field of photocatalysis through the hybridization of CTFs undergoes rapid expansion, there is a pressing and substantive need for a systematic retrospective analysis and forward-looking evaluation to elucidate pathways for enhancing performance. This comprehensive review commences by directing attention to diverse synthetic methodologies for the creation of composite materials. And then it delves into a thorough exploration of strategies geared towards augmenting performance, encompassing the introduction of electron donor-acceptor (D-A) units, heteroatom doping, defect Engineering, architecture of Heterojunction and optimization of morphology. Following this, it systematically elucidates applications primarily centered around the efficient generation of photocatalytic hydrogen, reduction of carbon dioxide through photocatalysis, and the degradation of organic pollutants. Ultimately, the discourse turns towards unresolved challenges and the prospects for further advancement, offering valuable guidance for the potent harnessing of CTFs in high-efficiency photocatalytic processes.}, }
@article {pmid38945180, year = {2024}, author = {Pearl, RL and Donze, LF and Rosas, LG and Agurs-Collins, T and Baskin, ML and Breland, JY and Byker Shanks, C and Cooksey Stowers, K and Johnson, S and Lee, BY and Martin, MY and Mujuru, P and Odoms-Young, A and Panza, E and Pronk, NP and Calicutt, K and Nadglowski, J and Nece, PM and Tedder, M and Chow, LS and Krishnamurti, H and Jay, M and Xi, D and Jastreboff, AM and Stanford, FC}, title = {Ending Weight Stigma to Advance Health Equity.}, journal = {American journal of preventive medicine}, volume = {67}, number = {5}, pages = {785-791}, pmid = {38945180}, issn = {1873-2607}, support = {P30 DK040561/DK/NIDDK NIH HHS/United States ; R01 DK099039/DK/NIDDK NIH HHS/United States ; R01 DK124484/DK/NIDDK NIH HHS/United States ; U24 DK132733/DK/NIDDK NIH HHS/United States ; UE5 DK137285/DK/NIDDK NIH HHS/United States ; UM1 TR004921/TR/NCATS NIH HHS/United States ; P50 MD017338/MD/NIMHD NIH HHS/United States ; K23 HL140176/HL/NHLBI NIH HHS/United States ; UL1 TR003142/TR/NCATS NIH HHS/United States ; K23 MD015092/MD/NIMHD NIH HHS/United States ; R03 HL160603/HL/NHLBI NIH HHS/United States ; U54 TR004279/TR/NCATS NIH HHS/United States ; R01 DK129668/DK/NIDDK NIH HHS/United States ; }, }
@article {pmid38941024, year = {2024}, author = {Holstein, T and Muth, T}, title = {Bioinformatic Workflows for Metaproteomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2820}, number = {}, pages = {187-213}, pmid = {38941024}, issn = {1940-6029}, mesh = {*Proteomics/methods ; *Computational Biology/methods ; *Workflow ; *Software ; *Microbiota/genetics ; Humans ; Databases, Protein ; Metagenomics/methods ; }, abstract = {The strong influence of microbiomes on areas such as ecology and human health has become widely recognized in the past years. Accordingly, various techniques for the investigation of the composition and function of microbial community samples have been developed. Metaproteomics, the comprehensive analysis of the proteins from microbial communities, allows for the investigation of not only the taxonomy but also the functional and quantitative composition of microbiome samples. Due to the complexity of the investigated communities, methods developed for single organism proteomics cannot be readily applied to metaproteomic samples. For this purpose, methods specifically tailored to metaproteomics are required. In this work, a detailed overview of current bioinformatic solutions and protocols in metaproteomics is given. After an introduction to the proteomic database search, the metaproteomic post-processing steps are explained in detail. Ten specific bioinformatic software solutions are focused on, covering various steps including database-driven identification and quantification as well as taxonomic and functional assignment.}, }
@article {pmid38938637, year = {2024}, author = {Yang, J and Deng, H and Zhang, Y and Zhou, Y and Miao, T}, title = {Application of amodal segmentation for shape reconstruction and occlusion recovery in occluded tomatoes.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1376138}, pmid = {38938637}, issn = {1664-462X}, abstract = {Common object detection and image segmentation methods are unable to accurately estimate the shape of the occluded fruit. Monitoring the growth status of shaded crops in a specific environment is challenging, and certain studies related to crop harvesting and pest detection are constrained by the natural shadow conditions. Amodal segmentation can focus on the occluded part of the fruit and complete the overall shape of the fruit. We proposed a Transformer-based amodal segmentation algorithm to infer the amodal shape of occluded tomatoes. Considering the high cost of amodal annotation, we only needed modal dataset to train the model. The dataset was taken from two greenhouses on the farm and contains rich occlusion information. We introduced boundary estimation in the hourglass structured network to provide a priori information about the completion of the amodal shapes, and reconstructed the occluded objects using a GAN network (with discriminator) and GAN loss. The model in this study showed accuracy, with average pairwise accuracy of 96.07%, mean intersection-over-union (mIoU) of 94.13% and invisible mIoU of 57.79%. We also examined the quality of pseudo-amodal annotations generated by our proposed model using Mask R-CNN. Its average precision (AP) and average precision with intersection over union (IoU) 0.5 (AP50) reached 63.91%,86.91% respectively. This method accurately and rationally achieves the shape of occluded tomatoes, saving the cost of manual annotation, and is able to deal with the boundary information of occlusion while decoupling the relationship of occluded objects from each other. Future work considers how to complete the amodal segmentation task without overly relying on the occlusion order and the quality of the modal mask, thus promising applications to provide technical support for the advancement of ecological monitoring techniques and ecological cultivation.}, }
@article {pmid38937989, year = {2024}, author = {Wu, H and Mu, C and Li, X and Fan, W and Shen, L and Zhu, W}, title = {Breed-Driven Microbiome Heterogeneity Regulates Intestinal Stem Cell Proliferation via Lactobacillus-Lactate-GPR81 Signaling.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {11}, number = {33}, pages = {e2400058}, pmid = {38937989}, issn = {2198-3844}, support = {32030104//National Natural Science Foundation of China/ ; 2022YFD1300402//National Key Research and Development Program of China/ ; }, mesh = {Animals ; *Cell Proliferation/physiology ; *Stem Cells/metabolism/cytology ; *Lactobacillus/metabolism/genetics ; *Receptors, G-Protein-Coupled/metabolism/genetics ; *Gastrointestinal Microbiome/physiology/genetics ; Swine ; *Lactic Acid/metabolism ; Signal Transduction/physiology ; Wnt Signaling Pathway/physiology/genetics ; Jejunum/microbiology/metabolism/cytology ; Obesity/metabolism/microbiology ; Intestinal Mucosa/metabolism/microbiology/cytology ; }, abstract = {Genetically lean and obese individuals have distinct intestinal microbiota and function. However, the underlying mechanisms of the microbiome heterogeneity and its regulation on epithelial function such as intestinal stem cell (ISC) fate remain unclear. Employing pigs of genetically distinct breeds (obese Meishan and lean Yorkshire), this study reveals transcriptome-wide variations in microbial ecology of the jejunum, characterized by enrichment of active Lactobacillus species, notably the predominant Lactobacillus amylovorus (L. amylovorus), and lactate metabolism network in obese breeds. The L. amylovorus-dominant heterogeneity is paralleled with epithelial functionality difference as reflected by highly expressed GPR81, more proliferative ISCs and activated Wnt/β-catenin signaling. Experiments using in-house developed porcine jejunal organoids prove that live L. amylovorus and its metabolite lactate promote intestinal organoid growth. Mechanistically, L. amylovorus and lactate activate Wnt/β-catenin signaling in a GPR81-dependent manner to promote ISC-mediated epithelial proliferation. However, heat-killed L. amylovorus fail to cause these changes. These findings uncover a previously underrepresented role of L. amylovorus in regulating jejunal stem cells via Lactobacillus-lactate-GPR81 axis, a key mechanism bridging breed-driven intestinal microbiome heterogeneity with ISC fate. Thus, results from this study provide new insights into the role of gut microbiome and stem cell interactions in maintaining intestinal homeostasis.}, }
@article {pmid38936731, year = {2024}, author = {Li, Y and Hou, K and Chang, Y and Yuan, B and Li, X}, title = {A methodological study on the identification of ecological security change processes and zoning control strategies -- Based on the perspective of sustainable development.}, journal = {The Science of the total environment}, volume = {946}, number = {}, pages = {174190}, doi = {10.1016/j.scitotenv.2024.174190}, pmid = {38936731}, issn = {1879-1026}, abstract = {Ecological security (ES) is a crucial indicator for assessing the sustainable development of a region. Currently, most studies on ES primarily focus on process analysis, and the integration of environmental variability into the development of tailored control strategies for regions with varying ecological quality is overlooked. Therefore, in this study, we identified regional ES change processes, employed an optimized system to calculate the ecological security index (ESI), and identified ecological corridors (ECs) through the Minimum Constrained Resource (MCR) model to determine zoning strategies for typical arid regions, using the Ningxia region in the Yellow River Basin of China as an example. The findings showed that (1) from 2006 to 2020, the ESI values of most regions were between 0.2 and 0.4, with small but consistent increases in the ESI values over the years. (2) The proportion of regions with high ES ratings increased by 9.08 % across all districts and counties, and the center of gravity of ES shifted in a north-south and east-west direction. (3) The ESI exhibited a strong positive spatial correlation, characterized by spatial diffusion and spillover effects in most regions. (4) The ECs were predominantly distributed in a north-south direction, involving a total of 20 districts and counties. Based on the principles of sustainable development, we developed a model for the dynamic identification and zoning control of regional ES, aiming to provide a practical framework for effective ecological restoration and protection measures. Additionally, the strategies and methodologies presented in this study serve as important references for similar regions worldwide to facilitate the zoning control of ES, highlighting the broader significance and applicability of the study.}, }
@article {pmid38936185, year = {2024}, author = {Hu, CJ and Lv, YQ and Xian, WD and Jiao, JY and Lian, ZH and Tan, S and Li, MM and Luo, ZH and Liu, ZT and Lv, AP and Liu, L and Ali, M and Liu, WQ and Li, WJ}, title = {Multi-omics insights into the function and evolution of sodium benzoate biodegradation pathway in Benzoatithermus flavus gen. nov., sp. nov. from hot spring.}, journal = {Journal of hazardous materials}, volume = {476}, number = {}, pages = {135017}, doi = {10.1016/j.jhazmat.2024.135017}, pmid = {38936185}, issn = {1873-3336}, mesh = {*Sodium Benzoate/metabolism ; *Biodegradation, Environmental ; *Hot Springs/microbiology ; *Phylogeny ; Water Pollutants, Chemical/metabolism ; Multiomics ; }, abstract = {Biodegradation stands as an eco-friendly and effective approach for organic contaminant remediation. However, research on microorganisms degrading sodium benzoate contaminants in extreme environments remains limited. In this study, we report to display the isolation of a novel hot spring enriched cultures with sodium benzoate (400 mg/L) as the sole carbon source. The results revealed that the phylum Pseudomonadota was the potential sodium benzoate degrader and a novel genus within the family Geminicoccaceae of this phylum. The isolated strain was named Benzoatithermus flavus SYSU G07066[T] and was isolated from HNT-2 hot spring samples. Genomic analysis revealed that SYSU G07066[T] carried benABC genes and physiological experiments indicated the ability to utilize sodium benzoate as a sole carbon source for growth, which was further confirmed by transcriptomic data with expression of benABC. Phylogenetic analysis suggested that Horizontal Gene Transfer (HGT) plays a significant role in acquiring sodium benzoate degradation capability among prokaryotes, and SYSU G07066[T] might have acquired benABC genes through HGT from the family Acetobacteraceae. The discovery of the first microorganism with sodium benzoate degradation function from a hot spring enhances our understanding of the diverse functions within the family Geminicoccaceae. This study unearths the first novel genus capable of efficiently degrading sodium benzoate and its evolution history at high temperatures, holding promising industrial applications, and provides a new perspective for further exploring the application potential of hot spring "microbial dark matter".}, }
@article {pmid38935782, year = {2024}, author = {Louvet, A and Mantoux, C and Machon, N}, title = {Assessing the extinction risk of the spontaneous flora in urban tree bases.}, journal = {PLoS computational biology}, volume = {20}, number = {6}, pages = {e1012191}, pmid = {38935782}, issn = {1553-7358}, mesh = {*Extinction, Biological ; *Trees ; *Bayes Theorem ; *Cities ; *Ecosystem ; Computational Biology ; Markov Chains ; Models, Biological ; Paris ; }, abstract = {As the spatial arrangement of trees planted along streets in cities makes their bases potential ecological corridors for the flora, urban tree bases may be a key contributor to the overall connectivity of the urban ecosystem. However, these tree bases are also a highly fragmented environment in which extinctions are frequent. The goal of this study was to assess the plant species' ability to survive and spread through urban tree bases. To do so, we developed a Bayesian framework to assess the extinction risk of a plant metapopulation using presence/absence data, assuming that the occupancy dynamics was described by a Hidden Markov Model. The novelty of our approach is to take into account the combined effect of low-distance dispersal and the potential presence of a seed bank on the extinction risk. We introduced a metric of the extinction risk and examined its performance over a wide range of metapopulation parameters. We applied our framework to yearly floristic inventories carried out in 1324 tree bases in Paris, France. While local extinction risks were generally high, extinction risks at the street scale varied greatly from one species to another. We identified 10 plant species that could survive and spread through urban tree bases, and three plant traits correlated with the extinction risk at the metapopulation scale: the maximal height, and the beginning and end of the flowering period. Our results suggest that some plant species can use urban tree bases as ecological corridors despite high local extinction risks by forming a seed bank. We also identified other plant traits correlated with the ability to survive in tree bases, related to the action of gardeners. Moreover, our findings demonstrate that our Bayesian estimation framework based on percolation theory has the potential to be extended to more general metapopulations.}, }
@article {pmid38932245, year = {2024}, author = {Conradie, T and Caparros-Martin, JA and Egan, S and Kicic, A and Koks, S and Stick, SM and Agudelo-Romero, P}, title = {Exploring the Complexity of the Human Respiratory Virome through an In Silico Analysis of Shotgun Metagenomic Data Retrieved from Public Repositories.}, journal = {Viruses}, volume = {16}, number = {6}, pages = {}, pmid = {38932245}, issn = {1999-4915}, support = {NHMRC115648//National Health and Medical Research Council/ ; Synergy grant APP118364//National Health and Medical Research Council/ ; Theme Collaboration Award 2023//Telethon Kids Institute/ ; N/A//Google cloud education program/ ; Investigator grant 2021/GR000216//National Health and Medical Research Council/ ; }, mesh = {Humans ; *Metagenomics/methods ; *Virome ; *Genome, Viral ; *Respiratory System/virology ; *Viruses/genetics/classification/isolation &amp; purification ; Metagenome ; Computer Simulation ; Phylogeny ; Computational Biology/methods ; Microbiota ; Bacteriophages/genetics/classification/isolation &amp; purification ; }, abstract = {BACKGROUND: Respiratory viruses significantly impact global morbidity and mortality, causing more disease in humans than any other infectious agent. Beyond pathogens, various viruses and bacteria colonize the respiratory tract without causing disease, potentially influencing respiratory diseases' pathogenesis. Nevertheless, our understanding of respiratory microbiota is limited by technical constraints, predominantly focusing on bacteria and neglecting crucial populations like viruses. Despite recent efforts to improve our understanding of viral diversity in the human body, our knowledge of viral diversity associated with the human respiratory tract remains limited.<br><br>METHODS: Following a comprehensive search in bibliographic and sequencing data repositories using keyword terms, we retrieved shotgun metagenomic data from public repositories (n = 85). After manual curation, sequencing data files from 43 studies were analyzed using EVEREST (pipEline for Viral assEmbly and chaRactEriSaTion). Complete and high-quality contigs were further assessed for genomic and taxonomic characterization.<br><br>RESULTS: Viral contigs were obtained from 194 out of the 868 FASTQ files processed through EVEREST. Of the 1842 contigs that were quality assessed, 8% (n = 146) were classified as complete/high-quality genomes. Most of the identified viral contigs were taxonomically classified as bacteriophages, with taxonomic resolution ranging from the superkingdom level down to the species level. Captured contigs were spread across 25 putative families and varied between RNA and DNA viruses, including previously uncharacterized viral genomes. Of note, airway samples also contained virus(es) characteristic of the human gastrointestinal tract, which have not been previously described as part of the lung virome. Additionally, by performing a meta-analysis of the integrated datasets, ecological trends within viral populations linked to human disease states and their biogeographical distribution along the respiratory tract were observed.<br><br>CONCLUSION: By leveraging publicly available repositories of shotgun metagenomic data, the present study provides new insights into viral genomes associated with specimens from the human respiratory tract across different disease spectra. Further studies are required to validate our findings and evaluate the potential impact of these viral communities on respiratory tract physiology.}, }
@article {pmid38926582, year = {2024}, author = {Tian, SY and Yasuhara, M and Condamine, FL and Huang, HM and Fernando, AGS and Aguilar, YM and Pandita, H and Irizuki, T and Iwatani, H and Shin, CP and Renema, W and Kase, T}, title = {Cenozoic history of the tropical marine biodiversity hotspot.}, journal = {Nature}, volume = {632}, number = {8024}, pages = {343-349}, pmid = {38926582}, issn = {1476-4687}, mesh = {Animals ; *Aquatic Organisms/classification/isolation &amp; purification ; *Biodiversity ; Climate Change ; Datasets as Topic ; Extinction, Biological ; *Fossils ; Genetic Speciation ; History, Ancient ; Time Factors ; *Tropical Climate ; Pacific Ocean ; Coral Reefs ; }, abstract = {The region with the highest marine biodiversity on our planet is known as the Coral Triangle or Indo-Australian Archipelago (IAA)[1,2]. Its enormous biodiversity has long attracted the interest of biologists; however, the detailed evolutionary history of the IAA biodiversity hotspot remains poorly understood[3]. Here we present a high-resolution reconstruction of the Cenozoic diversity history of the IAA by inferring speciation-extinction dynamics using a comprehensive fossil dataset. We found that the IAA has exhibited a unidirectional diversification trend since about 25 million years ago, following a roughly logistic increase until a diversity plateau beginning about 2.6 million years ago. The growth of diversity was primarily controlled by diversity dependency and habitat size, and also facilitated by the alleviation of thermal stress after 13.9 million years ago. Distinct net diversification peaks were recorded at about 25, 20, 16, 12 and 5 million years ago, which were probably related to major tectonic events in addition to climate transitions. Key biogeographic processes had far-reaching effects on the IAA diversity as shown by the long-term waning of the Tethyan descendants versus the waxing of cosmopolitan and IAA taxa. Finally, it seems that the absence of major extinctions and the Cenozoic cooling have been essential in making the IAA the richest marine biodiversity hotspot on Earth.}, }
@article {pmid38924481, year = {2024}, author = {Ramos, SR and Reynolds, H and Johnson, C and Melkus, G and Kershaw, T and Thayer, JF and Vorderstrasse, A}, title = {Perceptions of HIV-Related Comorbidities and Usability of a Virtual Environment for Cardiovascular Disease Prevention Education in Sexual Minority Men With HIV: Formative Phases of a Pilot Randomized Controlled Trial.}, journal = {Journal of medical Internet research}, volume = {26}, number = {}, pages = {e57351}, pmid = {38924481}, issn = {1438-8871}, support = {K01 HL145580/HL/NHLBI NIH HHS/United States ; L30 HL149001/HL/NHLBI NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; Male ; *Cardiovascular Diseases/prevention &amp; control ; *HIV Infections/prevention &amp; control/psychology ; Pilot Projects ; *Sexual and Gender Minorities/psychology/statistics &amp; numerical data ; Adult ; Middle Aged ; Comorbidity ; Virtual Reality ; User-Computer Interface ; }, abstract = {BACKGROUND: Sexual minority men with HIV are at an increased risk of cardiovascular disease (CVD) and have been underrepresented in behavioral research and clinical trials.<br><br>OBJECTIVE: This study aims to explore perceptions of HIV-related comorbidities and assess the interest in and usability of a virtual environment for CVD prevention education in Black and Latinx sexual minority men with HIV.<br><br>METHODS: This is a 3-phase pilot behavioral randomized controlled trial. We report on formative phases 1 and 2 that informed virtual environment content and features using qualitative interviews, usability testing, and beta testing with a total of 25 individuals. In phase 1, a total of 15 participants completed interviews exploring HIV-related illnesses of concern that would be used to tailor the virtual environment. In phase 2, usability testing and beta testing were conducted with 10 participants to assess interest, features, and content.<br><br>RESULTS: In phase 1, we found that CVD risk factors included high blood pressure, myocardial infarction, stroke, and diabetes. Cancer (prostate, colon, and others) was a common concern, as were mental health conditions. In phase 2, all participants completed the 12-item usability checklist with favorable feedback within 30 to 60 minutes. Beta-testing interviews suggested (1) mixed perceptions of health and HIV, (2) high risk for comorbid conditions, (3) virtual environment features were promising, and (4) the need for diverse avatar representations.<br><br>CONCLUSIONS: We identified several comorbid conditions of concern, and findings carry significant implications for mitigating barriers to preventive health screenings, given the shared risk factors between HIV and related comorbidities. Highly rated aspects of the virtual environment were anonymity; meeting others with HIV who identify as gay or bisexual; validating lesbian, gay, bisexual, transgender, queer, and others (LGBTQ+) images and content; and accessibility to CVD prevention education. Critical end-user feedback from beta testing suggested more options for avatar customization in skin, hair, and body representation. Our next phase will test the virtual environment as a new approach to advancing cardiovascular health equity in ethnic and racial sexual minority men with HIV.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov NCT04061915; https://clinicaltrials.gov/study/NCT05242952.<br><br>RR2-10.2196/38348.}, }
@article {pmid38920364, year = {2024}, author = {Mau, RL and Hayer, M and Purcell, AM and Geisen, S and Hungate, BA and Schwartz, E}, title = {Measurements of soil protist richness and community composition are influenced by primer pair, annealing temperature, and bioinformatics choices.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {7}, pages = {e0080024}, pmid = {38920364}, issn = {1098-5336}, support = {DE-AC52-07NA27344//U.S. Department of Energy (DOE)/ ; DE-SC0020172//U.S. Department of Energy (DOE)/ ; DE-SC0023126//U.S. Department of Energy (DOE)/ ; }, mesh = {*RNA, Ribosomal, 18S/genetics ; *Computational Biology/methods ; *Eukaryota/genetics/classification ; *DNA Primers/genetics ; *Soil Microbiology ; Biodiversity ; Temperature ; Soil/parasitology/chemistry ; Polymerase Chain Reaction ; }, abstract = {Protists are a diverse and understudied group of microbial eukaryotic organisms especially in terrestrial environments. Advances in molecular methods are increasing our understanding of the distribution and functions of these creatures; however, there is a vast array of choices researchers make including barcoding genes, primer pairs, PCR settings, and bioinformatic options that can impact the outcome of protist community surveys. Here, we tested four commonly used primer pairs targeting the V4 and V9 regions of the 18S rRNA gene using different PCR annealing temperatures and processed the sequences with different bioinformatic parameters in 10 diverse soils to evaluate how primer pair, amplification parameters, and bioinformatic choices influence the composition and richness of protist and non-protist taxa using Illumina sequencing. Our results showed that annealing temperature influenced sequencing depth and protist taxon richness for most primer pairs, and that merging forward and reverse sequencing reads for the V4 primer pairs dramatically reduced the number of sequences and taxon richness of protists. The data sets of primers that targeted the same 18S rRNA gene region (e.g., V4 or V9) had similar protist community compositions; however, data sets from primers targeting the V4 18S rRNA gene region detected a greater number of protist taxa compared to those prepared with primers targeting the V9 18S rRNA region. There was limited overlap of protist taxa between data sets targeting the two different gene regions (80/549 taxa). Together, we show that laboratory and bioinformatic choices can substantially affect the results and conclusions about protist diversity and community composition using metabarcoding.IMPORTANCEEcosystem functioning is driven by the activity and interactions of the microbial community, in both aquatic and terrestrial environments. Protists are a group of highly diverse, mostly unicellular microbes whose identity and roles in terrestrial ecosystem ecology have been largely ignored until recently. This study highlights the importance of choices researchers make, such as primer pair, on the results and conclusions about protist diversity and community composition in soils. In order to better understand the roles protist taxa play in terrestrial ecosystems, biases in methodological and analytical choices should be understood and acknowledged.}, }
@article {pmid38917931, year = {2024}, author = {Wang, H and Li, Y and Huang, G and Ma, Y and Zhang, Q and Li, Y}, title = {Analyzing variation of water inflow to inland lakes under climate change: Integrating deep learning and time series data mining.}, journal = {Environmental research}, volume = {259}, number = {}, pages = {119478}, doi = {10.1016/j.envres.2024.119478}, pmid = {38917931}, issn = {1096-0953}, mesh = {*Lakes/chemistry ; *Climate Change ; *Deep Learning ; Data Mining ; Environmental Monitoring/methods ; }, abstract = {The alarming depletion of global inland lakes in recent decades makes it essential to predict water inflow from rivers to lakes (WIRL) trend and unveil the dominant influencing driver, particularly in the context of climate change. The raw time series data contains multiple components (i.e., long-term trend, seasonal periodicity, and random noise), which makes it challenging for traditional machine/deep learning techniques to effectively capture long-term trend information. In this study, a novel FactorConvSTLnet (FCS) method is developed through integrating STL decomposition, convolutional neural networks (CNN), and factorial analysis into a general framework. FCS is more robust in long-term WIRL trend prediction through separating trend information as a modeling predictor, as well as unveiling predominant drivers. FCS is applied to typical inland lakes (the Aral Sea and the Lake Balkhash) in Central Asia, and results indicate that FCS (Nash-Sutcliffe efficiency = 0.88, root mean squared error = 67m[3]/s, mean relative error = 10%) outperforms the traditional CNN. Some main findings are: (i) during 1960-1990, reservoir water storage (WSR) was the dominant driver for the two lakes, respectively contributing to 71% and 49%; during 1991-2014 and 2015-2099, evaporation (EVAP) would be the dominant driver, with the contribution of 30% and 47%; (ii) climate change would shift the dominant driver from human activities to natural factors, where EVAP and surface snow amount (SNW) have an increasing influence on WIRL; (iii) compared to SSP1-2.6, the SNW contribution would decrease by 26% under SSP5-8.5, while the EVAP contribution would increase by 9%. The findings reveal the main drivers of shrinkage of the inland lakes and provide the scientific basis for promoting regional ecological sustainability.}, }
@article {pmid38917628, year = {2024}, author = {Li, Q and Ma, Q and Zhou, Y and Jiang, X and Parales, RE and Zhao, S and Zhuang, Y and Ruan, Z}, title = {Isolation, identification, and degradation mechanism by multi-omics of mesotrione-degrading Amycolatopsis nivea La24.}, journal = {Journal of hazardous materials}, volume = {476}, number = {}, pages = {134951}, doi = {10.1016/j.jhazmat.2024.134951}, pmid = {38917628}, issn = {1873-3336}, mesh = {*Herbicides/metabolism/chemistry ; *Cyclohexanones/metabolism ; *Biodegradation, Environmental ; *Amycolatopsis/metabolism/genetics ; Metabolomics ; Sulfonylurea Compounds/metabolism ; Soil Pollutants/metabolism ; Multiomics ; }, abstract = {Mesotrione is a herbicide used in agricultural production; however, its stability and long-term residues pose ecological risks to soil health and subsequent crops. In this research, the strain Amycolatopsis nivea La24 was identified as capable of completely degrading 50 mg∙L[-1] mesotrione within 48 h. It exhibited a broad adaptability to various environment and could degrade three sulfonylurea herbicides (nicosulfuron, chlorimuron-methyl, and cinosulfuron). Non-target metabonomic and mass spectrometry demonstrated that La24 strain broke down the mesotrione parent molecule by targeting the β-diketone bond and nitro group, resulting in the production of five possible degradation products. The differentially expressed genes were significantly enriched in fatty acid degradation, amino acid metabolism, and other pathways, and the differentially metabolites in glutathione metabolism, arginine/proline metabolism, cysteine/methionine metabolism, and other pathways. Additionally, it was confirmed by heterologous expression that nitroreductase was directly involved in the mesotrione degradation, and NDMA-dependent methanol dehydrogenase would increase the resistance to mesotrione. Finally, the intracellular response of La24 during mesotrione degradation was proposed. This work provides insight for a comprehensive understanding of the mesotrione biodegradation mechanism, significantly expands the resources for pollutant degradation, and offers the potential for a more sustainable solution to address herbicide pollution in soil.}, }
@article {pmid38917233, year = {2024}, author = {Costa, IB and Pimenta, IDSF and Aiquoc, KM and Oliveira, &#xc2;GRDC}, title = {Congenital syphilis, syphilis in pregnancy and prenatal care in Brazil: An ecological study.}, journal = {PloS one}, volume = {19}, number = {6}, pages = {e0306120}, pmid = {38917233}, issn = {1932-6203}, mesh = {Humans ; Pregnancy ; Female ; Brazil/epidemiology ; *Syphilis, Congenital/epidemiology ; *Prenatal Care ; *Pregnancy Complications, Infectious/epidemiology ; Incidence ; Adult ; Socioeconomic Factors ; Syphilis/epidemiology/diagnosis ; Adolescent ; Young Adult ; }, abstract = {The aim of this research was to evaluate the incidence of congenital syphilis and the ratio between congenital syphilis and syphilis in pregnant women in Brazil according to socioeconomic indicators (inadequate water supply and sanitation; illiteracy at 15 years of age or older; household income per capita; proportion of poor people; Gini index; human development index; and average health expenditure per inhabitant by the health system) and prenatal quality-of-care indicators. We conducted an ecological study using a sample composed of 257 municipalities, each with ≥ 100,000 inhabitants. Data was collected from four public databases: the Brazilian Institute of Geography and Statistics, comprising socioeconomical data from the 2010 census; and the data of 2019 available in the databases of the Department of Informatics of the Brazilian Health System, Information and Management of Primary Care, and the Electronic Citizen Information System. Descriptive analysis of dependent and independent variables and bivariate analysis by Negative Binomial regression were carried out. The mean incidence of congenital syphilis was 38% higher in municipalities with a Human Development Index up to 0.785 (ratio of means [RM] = 1.38; p = 0.049) and 57% higher among populations where less than 50% of primary healthcare services provided a rapid test for syphilis (RM = 1.57; p < 0.001). The ratio between congenital syphilis and syphilis in pregnant women was 29% higher in municipalities with a low household income per capita (RM = 1.29; p < 0.001) and 28% higher in locations where less than 50% of the primary healthcare services provided a rapid test for syphilis (RM = 1.28; p < 0.001). There was no statistical significance of the quality of prenatal care compared to the outcomes. This result underscores the challenges in detecting syphilis infections among pregnant women during prenatal care, consequently increasing the risk of vertical transmission of the disease to the fetus. Traits of inequality in the occurrence of congenital syphilis also draw attention to strategies to reduce health inequities and improve prenatal care.}, }
@article {pmid38916705, year = {2024}, author = {Yu, J and Chen, S}, title = {The Use of Big Data Analysis in Digital Empowerment of Sustainable Technological Innovation Management of Ecological Enterprises.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {31}, pages = {43956-43966}, pmid = {38916705}, issn = {1614-7499}, mesh = {*Big Data ; China ; Inventions ; Ecology ; Empowerment ; Environmental Monitoring/methods ; Conservation of Natural Resources ; }, abstract = {With the social economy's rapid progress and the popularization of environmental awareness, ecological enterprises have gradually become a crucial trend in the development of modern enterprises. This work intends to promote the development of ecological enterprises to a higher level. This work first analyzes the management mode of ecological enterprises in the context of big data in China. Then, it establishes various indicators to analyze the role of sustainable technological innovation in enterprise development and the impact of digital empowerment on enterprise development. Finally, this work takes China's manufacturing industry and ecological enterprises in Hubei Province as examples to summarize the digital empowerment of sustainable technological innovation management of ecological enterprises under the background of big data. The final result indicates that sustainable technological innovation significantly reduces ecological enterprises' resource consumption and waste emissions. Additionally, it has a significant positive effect on improving enterprise output value and economic benefits. The digital empowerment of enterprises has a significant driving effect on sustainable technological innovation, with a digital driving coefficient of 26. This work provides a feasible scheme for the specific application of big data analysis in the technology innovation management of ecological enterprises, including market demand analysis, environmental monitoring and governance, technology assessment and risk management. This work expounds the role of big data analysis technology in improving decision-making efficiency, optimizing resource allocation and enhancing the competitiveness of enterprises in the digital empowerment of ecological enterprises.}, }
@article {pmid38915508, year = {2024}, author = {Shukla, HG and Chakraborty, M and Emerson, JJ}, title = {Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38915508}, issn = {2692-8205}, support = {S10 OD021718/OD/NIH HHS/United States ; R35 GM153327/GM/NIGMS NIH HHS/United States ; P30 AR075047/AR/NIAMS NIH HHS/United States ; R01 GM123303/GM/NIGMS NIH HHS/United States ; S10 OD010794/OD/NIH HHS/United States ; P30 CA062203/CA/NCI NIH HHS/United States ; R00 GM129411/GM/NIGMS NIH HHS/United States ; }, abstract = {Many essential functions of organisms are encoded in highly repetitive genomic regions, including histones involved in DNA packaging, centromeres that are core components of chromosome segregation, ribosomal RNA comprising the protein translation machinery, telomeres that ensure chromosome integrity, piRNA clusters encoding host defenses against selfish elements, and virtually the entire Y chromosome. These regions, formed by highly similar tandem arrays, pose significant challenges for experimental and informatic study, impeding sequence-level descriptions essential for understanding genetic variation. Here, we report the assembly and variation analysis of such repetitive regions in Drosophila melanogaster, offering significant improvements to the existing community reference assembly. Our work successfully recovers previously elusive segments, including complete reconstructions of the histone locus and the pericentric heterochromatin of the X chromosome, spanning the Stellate locus to the distal flank of the rDNA cluster. To infer structural changes in these regions where alignments are often not practicable, we introduce landmark anchors based on unique variants that are putatively orthologous. These regions display considerable structural variation between different D. melanogaster strains, exhibiting differences in copy number and organization of homologous repeat units between haplotypes. In the histone cluster, although we observe minimal genetic exchange indicative of crossing over, the variation patterns suggest mechanisms such as unequal sister chromatid exchange. We also examine the prevalence and scale of concerted evolution in the histone and Stellate clusters and discuss the mechanisms underlying these observed patterns.}, }
@article {pmid38915006, year = {2024}, author = {Reininghaus, U and Schwannauer, M and Barne, I and Beames, JR and Bonnier, RA and Brenner, M and Breznoščáková, D and Dančík, D and De Allegri, M and Di Folco, S and Durstewitz, D and Gugel, J and Hajdúk, M and Heretik, A and Izáková, &#x13d; and Katreniakova, Z and Kiekens, G and Koppe, G and Kurilla, A and Marelli, L and Nagyova, I and Nguyen, H and Pečeňák, J and Schulte-Strathaus, JCC and Sotomayor-Enriquez, K and Uyttebroek, L and Weermeijer, J and Wolters, M and Wensing, M and Boehnke, JR and Myin-Germeys, I and Schick, A}, title = {Strategies, processes, outcomes, and costs of implementing experience sampling-based monitoring in routine mental health care in four European countries: study protocol for the IMMERSE effectiveness-implementation study.}, journal = {BMC psychiatry}, volume = {24}, number = {1}, pages = {465}, pmid = {38915006}, issn = {1471-244X}, support = {945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 389624707//DFG/ ; 101063326//Marie Sk&#x142;odowska-Curie fellowship/ ; 1204924N//Research Foundation Flanders/ ; APVV-22-0587//Agent&#xfa;ra na Podporu V&#xfd;skumu a V&#xfd;voja/ ; }, mesh = {Humans ; Belgium ; Cost-Benefit Analysis/methods ; Ecological Momentary Assessment ; Europe ; Germany ; Mental Disorders/therapy/economics ; *Mental Health Services/economics ; Slovakia ; *Randomized Controlled Trials as Topic ; *Multicenter Studies as Topic ; }, abstract = {BACKGROUND: Recent years have seen a growing interest in the use of digital tools for delivering person-centred mental health care. Experience Sampling Methodology (ESM), a structured diary technique for capturing moment-to-moment variation in experience and behaviour in service users' daily life, reflects a particularly promising avenue for implementing a person-centred approach. While there is evidence on the effectiveness of ESM-based monitoring, uptake in routine mental health care remains limited. The overarching aim of this hybrid effectiveness-implementation study is to investigate, in detail, reach, effectiveness, adoption, implementation, and maintenance as well as contextual factors, processes, and costs of implementing ESM-based monitoring, reporting, and feedback into routine mental health care in four European countries (i.e., Belgium, Germany, Scotland, Slovakia).<br><br>METHODS: In this hybrid effectiveness-implementation study, a parallel-group, assessor-blind, multi-centre cluster randomized controlled trial (cRCT) will be conducted, combined with a process and economic evaluation. In the cRCT, 24 clinical units (as the cluster and unit of randomization) at eight sites in four European countries will be randomly allocated using an unbalanced 2:1 ratio to one of two conditions: (a) the experimental condition, in which participants receive a Digital Mobile Mental Health intervention (DMMH) and other implementation strategies in addition to treatment as usual (TAU) or (b) the control condition, in which service users are provided with TAU. Outcome data in service users and clinicians will be collected at four time points: at baseline (t0), 2-month post-baseline (t1), 6-month post-baseline (t2), and 12-month post-baseline (t3). The primary outcome will be patient-reported service engagement assessed with the service attachment questionnaire at 2-month post-baseline. The process and economic evaluation will provide in-depth insights into in-vivo context-mechanism-outcome configurations and economic costs of the DMMH and other implementation strategies in routine care, respectively.<br><br>DISCUSSION: If this trial provides evidence on reach, effectiveness, adoption, implementation and maintenance of implementing ESM-based monitoring, reporting, and feedback, it will form the basis for establishing its public health impact and has significant potential to bridge the research-to-practice gap and contribute to swifter ecological translation of digital innovations to real-world delivery in routine mental health care.<br><br>TRIAL REGISTRATION: ISRCTN15109760 (ISRCTN registry, date: 03/08/2022).}, }
@article {pmid38914930, year = {2024}, author = {Jiang, G and Zheng, JY and Ren, SN and Yin, W and Xia, X and Li, Y and Wang, HL}, title = {A comprehensive workflow for optimizing RNA-seq data analysis.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {631}, pmid = {38914930}, issn = {1471-2164}, mesh = {*Workflow ; *RNA-Seq/methods ; *Software ; Fungi/genetics ; Computational Biology/methods ; Sequence Analysis, RNA/methods ; Alternative Splicing ; }, abstract = {BACKGROUND: Current RNA-seq analysis software for RNA-seq data tends to use similar parameters across different species without considering species-specific differences. However, the suitability and accuracy of these tools may vary when analyzing data from different species, such as humans, animals, plants, fungi, and bacteria. For most laboratory researchers lacking a background in information science, determining how to construct an analysis workflow that meets their specific needs from the array of complex analytical tools available poses a significant challenge.<br><br>RESULTS: By utilizing RNA-seq data from plants, animals, and fungi, it was observed that different analytical tools demonstrate some variations in performance when applied to different species. A comprehensive experiment was conducted specifically for analyzing plant pathogenic fungal data, focusing on differential gene analysis as the ultimate goal. In this study, 288 pipelines using different tools were applied to analyze five fungal RNA-seq datasets, and the performance of their results was evaluated based on simulation. This led to the establishment of a relatively universal and superior fungal RNA-seq analysis pipeline that can serve as a reference, and certain standards for selecting analysis tools were derived for reference. Additionally, we compared various tools for alternative splicing analysis. The results based on simulated data indicated that rMATS remained the optimal choice, although consideration could be given to supplementing with tools such as SpliceWiz.<br><br>CONCLUSION: The experimental results demonstrate that, in comparison to the default software parameter configurations, the analysis combination results after tuning can provide more accurate biological insights. It is beneficial to carefully select suitable analysis software based on the data, rather than indiscriminately choosing tools, in order to achieve high-quality analysis results more efficiently.}, }
@article {pmid38911902, year = {2024}, author = {Boyes, D and Holland, PWH and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the White-point, Mythimna albipuncta (Denis &amp; Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {62}, pmid = {38911902}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Mythimna albipuncta (the White-point; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 698.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.38 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,679 protein coding genes.}, }
@article {pmid38909735, year = {2024}, author = {Su, F and Huo, D and Yang, H and Sun, L}, title = {CircRNA8388 functions as the sponge for miR-2392 during intestinal regeneration in sea cucumber Apostichopus japonicus.}, journal = {International journal of biological macromolecules}, volume = {274}, number = {Pt 2}, pages = {133302}, doi = {10.1016/j.ijbiomac.2024.133302}, pmid = {38909735}, issn = {1879-0003}, mesh = {Animals ; Gene Expression Profiling ; Gene Expression Regulation ; Gene Ontology ; *Intestines ; *MicroRNAs/genetics ; *Regeneration/genetics ; *RNA, Circular/genetics ; *Stichopus/genetics ; }, abstract = {The sea cucumber Apostichopus japonicus can expel internal organs under stress and regenerate them subsequently. However, growth is delayed during regeneration, significantly impacting the industry. Circular RNAs (circRNAs) are single-stranded circular RNA molecules produced through alternative splicing of mRNA precursors. They play crucial roles in regulating gene expression via the ceRNA mechanism. In this study, circRNA profiles of control and regenerated intestines were constructed. A total of 15,874 circRNAs were identified, with a length of 300-350 nucleotides (nt) being the most abundant. Sanger sequencing confirmed the circular structure of circRNA398. Compared with the normal intestine, 50 and 83 differentially expressed circRNAs (DE-circRNAs) were identified in the regenerated intestine at 1 and 3 days post evisceration (dpe), respectively. Gene ontology (GO) terms for signal transduction and development regulation were most significantly enriched in 1dpeVScon and 3dpeVScon treatments, respectively. The dual-luciferase assay revealed that circRNA8388 functions as a sponge for miR-2392, participating in the remodeling of the extracellular matrix (ECM). In conclusion, these findings will contribute to the enhancement of the non-coding RNA database for echinoderms and lay the groundwork for future investigations into circRNA regulation during intestinal regeneration.}, }
@article {pmid38908558, year = {2024}, author = {Yang, Y and Li, Z and Wen, J}, title = {Long term impact of Wenchuan earthquake on population mental and behavioral disorders in heavily-stricken areas: An ecological study based on big data.}, journal = {Journal of affective disorders}, volume = {361}, number = {}, pages = {589-595}, doi = {10.1016/j.jad.2024.06.070}, pmid = {38908558}, issn = {1573-2517}, mesh = {Humans ; *Earthquakes ; China/epidemiology ; Male ; Female ; Middle Aged ; Adult ; *Mental Disorders/epidemiology ; *Disasters/statistics &amp; numerical data ; *Survivors/psychology/statistics &amp; numerical data ; Prevalence ; Adolescent ; Aged ; *Big Data ; Young Adult ; Risk Factors ; Child ; Urbanization ; }, abstract = {BACKGROUND: This study aimed to explore and evaluate the development trends and differential changes in the prevalence of mental and behavioral disorders among the earthquake survivors in exposure groups (highly hard-hit areas) and control groups (general disaster areas) from 2015 to 2019, as well as to investigate the potential influencing factors.<br><br>METHODS: Data was obtained from the Sichuan Health Information System and the Sichuan Health Yearbook, the prevalence of the exposure group and the control group were calculated, the difference between the two groups was evaluated using the prevalence rate ratio, and a fixed effect model was developed to investigate the potential influencing factors of the prevalence.<br><br>RESULTS: The prevalence by gender and age in the exposure group was always greater than those in the control group (RR>1), although the disparity between the two proceeded to diminish with time. The urbanization rate (&#x3b2;&#xa0;=&#xa0;0.0448, P&#xa0;<&#xa0;0.05) and disaster area levels (&#x3b2;&#xa0;=&#xa0;0.0104, P&#xa0;<&#xa0;0.05) were risk factors for the prevalence of mental and behavioral disorders.<br><br>LIMITATIONS: The study only collected data at the group level following the Wenchuan earthquake. Consequently, the findings are only applicable at the group level. Furthermore, diagnostic criteria for various types of mental and behavioral disorders diseases were not provided.<br><br>CONCLUSIONS: The earthquake has a significant long-term impact on mental health. It is necessary to continuously monitor the mental health of Wenchuan earthquake survivors and take appropriate post-disaster intervention measures.}, }
@article {pmid38907904, year = {2024}, author = {Roved, J}, title = {MHCtools 1.5: Analysis of MHC Sequencing Data in R.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2809}, number = {}, pages = {275-295}, pmid = {38907904}, issn = {1940-6029}, mesh = {*Major Histocompatibility Complex/genetics ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Software ; Animals ; *Haplotypes/genetics ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; Genetic Variation ; Genotyping Techniques/methods ; Genotype ; }, abstract = {The genes of the major histocompatibility complex (MHC) play a vital role in the vertebrate immune system and have attracted considerable interest in evolutionary biology. While the MHC has been characterized in detail in humans (human leukocyte antigen, HLA) and in model organisms such as the mouse, studies in non-model organisms often lack prior knowledge about structure, genetic variability, and evolutionary properties of this locus. MHC genotyping in non-model species commonly relies on PCR-based amplicon sequencing, and while several published protocols facilitate generation of MHC sequence data, there is a lack of transparent and standardized tools for downstream data analysis.Here, I present the R package MHCtools version 1.5, which contains 15 tools that (i) assist accurate MHC genotyping from high-throughput amplicon sequencing data, and provide standardized methods to analyze (ii) MHC diversity, (iii) MHC supertypes, and (iv) MHC haplotypes.I hope that MHCtools will be helpful in future studies of the MHC in non-model species and that it may help to advance our understanding of the important roles of the MHC in ecology and evolution.}, }
@article {pmid38904377, year = {2024}, author = {Berasategui, A and Salem, H and Moller, AG and Christopher, Y and Vidaurre Montoya, Q and Conn, C and Read, TD and Rodrigues, A and Ziemert, N and Gerardo, N}, title = {Genomic insights into the evolution of secondary metabolism of Escovopsis and its allies, specialized fungal symbionts of fungus-farming ants.}, journal = {mSystems}, volume = {9}, number = {7}, pages = {e0057624}, pmid = {38904377}, issn = {2379-5077}, support = {BE6922/1-1//Deutsche Forschungsgemeinschaft (DFG)/ ; EXC 2124 - 390838134//Deutsche Forschungsgemeinschaft (DFG)/ ; 1711545//National Science Foundation (NSF)/ ; 1754595//National Science Foundation (NSF)/ ; 1927411//National Science Foundation (NSF)/ ; 2021/04706-1//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (FAPESP)/ ; 2019/03746-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (FAPESP)/ ; }, mesh = {*Symbiosis ; *Ants/microbiology ; Animals ; *Secondary Metabolism/genetics ; *Phylogeny ; *Genome, Fungal ; *Hypocreales/genetics/metabolism ; Evolution, Molecular ; Genomics ; Biosynthetic Pathways/genetics ; }, abstract = {The metabolic intimacy of symbiosis often demands the work of specialists. Natural products and defensive secondary metabolites can drive specificity by ensuring infection and propagation across host generations. But in contrast to bacteria, little is known about the diversity and distribution of natural product biosynthetic pathways among fungi and how they evolve to facilitate symbiosis and adaptation to their host environment. In this study, we define the secondary metabolism of Escovopsis and closely related genera, symbionts in the gardens of fungus-farming ants. We ask how the gain and loss of various biosynthetic pathways correspond to divergent lifestyles. Long-read sequencing allowed us to define the chromosomal features of representative Escovopsis strains, revealing highly reduced genomes composed of seven to eight chromosomes. The genomes are highly syntenic with macrosynteny decreasing with increasing phylogenetic distance, while maintaining a high degree of mesosynteny. An ancestral state reconstruction analysis of biosynthetic pathways revealed that, while many secondary metabolites are shared with non-ant-associated Sordariomycetes, 56 pathways are unique to the symbiotic genera. Reflecting adaptation to diverging ant agricultural systems, we observe that the stepwise acquisition of these pathways mirrors the ecological radiations of attine ants and the dynamic recruitment and replacement of their fungal cultivars. As different clades encode characteristic combinations of biosynthetic gene clusters, these delineating profiles provide important insights into the possible mechanisms underlying specificity between these symbionts and their fungal hosts. Collectively, our findings shed light on the evolutionary dynamic nature of secondary metabolism in Escovopsis and its allies, reflecting adaptation of the symbionts to an ancient agricultural system.IMPORTANCEMicrobial symbionts interact with their hosts and competitors through a remarkable array of secondary metabolites and natural products. Here, we highlight the highly streamlined genomic features of attine-associated fungal symbionts. The genomes of Escovopsis species, as well as species from other symbiont genera, many of which are common with the gardens of fungus-growing ants, are defined by seven chromosomes. Despite a high degree of metabolic conservation, we observe some variation in the symbionts' potential to produce secondary metabolites. As the phylogenetic distribution of the encoding biosynthetic gene clusters coincides with attine transitions in agricultural systems, we highlight the likely role of these metabolites in mediating adaptation by a group of highly specialized symbionts.}, }
@article {pmid38902323, year = {2024}, author = {Horváth, G and Sos, T and Bóné, G and Lőrincz, CE and Pap, PL and Herczeg, G}, title = {Integrating behavioural thermoregulatory strategy into the animal personality framework using the common lizard, Zootoca vivipara as a model.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {14200}, pmid = {38902323}, issn = {2045-2322}, support = {PD 132041//Nemzeti Kutat&#xe1;si, Fejleszt&#xe9;si &#xe9;s Innovaci&#xf3;s Alap/ ; }, mesh = {Animals ; *Lizards/physiology ; *Body Temperature Regulation/physiology ; *Behavior, Animal/physiology ; Personality/physiology ; Male ; Female ; }, abstract = {The study of consistent between-individual behavioural variation in single (animal personality) and across two or more behavioural traits (behavioural syndrome) is a central topic of behavioural ecology. Besides behavioural type (individual mean behaviour), behavioural predictability (environment-independent within-individual behavioural variation) is now also seen as an important component of individual behavioural strategy. Research focus is still on the 'Big Five' traits (activity, exploration, risk-taking, sociability and aggression), but another prime candidate to integrate to the personality framework is behavioural thermoregulation in small-bodied poikilotherms. Here, we found animal personality in thermoregulatory strategy (selected body temperature, voluntary thermal maximum, setpoint range) and 'classic' behavioural traits (activity, sheltering, risk-taking) in common lizards (Zootoca vivipara). Individual state did not explain the between-individual variation. There was a positive behavioural type-behavioural predictability correlation in selected body temperature. Besides an activity-risk-taking syndrome, we also found a risk-taking-selected body temperature syndrome. Our results suggest that animal personality and behavioural syndrome are present in common lizards, both including thermoregulatory and 'classic' behavioural traits, and selecting high body temperature with high predictability is part of the risk-prone behavioural strategy. We propose that thermoregulatory behaviour should be considered with equal weight to the 'classic' traits in animal personality studies of poikilotherms employing active behavioural thermoregulation.}, }
@article {pmid38899724, year = {2024}, author = {Parra, J and Jarmusch, SA and Duncan, KR}, title = {Multi-omics analysis of antagonistic interactions among free-living Pseudonocardia from diverse ecosystems.}, journal = {Environmental microbiology}, volume = {26}, number = {6}, pages = {e16635}, doi = {10.1111/1462-2920.16635}, pmid = {38899724}, issn = {1462-2920}, support = {2-1-4-17-1-037//Ministerio de Ciencia Tecnolog&#xed;a y Telecomunicaciones, Costa Rica/ ; NNF19OC0055625//Novo Nordisk Fonden/ ; DNRF137//Danmarks Grundforskningsfond/ ; }, mesh = {Antibiosis ; *Ecosystem ; Genomics ; Geologic Sediments/microbiology ; *Metabolomics ; Multigene Family ; Multiomics ; *Phylogeny ; *Pseudonocardia/genetics ; }, abstract = {Actinomycetes are a phylogenetically diverse bacterial group which are widely distributed across terrestrial and aquatic ecosystems. Within this order, the genus Pseudonocardia and their specialised metabolites have been the focus of previous ecological studies due to their antagonistic interactions with other microorganisms and their mutualistic interactions with insects. However, the chemical ecology of free-living Pseudonocardia remains understudied. This study applies a multi-omics approach to investigate the chemical ecology of free-living actinomycetes from the genus Pseudonocardia. In a comparative genomics analysis, it was observed that the biosynthetic gene cluster family distribution was influenced mainly by phylogenetic distance rather than the geographic or ecological origin of strains. This finding was also observed in the mass spectrometry-based metabolomic profiles of nine Pseudonocardia species isolated from marine sediments and two terrestrial species. Antagonist interactions between these 11 species were examined, and matrix-assisted laser desorption/ionisation-mass spectrometry imaging was used to examine in situ chemical interactions between the Southern Ocean strains and their phylogenetically close relatives. Overall, it was demonstrated that phylogeny was the main predictor of antagonistic interactions among free-living Pseudonocardia. Moreover, two features at m/z 441.15 and m/z 332.20 were identified as metabolites related to these interspecies interactions.}, }
@article {pmid38897481, year = {2024}, author = {Kepp, KP and Aavitsland, P and Ballin, M and Balloux, F and Baral, S and Bardosh, K and Bauchner, H and Bendavid, E and Bhopal, R and Blumstein, DT and Boffetta, P and Bourgeois, F and Brufsky, A and Collignon, PJ and Cripps, S and Cristea, IA and Curtis, N and Djulbegovic, B and Faude, O and Flacco, ME and Guyatt, GH and Hajishengallis, G and Hemkens, LG and Hoffmann, T and Joffe, AR and Klassen, TP and Koletsi, D and Kontoyiannis, DP and Kuhl, E and La Vecchia, C and Lallukka, T and Lambris, J and Levitt, M and Makridakis, S and Maltezou, HC and Manzoli, L and Marusic, A and Mavragani, C and Moher, D and Mol, BW and Muka, T and Naudet, F and Noble, PW and Nordström, A and Nordström, P and Pandis, N and Papatheodorou, S and Patel, CJ and Petersen, I and Pilz, S and Plesnila, N and Ponsonby, AL and Rivas, MA and Saltelli, A and Schabus, M and Schippers, MC and Schünemann, H and Solmi, M and Stang, A and Streeck, H and Sturmberg, JP and Thabane, L and Thombs, BD and Tsakris, A and Wood, SN and Ioannidis, JPA}, title = {Panel stacking is a threat to consensus statement validity.}, journal = {Journal of clinical epidemiology}, volume = {173}, number = {}, pages = {111428}, pmid = {38897481}, issn = {1878-5921}, support = {R35 GM122543/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Conflict of Interest ; *Consensus ; *COVID-19/prevention &amp; control ; *Delphi Technique ; Pandemics ; Reproducibility of Results ; SARS-CoV-2 ; Consensus Statements as Topic ; }, abstract = {Consensus statements can be very influential in medicine and public health. Some of these statements use systematic evidence synthesis but others fail on this front. Many consensus statements use panels of experts to deduce perceived consensus through Delphi processes. We argue that stacking of panel members toward one particular position or narrative is a major threat, especially in absence of systematic evidence review. Stacking may involve financial conflicts of interest, but nonfinancial conflicts of strong advocacy can also cause major bias. Given their emerging importance, we describe here how such consensus statements may be misleading, by analyzing in depth a recent high-impact Delphi consensus statement on COVID-19 recommendations as a case example. We demonstrate that many of the selected panel members and at least 35% of the core panel members had advocated toward COVID-19 elimination (Zero-COVID) during the pandemic and were leading members of aggressive advocacy groups. These advocacy conflicts were not declared in the Delphi consensus publication, with rare exceptions. Therefore, we propose that consensus statements should always require rigorous evidence synthesis and maximal transparency on potential biases toward advocacy or lobbyist groups to be valid. While advocacy can have many important functions, its biased impact on consensus panels should be carefully avoided.}, }
@article {pmid38896539, year = {2024}, author = {Sänger, M and De Mecquenem, N and Lewińska, KE and Bountris, V and Lehmann, F and Leser, U and Kosch, T}, title = {A qualitative assessment of using ChatGPT as large language model for scientific workflow development.}, journal = {GigaScience}, volume = {13}, number = {}, pages = {}, pmid = {38896539}, issn = {2047-217X}, support = {//German Research Foundation/ ; }, mesh = {*Workflow ; Programming Languages ; Software ; Computational Biology/methods ; Humans ; }, abstract = {BACKGROUND: Scientific workflow systems are increasingly popular for expressing and executing complex data analysis pipelines over large datasets, as they offer reproducibility, dependability, and scalability of analyses by automatic parallelization on large compute clusters. However, implementing workflows is difficult due to the involvement of many black-box tools and the deep infrastructure stack necessary for their execution. Simultaneously, user-supporting tools are rare, and the number of available examples is much lower than in classical programming languages.<br><br>RESULTS: To address these challenges, we investigate the efficiency of large language models (LLMs), specifically ChatGPT, to support users when dealing with scientific workflows. We performed 3 user studies in 2 scientific domains to evaluate ChatGPT for comprehending, adapting, and extending workflows. Our results indicate that LLMs efficiently interpret workflows but achieve lower performance for exchanging components or purposeful workflow extensions. We characterize their limitations in these challenging scenarios and suggest future research directions.<br><br>CONCLUSIONS: Our results show a high accuracy for comprehending and explaining scientific workflows while achieving a reduced performance for modifying and extending workflow descriptions. These findings clearly illustrate the need for further research in this area.}, }
@article {pmid38892087, year = {2024}, author = {Suárez, I and Collado, IG and Garrido, C}, title = {Revealing Hidden Genes in Botrytis cinerea: New Insights into Genes Involved in the Biosynthesis of Secondary Metabolites.}, journal = {International journal of molecular sciences}, volume = {25}, number = {11}, pages = {}, pmid = {38892087}, issn = {1422-0067}, support = {PID-2021-1228990-B-C21 and PID-2021-1228990-B-C22//MCIN/AEI/ 10.13039/501100011033 and ERDF A way of making Europe/ ; }, mesh = {*Botrytis/genetics/pathogenicity ; *Secondary Metabolism/genetics ; *Peptide Synthases/genetics/metabolism ; *Polyketide Synthases/genetics/metabolism ; Fungal Proteins/genetics/metabolism ; Computational Biology/methods ; Multigene Family ; Genes, Fungal ; }, abstract = {Utilizing bioinformatics tools, this study expands our understanding of secondary metabolism in Botrytis cinerea, identifying novel genes within polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS), sesquiterpene cyclase (STC), diterpene cyclase (DTC), and dimethylallyltryptophan synthase (DMATS) families. These findings enrich the genetic framework associated with B. cinerea's pathogenicity and ecological adaptation, offering insights into uncharted metabolic pathways. Significantly, the discovery of previously unannotated genes provides new molecular targets for developing targeted antifungal strategies, promising to enhance crop protection and advance our understanding of fungal biochemistry. This research not only broadens the scope of known secondary metabolites but also opens avenues for future exploration into B. cinerea's biosynthetic capabilities, potentially leading to novel antifungal compounds. Our work underscores the importance of integrating bioinformatics and genomics for fungal research, paving the way for sustainable agricultural practices by pinpointing precise molecular interventions against B. cinerea. This study sets a foundation for further investigations into the fungus's secondary metabolism, with implications for biotechnology and crop disease management.}, }
@article {pmid38888768, year = {2024}, author = {Sanderson, H and White, AP}, title = {Methods for Genomic Epidemiology of Bacterial Pathogens: Example Salmonella.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2813}, number = {}, pages = {19-37}, pmid = {38888768}, issn = {1940-6029}, mesh = {*Salmonella/genetics ; Humans ; *Genomics/methods ; *Salmonella Infections/microbiology/epidemiology ; *Phylogeny ; *Genome, Bacterial ; *Molecular Epidemiology/methods ; Virulence Factors/genetics ; Disease Outbreaks ; Drug Resistance, Bacterial/genetics ; Interspersed Repetitive Sequences/genetics ; }, abstract = {Genomics has revolutionized how we characterize and monitor infectious diseases for public health. The surveillance and characterization of Salmonella has improved drastically within the past decade. In this chapter, we discuss the prerequisites for good bacterial genomics studies and make note of advantages and disadvantages of this research approach. We discuss methods for outbreak detection and the evolutionary and epidemiological characterization of Salmonella spp. We provide an outline for determining the sequence type and serotype of isolates, building a core genome phylogenetic tree, and detecting antimicrobial resistance genes, virulence factors, and mobile genetic elements. These methods can be used to study other pathogenic bacterial species.}, }
@article {pmid38882711, year = {2023}, author = {Waterhouse, RM and Adam-Blondon, AF and Balech, B and Barta, E and Ying Shi Chua, P and Di Cola, V and Heil, KF and Hughes, GM and Jermiin, LS and Kalaš, M and Lanfear, J and Pafilis, E and Palagi, PM and Papageorgiou, AC and Paupério, J and Psomopoulos, F and Raes, N and Burgin, J and Gabaldón, T}, title = {The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity.}, journal = {F1000Research}, volume = {12}, number = {}, pages = {}, pmid = {38882711}, issn = {2046-1402}, mesh = {Humans ; *Biodiversity ; Conservation of Natural Resources ; }, abstract = {Biodiversity loss is now recognised as one of the major challenges for humankind to address over the next few decades. Unless major actions are taken, the sixth mass extinction will lead to catastrophic effects on the Earth's biosphere and human health and well-being. ELIXIR can help address the technical challenges of biodiversity science, through leveraging its suite of services and expertise to enable data management and analysis activities that enhance our understanding of life on Earth and facilitate biodiversity preservation and restoration. This white paper, prepared by the ELIXIR Biodiversity Community, summarises the current status and responses, and presents a set of plans, both technical and community-oriented, that should both enhance how ELIXIR Services are applied in the biodiversity field and how ELIXIR builds connections across the many other infrastructures active in this area. We discuss the areas of highest priority, how they can be implemented in cooperation with the ELIXIR Platforms, and their connections to existing ELIXIR Communities and international consortia. The article provides a preliminary blueprint for a Biodiversity Community in ELIXIR and is an appeal to identify and involve new stakeholders.}, }
@article {pmid38882082, year = {2024}, author = {Fei, J and Jiang, X and Yang, H and Fan, K and Che, Y and Sun, B and Guo, T}, title = {Research and Development of a Big Data Application Platform for Intelligent Blast Furnace Intensive Management and Control.}, journal = {ACS omega}, volume = {9}, number = {23}, pages = {24674-24684}, pmid = {38882082}, issn = {2470-1343}, abstract = {The blast furnaces of Anshan Iron and Steel have completed large-scale modernization, and a large amount of information technology has been popularized and applied to the process of blast furnaces. This paper takes the Anshan Iron and Steel blast furnace group as the research background. Based on big data and industrial Internet technology, combining the smelting process mechanism of blast furnace production and using artificial intelligence, cloud analysis, and other technologies, the data management platform was used to effectively integrate the data of each process of the blast furnace and design the data asset catalogue. The big data application platform for the intensive control of the blast furnace was established. The data were in multidimensional in-depth mining, and the intelligent application model of the blast furnace was established. The visual intelligent monitoring of the safe production and operation of the blast furnace was realized, and the production operation of the blast furnace was guided. The overall information and intelligent level of production operation and management of the blast furnace have been improved.}, }
@article {pmid38880940, year = {2024}, author = {Medo, A and Ohte, N and Doi, H and Kamdee, K and Koba, K and Arai, N and Mitsunaga, Y and Kume, M and Kojima, D and Nose, T and Yokoyama, A and Viputhanumas, T and Mitamura, H}, title = {Trophic niche partitioning and intraspecific variation in food resource use in the genus Pangasianodon in a reservoir revealed by stable isotope analysis of multiple tissues.}, journal = {Journal of fish biology}, volume = {105}, number = {3}, pages = {814-824}, doi = {10.1111/jfb.15842}, pmid = {38880940}, issn = {1095-8649}, support = {16H05792//Japan Society for the Promotion of Science/ ; 22J13642//Japan Society for the Promotion of Science/ ; 202180216//Japan Society for the Promotion of Science/ ; //Shikata Memorial Trust for Nature Conservation/ ; 25610919060008//Thailand Institute of Nuclear Technology/ ; }, mesh = {Animals ; *Nitrogen Isotopes/analysis ; *Carbon Isotopes/analysis ; *Diet/veterinary ; Food Chain ; Thailand ; Liver/chemistry ; Ecosystem ; Catfishes ; }, abstract = {Understanding the mechanism by which non-native fish species integrate into native communities is crucial for evaluating the possibility of their establishment success. The genus Pangasianodon, comprising Pangasianodon gigas and Pangasianodon hypophthalmus, has been introduced into reservoirs, which are non-native habitats, for fishery stock enhancement. P. gigas and P. hypophthalmus often successfully establish and co-occur in several Thai reservoirs, but there is little information on differences in food resource use between the two species. To investigate the trophic niche width of P. gigas and P. hypophthalmus in a Thai reservoir, we conducted stable carbon and nitrogen ratio (δ[13]C and δ[15]N) analyses. We examined the degree of individual specialization in both species using the δ[13]C and δ[15]N values of muscle and liver tissues, which provides long- and short-term diet information. The isotopic niches did not overlap between P. gigas and P. hypophthalmus. The δ[15]N value of P. gigas was significantly higher than that of P. hypophthalmus, whereas the δ[13]C value did not significantly differ between the two species. The isotopic niche sizes were larger in P. hypophthalmus than in P. gigas. Individual specialization was observed in P. hypophthalmus but not in P. gigas, indicating that intraspecific variation in food resource use was larger in P. hypophthalmus compared to P. gigas. These findings suggest that trophic niche partitioning was one of the factors facilitating the establishment success of P. gigas and P. hypophthalmus in a reservoir, but the establishment process may differ between the two species.}, }
@article {pmid38873190, year = {2023}, author = {Boyes, D and Hammond, J and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Notch-wing Button, Acleris emargana (Fabricius, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {376}, pmid = {38873190}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Acleris emargana (the Notch-wing Button; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 691.4 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.34 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,886 protein coding genes.}, }
@article {pmid38870844, year = {2024}, author = {Rocha, LP and Machado, &#xcd;E and Fogal, AS and Malta, DC and Velasquez-Melendez, G and Felisbino-Mendes, MS}, title = {Burden of disease and direct costs to the health system attributable to high body mass index in Brazil.}, journal = {Public health}, volume = {233}, number = {}, pages = {121-129}, doi = {10.1016/j.puhe.2024.05.013}, pmid = {38870844}, issn = {1476-5616}, mesh = {Humans ; Brazil/epidemiology ; *Body Mass Index ; Cross-Sectional Studies ; Male ; *Cost of Illness ; Female ; Middle Aged ; Adult ; *Health Care Costs/statistics &amp; numerical data ; Hospitalization/statistics &amp; numerical data/economics ; National Health Programs/economics/statistics &amp; numerical data ; Obesity/epidemiology/economics ; Aged ; Disability-Adjusted Life Years ; }, abstract = {OBJECTIVES: Excess weight, measured by a high body mass index (BMI), is associated with the onset of many diseases, which can, in turn, lead to disability and premature death, subsequently placing a significant burden on healthcare services. This study analysed the burden of disease and the direct costs to the Brazilian Unified Health System (Sistema Único de Saúde [SUS]) attributable to high BMI in the Brazilian population.<br><br>STUDY DESIGN: Ecological study.<br><br>METHODS: This ecological study had two components: (1) a time-series assessment to analyse the burden of diseases attributable to high BMI from 1990 to 2019 in Brazil; and (2) a cross-sectional design to estimate the direct costs of SUS hospitalisations and outpatient procedures attributable to high BMI in 2019. Estimates from the Global Burden of Disease study and the costs of hospital admissions and outpatient procedures from the Department of Informatics of the Brazilian Unified Health System were used. Deaths, years of life lost to premature death (YLLs), years lived with disability (YLDs), and years of life lost adjusted for disability (DALYs) were analysed. The direct health cost was obtained in Brazilian Real (R$) and converted in international Dollars (INT$).<br><br>RESULTS: The current study found a reduction in the number of DALYs, YLLs, and deaths per 100,000 population of cardiovascular disease (CVD) attributable to high BMI and an increase in YLD due to diabetes and cardiovascular disease attributable to high BMI from 1990 to 2019. In 2019, high BMI resulted in 2404 DALYs, 658 YLDs, 1746 YLLs, and 76 deaths per 100,000 inhabitants. In the same year, INT$377.30 million was spent on hospitalisations and high- and medium-complexity procedures to control non-communicable diseases attributable to high BMI. The states in the South and Southeast regions of Brazil presented the highest total cost per 10,000 inhabitants. CVDs and chronic kidney disease showed the highest costs per hospital admission, whereas neoplasms and CVDs presented the highest costs for outpatient procedures.<br><br>CONCLUSIONS: High BMI causes significant disease burden and financial costs. The highest expenses observed were not in locations with the highest burden of disease attributable to high BMI. These findings highlight the need to improve current public policies and apply cost-effective intervention packages, focussing on equity and the promotion of healthier lifestyles to reduce overweight/obesity, especially in localities with low socioeconomic status.}, }
@article {pmid38870774, year = {2024}, author = {Bucci, S and Berry, N and Ainsworth, J and Berry, K and Edge, D and Eisner, E and Emsley, R and Forbes, G and Hassan, L and Lewis, S and Machin, M and Haddock, G}, title = {Effects of Actissist, a digital health intervention for early psychosis: A randomized clinical trial.}, journal = {Psychiatry research}, volume = {339}, number = {}, pages = {116025}, doi = {10.1016/j.psychres.2024.116025}, pmid = {38870774}, issn = {1872-7123}, support = {MR/P026664/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; Female ; Male ; Adult ; *Psychotic Disorders/therapy ; *Schizophrenia/therapy ; *Mobile Applications ; *Cognitive Behavioral Therapy/methods ; *Telemedicine ; Young Adult ; Middle Aged ; Outcome Assessment, Health Care ; Treatment Outcome ; Digital Health ; }, abstract = {Schizophrenia affects 24 million people worldwide. Digital health interventions drawing on psychological principles have been developed, but their effectiveness remains unclear. This parallel, assessor-blinded, randomized clinical trial aimed to investigate whether a cognitive behaviour therapy-informed digital health intervention (Actissist app) confers added benefit on psychotic symptoms over and above remote symptom monitoring (ClinTouch app). Participants recruited from UK community health services were randomized 1:1 to receive either Actissist plus treatment as usual (TAU) or ClinTouch plus TAU. Eligible participants were adults with schizophrenia-spectrum psychosis within five years of first episode onset meeting a criterion level of positive symptoms severity. The primary outcome was Positive and Negative Syndrome Scale (PANSS) symptoms total score at 12 weeks post-randomization. Intention-to-treat analysis included 172 participants, with 149 participants (86.6 %) providing primary outcome data. Actissist plus TAU was not associated with greater reduction than an active control remote symptom monitoring app (ClinTouch) in PANSS total score at post-randomization. There were no significant effects between groups across secondary measures. There were no serious adverse reactions. Both groups improved on the primary psychotic symptoms measure at primary end-point and on secondary measures over time. The Actissist app is safe but not superior to digital symptom monitoring.}, }
@article {pmid38868628, year = {2023}, author = {Obbard, DJ and ,  and ,  and ,  and , }, title = {The genome sequence of a drosophilid fruit fly, Hirtodrosophila cameraria (Haliday, 1833).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {361}, pmid = {38868628}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Hirtodrosophila cameraria (a drosophilid fruit fly; Arthropoda; Insecta; Diptera; Drosophilidae). The genome sequence is 214.5 megabases in span. Most of the assembly is scaffolded into 4 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.94 kilobases in length.}, }
@article {pmid38867756, year = {2024}, author = {Boyes, D and Lewis, OT and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Marbled White Spot, Protodeltote pygarga (Hufnagel, 1766).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {7}, pmid = {38867756}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Protodeltote pygarga (the Marbled White Spot; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 421.1 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.48 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,784 protein coding genes.}, }
@article {pmid38867206, year = {2024}, author = {Anjos, C and Duarte, D and Fatsini, E and Matias, D and Cabrita, E}, title = {Comparative transcriptome analysis reveals molecular damage associated with cryopreservation in Crassostrea angulata D-larvae rather than to cryoprotectant exposure.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {591}, pmid = {38867206}, issn = {1471-2164}, support = {SFRH/BD/130910/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; CCMAR/Multi/04326/2022//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 0139_VENUS_5_E//Interreg POCTEP/ ; JRA2-H2020-INFRAIA-2016-2017//European Commission/ ; EBB-EAPA_501/2016//Interreg Atlantic Area/ ; }, mesh = {Animals ; *Cryopreservation ; *Crassostrea/genetics/growth &amp; development ; *Cryoprotective Agents/pharmacology/toxicity ; *Larva/genetics/drug effects/growth &amp; development ; *Gene Expression Profiling ; Transcriptome ; Gene Ontology ; }, abstract = {BACKGROUND: The Portuguese oyster Crassostrea angulata, a bivalve of significant economic and ecological importance, has faced a decline in both production and natural populations due to pathologies, climate change, and anthropogenic factors. To safeguard its genetic diversity and improve reproductive management, cryopreservation emerges as a valuable strategy. However, the cryopreservation methodologies lead to some damage in structures and functions of the cells and tissues that can affect post-thaw quality. Transcriptomics may help to understand the molecular consequences related to cryopreservation steps and therefore to identify different freezability biomarkers. This study investigates the molecular damage induced by cryopreservation in C. angulata D-larvae, focusing on two critical steps: exposure to cryoprotectant solution and the freezing/thawing process.<br><br>RESULTS: Expression analysis revealed 3 differentially expressed genes between larvae exposed to cryoprotectant solution and fresh larvae and 611 differentially expressed genes in cryopreserved larvae against fresh larvae. The most significantly enriched gene ontology terms were "carbohydrate metabolic process", "integral component of membrane" and "chitin binding" for biological processes, cellular components and molecular functions, respectively. Kyoto Encyclopedia of Genes and Genomes enrichment analysis identified the "neuroactive ligand receptor interaction", "endocytosis" and "spliceosome" as the most enriched pathways. RNA sequencing results were validate by quantitative RT-PCR, once both techniques presented the same gene expression tendency and a group of 11 genes were considered important molecular biomarkers to be used in further studies for the evaluation of cryodamage.<br><br>CONCLUSIONS: The current work provided valuable insights into the molecular repercussions of cryopreservation on D-larvae of Crassostrea angulata, revealing that the freezing process had a more pronounced impact on larval quality compared to any potential cryoprotectant-induced toxicity. Additionally, was identify 11 genes serving as biomarkers of freezability for D-larvae quality assessment. This research contributes to the development of more effective cryopreservation protocols and detection methods for cryodamage in this species.}, }
@article {pmid38866716, year = {2024}, author = {Brock, MT and Morrison, HG and Maignien, L and Weinig, C}, title = {Impacts of sample handling and storage conditions on archiving physiologically active soil microbial communities.}, journal = {FEMS microbiology letters}, volume = {371}, number = {}, pages = {}, doi = {10.1093/femsle/fnae044}, pmid = {38866716}, issn = {1574-6968}, support = {IOS-1444571//NSF/ ; }, mesh = {*Specimen Handling ; *Soil Microbiology ; *Microbiota ; *Preservation, Biological ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA ; Data Curation ; Phylogeny ; Biodiversity ; Principal Component Analysis ; }, abstract = {Soil microbial communities are fundamental to ecosystem processes and plant growth, yet community composition is seasonally and successionally dynamic, which interferes with long-term iterative experimentation of plant-microbe interactions. We explore how soil sample handling (e.g. filtering) and sample storage conditions impact the ability to revive the original, physiologically active, soil microbial community. We obtained soil from agricultural fields in Montana and Oklahoma, USA and samples were sieved to 2 mm or filtered to 45 µm. Sieved and filtered soil samples were archived at -20°C or -80°C for 50 days and revived for 2 or 7 days. We extracted DNA and the more transient RNA pools from control and treatment samples and characterized microbial communities using 16S amplicon sequencing. Filtration and storage treatments significantly altered soil microbial communities, impacting both species richness and community composition. Storing sieved soil at -20°C did not alter species richness and resulted in the least disruption to the microbial community composition in comparison to nonarchived controls as characterized by RNA pools from soils of both sites. Filtration significantly altered composition but not species richness. Archiving sieved soil at -20°C could allow for long-term and repeated experimentation on preserved physiologically active microbial communities.}, }
@article {pmid38865434, year = {2024}, author = {Iverson, AR and Humple, DL and Cormier, RL and Hahn, TP and Block, TA and Shizuka, D and Lyon, BE and Chaine, AS and Hudson, EJ and Hull, EM}, title = {Winter GPS tagging reveals home ranges during the breeding season for a boreal-nesting migrant songbird, the Golden-crowned Sparrow.}, journal = {PloS one}, volume = {19}, number = {6}, pages = {e0305369}, pmid = {38865434}, issn = {1932-6203}, mesh = {Animals ; *Seasons ; *Geographic Information Systems ; *Animal Migration/physiology ; *Sparrows/physiology ; *Homing Behavior/physiology ; Breeding ; Ecosystem ; British Columbia ; Alaska ; Nesting Behavior/physiology ; }, abstract = {Determining space use for species is fundamental to understanding their ecology, and tracking animals can reveal insights into their spatial ecology on home ranges and territories. Recent technological advances have led to GPS-tracking devices light enough for birds as small as ~30 g, creating novel opportunities to remotely monitor fine-scale movements and space use for these smaller species. We tested whether miniaturized GPS tags can allow us to understand space use of migratory birds away from their capture sites and sought to understand both pre-breeding space use as well as territory and habitat use on the breeding grounds. We used GPS tags to characterize home ranges on the breeding grounds for a migratory songbird with limited available breeding information, the Golden-crowned Sparrow (Zonotrichia atricapilla). Using GPS points from 23 individuals across 26 tags (three birds tagged twice), we found home ranges in Alaska and British Columbia were on average 44.1 ha (95% kernel density estimate). In addition, estimates of territory sizes based on field observations (mean 2.1 ha, 95% minimum convex polygon [MCP]) were three times smaller than 95% MCPs created using GPS tags (mean 6.5 ha). Home ranges included a variety of land cover classes, with shrubland particularly dominant (64-100% of home range cover for all but one bird). Three birds tracked twice returned to the same breeding area each year, supporting high breeding site fidelity for this species. We found reverse spring migration for five birds that flew up to 154 km past breeding destinations before returning. GPS-tracking technology allowed for critical ecological insights into this migratory species that breeds in very remote locations.}, }
@article {pmid38865431, year = {2024}, author = {Tedersoo, L and Hosseyni Moghaddam, MS and Mikryukov, V and Hakimzadeh, A and Bahram, M and Nilsson, RH and Yatsiuk, I and Geisen, S and Schwelm, A and Piwosz, K and Prous, M and Sildever, S and Chmolowska, D and Rueckert, S and Skaloud, P and Laas, P and Tines, M and Jung, JH and Choi, JH and Alkahtani, S and Anslan, S}, title = {EUKARYOME: the rRNA gene reference database for identification of all eukaryotes.}, journal = {Database : the journal of biological databases and curation}, volume = {2024}, number = {}, pages = {}, pmid = {38865431}, issn = {1758-0463}, support = {Distinguished Scientist Fellowship Programme//King Saud University/ ; MOBERC66 MOBTP198//European Regional Development Fund/ ; //LOEWE Zentrum AdRIA/ ; Distinguished Scientist Fellowship Programme//King Saud University/ ; MOBERC66 MOBTP198//European Regional Development Fund/ ; //LOEWE Zentrum AdRIA/ ; }, mesh = {*Eukaryota/genetics ; RNA, Ribosomal, 18S/genetics ; Databases, Genetic ; Databases, Nucleic Acid ; Animals ; Genes, rRNA/genetics ; Phylogeny ; }, abstract = {Molecular identification of micro- and macroorganisms based on nuclear markers has revolutionized our understanding of their taxonomy, phylogeny and ecology. Today, research on the diversity of eukaryotes in global ecosystems heavily relies on nuclear ribosomal RNA (rRNA) markers. Here, we present the research community-curated reference database EUKARYOME for nuclear ribosomal 18S rRNA, internal transcribed spacer (ITS) and 28S rRNA markers for all eukaryotes, including metazoans (animals), protists, fungi and plants. It is particularly useful for the identification of arbuscular mycorrhizal fungi as it bridges the four commonly used molecular markers-ITS1, ITS2, 18S V4-V5 and 28S D1-D2 subregions. The key benefits of this database over other annotated reference sequence databases are that it is not restricted to certain taxonomic groups and it includes all rRNA markers. EUKARYOME also offers a number of reference long-read sequences that are derived from (meta)genomic and (meta)barcoding-a unique feature that can be used for taxonomic identification and chimera control of third-generation, long-read, high-throughput sequencing data. Taxonomic assignments of rRNA genes in the database are verified based on phylogenetic approaches. The reference datasets are available in multiple formats from the project homepage, http://www.eukaryome.org.}, }
@article {pmid38863181, year = {2024}, author = {Wong, RE and Berner, LT and Sullivan, PF and Potter, CS and Dial, RJ}, title = {Pixel walking along the boreal forest-Arctic tundra ecotone: Large scale ground-truthing of satellite-derived greenness (NDVI).}, journal = {Global change biology}, volume = {30}, number = {6}, pages = {e17374}, doi = {10.1111/gcb.17374}, pmid = {38863181}, issn = {1365-2486}, support = {80NSSC22K1247/NASA/NASA/United States ; 80NSSC20M0070//Alaska Space Grant Program/ ; DEB-2133494//National Science Foundation/ ; OPP-1748773//National Science Foundation/ ; OPP-1748849//National Science Foundation/ ; 80NSSC19M0062//Alaska NASA EPSCoR/ ; }, mesh = {Alaska ; Arctic Regions ; *Satellite Imagery ; *Tundra ; Remote Sensing Technology/methods ; Taiga ; Environmental Monitoring/methods ; }, abstract = {In this Technical Advance, we describe a novel method to improve ecological interpretation of remotely sensed vegetation greenness measurements that involved sampling 24,395 Landsat pixels (30 m) across 639 km of Alaska's central Brooks Range. The method goes well beyond the spatial scale of traditional plot-based sampling and thereby more thoroughly relates ground-based observations to satellite measurements. Our example dataset illustrates that, along the boreal-Arctic boundary, vegetation with the greatest Landsat Normalized Difference Vegetation Index (NDVI) is taller than 1 m, woody, and deciduous; whereas vegetation with lower NDVI tends to be shorter, evergreen, or non-woody. The field methods and associated analyses advance efforts to inform satellite data with ground-based vegetation observations using field samples collected at spatial scales that closely match the resolution of remotely sensed imagery.}, }
@article {pmid38862613, year = {2024}, author = {Venu, V and Roth, C and Adikari, SH and Small, EM and Starkenburg, SR and Sanbonmatsu, KY and Steadman, CR}, title = {Multi-omics analysis reveals the dynamic interplay between Vero host chromatin structure and function during vaccinia virus infection.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {721}, pmid = {38862613}, issn = {2399-3642}, support = {20210134ER//DOE | LDRD | Los Alamos National Laboratory (Los Alamos Lab)/ ; }, mesh = {*Chromatin/metabolism/genetics ; Animals ; *Vaccinia virus/genetics/physiology ; Chlorocebus aethiops ; Vero Cells ; Vaccinia/virology/immunology ; Host-Pathogen Interactions/genetics ; Multiomics ; }, abstract = {The genome folds into complex configurations and structures thought to profoundly impact its function. The intricacies of this dynamic structure-function relationship are not well understood particularly in the context of viral infection. To unravel this interplay, here we provide a comprehensive investigation of simultaneous host chromatin structural (via Hi-C and ATAC-seq) and functional changes (via RNA-seq) in response to vaccinia virus infection. Over time, infection significantly impacts global and local chromatin structure by increasing long-range intra-chromosomal interactions and B compartmentalization and by decreasing chromatin accessibility and inter-chromosomal interactions. Local accessibility changes are independent of broad-scale chromatin compartment exchange (~12% of the genome), underscoring potential independent mechanisms for global and local chromatin reorganization. While infection structurally condenses the host genome, there is nearly equal bidirectional differential gene expression. Despite global weakening of intra-TAD interactions, functional changes including downregulated immunity genes are associated with alterations in local accessibility and loop domain restructuring. Therefore, chromatin accessibility and local structure profiling provide impactful predictions for host responses and may improve development of efficacious anti-viral counter measures including the optimization of vaccine design.}, }
@article {pmid38862357, year = {2024}, author = {Knight, E and Rhinehart, T and de Zwaan, DR and Weldy, MJ and Cartwright, M and Hawley, SH and Larkin, JL and Lesmeister, D and Bayne, E and Kitzes, J}, title = {Individual identification in acoustic recordings.}, journal = {Trends in ecology &amp; evolution}, volume = {39}, number = {10}, pages = {947-960}, doi = {10.1016/j.tree.2024.05.007}, pmid = {38862357}, issn = {1872-8383}, mesh = {*Acoustics ; Animals ; Vocalization, Animal ; }, abstract = {Recent advances in bioacoustics combined with acoustic individual identification (AIID) could open frontiers for ecological and evolutionary research because traditional methods of identifying individuals are invasive, expensive, labor-intensive, and potentially biased. Despite overwhelming evidence that most taxa have individual acoustic signatures, the application of AIID remains challenging and uncommon. Furthermore, the methods most commonly used for AIID are not compatible with many potential AIID applications. Deep learning in adjacent disciplines suggests opportunities to advance AIID, but such progress is limited by training data. We suggest that broadscale implementation of AIID is achievable, but researchers should prioritize methods that maximize the potential applications of AIID, and develop case studies with easy taxa at smaller spatiotemporal scales before progressing to more difficult scenarios.}, }
@article {pmid38860489, year = {2024}, author = {Toga, K and Sakamoto, T and Kanda, M and Tamura, K and Okuhara, K and Tabunoki, H and Bono, H}, title = {Long-read genome assembly of the Japanese parasitic wasp Copidosoma floridanum (Hymenoptera: Encyrtidae).}, journal = {G3 (Bethesda, Md.)}, volume = {14}, number = {8}, pages = {}, pmid = {38860489}, issn = {2160-1836}, support = {JPMJPF2010//Center of Innovation for Bio-Digital Transformation/ ; 23K17418//JSPS KAKENHI/ ; }, mesh = {Animals ; Genome, Insect ; Genomics/methods ; Japan ; *Molecular Sequence Annotation ; *Wasps/genetics ; }, abstract = {Copidosoma floridanum is a cosmopolitan species and an egg-larval parasitoid of the Plusiine moth. C. floridanum has a unique development mode called polyembryony, in which over two thousand genetically identical embryos are produced from a single egg. Some embryos develop into sterile soldier larvae precociously, and their emergence period and aggressive behavior differ between the US and Japanese C. floridanum strains. Genome sequencing expects to contribute to our understanding of the molecular bases underlying the progression of polyembryony. However, only the genome sequence of the US strain generated by the short-read assembly has been reported. In the present study, we determined the genome sequence of the Japanese strain using Pacific Biosciences high-fidelity reads and generating a highly contiguous assembly (552.7 Mb, N50: 17.9 Mb). Gene prediction and annotation identified 13,886 transcripts derived from 10,786 gene models. We searched the genomic differences between US and Japanese strains. Among gene models predicted in this study, 100 gene loci in the Japanese strain had extremely different gene structures from those in the US strain. This was accomplished through functional annotation (GGSEARCH) and long-read sequencing. Genomic differences between strains were also reflected in amino acid sequences of vasa that play a central role in caste determination in this species. The genome assemblies constructed in this study will facilitate the genomic comparisons between Japanese and US strains, leading to our understanding of detailed genomic regions responsible for the ecological and physiological characteristics of C. floridanum.}, }
@article {pmid38856681, year = {2024}, author = {Dasgupta, S}, title = {Thinking Beyond Disease Silos: Dysregulated Genes Common in Tuberculosis and Lung Cancer as Identified by Systems Biology and Machine Learning.}, journal = {Omics : a journal of integrative biology}, volume = {28}, number = {7}, pages = {347-356}, doi = {10.1089/omi.2024.0116}, pmid = {38856681}, issn = {1557-8100}, mesh = {Humans ; *Machine Learning ; *Lung Neoplasms/genetics ; *Tuberculosis/genetics ; *Systems Biology/methods ; Computational Biology/methods ; Gene Expression Profiling/methods ; Gene Regulatory Networks ; }, abstract = {The traditional way of thinking about human diseases across clinical and narrow phenomics silos often masks the underlying shared molecular substrates across human diseases. One Health and planetary health fields particularly address such complexities and invite us to think across the conventional disease nosologies. For example, tuberculosis (TB) and lung cancer (LC) are major pulmonary diseases with significant planetary health implications. Despite distinct etiologies, they can coexist in a given community or patient. This is both a challenge and an opportunity for preventive medicine, diagnostics, and therapeutics innovation. This study reports a bioinformatics analysis of publicly available gene expression data, identifying overlapping dysregulated genes, downstream regulators, and pathways in TB and LC. Analysis of NCBI-GEO datasets (GSE83456 and GSE103888) unveiled differential expression of CEACAM6, MUC1, ADM, DYSF, PLOD2, and GAS6 genes in both diseases, with pathway analysis indicating association with lysine degradation pathway. Random forest, a machine-learning-based classification, achieved accuracies of 84% for distinguishing TB from controls and 83% for discriminating LC from controls using these specific genes. Additionally, potential drug targets were identified, with molecular docking confirming the binding affinity of warfarin to GAS6. Taken together, the present study speaks of the pressing need to rethink clinical diagnostic categories of human diseases and that TB and LC might potentially share molecular substrates. Going forward, planetary health and One Health scholarship are poised to cultivate new ways of thinking about diseases not only across medicine and ecology but also across traditional diagnostic conventions.}, }
@article {pmid38855721, year = {2023}, author = {Boyes, D and Broad, GR and Holland, PWH and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Cloaked Minor, Mesoligia furuncula (Denis &amp; Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {251}, pmid = {38855721}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Mesoligia furuncula (the Cloaked Minor; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 889.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,903 protein coding genes.}, }
@article {pmid38854694, year = {2024}, author = {Christenhusz, MJM and Pannell, JR and Twyford, AD and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Annual Mercury, Mercurialis annua L., 1753 (Euphorbiaceae).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {102}, pmid = {38854694}, issn = {2398-502X}, abstract = {We present a genome assembly from a diploid female Mercurialis annua (the Annual Mercury; Tracheophyta; Magnoliopsida; Malpighiales; Euphorbiaceae). The genome sequence is 453.2 megabases in span. Most of the assembly is scaffolded into 8 chromosomal pseudomolecules, including the X chromosome. The organelle genomes have also been assembled, and the mitochondrial genome is 435.28 kilobases in length, while the plastid genome is 169.65 kilobases in length.}, }
@article {pmid38853065, year = {2024}, author = {O'Connor, JB and Mottlowitz, M and Wagner, BD and Harris, JK and Laguna, TA}, title = {Metabolomics analysis of bronchoalveolar lavage fluid predicts unique features of the lower airway in pediatric cystic fibrosis.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {23}, number = {6}, pages = {1087-1094}, doi = {10.1016/j.jcf.2024.04.017}, pmid = {38853065}, issn = {1873-5010}, mesh = {Humans ; *Cystic Fibrosis/microbiology/metabolism/physiopathology ; *Bronchoalveolar Lavage Fluid/chemistry/microbiology ; Child ; Female ; Male ; *Metabolomics/methods ; Microbiota ; Adolescent ; Bronchoscopy/methods ; RNA, Ribosomal, 16S/analysis ; Respiratory Function Tests/methods ; }, abstract = {BACKGROUND: Progressive, obstructive lung disease resulting from chronic infection and inflammation is the leading cause of morbidity and mortality in persons with cystic fibrosis (PWCF). Metabolomics and next -generation sequencing (NGS) of airway secretions can allow for better understanding of cystic fibrosis (CF) pathophysiology. In this study, global metabolomic profiling on bronchoalveolar lavage fluid (BALF) obtained from pediatric PWCF and disease controls (DCs) was performed and compared to lower airway microbiota, inflammation, and lung function.<br><br>METHODS: BALF was collected from children undergoing flexible bronchoscopies for clinical indications. Metabolomic profiling was performed using a platform developed by Metabolon Inc. Total bacterial load (TBL) was measured using quantitative polymerase chain reaction (qPCR), and bacterial communities were characterized using 16S ribosomal RNA (rRNA) sequencing. Random Forest Analysis (RFA), principal component analysis (PCA), and hierarchical clustering analysis (HCA) were performed.<br><br>RESULTS: One hundred ninety-five BALF samples were analyzed, 142 (73 %) from PWCF. Most metabolites (425/665) and summed categories (7/9) were significantly increased in PWCF. PCA of the metabolomic data revealed CF BALF exhibited more dispersed clustering compared to DC BALF. Higher metabolite concentrations correlated with increased inflammation, increased abundance of Staphylococcus, and decreased lung function.<br><br>CONCLUSIONS: The lower airway metabolome of PWCF was defined by a complex expansion of metabolomic activity. These findings could be attributed to heightened inflammation in PWCF and aspects of the CF airway polymicrobial ecology. CF-specific metabolomic features are associated with the unique underlying biology of the CF airway.}, }
@article {pmid38852834, year = {2024}, author = {Goodus, MT and Alfredo, AN and Carson, KE and Dey, P and Pukos, N and Schwab, JM and Popovich, PG and Gao, J and Mo, X and Bruno, RS and McTigue, DM}, title = {Spinal cord injury-induced metabolic impairment and steatohepatitis develops in non-obese rats and is exacerbated by premorbid obesity.}, journal = {Experimental neurology}, volume = {379}, number = {}, pages = {114847}, pmid = {38852834}, issn = {1090-2430}, support = {R01 DK126008/DK/NIDDK NIH HHS/United States ; R35 NS111582/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; *Spinal Cord Injuries/complications/metabolism/pathology ; Rats ; *Obesity/complications/metabolism/pathology ; Male ; Fatty Liver/metabolism/pathology/etiology ; Rats, Sprague-Dawley ; Metabolic Syndrome/metabolism/complications/pathology ; Disease Models, Animal ; Insulin Resistance/physiology ; }, abstract = {Impaired sensorimotor functions are prominent complications of spinal cord injury (SCI). A clinically important but less obvious consequence is development of metabolic syndrome (MetS), including increased adiposity, hyperglycemia/insulin resistance, and hyperlipidemia. MetS predisposes SCI individuals to earlier and more severe diabetes and cardiovascular disease compared to the general population, which trigger life-threatening complications (e.g., stroke, myocardial infarcts). Although each comorbidity is known to be a risk factor for diabetes and other health problems in obese individuals, their relative contribution or perceived importance in propagating systemic pathology after SCI has received less attention. This could be explained by an incomplete understanding of MetS promoted by SCI compared with that from the canonical trigger diet-induced obesity (DIO). Thus, here we compared metabolic-related outcomes after SCI in lean rats to those of uninjured rats with DIO. Surprisingly, SCI-induced MetS features were equal to or greater than those in obese uninjured rats, including insulin resistance, endotoxemia, hyperlipidemia, liver inflammation and steatosis. Considering the endemic nature of obesity, we also evaluated the effect of premorbid obesity in rats receiving SCI; the combination of DIO + SCI exacerbated MetS and liver pathology compared to either alone, suggesting that obese individuals that sustain a SCI are especially vulnerable to metabolic dysfunction. Notably, premorbid obesity also exacerbated intraspinal lesion pathology and worsened locomotor recovery after SCI. Overall, these results highlight that normal metabolic function requires intact spinal circuitry and that SCI is not just a sensory-motor disorder, but also has significant metabolic consequences.}, }
@article {pmid38850116, year = {2024}, author = {Yi, X and Kemppainen, P and Merilä, J}, title = {SLRfinder: A method to detect candidate sex-linked regions with linkage disequilibrium clustering.}, journal = {Molecular ecology resources}, volume = {24}, number = {6}, pages = {e13985}, doi = {10.1111/1755-0998.13985}, pmid = {38850116}, issn = {1755-0998}, support = {N_HKU763/21//National Natural Science Foundation of China/Research Grants Council (RGC) Joint Research Scheme/ ; }, mesh = {*Linkage Disequilibrium ; *Sex Chromosomes/genetics ; Computational Biology/methods ; Animals ; Male ; Female ; Cluster Analysis ; }, abstract = {Despite their critical roles in genetic sex determination, sex chromosomes remain unknown in many non-model organisms, especially those having recently evolved sex-linked regions (SLRs). These evolutionarily young and labile sex chromosomes are important for understanding early sex chromosome evolution but are difficult to identify due to the lack of Y/W degeneration and SLRs limited to small genomic regions. Here, we present SLRfinder, a method to identify candidate SLRs using linkage disequilibrium (LD) clustering, heterozygosity and genetic divergence. SLRfinder does not rely on specific sequencing methods or a specific type of reference genome (e.g., from the homomorphic sex). In addition, the input of SLRfinder does not require phenotypic sexes, which may be unknown from population sampling, but sex information can be incorporated and is necessary to validate candidate SLRs. We tested SLRfinder using various published datasets and compared it to the local principal component analysis (PCA) method and the depth-based method Sex Assignment Through Coverage (SATC). As expected, the local PCA method could not be used to identify unknown SLRs. SATC works better on conserved sex chromosomes, whereas SLRfinder outperforms SATC in analysing labile sex chromosomes, especially when SLRs harbour inversions. Power analyses showed that SLRfinder worked better when sampling more populations that share the same SLR. If analysing one population, a relatively larger sample size (around 50) is needed for sufficient statistical power to detect significant SLR candidates, although true SLRs are likely always top-ranked. SLRfinder provides a novel and complementary approach for identifying SLRs and uncovering additional sex chromosome diversity in nature.}, }
@article {pmid38845010, year = {2024}, author = {Wang, S and Lee, HC and Lee, S}, title = {Predicting herb-disease associations using network-based measures in human protein interactome.}, journal = {BMC complementary medicine and therapies}, volume = {24}, number = {Suppl 2}, pages = {218}, pmid = {38845010}, issn = {2662-7671}, support = {GIST Research Institute IIBR//Gwangju Institute of Science and Technology/ ; GIST Research Institute (GRI) GIST-MIT research Collaboration//Gwangju Institute of Science and Technology/ ; 2021M3A9G8022959//Ministry of Science and ICT, South Korea/ ; 2021R1C1C1006336//Ministry of Science and ICT, South Korea/ ; HR22C141105//Ministry of Health and Welfare/ ; }, mesh = {Humans ; *Protein Interaction Maps ; Computer Simulation ; Computational Biology/methods ; }, abstract = {BACKGROUND: Natural herbs are frequently used to treat diseases or to relieve symptoms in many countries. Moreover, as their safety has been proven for a long time, they are considered as main sources of new drug development. However, in many cases, the herbs are still prescribed relying on ancient records and/or traditional practices without scientific evidences. More importantly, the medicinal efficacy of the herbs has to be evaluated in the perspective of MCMT (multi-compound multi-target) effects, but most efforts focus on identifying and analyzing a single compound experimentally. To overcome these hurdles, computational approaches which are based on the scientific evidences and are able to handle the MCMT effects are needed to predict the herb-disease associations.<br><br>RESULTS: In this study, we proposed a network-based in silico method to predict the herb-disease associations. To this end, we devised a new network-based measure, WACP (weighted average closest path length), which not only quantifies proximity between herb-related genes and disease-related genes but also considers compound compositions of each herb. As a result, we confirmed that our method successfully predicts the herb-disease associations in the human protein interactome (AUROC&#x2009;=&#x2009;0.777). In addition, we observed that our method is superior than the other simple network-based proximity measures (e.g. average shortest and closest path length). Additionally, we analyzed the associations between Brassica oleracea var. italica and its known associated diseases more specifically as case studies. Finally, based on the prediction results of the WACP, we suggested novel herb-disease pairs which are expected to have potential relations and their literature evidences.<br><br>CONCLUSIONS: This method could be a promising solution to modernize the use of the natural herbs by providing the scientific evidences about the molecular associations between the herb-related genes targeted by multiple compounds and the disease-related genes in the human protein interactome.}, }
@article {pmid38844398, year = {2024}, author = {Xiao, Z and Robertson, S and Long, E and Flaig, R and Kirby, L and Romaniuk, L and Murray, A and Whalley, H}, title = {Loneliness in the Digital World: protocol for a co-produced ecological momentary assessment study in adolescents.}, journal = {BMJ open}, volume = {14}, number = {6}, pages = {e087374}, pmid = {38844398}, issn = {2044-6055}, support = {/WT_/Wellcome Trust/United Kingdom ; /MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; *Loneliness/psychology ; Adolescent ; *Ecological Momentary Assessment ; *Mental Health ; Female ; Child ; Male ; Social Interaction ; Surveys and Questionnaires ; Research Design ; Depression ; Scotland ; Anxiety ; }, abstract = {INTRODUCTION: Loneliness has been identified as an important public health issue, peaking during adolescence. Previous research has suggested that social interaction is a key factor in loneliness, and positive social interaction can act as a protective factor against loneliness. However, it is unclear whether there are differing impacts of in-person and online social interaction on adolescents' loneliness and mental health. Ecological Momentary Assessment (EMA) designs are ideally suited for better understanding these associations.<br><br>METHOD AND ANALYSIS: In the 'Loneliness in the Digital World' study, we will use a co-developed EMA design to capture daily social interactions, loneliness and mental health such as positive and negative emotions, depression and anxiety in approximately 200 adolescents aged 12-15 years. We will combine this with comprehensive information gathered from online surveys. Analysing the data using techniques such as dynamic structural equation modelling, we will examine, among other research questions, the associations between online and in-person social interaction and feelings of loneliness. The results can help inform interventions to support adolescents with high levels of loneliness and poor mental health.<br><br>ETHICS AND DISSEMINATION: We received the ethics approval for the data collection from The Academic and Clinical Central Office for Research and Development, followed by the College of Medicine and Veterinary Medicine Ethics panel at University of Edinburgh, and finally reviewed by East of Scotland Research Ethics Service. The results will be disseminated through journal publications, conferences and seminar presentations and to relevant stakeholders such as teachers.}, }
@article {pmid38841890, year = {2024}, author = {Pedersen, MB and Beedholm, K and Hubancheva, A and Koseva, K and Uebel, AS and Hochradel, K and Madsen, PT and Stidsholt, L}, title = {Clutter resilience via auditory stream segregation in echolocating greater mouse-eared bats.}, journal = {The Journal of experimental biology}, volume = {227}, number = {12}, pages = {}, doi = {10.1242/jeb.246889}, pmid = {38841890}, issn = {1477-9145}, support = {//Frands Christian Frantsen Foundation/ ; FP2 0135-00343B//Natur og Univers, Det Frie Forskningsr&#xe5;d/ ; AU337272//Fonden Frands Christian Frantsens Legat/ ; 41386//Villum Fonden/ ; CF16-0405//Carlsbergfondet/ ; }, mesh = {Animals ; *Chiroptera/physiology ; *Echolocation/physiology ; Male ; Female ; Vocalization, Animal/physiology ; }, abstract = {Bats use echolocation to navigate and hunt in darkness, and must in that process segregate target echoes from unwanted clutter echoes. Bats may do this by approaching a target at steep angles relative to the plane of the background, utilizing their directional transmission and receiving systems to minimize clutter from background objects, but it remains unknown how bats negotiate clutter that cannot be spatially avoided. Here, we tested the hypothesis that when movement no longer offers spatial release, echolocating bats mitigate clutter by calling at lower source levels and longer call intervals to ease auditory streaming. We trained five greater mouse-eared bats (Myotis myotis) to land on a spherical loudspeaker with two microphones attached. We used a phantom-echo setup, where the loudspeaker/target transmitted phantom clutter echoes by playing back the bats' own calls at time delays of 1, 3 and 5 ms with a virtual target strength 7 dB higher than the physical target. We show that the bats successfully landed on the target, irrespective of the clutter echo delays. Rather than decreasing their source levels, the bats used similar source level distributions in clutter and control trials. Similarly, the bats did not increase their call intervals, but instead used the same distribution of call intervals across control and clutter trials. These observations reject our hypothesis, leading us to conclude that bats display great resilience to clutter via short auditory integration times and acute auditory stream segregation rather than via biosonar adjustments.}, }
@article {pmid38840517, year = {2024}, author = {Walker, XJ and Hart, S and Hansen, WD and Jean, M and Brown, CD and Stuart Chapin, F and Hewitt, R and Hollingsworth, TN and Mack, MC and Johnstone, JF}, title = {Factors limiting the potential range expansion of lodgepole pine in Interior Alaska.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {34}, number = {5}, pages = {e2983}, doi = {10.1002/eap.2983}, pmid = {38840517}, issn = {1051-0761}, support = {05-1-2-06//Joint Fire Science Program/ ; //Natural Sciences and Engineering Research Council of Canada/ ; PNW01-JV11261952-23//U.S. Fish and Wildlife Service/ ; RC-2109//Strategic Environmental Research and Development Program/ ; RC-2754//Strategic Environmental Research and Development Program/ ; DEB-0620579//National Science Foundation/ ; DEB-1636476//National Science Foundation/ ; DEB-2224776//National Science Foundation/ ; USFS-PNW01-JV11261952-23//National Science Foundation/ ; RJVA-PNW-20-JV-11261932-018//National Science Foundation/ ; OPP-2116862//National Science Foundation/ ; NNX15AT71A/NASA/NASA/United States ; }, mesh = {*Pinus/physiology ; Alaska ; Climate Change ; Models, Biological ; Seedlings ; Demography ; Animals ; Ecosystem ; }, abstract = {Understanding the factors influencing species range limits is increasingly crucial in anticipating migrations due to human-caused climate change. In the boreal biome, ongoing climate change and the associated increases in the rate, size, and severity of disturbances may alter the distributions of boreal tree species. Notably, Interior Alaska lacks native pine, a biogeographical anomaly that carries implications for ecosystem structure and function. The current range of lodgepole pine (Pinus contorta var. latifolia) in the adjacent Yukon Territory may expand into Interior Alaska, particularly with human assistance. Evaluating the potential for pine expansion in Alaska requires testing constraints on range limits such as dispersal limitations, environmental tolerance limits, and positive or negative biotic interactions. In this study, we used field experiments with pine seeds and transplanted seedlings, complemented by model simulations, to assess the abiotic and biotic factors influencing lodgepole pine seedling establishment and growth after fire in Interior Alaska. We found that pine could successfully recruit, survive, grow, and reproduce across our broadly distributed network of experimental sites. Our results show that both mammalian herbivory and competition from native tree species are unlikely to constrain pine growth and that environmental conditions commonly found in Interior Alaska fall well within the tolerance limits for pine. If dispersal constraints are released, lodgepole pine could have a geographically expansive range in Alaska, and once established, its growth is sufficient to support pine-dominated stands. Given the impacts of lodgepole pine on ecosystem processes such as increases in timber production, carbon sequestration, landscape flammability, and reduced forage quality, natural or human-assisted migration of this species is likely to substantially alter responses of Alaskan forest ecosystems to climate change.}, }
@article {pmid38839953, year = {2024}, author = {Senior, RA and Bagwyn, R and Leng, D and Killion, AK and Jetz, W and Wilcove, DS}, title = {Global shortfalls in documented actions to conserve biodiversity.}, journal = {Nature}, volume = {630}, number = {8016}, pages = {387-391}, pmid = {38839953}, issn = {1476-4687}, mesh = {Animals ; *Biodiversity ; *Conservation of Natural Resources/methods/statistics &amp; numerical data ; Databases, Factual ; *Endangered Species/statistics &amp; numerical data ; Extinction, Biological ; *Internationality ; Introduced Species/statistics &amp; numerical data ; }, abstract = {Threatened species are by definition species that are in need of assistance. In the absence of suitable conservation interventions, they are likely to disappear soon[1]. There is limited understanding of how and where conservation interventions are applied globally, or how well they work[2,3]. Here, using information from the International Union for Conservation of Nature Red List and other global databases, we find that for species at risk from three of the biggest drivers of biodiversity loss-habitat loss, overexploitation for international trade and invasive species[4]-many appear to lack the appropriate types of conservation interventions. Indeed, although there has been substantial recent expansion of the protected area network, we still find that 91% of threatened species have insufficient representation of their habitats within protected areas. Conservation interventions are not implemented uniformly across different taxa and regions and, even when present, have infrequently led to substantial improvements in the status of species. For 58% of the world's threatened terrestrial species, we find conservation interventions to be notably insufficient or absent. We cannot determine whether such species are truly neglected, or whether efforts to recover them are not included in major conservation databases. If they are indeed neglected, the outlook for many of the world's threatened species is grim without more and better targeted action.}, }
@article {pmid38838462, year = {2024}, author = {Runge, MC and Shea, K and Howerton, E and Yan, K and Hochheiser, H and Rosenstrom, E and Probert, WJM and Borchering, R and Marathe, MV and Lewis, B and Venkatramanan, S and Truelove, S and Lessler, J and Viboud, C}, title = {Scenario design for infectious disease projections: Integrating concepts from decision analysis and experimental design.}, journal = {Epidemics}, volume = {47}, number = {}, pages = {100775}, pmid = {38838462}, issn = {1878-0067}, support = {U24 GM132013/GM/NIGMS NIH HHS/United States ; Z99 TW999999/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Humans ; *COVID-19/epidemiology/prevention &amp; control/transmission ; *Decision Support Techniques ; Forecasting ; SARS-CoV-2 ; Communicable Diseases/epidemiology ; Pandemics/prevention &amp; control ; Decision Making ; Research Design ; }, abstract = {Across many fields, scenario modeling has become an important tool for exploring long-term projections and how they might depend on potential interventions and critical uncertainties, with relevance to both decision makers and scientists. In the past decade, and especially during the COVID-19 pandemic, the field of epidemiology has seen substantial growth in the use of scenario projections. Multiple scenarios are often projected at the same time, allowing important comparisons that can guide the choice of intervention, the prioritization of research topics, or public communication. The design of the scenarios is central to their ability to inform important questions. In this paper, we draw on the fields of decision analysis and statistical design of experiments to propose a framework for scenario design in epidemiology, with relevance also to other fields. We identify six different fundamental purposes for scenario designs (decision making, sensitivity analysis, situational awareness, horizon scanning, forecasting, and value of information) and discuss how those purposes guide the structure of scenarios. We discuss other aspects of the content and process of scenario design, broadly for all settings and specifically for multi-model ensemble projections. As an illustrative case study, we examine the first 17 rounds of scenarios from the U.S. COVID-19 Scenario Modeling Hub, then reflect on future advancements that could improve the design of scenarios in epidemiological settings.}, }
@article {pmid38837409, year = {2024}, author = {Rico-Jiménez, M and Udaondo, Z and Krell, T and Matilla, MA}, title = {Auxin-mediated regulation of susceptibility to toxic metabolites, c-di-GMP levels, and phage infection in the rhizobacterium Serratia plymuthica.}, journal = {mSystems}, volume = {9}, number = {7}, pages = {e0016524}, pmid = {38837409}, issn = {2379-5077}, support = {PID2020-112612GB-I00//Spanish Ministry for Science and Innovation/ ; PID2019-103972GA-I00//Spanish Ministry for Science and Innovation/ ; 2023AEP002//Consejo Superior de Investigaciones Cient&#xed;ficas (CSIC)/ ; P18-FR-1621//Junta de Andalucia/ ; }, mesh = {*Indoleacetic Acids/metabolism ; *Serratia/metabolism/genetics/drug effects/pathogenicity ; *Cyclic GMP/metabolism/analogs &amp; derivatives ; Gene Expression Regulation, Bacterial/drug effects ; Bacteriophages ; Signal Transduction/drug effects ; Biofilms/drug effects/growth &amp; development ; Bacterial Proteins/metabolism/genetics ; Plant Growth Regulators/metabolism ; Transcriptome/drug effects ; }, abstract = {UNLABELLED: The communication between plants and their microbiota is highly dynamic and involves a complex network of signal molecules. Among them, the auxin indole-3-acetic acid (IAA) is a critical phytohormone that not only regulates plant growth and development, but is emerging as an important inter- and intra-kingdom signal that modulates many bacterial processes that are important during interaction with their plant hosts. However, the corresponding signaling cascades remain largely unknown. Here, we advance our understanding of the largely unknown mechanisms by which IAA carries out its regulatory functions in plant-associated bacteria. We showed that IAA caused important changes in the global transcriptome of the rhizobacterium Serratia plymuthica and multidisciplinary approaches revealed that IAA sensing interferes with the signaling mediated by other pivotal plant-derived signals such as amino acids and 4-hydroxybenzoic acid. Exposure to IAA caused large alterations in the transcript levels of genes involved in amino acid metabolism, resulting in significant metabolic alterations. IAA treatment also increased resistance to toxic aromatic compounds through the induction of the AaeXAB pump, which also confers resistance to IAA. Furthermore, IAA promoted motility and severely inhibited biofilm formation; phenotypes that were associated with decreased c-di-GMP levels and capsule production. IAA increased capsule gene expression and enhanced bacterial sensitivity to a capsule-dependent phage. Additionally, IAA induced the expression of several genes involved in antibiotic resistance and led to changes in the susceptibility and responses to antibiotics with different mechanisms of action. Collectively, our study illustrates the complexity of IAA-mediated signaling in plant-associated bacteria.<br><br>IMPORTANCE: Signal sensing plays an important role in bacterial adaptation to ecological niches and hosts. This communication appears to be particularly important in plant-associated bacteria since they possess a large number of signal transduction systems that respond to a wide diversity of chemical, physical, and biological stimuli. IAA is emerging as a key inter- and intra-kingdom signal molecule that regulates a variety of bacterial processes. However, despite the extensive knowledge of the IAA-mediated regulatory mechanisms in plants, IAA signaling in bacteria remains largely unknown. Here, we provide insight into the diversity of mechanisms by which IAA regulates primary and secondary metabolism, biofilm formation, motility, antibiotic susceptibility, and phage sensitivity in a biocontrol rhizobacterium. This work has important implications for our understanding of bacterial ecology in plant environments and for the biotechnological and clinical applications of IAA, as well as related molecules.}, }
@article {pmid38831386, year = {2024}, author = {Duo, H and Li, Y and Lan, Y and Tao, J and Yang, Q and Xiao, Y and Sun, J and Li, L and Nie, X and Zhang, X and Liang, G and Liu, M and Hao, Y and Li, B}, title = {Systematic evaluation with practical guidelines for single-cell and spatially resolved transcriptomics data simulation under multiple scenarios.}, journal = {Genome biology}, volume = {25}, number = {1}, pages = {145}, pmid = {38831386}, issn = {1474-760X}, support = {KJQN202100538//Science and Technology Research Program of Chongqing Municipal Education Commission/ ; 62101087//National Natural Science Foundation of China/ ; 2021MD703942//China Postdoctoral Science Foundation/ ; YKC23027//Graduate Research Innovation Project of Chongqing Normal University/ ; YNPRAEC-2023004//Open Fund of Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology/ ; }, mesh = {*Single-Cell Analysis/methods ; *Gene Expression Profiling/methods ; Humans ; Software ; Computer Simulation ; Transcriptome ; Computational Biology/methods ; Sequence Analysis, RNA/methods ; RNA-Seq/methods/standards ; }, abstract = {BACKGROUND: Single-cell RNA sequencing (scRNA-seq) and spatially resolved transcriptomics (SRT) have led to groundbreaking advancements in life sciences. To develop bioinformatics tools for scRNA-seq and SRT data and perform unbiased benchmarks, data simulation has been widely adopted by providing explicit ground truth and generating customized datasets. However, the performance of simulation methods under multiple scenarios has not been comprehensively assessed, making it challenging to choose suitable methods without practical guidelines.<br><br>RESULTS: We systematically evaluated 49 simulation methods developed for scRNA-seq and/or SRT data in terms of accuracy, functionality, scalability, and usability using 152 reference datasets derived from 24 platforms. SRTsim, scDesign3, ZINB-WaVE, and scDesign2 have the best accuracy performance across various platforms. Unexpectedly, some methods tailored to scRNA-seq data have potential compatibility for simulating SRT data. Lun, SPARSim, and scDesign3-tree outperform other methods under corresponding simulation scenarios. Phenopath, Lun, Simple, and MFA yield high scalability scores but they cannot generate realistic simulated data. Users should consider the trade-offs between method accuracy and scalability (or functionality) when making decisions. Additionally, execution errors are mainly caused by failed parameter estimations and appearance of missing or infinite values in calculations. We provide practical guidelines for method selection, a standard pipeline Simpipe (https://github.com/duohongrui/simpipe ; https://doi.org/10.5281/zenodo.11178409), and an online tool Simsite (https://www.ciblab.net/software/simshiny/) for data simulation.<br><br>CONCLUSIONS: No method performs best on all criteria, thus a good-yet-not-the-best method is recommended if it solves problems effectively and reasonably. Our comprehensive work provides crucial insights for developers on modeling gene expression data and fosters the simulation process for users.}, }
@article {pmid38826163, year = {2024}, author = {Onyango, B and Copeland, R and Mbogholi, J and Wamalwa, M and Kibet, C and Tonnang, HEZ and Senagi, K}, title = {WiPFIM: A digital platform for interlinking biocollections of wild plants, fruits, associated insects, and their molecular barcodes.}, journal = {Ecology and evolution}, volume = {14}, number = {6}, pages = {e11457}, pmid = {38826163}, issn = {2045-7758}, abstract = {The current knowledge on insects feeding on fruits is limited, and some of the scarce existing data on the fruit-associated insects are secluded within the host institutions. Consequently, their value is not fully realized. Moreover, in countries like Kenya, the integration of biocollections data within a digital framework has not been fully exploited. To address these gaps, this article presents a description of the development of a web-based platform for data sharing and integrating biodiversity historical data of wild plants, fruits, associated insects, and their molecular barcodes (WiPFIM) while leveraging data science technologies. The barcodes corresponding to the biocollections data were retrieved from BOLD database. The platform is an online resource about fruit-insect interactions that can be of interest to a worldwide community of users and can be useful in building innovative tools. The platform is accessible online at https://test-dmmg.icipe.org/wpfhi.}, }
@article {pmid38825206, year = {2024}, author = {Wei, Q and Xue, L and Liao, S and Liu, Y}, title = {Ecohydrological indicators and environmental flow assessment in the middle and lower reaches of the Huai River, China.}, journal = {The Science of the total environment}, volume = {940}, number = {}, pages = {173639}, doi = {10.1016/j.scitotenv.2024.173639}, pmid = {38825206}, issn = {1879-1026}, abstract = {The vitality of river ecosystems is vital for the sustainable development of river basins, with the assessment of environmental flow (EF) playing a pivotal role in eco-informatics. This study delves into the middle and lower reaches (MLR) of the Huai River basin (HRB) in China, utilizing hydrological data spanning from 1950 to 2020. Its principal objective lies in the selection of ecohydrological indicators to refine the estimation of EF in the HRB. Employing principal component analysis (PCA), ecologically relevant hydrological indicators (ERHIs) were discerned and scrutinized for their hydrological characteristics. The analysis extended to evaluating hydrological shifts at different stations using ERHIs, determining suitable EF in the MLR, and delineating the trajectories of appropriate intra-annual flows in different hydrological years through HEC-RPT. Based on a variety of mutation test methods, the change point of runoff sequence was determined in 1991. The PCA analysis identified eight ERHIs, reflecting hydrological changes of 49.79 % and 56.26 % at Bengbu and Sanhezha, respectively, which indicate a moderate alteration. Based on ERHIs, the other stations in the HRB exhibited hydrological alterations ranging from 33 % to 47 %, notably highlighting substantial changes in maximal 30d flow and flow fall rate. The optimal flood pulse discharge in the middle reaches is 4150 m[3]/s, 3140 m[3]/s and 2150 m[3]/s in wet, dry and dry years, respectively. Downstream, flood pulse flow in wet, normal and dry years should exceed 4070 m[3]/s, 3110 m[3]/s and 1980 m[3]/s, respectively. The research contributes significantly to the management of rivers and the sustainable conservation of the ecological milieu.}, }
@article {pmid38824636, year = {2024}, author = {Xie, PZ and Fan, YX and Chapman, C and Ma, C and Wu, CF and Hu, P and Hu, LL and Fan, PF}, title = {Determinants of macaques' space use: A test for the ecological constraints model using GPS collars.}, journal = {American journal of primatology}, volume = {86}, number = {8}, pages = {e23636}, doi = {10.1002/ajp.23636}, pmid = {38824636}, issn = {1098-2345}, support = {33000-42090019//Forestry Administration of Guangdong Province/ ; Basic Research 20180285//Shenzhen Science and Technology Innovation Committee/ ; 23lgzy002//Fundamental Research Funds for the Central Universities, Sun Yat-sun University/ ; }, mesh = {Animals ; *Macaca mulatta/physiology ; *Geographic Information Systems ; *Homing Behavior ; China ; Male ; Female ; Ecosystem ; Temperature ; Seasons ; Islands ; }, abstract = {As a central topic in Behavioral Ecology, animal space use involves dynamic responses to social and ecological factors. We collared 22 rhesus macaques (Macaca mulatta) from six groups on Neilingding Island, China, and collected 80,625 hourly fixes over a year. Using this high-resolution location data set, we quantified the macaques' space use at the individual level and tested the ecological constraints model while considering various environmental and human interfering factors. As predicted by the ecological constraints model, macaques in larger groups had longer daily path lengths (DPLs) and larger home ranges. We found an inverted U-shape relationship between mean daily temperatures and DPLs, indicating that macaques traveled farther on mild temperature days, while they decreased DPLs when temperatures were too high or too low. Anthropogenic food subsidies were positively correlated to DPLs, while the effect of rainfall was negative. Macaques decreased their DPLs and core areas when more flowers and less leaves were available, suggesting that macaques shifted their space use patterns to adapt to the seasonal differences in food resources. By applying GPS collars on a large number of individuals living on a small island, we gained valuable insights into within-group exploitation competition in wild rhesus macaques.}, }
@article {pmid38823656, year = {2024}, author = {Sundar Panja, A}, title = {The systematic codon usage bias has an important effect on genetic adaption in native species.}, journal = {Gene}, volume = {926}, number = {}, pages = {148627}, doi = {10.1016/j.gene.2024.148627}, pmid = {38823656}, issn = {1879-0038}, mesh = {*Codon Usage ; *Selection, Genetic ; *Evolution, Molecular ; Endangered Species ; Mutation ; Animals ; Codon/genetics ; Adaptation, Physiological/genetics ; Extremophiles/genetics ; }, abstract = {Random mutations increase genetic variety and natural selection enhances adaption over generations. Codon usage biases (CUB) provide clues about the genome adaptation mechanisms of native species and extremophile species. Significant numbers of gene (CDS) of nine classes of endangered, native species, including extremophiles and mesophiles were utilised to compute CUB. Codon usage patterns differ among the lineages of endangered and extremophiles with native species. Polymorphic usage of nucleotides with codon burial suggests parallelism of native species within relatively confined taxonomic groups. Utilizing the deviation pattern of CUB of endangered and native species, I present a calculation parameter to estimate the extinction risk of endangered species. Species diversity and extinction risk are both positively associated with the propensity of random mutation in CDS (Coding DNA sequence). Codon bias tenet profoundly selected and it governs to adaptive evolution of native species.}, }
@article {pmid38823290, year = {2024}, author = {Lopez-Labrador, FX and Huber, M and Sidorov, IA and Brown, JR and Cuypers, L and Laenen, L and Vanmechelen, B and Maes, P and Fischer, N and Pichler, I and Storey, N and Atkinson, L and Schmutz, S and Kufner, V and van Boheemen, S and Mulders, CE and Grundhoff, A and Blümke, P and Robitaille, A and Cinek, O and Hubáčková, K and Mourik, K and Boers, SA and Stauber, L and Salmona, M and Cappy, P and Ramette, A and Franze', A and LeGoff, J and Claas, ECJ and Rodriguez, C and de Vries, JJC and , }, title = {Multicenter benchmarking of short and long read wet lab protocols for clinical viral metagenomics.}, journal = {Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology}, volume = {173}, number = {}, pages = {105695}, doi = {10.1016/j.jcv.2024.105695}, pmid = {38823290}, issn = {1873-5967}, mesh = {*Metagenomics/methods/standards ; Humans ; *Benchmarking ; *Viruses/genetics/classification/isolation &amp; purification ; *Sensitivity and Specificity ; High-Throughput Nucleotide Sequencing/methods/standards ; Virus Diseases/diagnosis/virology ; Computational Biology/methods ; }, abstract = {Metagenomics is gradually being implemented for diagnosing infectious diseases. However, in-depth protocol comparisons for viral detection have been limited to individual sets of experimental workflows and laboratories. In this study, we present a benchmark of metagenomics protocols used in clinical diagnostic laboratories initiated by the European Society for Clinical Virology (ESCV) Network on NGS (ENNGS). A mock viral reference panel was designed to mimic low biomass clinical specimens. The panel was used to assess the performance of twelve metagenomic wet lab protocols currently in use in the diagnostic laboratories of participating ENNGS member institutions. Both Illumina and Nanopore, shotgun and targeted capture probe protocols were included. Performance metrics sensitivity, specificity, and quantitative potential were assessed using a central bioinformatics pipeline. Overall, viral pathogens with loads down to 10[4] copies/ml (corresponding to CT values of 31 in our PCR assays) were detected by all the evaluated metagenomic wet lab protocols. In contrast, lower abundant mixed viruses of CT values of 35 and higher were detected only by a minority of the protocols. Considering the reference panel as the gold standard, optimal thresholds to define a positive result were determined per protocol, based on the horizontal genome coverage. Implementing these thresholds, sensitivity and specificity of the protocols ranged from 67 to 100 % and 87 to 100 %, respectively. A variety of metagenomic protocols are currently in use in clinical diagnostic laboratories. Detection of low abundant viral pathogens and mixed infections remains a challenge, implying the need for standardization of metagenomic analysis for use in clinical settings.}, }
@article {pmid38822995, year = {2024}, author = {Meier, TA and Refahi, MS and Hearne, G and Restifo, DS and Munoz-Acuna, R and Rosen, GL and Woloszynek, S}, title = {The Role and Applications of Artificial Intelligence in the Treatment of Chronic Pain.}, journal = {Current pain and headache reports}, volume = {28}, number = {8}, pages = {769-784}, pmid = {38822995}, issn = {1534-3081}, mesh = {Humans ; *Chronic Pain/therapy ; *Artificial Intelligence ; Pain Management/methods ; Precision Medicine/methods ; }, abstract = {PURPOSE OF REVIEW: This review aims to explore the interface between artificial intelligence (AI) and chronic pain, seeking to identify areas of focus for enhancing current treatments and yielding novel therapies.<br><br>RECENT FINDINGS: In the United States, the prevalence of chronic pain is estimated to be upwards of 40%. Its impact extends to increased healthcare costs, reduced economic productivity, and strain on healthcare resources. Addressing this condition is particularly challenging due to its complexity and the significant variability in how patients respond to treatment. Current options often struggle to provide long-term relief, with their benefits rarely outweighing the risks, such as dependency or other side effects. Currently, AI has impacted four key areas of chronic pain treatment and research: (1) predicting outcomes based on clinical information; (2) extracting features from text, specifically clinical notes; (3) modeling 'omic data to identify meaningful patient subgroups with potential for personalized treatments and improved understanding of disease processes; and (4) disentangling complex neuronal signals responsible for pain, which current therapies attempt to modulate. As AI advances, leveraging state-of-the-art architectures will be essential for improving chronic pain treatment. Current efforts aim to extract meaningful representations from complex data, paving the way for personalized medicine. The identification of unique patient subgroups should reveal targets for tailored chronic pain treatments. Moreover, enhancing current treatment approaches is achievable by gaining a more profound understanding of patient physiology and responses. This can be realized by leveraging AI on the increasing volume of data linked to chronic pain.}, }
@article {pmid38822898, year = {2024}, author = {Asefa, A and Reuber, VM and Miehe, G and Wraase, L and Wube, T and Farwig, N and Schabo, DG}, title = {Giant root-rat engineering and livestock grazing activities regulate plant functional trait diversity of an Afroalpine vegetation community in the Bale Mountains, Ethiopia.}, journal = {Oecologia}, volume = {205}, number = {2}, pages = {281-293}, pmid = {38822898}, issn = {1432-1939}, support = {NA 783/12-2, FA-925/14-1 und SCHA-2085/3-1, MI271/33-2]//German Research Council (DFG) within the Research Unit 2358 ("The Mountain Exile Hypothesis")/ ; }, mesh = {Ethiopia ; Animals ; *Livestock ; *Ecosystem ; Rodentia/physiology ; }, abstract = {Disturbances from rodent engineering and human activities profoundly impact ecosystem structure and functioning. Whilst we know that disturbances modulate plant communities, comprehending the mechanisms through which rodent and human disturbances influence the functional trait diversity and trait composition of plant communities is important to allow projecting future changes and to enable informed decisions in response to changing intensity of the disturbances. Here, we evaluated the changes in functional trait diversity and composition of Afroalpine plant communities in the Bale Mountains of Ethiopia along gradients of engineering disturbances of a subterranean endemic rodent, the giant root-rat (Tachyoryctes macrocephalus Rüppell 1842) and human activities (settlement establishment and livestock grazing). We conducted RLQ (co-inertia analysis) and fourth-corner analyses to test for trait-disturbance (rodent engineering/human activities) covariation. Overall, our results show an increase in plant functional trait diversity with increasing root-rat engineering and increasing human activities. We found disturbance specific association with traits. Specifically, we found strong positive association of larger seed mass with increasing root-rat fresh burrow density, rhizomatous vegetative propagation negatively associated with increasing root-rat old burrow, and stolonifereous vegetative propagation positively associated with presence of root-rat mima mound. Moreover, both leaf size and leaf nitrogen content were positively associated with livestock dung abundance but negatively with distance from settlement. Overall, our results suggest that disturbances by rodents filter plant traits related to survival and reproduction strategies, whereas human activities such as livestock grazing act as filters for traits related to leaf economics spectrum along acquisitive resource-use strategy.}, }
@article {pmid38822152, year = {2024}, author = {Li, X and Bai, Y and Xu, C and Liu, S and Yu, H and Kong, L and Du, S and Li, Q}, title = {OysterDB: A Genome Database for Ostreidae.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {26}, number = {4}, pages = {827-834}, pmid = {38822152}, issn = {1436-2236}, support = {2022LZGCQY010, 2021ZLGX03 and 2021TSGC1240//Shandong Province Agriculture Research System Project/ ; CARS-49//China Agriculture Research System Project/ ; }, mesh = {Animals ; *Databases, Genetic ; *Ostreidae/genetics ; *Genome ; Molecular Sequence Annotation ; Computational Biology ; Genomics ; }, abstract = {The molluscan family Ostreidae, commonly known as oysters, is an important molluscan group due to its economic and ecological importance. In recent years, an abundance of genomic data of Ostreidae species has been generated and available in public domain. However, there is still a lack of a high-efficiency database platform to store and distribute these data with comprehensive tools. In this study, we developed an oyster genome database (OysterDB) to consolidate oyster genomic data. This database includes eight oyster genomes and 208,923 protein-coding gene annotations. Bioinformatic tools, such as BLAST and JBrowse, are integrated into the database to provide a user-friendly platform for homologous sequence searching, visualization of genomes, and screen for candidate gene information. Moreover, OysterDB will be continuously updated with ever-growing oyster genomic resources and facilitate future studies for comparative and functional genomic analysis of oysters (http://oysterdb.com.cn/).}, }
@article {pmid38820292, year = {2023}, author = {Damian-Serrano, A and Sutherland, KR}, title = {A Developmental Ontology for the Colonial Architecture of Salps.}, journal = {The Biological bulletin}, volume = {245}, number = {1}, pages = {9-18}, doi = {10.1086/730459}, pmid = {38820292}, issn = {1939-8697}, mesh = {Animals ; *Urochordata/growth &amp; development/physiology/anatomy &amp; histology ; Life Cycle Stages/physiology ; Biological Ontologies ; }, abstract = {AbstractColonial animals are composed of clonal individuals that remain physically connected and physiologically integrated. Salps are tunicates with a dual life cycle, including an asexual solitary stage that buds sexual colonies composed of jet-propelling zooids that efficiently swim together as a single unit by multijet propulsion. Colonies from different species develop distinct architectures characterized by their zooid arrangement patterns, but this diversity has received little attention. Thus, these architectures have never been formally defined using a framework of variables and axes that would allow comparative analyses. We set out to define an ontology of the salp colony architecture morphospace and describe the developmental pathways that build the different architectures. To inform these definitions, we collected and photographed live specimens of adult and developing colonies through offshore scuba diving. Since all salp colonies begin their development as a transversal double chain, we characterized each adult colonial architecture as a series of developmental transitions, such as rotations and translations of zooids, relative to their orientation at this early shared stage. We hypothesize that all adult architectures are either final or intermediate stages within three developmental pathways toward bipinnate, cluster, or helical forms. This framework will enable comparative studies on the biomechanical implications, ecological functions, evolutionary history, and engineering applications of the diversity of salp colony architectures.}, }
@article {pmid38819974, year = {2024}, author = {Tang, Z and Tang, S and Wang, H and Li, R and Zhang, X and Zhang, W and Yuan, X and Zang, Y and Li, Y and Zhou, T and Li, Y}, title = {S2VQ-VAE: Semi-Supervised Vector Quantised-Variational AutoEncoder for Automatic Evaluation of Trail Making Test.}, journal = {IEEE journal of biomedical and health informatics}, volume = {28}, number = {8}, pages = {4456-4470}, doi = {10.1109/JBHI.2024.3407881}, pmid = {38819974}, issn = {2168-2208}, mesh = {Humans ; *Cognitive Dysfunction/diagnosis ; Aged ; Male ; Female ; *Trail Making Test ; Supervised Machine Learning ; Aged, 80 and over ; Algorithms ; Deep Learning ; Diagnosis, Computer-Assisted/methods ; Signal Processing, Computer-Assisted ; }, abstract = {BACKGROUND: Computer-aided detection of cognitive impairment garnered increasing attention, offering older adults in the community access to more objective, ecologically valid, and convenient cognitive assessments using multimodal sensing technology on digital devices.<br><br>METHODOLOGY: In this study, we aimed to develop an automated method for screening cognitive impairment, building on paper- and electronic TMTs. We proposed a novel deep representation learning approach named Semi-Supervised Vector Quantised-Variational AutoEncoder (S2VQ-VAE). Within S2VQ-VAE, we incorporated intra- and inter-class correlation losses to disentangle class-related factors. These factors were then combined with various real-time obtainable features (including demographic, time-related, pressure-related, and jerk-related features) to create a robust feature engineering block. Finally, we identified the light gradient boosting machine as the optimal classifier. The experiments were conducted on a dataset collected from older adults in the community.<br><br>RESULTS: The experimental results showed that the proposed multi-type feature fusion method outperformed the conventional method used in paper-based TMTs and the existing VAE-based feature extraction in terms of screening performance.<br><br>CONCLUSIONS: In conclusion, the proposed deep representation learning method significantly enhances the cognitive diagnosis capabilities of behavior-based TMTs and streamlines large-scale community-based cognitive impairment screening while reducing the workload of professional healthcare staff.}, }
@article {pmid38819559, year = {2024}, author = {Sanchez, FB and Sato Guima, SE and Setubal, JC}, title = {How to Obtain and Compare Metagenome-Assembled Genomes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2802}, number = {}, pages = {135-163}, pmid = {38819559}, issn = {1940-6029}, mesh = {*Metagenome/genetics ; *Metagenomics/methods ; Software ; Computational Biology/methods ; Databases, Genetic ; Sequence Analysis, DNA/methods ; Genome, Bacterial ; }, abstract = {Metagenome-assembled genomes, or MAGs, are genomes retrieved from metagenome datasets. In the vast majority of cases, MAGs are genomes from prokaryotic species that have not been isolated or cultivated in the lab. They, therefore, provide us with information on these species that are impossible to obtain otherwise, at least until new cultivation methods are devised. Thanks to improvements and cost reductions of DNA sequencing technologies and growing interest in microbial ecology, the rise in number of MAGs in genome repositories has been exponential. This chapter covers the basics of MAG retrieval and processing and provides a practical step-by-step guide using a real dataset and state-of-the-art tools for MAG analysis and comparison.}, }
@article {pmid38818975, year = {2024}, author = {Shi, H and Zhu, Y and Wu, X and Jiang, T and Li, X and Liu, J and Di, Y and Chen, F and Gao, J and Xu, X and Xiao, N and Feng, X and Zhang, P and Wu, Y and La, Q and Li, A and Chen, P and Li, X}, title = {CropMetabolome: a comprehensive metabolome database for major crops cross eight categories.}, journal = {The Plant journal : for cell and molecular biology}, volume = {119}, number = {3}, pages = {1613-1626}, doi = {10.1111/tpj.16858}, pmid = {38818975}, issn = {1365-313X}, support = {2023ZD04073//National Key R&amp;D Program of China/ ; XDA24010400//Strategic Priority Research Program of Chinese Academy of Sciences/ ; BE2023336//Key R&amp;D Program of Jiangsu Province Modern Agriculture/ ; 32270719//National Natural Science Foundation of China/ ; 31900470//National Natural Science Foundation of China/ ; 32200093//National Natural Science Foundation of China/ ; CARS-11//Earmarked Fund for China Agriculture Research System/ ; 2022M713144//China Postdoctoral Science Foundation/ ; }, mesh = {*Crops, Agricultural/metabolism/genetics ; *Metabolome ; *Metabolomics/methods ; *Databases, Factual ; Flavonoids/metabolism ; Mass Spectrometry ; }, abstract = {Chemical compositions of crops are of great agronomical importance, as crops serve as resources for nutrition, energy, and medicines for human and livestock. For crop metabolomics research, the lack of crop reference metabolome and high-quality reference compound mass spectra, as well as utilities for metabolic profiling, has hindered the discovery and functional study of phytochemicals in crops. To meet these challenging needs, we have developed the Crop Metabolome database (abbreviated as CropMetabolome) that is dedicated to the construction of crop reference metabolome, repository, and dissemination of crop metabolomic data, and profiling and analytic tools for metabolomics research. CropMetabolome contains a metabolomics database for more than 50 crops (belonging to eight categories) that integrated self-generated raw mass spectral data and public-source datasets. The reference metabolome for 59 crop species was constructed, which have functions that parallel those of reference genome in genomic studies. CropMetabolome also contains 'Standard compound mass spectral library', 'Flavonoids library', 'Pesticide library', and a set of related analytical tools that enable metabolic profiling based on a reference metabolome (CropRefMetaBlast), annotation and identification of new metabolites (CompoundLibBlast), deducing the structure of novel flavonoid derivatives (FlavoDiscover), and detecting possible residual pesticides in crop samples (PesticiDiscover). In addition, CropMetabolome is a repository to share and disseminate metabolomics data and a platform to promote collaborations to develop reference metabolome for more crop species. CropMetabolome is a comprehensive platform that offers important functions in crop metabolomics research and contributes to improve crop breeding, nutrition, and safety. CropMetabolome is freely available at https://www.cropmetabolome.com/.}, }
@article {pmid38816346, year = {2024}, author = {Locke, MA and Witthaus, LM and Lizotte, RE and Heintzman, LJ and Moore, MT and O'Reilly, A and Wells, RR and Langendoen, EJ and Bingner, RL and Gholson, DM and Taylor, JM and Johnson, FE}, title = {The LTAR Cropland Common Experiment in the Lower Mississippi River Basin.}, journal = {Journal of environmental quality}, volume = {53}, number = {6}, pages = {957-967}, doi = {10.1002/jeq2.20577}, pmid = {38816346}, issn = {1537-2537}, mesh = {*Rivers ; *Agriculture/methods ; *Crops, Agricultural ; Conservation of Natural Resources/methods ; }, abstract = {The Lower Mississippi River Basin Long-Term Agroecosystem Research Site (LMRB-LTAR) encompasses six states from Missouri to the Gulf of Mexico and is coordinated by the USDA-ARS National Sedimentation Laboratory, Oxford, MS. The overarching goal of LTAR is to assess regionally diverse and geographically scalable farming practices for enhanced sustainability of agroecosystem goods and services under changing environment and resource-use conditions. The LMRB-LTAR overall goal is to assess sustainable row crop agricultural production systems that integrate regional environmental and socioeconomic needs. Primary row crops in the region include soybeans, corn, cotton, rice, and sugarcane with crop rotations influenced by commodity crop price and other factors. The field-scale common experiment (CE) includes four row crop farms (26-101 ha) established in 2021 and 2023. Three fields are managed with alternative practices, including reduced tillage, cover crops, and automated prescription irrigation, and three fields are managed with prevailing farming practices, consisting of conventional tillage, no cover crop, and nonprescription irrigation. Treatment effects on crop productivity, soil quality, water use efficiency, water quality, and carbon storage are assessed. Research from the LMRB CE will deliver outcomes linked to overarching LTAR network goals, including innovative agricultural systems, strengthened partnerships, data management technologies, and precision environmental tools.}, }
@article {pmid38814981, year = {2024}, author = {Mullon, C and Peña, J and Lehmann, L}, title = {The evolution of environmentally mediated social interactions and posthumous spite under isolation by distance.}, journal = {PLoS computational biology}, volume = {20}, number = {5}, pages = {e1012071}, pmid = {38814981}, issn = {1553-7358}, mesh = {*Biological Evolution ; *Social Interaction ; Computational Biology ; Phenotype ; Animals ; Environment ; Humans ; }, abstract = {Many social interactions happen indirectly via modifications of the environment, e.g. through the secretion of functional compounds or the depletion of renewable resources. Here, we derive the selection gradient on a quantitative trait affecting dynamical environmental variables that feed back on reproduction and survival in a finite patch-structured population subject to isolation by distance. Our analysis shows that the selection gradient depends on how a focal individual influences the fitness of all future individuals in the population through modifications of the environmental variables they experience, weighted by the neutral relatedness between recipients and the focal. The evolutionarily relevant trait-driven environmental modifications are formalized as the extended phenotypic effects of an individual, quantifying how a trait change in an individual in the present affects the environmental variables in all patches at all future times. When the trait affects reproduction and survival through a payoff function, the selection gradient can be expressed in terms of extended phenotypic effects weighted by scaled relatedness. We show how to compute extended phenotypic effects, relatedness, and scaled relatedness using Fourier analysis, which allow us to investigate a broad class of environmentally mediated social interactions in a tractable way. We use our approach to study the evolution of a trait controlling the costly production of some lasting commons (e.g. a common-pool resource or a toxic compound) that can diffuse in space and persist in time. We show that indiscriminate posthumous spite readily evolves in this scenario. More generally, whether selection favours environmentally mediated altruism or spite is determined by the spatial correlation between an individual's lineage and the commons originating from its patch. The sign of this correlation depends on interactions between dispersal patterns and the commons' renewal dynamics. More broadly, we suggest that selection can favour a wide range of social behaviours when these have carry-over effects in space and time.}, }
@article {pmid38814957, year = {2024}, author = {Schoenecker, KA and King, SRB and Hennig, JD and Cole, MJ and Scasta, JD and Beck, JL}, title = {Effects of telemetry collars on two free-roaming feral equid species.}, journal = {PloS one}, volume = {19}, number = {5}, pages = {e0303312}, pmid = {38814957}, issn = {1932-6203}, mesh = {Animals ; *Telemetry ; *Equidae/physiology ; *Geographic Information Systems ; Horses ; Female ; Male ; }, abstract = {There are two species of free-roaming feral equids in North America: horses (Equus caballus) and donkeys or "burros" (E. asinus). Both species were introduced as domestic animals to North America in the early 1500s and currently inhabit rangelands across the western United States, Canada, and all continents except Antarctica. Despite their global distribution, little is known about their fine scale spatial ecology. Contemporary research tools to assess space use include global positioning system (GPS) tracking collars, but older models were problematic due to stiff collar belting causing poor fit. We tested modern designs of GPS collars on n = 105 horses and n = 60 burros for 4 years in five populations (3 horse, 2 burro) across the western United States, to assess whether collars posed welfare risks to horses or burros. We found no difference in survival of collared versus uncollared mares and jennies, and no difference in survival of their foals. In 4036 of 4307 observations for horses (93.7%) and 2115 of 2258 observations for burros (93.6%), collars were observed symmetrical, maintaining proper fit on the neck. Fur effects from collars (sweaty neck, indented fur, broken fur) were seen in 3% of horse observations and 25% of burro observations. Superficial effects (chafes and marks on skin surface) were seen in 2% of horse observations and 11% of burro observations; no severe effects from collars were seen. Body condition was not affected by collars; mean body condition of collared horses was 4.70 ± 0.54 (mean ± s.d) and 4.71 ± 0.65 for collared burros. Behavior results indicated minimal effects; collared horses stood slightly more than uncollared, and collared burros stood and foraged more in one population, but not in the other. For 6.3% of observations of horses and 6.4% of observations of burros, we found an effect of time wearing a collar on the cumulative sum of fur effects which increased over time (burros: rs = 0.87, P = <0.0001; horses: rs = 0.31, P = 0.002). Burros also showed an increase over time in the number of superficial effects, but horses did not. Collars occasionally moved into the wrong position, shifting forward over the ears; we observed this on 19 horses and 1 burro. Of those, most collars went over the ears in summer (n = 12). All collars were equipped with a remote release mechanism as well as a timed-release mechanism for redundancy, thus removed when observed in wrong position to avoid rubbing or discomfort. Our finding of no consequential physical effects in 98% of horse observations, and 89% of burro observations suggests the consequences of collars on free-roaming equid welfare and survival is biologically insignificant, although collars should be monitored regularly and continue to be equipped with a remote release mechanism to remove a collar if needed. With frequent welfare-driven, visual monitoring, collaring of free-roaming equids can be a safe and useful tool to increase our understanding of their spatial ecology, demography, habitat use, behavior, and interactions with other wildlife.}, }
@article {pmid38813661, year = {2024}, author = {Cong, Y and Endo, T}, title = {A Quadruple Revolution: Deciphering Biological Complexity with Artificial Intelligence, Multiomics, Precision Medicine, and Planetary Health.}, journal = {Omics : a journal of integrative biology}, volume = {28}, number = {6}, pages = {257-260}, doi = {10.1089/omi.2024.0110}, pmid = {38813661}, issn = {1557-8100}, mesh = {*Precision Medicine/methods/trends ; *Artificial Intelligence ; Humans ; Systems Biology/methods ; Genomics/methods ; Machine Learning ; Multiomics ; }, abstract = {A quiet quadruple revolution has been in the making in systems science with convergence of (1) artificial intelligence, machine learning, and other digital technologies; (2) multiomics big data integration; (3) growing interest in the "variability science" of precision/personalized medicine that aims to account for patient-to-patient and between-population differences in disease susceptibilities and responses to health interventions such as drugs, nutrition, vaccines, and radiation; and (4) planetary health scholarship that both scales up and integrates biological, clinical, and ecological contexts of health and disease. Against this overarching background, this article presents and highlights some of the salient challenges and prospects of multiomics research, emphasizing the attendant pivotal role of systems medicine and systems biology. In addition, we emphasize the rapidly growing importance of planetary health research for systems medicine, particularly amid climate emergency, ecological degradation, and loss of planetary biodiversity. Looking ahead, we anticipate that the integration and utilization of multiomics big data and artificial intelligence will drive further progress in systems medicine and systems biology, heralding a promising future for both human and planetary health.}, }
@article {pmid38813550, year = {2023}, author = {Boyes, D and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Six-belted Clearwing, Bembecia ichneumoniformis (Denis &amp; Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {515}, pmid = {38813550}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Bembecia ichneumoniformis (the Six-belted Clearwing; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 511.4 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.32 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,114 protein coding genes.}, }
@article {pmid38813548, year = {2023}, author = {Boyes, D and Holland, PWH and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the July Highflyer, Hydriomena furcata (Thunberg, 1784).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {496}, pmid = {38813548}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Hydriomena furcata (the July Highflyer; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 423.3 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.89 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,324 protein coding genes.}, }
@article {pmid38813465, year = {2024}, author = {Falk, S and Poole, O and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the parsley Cheilosia, Cheilosia pagana (Meigen, 1822).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {54}, pmid = {38813465}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Cheilosia pagana (the parsley Cheilosia; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 354.1 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.76 kilobases in length.}, }
@article {pmid38808804, year = {2024}, author = {Freitas, GA and Marcon, GEB and Welch, JR and Silva, CMFPD}, title = {Analysis of the completeness and consistency of records of violence against indigenous women in the health macro-region of Dourados, Mato Grosso do Sul state, Brazil, 2009-2020.}, journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil}, volume = {33}, number = {}, pages = {e20231075}, pmid = {38808804}, issn = {2237-9622}, mesh = {Adult ; Indians, South American/statistics &amp; numerical data ; Information Systems ; Time Factors ; Female ; South American People ; Humans ; Brazil ; Communication ; Indigenous Peoples/statistics &amp; numerical data ; *Violence/statistics &amp; numerical data ; Educational Status ; Gender-Based Violence/statistics &amp; numerical data ; }, abstract = {OBJECTIVE: To analyze the temporal trend of completeness and consistency of data on notifications of violence against indigenous women in the health macro-region of Dourados, state of Mato Grosso do Sul, Brazil, between 2009 and 2020.<br><br>METHODS: An ecological time series study was conducted using data from the Notifiable Health Conditions Information System; Prais-Winsten regression was used to analyze the trend of data completeness and consistency, as well as the proportion of completed and coherent fields.<br><br>RESULTS: A total of 2,630 cases were reported; completeness was found to be very poor in the variable "occupation" (48.9%) and poor in the variables "schooling" (68.3%) and "time of occurrence" (67.9%); in the analysis of temporal trends, only the variable "occupation" showed a decreasing trend (p = 0.045).<br><br>CONCLUSION: The data analyzed demonstrated the need for improvement in the completeness of the variables "schooling", "occupation" and "time of occurrence" of the violent act.<br><br>MAIN RESULTS: There was a progressive increase in notifications over the years. Most of the variables showed regular or excellent completeness and consistency. In the analysis of temporal trend, only the "occupation" variable showed a decreasing trend.<br><br>IMPLICATIONS FOR SERVICES: Care for victims of violence is part of the daily routine of health services, and it is essential for health professionals to provide adequate compulsory notification for a comprehensive understanding of the victims' profile, thus assisting in addressing this issue.<br><br>PERSPECTIVES: Further studies are needed to understand the factors associated with violence against indigenous women, which could help the development of health promotion actions and violence prevention strategies targeting these women.}, }
@article {pmid38808214, year = {2024}, author = {Kyalo, H and Tonnang, HEZ and Egonyu, JP and Olukuru, J and Tanga, CM and Senagi, K}, title = {A convolutional neural network with image and numerical data to improve farming of edible crickets as a source of food-A decision support system.}, journal = {Frontiers in artificial intelligence}, volume = {7}, number = {}, pages = {1403593}, pmid = {38808214}, issn = {2624-8212}, abstract = {Crickets (Gryllus bimaculatus) produce sounds as a natural means to communicate and convey various behaviors and activities, including mating, feeding, aggression, distress, and more. These vocalizations are intricately linked to prevailing environmental conditions such as temperature and humidity. By accurately monitoring, identifying, and appropriately addressing these behaviors and activities, the farming and production of crickets can be enhanced. This research implemented a decision support system that leverages machine learning (ML) algorithms to decode and classify cricket songs, along with their associated key weather variables (temperature and humidity). Videos capturing cricket behavior and weather variables were recorded. From these videos, sound signals were extracted and classified such as calling, aggression, and courtship. Numerical and image features were extracted from the sound signals and combined with the weather variables. The extracted numerical features, i.e., Mel-Frequency Cepstral Coefficients (MFCC), Linear Frequency Cepstral Coefficients, and chroma, were used to train shallow (support vector machine, k-nearest neighbors, and random forest (RF)) ML algorithms. While image features, i.e., spectrograms, were used to train different state-of-the-art deep ML models, i,e., convolutional neural network architectures (ResNet152V2, VGG16, and EfficientNetB4). In the deep ML category, ResNet152V2 had the best accuracy of 99.42%. The RF algorithm had the best accuracy of 95.63% in the shallow ML category when trained with a combination of MFCC+chroma and after feature selection. In descending order of importance, the top 6 ranked features in the RF algorithm were, namely humidity, temperature, C#, mfcc11, mfcc10, and D. From the selected features, it is notable that temperature and humidity are necessary for growth and metabolic activities in insects. Moreover, the songs produced by certain cricket species naturally align to musical tones such as C# and D as ranked by the algorithm. Using this knowledge, a decision support system was built to guide farmers about the optimal temperature and humidity ranges and interpret the songs (calling, aggression, and courtship) in relation to weather variables. With this information, farmers can put in place suitable measures such as temperature regulation, humidity control, addressing aggressors, and other relevant interventions to minimize or eliminate losses and enhance cricket production.}, }
@article {pmid38807051, year = {2024}, author = {Xie, J and Lan, Y and Zou, C and He, J and Huang, Q and Zeng, J and Pan, M and Mei, Y and Luo, J and Zou, D}, title = {Single-nucleus analysis reveals microenvironment-specific neuron and glial cell enrichment in Alzheimer's disease.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {526}, pmid = {38807051}, issn = {1471-2164}, support = {YCSW2023244//the Innovation Project of Guangxi Graduate Education/ ; 2024GXNSFBA010054//the Joint Project on Regional High-Incidence Diseases Research of Guangxi Natural Science Foundation/ ; 2024GXNSFDA010001//the Joint Project on Regional High-Incidence Diseases Research of Guangxi Natural Science Foundation/ ; }, mesh = {*Alzheimer Disease/genetics/pathology/metabolism ; Humans ; *Neuroglia/metabolism/pathology ; *Neurons/metabolism ; *Single-Cell Analysis ; Cellular Microenvironment/genetics ; Computational Biology/methods ; }, abstract = {BACKGROUND: Alzheimer's disease (AD) is a complicated neurodegenerative disease. Neuron-glial cell interactions are an important but not fully understood process in the progression of AD. We used bioinformatic methods to analyze single-nucleus RNA sequencing (snRNA-seq) data to investigate the cellular and molecular biological processes of AD.<br><br>METHOD: snRNA-seq data were downloaded from Gene Expression Omnibus (GEO) datasets and reprocessed to identify 240,804 single nuclei from healthy controls and patients with AD. The cellular composition of AD was further explored using Uniform Manifold Approximation and Projection (UMAP). Enrichment analysis for the functions of the DEGs was conducted and cell development trajectory analyses were used to reveal underlying cell fate decisions. iTALK was performed to identify ligand-receptor pairs among various cell types in the pathological ecological microenvironment of AD.<br><br>RESULTS: Six cell types and multiple subclusters were identified based on the snRNA-seq data. A subcluster of neuron and glial cells co-expressing lncRNA-SNHG14, myocardin-related transcription factor A (MRTFA), and MRTFB was found to be more abundant in the AD group. This subcluster was enriched in mitogen-activated protein kinase (MAPK)-, immune-, and apoptosis-related pathways. Through molecular docking, we found that lncRNA-SNHG14 may bind MRTFA and MRTFB, resulting in an interaction between neurons and glial cells.<br><br>CONCLUSIONS: The findings of this study describe a regulatory relationship between lncRNA-SNHG14, MRTFA, and MRTFB in the six main cell types of AD. This relationship may contribute to microenvironment remodeling in AD and provide a theoretical basis for a more in-depth analysis of AD.}, }
@article {pmid38805961, year = {2024}, author = {Edwin, IE and Chukwuka, O and Ochege, FU and Ling, Q and Chen, B and Nzabarinda, V and Ajaero, C and Hamdi, R and Luo, G}, title = {Quantifying land change dynamics, resilience and feedback: A comparative analysis of the lake Chad basin in Africa and Aral Sea basin in Central Asia.}, journal = {Journal of environmental management}, volume = {361}, number = {}, pages = {121218}, doi = {10.1016/j.jenvman.2024.121218}, pmid = {38805961}, issn = {1095-8630}, mesh = {*Lakes ; *Climate Change ; Africa ; Geographic Information Systems ; Conservation of Natural Resources ; Asia ; }, abstract = {The intricate interaction of natural and anthropogenic factors drives changes in land and water in response to societal demands and climate change. However, there has been insufficient information on the feedback effects in dryland hotspots altered by land change dynamics. This research compared two transboundary inland lakes, the Lake Chad basin (LCB) in Africa and the Aral Sea basin (ASB) in Central Asia, using remote sensing and geographic information system techniques to analyze and quantify present and future land cover dynamics, resilience, and their feedback effects. The study integrated Cellular Automata, Markov Chain, and Multilayer Perceptron models to predict LULC changes up to 2030. Descriptive statistics, ordinary least squares regression, hotspot Gi-Bin, trend analysis, and advanced geostatistical methods were utilized to identify relationships, patterns, magnitudes, and directions of observed changes in the feedback effects. From 2000 to 2030, the analysis unveils intriguing trends, including an increase in cropland from 48% to 51% and a decrease in shrubland from 18% to 15% in the LCB. The grassland increased from 21% to 22%, and the settlement expanded from 0.10 to 0.60% in the ASB. Water bodies remained stable at 1.60 % in LCB, while in ASB, it declined from 3% to 2%. These changes were significantly influenced by population, elevation, and temperature in both basins, with irrigation also playing a significant role in the ASB and slope in LCB. The study further revealed discernible shifts in normalized difference vegetation index, temperature, and precipitation linked to specific land cover conversions, suggesting alterations in surface properties and vegetation health. This study underscores the complex interplay between land cover dynamics, resilience, climate variability, and feedback mechanisms in LCB and ASB.}, }
@article {pmid38805695, year = {2024}, author = {McElroy, KE and Masonbrink, R and Chudalayandi, S and Severin, AJ and Serb, JM}, title = {A chromosome-level genome assembly of the disco clam, Ctenoides ales.}, journal = {G3 (Bethesda, Md.)}, volume = {14}, number = {9}, pages = {}, pmid = {38805695}, issn = {2160-1836}, support = {DEB 1754331//National Science Foundation/ ; 1726447//NSF/ ; }, mesh = {Animals ; *Bivalvia/genetics ; *Genome ; *Molecular Sequence Annotation ; Chromosomes/genetics ; Genomics/methods ; Phylogeny ; }, abstract = {The bivalve subclass Pteriomorphia, which includes the economically important scallops, oysters, mussels, and ark clams, exhibits extreme ecological, morphological, and behavioral diversity. Among this diversity are five morphologically distinct eye types, making Pteriomorphia an excellent setting to explore the molecular basis for the evolution of novel traits. Of pteriomorphian bivalves, Limida is the only order lacking genomic resources, greatly limiting the potential phylogenomic analyses related to eyes and phototransduction. Here, we present a limid genome assembly, the disco clam, Ctenoides ales (C. ales), which is characterized by invaginated eyes, exceptionally long tentacles, and a flashing light display. This genome assembly was constructed with PacBio long reads and Dovetail Omni-CTM proximity-ligation sequencing. The final assembly is ∼2.3Gb and over 99% of the total length is contained in 18 pseudomolecule scaffolds. We annotated 41,064 protein coding genes and reported a BUSCO completeness of 91.9% for metazoa_obd10. Additionally, we report a complete and annotated mitochondrial genome, which also had been lacking from Limida. The ∼20Kb mitogenome has 12 protein coding genes, 22 tRNAs, 2 rRNA genes, and a 1,589 bp duplicated sequence containing the origin of replication. The C. ales nuclear genome size is substantially larger than other pteriomorphian genomes, mainly accounted for by transposable element sequences. We inventoried the genome for opsins, the signaling proteins that initiate phototransduction, and found that, unlike its closest eyed-relatives, the scallops, C. ales lacks duplication of the rhabdomeric Gq-protein-coupled opsin that is typically used for invertebrate vision. In fact, C. ales has uncharacteristically few opsins relative to the other pteriomorphian families, all of which have unique expansions of xenopsins, a recently discovered opsin subfamily. This chromosome-level assembly, along with the mitogenome, is a valuable resource for comparative genomics and phylogenetics in bivalves and particularly for the understudied but charismatic limids.}, }
@article {pmid38805543, year = {2024}, author = {Lansch-Justen, L and El Karoui, M and Alexander, HK}, title = {Estimating mutation rates under heterogeneous stress responses.}, journal = {PLoS computational biology}, volume = {20}, number = {5}, pages = {e1012146}, pmid = {38805543}, issn = {1553-7358}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Mutation Rate ; *Escherichia coli/genetics ; *Stress, Physiological/genetics ; *Models, Genetic ; SOS Response, Genetics/genetics ; Computer Simulation ; Computational Biology/methods ; Mutation ; }, abstract = {Exposure to environmental stressors, including certain antibiotics, induces stress responses in bacteria. Some of these responses increase mutagenesis and thus potentially accelerate resistance evolution. Many studies report increased mutation rates under stress, often using the standard experimental approach of fluctuation assays. However, single-cell studies have revealed that many stress responses are heterogeneously expressed in bacterial populations, which existing estimation methods have not yet addressed. We develop a population dynamic model that considers heterogeneous stress responses (subpopulations of cells with the response off or on) that impact both mutation rate and cell division rate, inspired by the DNA-damage response in Escherichia coli (SOS response). We derive the mutant count distribution arising in fluctuation assays under this model and then implement maximum likelihood estimation of the mutation-rate increase specifically associated with the expression of the stress response. Using simulated mutant count data, we show that our inference method allows for accurate and precise estimation of the mutation-rate increase, provided that this increase is sufficiently large and the induction of the response also reduces the division rate. Moreover, we find that in many cases, either heterogeneity in stress responses or mutant fitness costs could explain similar patterns in fluctuation assay data, suggesting that separate experiments would be required to identify the true underlying process. In cases where stress responses and mutation rates are heterogeneous, current methods still correctly infer the effective increase in population mean mutation rate, but we provide a novel method to infer distinct stress-induced mutation rates, which could be important for parameterising evolutionary models.}, }
@article {pmid38805169, year = {2025}, author = {Peng, X and Yang, Y and Zhong, R and Yang, Y and Yan, F and Liang, N and Yuan, S}, title = {Zinc and Inflammatory Bowel Disease: From Clinical Study to Animal Experiment.}, journal = {Biological trace element research}, volume = {203}, number = {2}, pages = {624-634}, doi = {10.1007/s12011-024-04193-6}, pmid = {38805169}, issn = {1559-0720}, support = {2081921001//Chengdu University/ ; CDUCX2024759//Training Program for Innovation and Entrepreneurship of Chengdu University/ ; 32370557//National Natural Science Foundation of China/ ; NCKL202201//Nanchong Key Laboratory of Wildlife Nutrition Ecology and Disease Control/ ; }, mesh = {*Zinc/deficiency/therapeutic use ; Animals ; *Inflammatory Bowel Diseases/drug therapy/metabolism/pathology ; Humans ; Dietary Supplements ; Disease Models, Animal ; }, abstract = {Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the gastrointestinal tract (GI) with a high incidence rate globally, and IBD patients are often accompanied by zinc deficiency. This review aims to summarize the potential therapeutic value of zinc supplementation in IBD clinical patients and animal models. Zinc supplementation can relieve the severity of IBD especially in patients with zinc deficiency. The clinical severity of IBD were mainly evaluated through some scoring methods involving clinical performance, endoscopic observation, blood biochemistry, and pathologic biopsy. Through conducting animal experiments, it has been found that zinc plays an important role in alleviating clinical symptoms and improving pathological lesions. In both clinical observation and animal experiment of IBD, the therapeutic mechanisms of zinc interventions have been found to be related to immunomodulation, intestinal epithelial repair, and gut microbiota's balance. Furthermore, the antioxidant activity of zinc was clarified in animal experiment. Appropriate zinc supplementation is beneficial for IBD therapy, and the present evidence highlights that alleviating zinc-deficient status can effectively improve the severity of clinical symptoms in IBD patients and animal models.}, }
@article {pmid38803273, year = {2024}, author = {Wang, Y and Yang, Y and Liu, Y and Liu, C and Xu, M and Fang, M and Mu, X}, title = {CoSFISH: a comprehensive reference database of COI and 18S rRNA barcodes for fish.}, journal = {Database : the journal of biological databases and curation}, volume = {2024}, number = {}, pages = {}, pmid = {38803273}, issn = {1758-0463}, support = {2022SBH00001//Guangdong Rural Revitalization Strategy Special Provincial Organization/ ; 2023KJ134 2023KJ150//Modern Agriculture Industry Technology Innovation Team/ ; CAMC-2018F//China-ASEAN Maritime Cooperation Fund/ ; FGRC18537//National Freshwater Genetic Resource Center/ ; 2022SBH00001//Guangdong Rural Revitalization Strategy Special Provincial Organization/ ; 2023KJ134 2023KJ150//Modern Agriculture Industry Technology Innovation Team/ ; CAMC-2018F//China-ASEAN Maritime Cooperation Fund/ ; FGRC18537//National Freshwater Genetic Resource Center/ ; }, mesh = {Animals ; *Fishes/genetics/classification ; *RNA, Ribosomal, 18S/genetics ; *Electron Transport Complex IV/genetics ; *DNA Barcoding, Taxonomic/methods ; Databases, Genetic ; Phylogeny ; Databases, Nucleic Acid ; }, abstract = {Fish, being a crucial component of aquatic ecosystems, holds significant importance from both economic and ecological perspectives. However, the identification of fish at the species level remains challenging, and there is a lack of a taxonomically complete and comprehensive reference sequence database for fish. Therefore, we developed CoSFISH, an online fish database. Currently, the database contains 21 535 cytochrome oxidase I sequences and 1074 18S rRNA sequences of 21 589 species, belonging to 8 classes and 90 orders. We additionally incorporate online analysis tools to aid users in comparing, aligning and analyzing sequences, as well as designing primers. Users can upload their own data for analysis, in addition to using the data stored in the database directly. CoSFISH offers an extensive fish database and incorporates online analysis tools, making it a valuable resource for the study of fish diversity, phylogenetics and biological evolution. Database URL: http://210.22.121.250:8888/CoSFISH/home/indexPage.}, }
@article {pmid38803140, year = {2024}, author = {Jacobson, OT and Barrett, BJ and Perry, SE and Finerty, GE and Tiedeman, KM and Crofoot, MC}, title = {A new approach to geostatistical synthesis of historical records reveals capuchin spatial responses to climate and demographic change.}, journal = {Ecology letters}, volume = {27}, number = {5}, pages = {e14443}, doi = {10.1111/ele.14443}, pmid = {38803140}, issn = {1461-0248}, support = {//Wenner-Gren Foundation/ ; //American Society of Primatologists/ ; //Alexander von Humboldt-Stiftung/ ; //Max-Planck-Gesellschaft/ ; //Department of Anthropology, University of California, Los Angeles/ ; 20113909//National Geographic Society/ ; 45176R-18//National Geographic Society/ ; 7968-06//National Geographic Society/ ; 8671-09//National Geographic Society/ ; 9795-15//National Geographic Society/ ; 9633991//National Science Foundation/ ; BCS-0613226//National Science Foundation/ ; BCS-1638428//National Science Foundation/ ; BCS-848360//National Science Foundation/ ; DDIG 1232371//National Science Foundation/ ; SE9870429//National Science Foundation/ ; //Achievement Rewards for College Scientists Foundation/ ; //Leakey Foundation/ ; 1650042//National Science Foundation Graduate Research Fellowship Program/ ; Grant 0208/TWCF/TWCF/United States ; }, mesh = {Animals ; Costa Rica ; *Climate Change ; *Cebus/physiology ; Homing Behavior ; Geographic Information Systems ; Population Dynamics ; Demography ; }, abstract = {Recent proliferation of GPS technology has transformed animal movement research. Yet, time-series data from this recent technology rarely span beyond a decade, constraining longitudinal research. Long-term field sites hold valuable historic animal location records, including hand-drawn maps and semantic descriptions. Here, we introduce a generalised workflow for converting such records into reliable location data to estimate home ranges, using 30 years of sleep-site data from 11 white-faced capuchin (Cebus imitator) groups in Costa Rica. Our findings illustrate that historic sleep locations can reliably recover home range size and geometry. We showcase the opportunity our approach presents to resolve open questions that can only be addressed with very long-term data, examining how home ranges are affected by climate cycles and demographic change. We urge researchers to translate historical records into usable movement data before this knowledge is lost; it is essential to understanding how animals are responding to our changing world.}, }
@article {pmid38802965, year = {2024}, author = {Hosseinzadeh-Shanjani, Z and Khodayari-Zarnaq, R and Khosravi, MF and Arab-Zozani, M and Alizadeh, G}, title = {Factors affecting major depression in Iran: a mixed-method study.}, journal = {Journal of health, population, and nutrition}, volume = {43}, number = {1}, pages = {73}, pmid = {38802965}, issn = {2072-1315}, mesh = {Humans ; Iran/epidemiology ; *Major Depressive Disorder/epidemiology ; Risk Factors ; Health Policy ; Socioeconomic Factors ; Economic Recession ; Politics ; Female ; Male ; }, abstract = {Depression is a major cause of disability and, if left untreated, can increase the risk of suicide. Evidence on the determinants of depression is incomplete, making it challenging to interpret results across studies. This study aims to identify the social, economic, environmental, political, and technological factors influencing the great recession in Iran. The study was conducted in two parts. The first step involved a literature review to identify the factors, using PubMed, Scopus, and Web of Science for the search. The reference lists of all identified articles were reviewed to find relevant studies, and the extracted information was summarized and reported descriptively. The second steps involved compiling and consulting 14 experts from different fields, using a framework analysis method. Twenty-four articles were used as primary sources of information, and a total of 28 factors were found to exist. After removing duplicates and related factors, 19 of these were subsequently declared as factors, resulting in a total of 36 determinants being identified. Most of these factors belong to the social category. The health policies implemented have a significant impact on disease risk factors and ultimately their occurrence. Political decisions and policy-making processes play a crucial role in all areas, particularly in addressing disease risk factors. Severe depression can disrupt all aspects of the healthcare system, underscoring the importance of access to care. Policies concerning physical education, transportation, nutrition, employment, green spaces, recreational facilities, and tobacco are vital in this context. The influence of health policies on disease risk factors and disease occurrence is profound. Severe depression can have far-reaching effects on the healthcare system, emphasizing the critical need for access to care. The formulation of policies to combat depression must be thoroughly evaluated in terms of economic, political, social, technological, and environmental factors. The findings suggest that addressing social inequalities and emphasizing the role of political action, as highlighted by the social determinants of health, should be top priorities in addressing depression. Efforts to prevent depression should incorporate ecological approaches that consider the impact of the socioeconomic environment on depressive symptoms.}, }
@article {pmid38802223, year = {2024}, author = {Lv, H and Lu, Z and Fu, G and Lv, S and Jiang, J and Xie, Y and Luo, X and Zeng, J and Xue, S}, title = {Pollution characteristics and quantitative source apportionment of heavy metals within a zinc smelting site by GIS-based PMF and APCS-MLR models.}, journal = {Journal of environmental sciences (China)}, volume = {144}, number = {}, pages = {100-112}, doi = {10.1016/j.jes.2023.09.033}, pmid = {38802223}, issn = {1001-0742}, mesh = {*Metals, Heavy/analysis ; *Zinc/analysis ; *Environmental Monitoring/methods ; *Soil Pollutants/analysis ; *Metallurgy ; Geographic Information Systems ; Models, Chemical ; }, abstract = {The abandoned smelters present a substantial pollution threat to the nearby soil and groundwater. In this study, 63 surface soil samples were collected from a zinc smelter to quantitatively describe the pollution characteristics, ecological risks, and source apportionment of heavy metal(loid)s (HMs). The results revealed that the average contents of Zn, Cd, Pb, As, and Hg were 0.4, 12.2, 3.3, 5.3, and 12.7 times higher than the risk screening values of the construction sites, respectively. Notably, the smelter was accumulated heavily with Cd and Hg, and the contribution of Cd (0.38) and Hg (0.53) to ecological risk was 91.58%. ZZ3 and ZZ7 were the most polluted workshops, accounting for 25.7% and 35.0% of the pollution load and ecological risk, respectively. The influence of soil parent materials on pollution was minor compared to various workshops within the smelter. Combined with PMF, APCS-MLR and GIS analysis, four sources of HMs were identified: P1(25.5%) and A3(18.4%) were atmospheric deposition from the electric defogging workshop and surface runoff from the smelter; P2(32.7%) and A2(20.9%) were surface runoff of As-Pb foul acid; P3(14.5%) and A4(49.8%) were atmospheric deposition from the leach slag drying workshop; P4(27.3%) and A1(10.8%) were the smelting process of zinc products. This paper described the distribution characteristics and specific sources of HMs in different process workshops, providing a new perspective for the precise remediation of the smelter by determining the priority control factors.}, }
@article {pmid38800997, year = {2025}, author = {Madrigal, G and Minhas, BF and Catchen, J}, title = {Klumpy: A tool to evaluate the integrity of long-read genome assemblies and illusive sequence motifs.}, journal = {Molecular ecology resources}, volume = {25}, number = {1}, pages = {e13982}, pmid = {38800997}, issn = {1755-0998}, support = {1645087//Division of Antarctic Sciences/ ; }, mesh = {Animals ; Bees/genetics ; *Computational Biology/methods ; Sequence Analysis, DNA/methods ; Antifreeze Proteins/genetics/chemistry ; High-Throughput Nucleotide Sequencing/methods ; Genome/genetics ; Genomics/methods ; Software ; Fishes/genetics ; }, abstract = {The improvement and decreasing costs of third-generation sequencing technologies has widened the scope of biological questions researchers can address with de novo genome assemblies. With the increasing number of reference genomes, validating their integrity with minimal overhead is vital for establishing confident results in their applications. Here, we present Klumpy, a tool for detecting and visualizing both misassembled regions in a genome assembly and genetic elements (e.g. genes) of interest in a set of sequences. By leveraging the initial raw reads in combination with their respective genome assembly, we illustrate Klumpy's utility by investigating antifreeze glycoprotein (afgp) loci across two icefishes, by searching for a reported absent gene in the northern snakehead fish, and by scanning the reference genomes of a mudskipper and bumblebee for misassembled regions. In the two former cases, we were able to provide support for the noncanonical placement of an afgp locus in the icefishes and locate the missing snakehead gene. Furthermore, our genome scans were able identify an unmappable locus in the mudskipper reference genome and identify a putative repetitive element shared among several species of bees.}, }
@article {pmid38800521, year = {2024}, author = {Obbard, DJ and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the drosophilid fruit fly, Drosophila phalerata (Meigen, 1830).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {63}, pmid = {38800521}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Drosophila phalerata (drosophilid fruit fly, Arthropoda; Insecta; Diptera; Drosophilidae). The genome sequence is 223.9 megabases in span. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.14 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,973 protein coding genes.}, }
@article {pmid38800516, year = {2024}, author = {Li, R and Li, J and Lopez, JV and Oatley, G and Clayton-Lucey, IA and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the giant clam, Tridacna gigas (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {145}, pmid = {38800516}, issn = {2398-502X}, abstract = {We present a chromosomal-level genome assembly from an individual Tridacna gigas (the giant clam; Mollusca; Bivalvia; Veneroida; Cardiidae). The genome sequence is 1,175.9 megabases in span. Most of the assembly is scaffolded into 17 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 25.34 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,177 protein coding genes.}, }
@article {pmid38798998, year = {2023}, author = {Obbard, DJ and ,  and ,  and ,  and , }, title = {The genome sequence of a drosophilid fruit fly, Drosophila funebris (Fabricius, 1789).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {437}, pmid = {38798998}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Drosophila funebris (drosophilid fruit fly; Arthropoda; Insecta; Diptera; Drosophilidae). The genome sequence is 181.1 megabases in span. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.15 kilobases in length.}, }
@article {pmid38798994, year = {2023}, author = {Hawkes, WLS and Wotton, KR and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Common Spotted Hoverfly, Eupeodes luniger (Meigen, 1822).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {472}, pmid = {38798994}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Eupeodes luniger (the Common Spotted Hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 616.9 megabases in span. Most of the assembly is scaffolded into 4 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 17.45 kilobases in length.}, }
@article {pmid38798992, year = {2023}, author = {Hawkes, WLS and Wotton, KR and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the slender grass hoverfly, Melanostoma scalare (Fabricius, 1794).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {489}, pmid = {38798992}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Melanostoma scalare (the slender grass hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 738.2 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.08 kilobases in length.}, }
@article {pmid38796535, year = {2024}, author = {Wenk, EH and Sauquet, H and Gallagher, RV and Brownlee, R and Boettiger, C and Coleman, D and Yang, S and Auld, T and Barrett, R and Brodribb, T and Choat, B and Dun, L and Ellsworth, D and Gosper, C and Guja, L and Jordan, GJ and Le Breton, T and Leigh, A and Lu-Irving, P and Medlyn, B and Nolan, R and Ooi, M and Sommerville, KD and Vesk, P and White, M and Wright, IJ and Falster, DS}, title = {The AusTraits plant dictionary.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {537}, pmid = {38796535}, issn = {2052-4463}, mesh = {*Plants ; Databases, Factual ; Dictionaries as Topic ; }, abstract = {Traits with intuitive names, a clear scope and explicit description are essential for all trait databases. The lack of unified, comprehensive, and machine-readable plant trait definitions limits the utility of trait databases, including reanalysis of data from a single database, or analyses that integrate data across multiple databases. Both can only occur if researchers are confident the trait concepts are consistent within and across sources. Here we describe the AusTraits Plant Dictionary (APD), a new data source of terms that extends the trait definitions included in a recent trait database, AusTraits. The development process of the APD included three steps: review and formalisation of the scope of each trait and the accompanying trait description; addition of trait metadata; and publication in both human and machine-readable forms. Trait definitions include keywords, references, and links to related trait concepts in other databases, enabling integration of AusTraits with other sources. The APD will both improve the usability of AusTraits and foster the integration of trait data across global and regional plant trait databases.}, }
@article {pmid38796014, year = {2024}, author = {Graham, CC}, title = {The role of Geographic Information Systems in mitigating plastics pollution in the Global South-A spatial analysis of recycling facilities in Costa Rica.}, journal = {The Science of the total environment}, volume = {937}, number = {}, pages = {173396}, doi = {10.1016/j.scitotenv.2024.173396}, pmid = {38796014}, issn = {1879-1026}, mesh = {Costa Rica ; *Plastics/analysis ; *Geographic Information Systems ; *Recycling ; *Environmental Pollution/statistics &amp; numerical data ; Spatial Analysis ; Conservation of Natural Resources/methods ; Environmental Monitoring ; }, abstract = {Costa Rica is at the forefront of environmental conservation in Central America, with its focus on sustainability and green practices. Building on this foundation, the country joins a cohort of middle-income developing countries that have set forth ambitious goals to eliminate plastic pollution and become plastics-free. Recycling remains one of the most effective ways of removing plastic waste from the environment. Although GIS has been utilized in environmental research, its use is still expanding in developing countries of the Global South. These countries are experiencing unprecedented adverse climate and ecological impacts while also pursuing fundamental socioeconomic growth. The application of more cost-effective and strategic technological solutions, as well as data-driven decision-making, could fast-track the achievement of their urgent environmental goals. Using Geographic Information Systems (GIS) analysis, this study applies hot spot, location-allocation, and time-distance measures to examine Costa Rica's capacity to recycle plastic waste. Focusing specifically on availability and the public's access to recycling facilities, this article offers insights into the resource constraints and evolution of plastics governance in developing countries with environmentally-focused priorities. The findings of this study suggest that while Costa Rica is implementing progressive plastics regulatory policies, the ability to achieve plastics-free status is hampered by shortfalls in the number and distribution of recycling facilities and the public's access to recycling services. Expanding recycling infrastructure, including transportation, and adopting a less canton-centric waste administration system could contribute to resolving these challenges. This study contributes to discourses on global plastics governance and environmental change management in the Global South.}, }
@article {pmid38795997, year = {2024}, author = {Lu, J and Peng, Q and Song, Y and Lyu, L and Chen, D and Huang, P and Peng, F and Liu, Y}, title = {Characteristics and effects of global sloping land urbanization from 2000 to 2020.}, journal = {The Science of the total environment}, volume = {937}, number = {}, pages = {173348}, doi = {10.1016/j.scitotenv.2024.173348}, pmid = {38795997}, issn = {1879-1026}, abstract = {Cities usually expand on flat land. However, in recent decades, the increasing scarcity of available flat land has compelled many cities to expand to sloping land (sloping land urbanization, SLU), and the understanding for global SLU is still unclear. This study, based on the currently available high-precision global Digital Elevation Model (FABDEM) and global land cover dataset (GlobeLand30), investigated the characteristics and impacts of SLU in 26,402 urban residential areas worldwide from 2000 to 2020. Results show that the total area of SLU globally is 16,383 km[2], accounting for 9.54 % of the overall urban expansion. This phenomenon is widespread globally and relatively concentrated in a few countries, with 42.78 %, 24.35 %, and 21.83 % of the area coming from cultivated land, forest, and grassland respectively. Global SLU has accommodated 34.78 million urban population, and indirectly protected 8922 km[2] of flat cultivated land, while causing a net loss of 4373 km[2] of green ecological land. Deliberately balancing the dual effects of SLU is crucial for advancing sustainable global urbanization.}, }
@article {pmid38791265, year = {2024}, author = {Bartas, M and Brázda, V and Pečinka, P}, title = {Special Issue "Bioinformatics of Unusual DNA and RNA Structures".}, journal = {International journal of molecular sciences}, volume = {25}, number = {10}, pages = {}, pmid = {38791265}, issn = {1422-0067}, support = {CZ.10.03.01/00/22_003/0000003//Operational Programme Just Transition, European Union/ ; }, mesh = {*RNA/chemistry/metabolism ; *DNA/chemistry/metabolism ; *Computational Biology/methods ; *Nucleic Acid Conformation ; Humans ; }, abstract = {Nucleic acids are not only static carriers of genetic information but also play vital roles in controlling cellular lifecycles through their fascinating structural diversity [...].}, }
@article {pmid38789640, year = {2024}, author = {Leigh, DM and Vandergast, AG and Hunter, ME and Crandall, ED and Funk, WC and Garroway, CJ and Hoban, S and Oyler-McCance, SJ and Rellstab, C and Segelbacher, G and Schmidt, C and Vázquez-Domínguez, E and Paz-Vinas, I}, title = {Best practices for genetic and genomic data archiving.}, journal = {Nature ecology &amp; evolution}, volume = {8}, number = {7}, pages = {1224-1232}, pmid = {38789640}, issn = {2397-334X}, support = {31BD30_193900//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; }, mesh = {*Genomics ; Databases, Genetic ; Data Management ; Metadata ; }, abstract = {Genetic and genomic data are collected for a vast array of scientific and applied purposes. Despite mandates for public archiving, data are typically used only by the generating authors. The reuse of genetic and genomic datasets remains uncommon because it is difficult, if not impossible, due to non-standard archiving practices and lack of contextual metadata. But as the new field of macrogenetics is demonstrating, if genetic data and their metadata were more accessible and FAIR (findable, accessible, interoperable and reusable) compliant, they could be reused for many additional purposes. We discuss the main challenges with existing genetic and genomic data archives, and suggest best practices for archiving genetic and genomic data. Recognizing that this is a longstanding issue due to little formal data management training within the fields of ecology and evolution, we highlight steps that research institutions and publishers could take to improve data archiving.}, }
@article {pmid38787862, year = {2024}, author = {Wang, L and Cui, H}, title = {Identification and classification of urban employment centers based on big data: A case study of Beijing.}, journal = {PloS one}, volume = {19}, number = {5}, pages = {e0299726}, pmid = {38787862}, issn = {1932-6203}, mesh = {Beijing ; Humans ; *Employment/statistics &amp; numerical data ; *Transportation/statistics &amp; numerical data ; Big Data ; Workplace ; Urban Population ; }, abstract = {The layout, scale and spatial form of urban employment centers are important guidelines for the rational layout of public service facilities such as urban transportation, medical care, and education. In this paper, we use Internet cell phone positioning data to identify the workplace and residence of users in the Beijing city area and obtain commuting data of the employed to measure the employment center system in Beijing. Firstly, the employment density distribution is generated using the data of the working places of the employed persons, and the employment centers are identified based on the employment density of Beijing. Then, we use the business registration data of employment centers to measure the industrial diversity within the employment centers by using the ecological Shannon Wiener Diversity Index, and combine the commuting links between employment centers and places of residence to measure the energy level of each employment center, analyze the hinterland and sphere of influence of each center, and finally using the industrial diversity index of employment centers and the average commuting time of employed persons, combined with the K-Means clustering algorithm, to classify the employment centers in Beijing. The employment center identification and classification method based on big data constructed in this study can help solve the limitations of the previous employment center system research in terms of center identification and commuting linkage measurement due to large spatial units and lack of commuting data to a certain extent. The study can provide reference for the regular understanding and technical analysis of employment centers and provide help for the employment multi-center system in Beijing in terms of quantifying the employment spatial structure, guiding the construction of multi-center system, and adjusting the land use rules.}, }
@article {pmid38785034, year = {2024}, author = {McEachran, MC and Harvey, JA and Mummah, RO and Bletz, MC and Teitelbaum, CS and Rosenblatt, E and Rudolph, FJ and Arce, F and Yin, S and Prosser, DJ and Mosher, BA and Mullinax, JM and DiRenzo, GV and Couret, J and Runge, MC and Grant, EHC and Cook, JD}, title = {Reframing wildlife disease management problems with decision analysis.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {38}, number = {4}, pages = {e14284}, doi = {10.1111/cobi.14284}, pmid = {38785034}, issn = {1523-1739}, support = {//National Science Foundation/ ; 2200310//PIPP Phase 1: International Center for Avian Influenza Pandemic Prediction and Prevention/ ; P.L. 116-136//Coronavirus Aid, Relief, and Economic Security Act/ ; }, mesh = {Animals ; *Animals, Wild ; *Decision Support Techniques ; *Conservation of Natural Resources/methods ; *Decision Making ; COVID-19/epidemiology ; SARS-CoV-2 ; Uncertainty ; }, abstract = {Contemporary wildlife disease management is complex because managers need to respond to a wide range of stakeholders, multiple uncertainties, and difficult trade-offs that characterize the interconnected challenges of today. Despite general acknowledgment of these complexities, managing wildlife disease tends to be framed as a scientific problem, in which the major challenge is lack of knowledge. The complex and multifactorial process of decision-making is collapsed into a scientific endeavor to reduce uncertainty. As a result, contemporary decision-making may be oversimplified, rely on simple heuristics, and fail to account for the broader legal, social, and economic context in which the decisions are made. Concurrently, scientific research on wildlife disease may be distant from this decision context, resulting in information that may not be directly relevant to the pertinent management questions. We propose reframing wildlife disease management challenges as decision problems and addressing them with decision analytical tools to divide the complex problems into more cognitively manageable elements. In particular, structured decision-making has the potential to improve the quality, rigor, and transparency of decisions about wildlife disease in a variety of systems. Examples of management of severe acute respiratory syndrome coronavirus 2, white-nose syndrome, avian influenza, and chytridiomycosis illustrate the most common impediments to decision-making, including competing objectives, risks, prediction uncertainty, and limited resources.}, }
@article {pmid38784435, year = {2024}, author = {Boyes, D and Crowley, LM and Holland, PWH and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Summer Chafer, Amphimallon solstitiale (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {138}, pmid = {38784435}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Amphimallon solstitiale (the Summer Chafer; Arthropoda; Insecta; Coleoptera; Scarabaeidae). The genome sequence is 1,584.1 megabases in span. Most of the assembly is scaffolded into 11 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 19.29 kilobases in length.}, }
@article {pmid38781445, year = {2024}, author = {Vuruputoor, VS and Starovoitov, A and Cai, Y and Liu, Y and Rahmatpour, N and Hedderson, TA and Wilding, N and Wegrzyn, JL and Goffinet, B}, title = {Crossroads of assembling a moss genome: navigating contaminants and horizontal gene transfer in the moss Physcomitrellopsis africana.}, journal = {G3 (Bethesda, Md.)}, volume = {14}, number = {7}, pages = {}, pmid = {38781445}, issn = {2160-1836}, support = {DEB-0919284//US National Science Foundation/ ; }, mesh = {*Gene Transfer, Horizontal ; *Bryopsida/genetics ; *Genome, Plant ; *Phylogeny ; Genomics/methods ; Molecular Sequence Annotation ; }, abstract = {The first chromosome-scale reference genome of the rare narrow-endemic African moss Physcomitrellopsis africana (P. africana) is presented here. Assembled from 73 × Oxford Nanopore Technologies (ONT) long reads and 163 × Beijing Genomics Institute (BGI)-seq short reads, the 414 Mb reference comprises 26 chromosomes and 22,925 protein-coding genes [Benchmarking Universal Single-Copy Ortholog (BUSCO) scores: C:94.8% (D:13.9%)]. This genome holds 2 genes that withstood rigorous filtration of microbial contaminants, have no homolog in other land plants, and are thus interpreted as resulting from 2 unique horizontal gene transfers (HGTs) from microbes. Further, P. africana shares 176 of the 273 published HGT candidates identified in Physcomitrium patens (P. patens), but lacks 98 of these, highlighting that perhaps as many as 91 genes were acquired in P. patens in the last 40 million years following its divergence from its common ancestor with P. africana. These observations suggest rather continuous gene gains via HGT followed by potential losses during the diversification of the Funariaceae. Our findings showcase both dynamic flux in plant HGTs over evolutionarily "short" timescales, alongside enduring impacts of successful integrations, like those still functionally maintained in extant P. africana. Furthermore, this study describes the informatic processes employed to distinguish contaminants from candidate HGT events.}, }
@article {pmid38781323, year = {2024}, author = {Edwards, SV and Cloutier, A and Cockburn, G and Driver, R and Grayson, P and Katoh, K and Baldwin, MW and Sackton, TB and Baker, AJ}, title = {A nuclear genome assembly of an extinct flightless bird, the little bush moa.}, journal = {Science advances}, volume = {10}, number = {21}, pages = {eadj6823}, pmid = {38781323}, issn = {2375-2548}, mesh = {Animals ; *Birds/genetics ; *Genome ; *Extinction, Biological ; Cell Nucleus/genetics ; Phylogeny ; Fossils ; Genome, Mitochondrial ; Flight, Animal ; New Zealand ; Male ; DNA Transposable Elements/genetics ; Genomics/methods ; }, abstract = {We present a draft genome of the little bush moa (Anomalopteryx didiformis)-one of approximately nine species of extinct flightless birds from Aotearoa, New Zealand-using ancient DNA recovered from a fossil bone from the South Island. We recover a complete mitochondrial genome at 249.9× depth of coverage and almost 900 megabases of a male moa nuclear genome at ~4 to 5× coverage, with sequence contiguity sufficient to identify more than 85% of avian universal single-copy orthologs. We describe a diverse landscape of transposable elements and satellite repeats, estimate a long-term effective population size of ~240,000, identify a diverse suite of olfactory receptor genes and an opsin repertoire with sensitivity in the ultraviolet range, show that the wingless moa phenotype is likely not attributable to gene loss or pseudogenization, and identify potential function-altering coding sequence variants in moa that could be synthesized for future functional assays. This genomic resource should support further studies of avian evolution and morphological divergence.}, }
@article {pmid38779566, year = {2024}, author = {Scanu, M and Toto, F and Petito, V and Masi, L and Fidaleo, M and Puca, P and Baldelli, V and Reddel, S and Vernocchi, P and Pani, G and Putignani, L and Scaldaferri, F and Del Chierico, F}, title = {An integrative multi-omic analysis defines gut microbiota, mycobiota, and metabolic fingerprints in ulcerative colitis patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1366192}, pmid = {38779566}, issn = {2235-2988}, mesh = {Humans ; *Colitis, Ulcerative/microbiology/metabolism ; *Gastrointestinal Microbiome ; Male ; Adult ; Female ; *Bacteria/classification/isolation &amp; purification/metabolism/genetics ; Middle Aged ; *Metabolomics/methods ; *RNA, Ribosomal, 16S/genetics ; *Gas Chromatography-Mass Spectrometry ; *Feces/microbiology ; *Fungi/classification/isolation &amp; purification/metabolism ; Dysbiosis/microbiology ; Metabolome ; Aged ; Young Adult ; Solid Phase Microextraction ; Mycobiome ; Multiomics ; }, abstract = {BACKGROUND: Ulcerative colitis (UC) is a multifactorial chronic inflammatory bowel disease (IBD) that affects the large intestine with superficial mucosal inflammation. A dysbiotic gut microbial profile has been associated with UC. Our study aimed to characterize the UC gut bacterial, fungal, and metabolic fingerprints by omic approaches.<br><br>METHODS: The 16S rRNA- and ITS2-based metataxonomics and gas chromatography-mass spectrometry/solid phase microextraction (GC-MS/SPME) metabolomic analysis were performed on stool samples of 53 UC patients and 37 healthy subjects (CTRL). Univariate and multivariate approaches were applied to separated and integrated omic data, to define microbiota, mycobiota, and metabolic signatures in UC. The interaction between gut bacteria and fungi was investigated by network analysis.<br><br>RESULTS: In the UC cohort, we reported the increase of Streptococcus, Bifidobacterium, Enterobacteriaceae, TM7-3, Granulicatella, Peptostreptococcus, Lactobacillus, Veillonella, Enterococcus, Peptoniphilus, Gemellaceae, and phenylethyl alcohol; and we also reported the decrease of Akkermansia; Ruminococcaceae; Ruminococcus; Gemmiger; Methanobrevibacter; Oscillospira; Coprococus; Christensenellaceae; Clavispora; Vishniacozyma; Quambalaria; hexadecane; cyclopentadecane; 5-hepten-2-ol, 6 methyl; 3-carene; caryophyllene; p-Cresol; 2-butenal; indole, 3-methyl-; 6-methyl-3,5-heptadiene-2-one; 5-octadecene; and 5-hepten-2-one, 6 methyl. The integration of the multi-omic data confirmed the presence of a distinctive bacterial, fungal, and metabolic fingerprint in UC gut microbiota. Moreover, the network analysis highlighted bacterial and fungal synergistic and/or divergent interkingdom interactions.<br><br>CONCLUSION: In this study, we identified intestinal bacterial, fungal, and metabolic UC-associated biomarkers. Furthermore, evidence on the relationships between bacterial and fungal ecosystems provides a comprehensive perspective on intestinal dysbiosis and ecological interactions between microorganisms in the framework of UC.}, }
@article {pmid38779149, year = {2024}, author = {Boyes, D and Mulhair, PO and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Water Veneer, Acentria ephemerella (Denis &amp; Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {134}, pmid = {38779149}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Acentria ephemerella (the Water Veneer; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 340.8 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.35 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,748 protein coding genes.}, }
@article {pmid38779060, year = {2023}, author = {Boyes, D and Mulhair, PO and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Scarce Umber, Agriopis aurantiaria (Hübner, 1799).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {463}, pmid = {38779060}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Agriopis aurantiaria (the Scarce Umber; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 485.4 megabases in span. The whole assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.44 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,963 protein coding genes.}, }
@article {pmid38779056, year = {2023}, author = {Boyes, D and Holland, PWH and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Pinion-streaked Snout, Schrankia costaestrigalis (Stephens, 1834).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {203}, pmid = {38779056}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Schrankia costaestrigalis (the Pinion-streaked Snout; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 572.0 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.1 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,453 protein coding genes.}, }
@article {pmid38779055, year = {2023}, author = {Boyes, D and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Diamondback Moth, Plutella xylostella (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {404}, pmid = {38779055}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Plutella xylostella (the Diamondback Moth; Arthropoda; Insecta; Lepidoptera; Plutellidae). The genome sequence is 323.3 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 35.12 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,190 protein coding genes.}, }
@article {pmid38779054, year = {2023}, author = {Boyes, D and Boyes, C and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Coxcomb Prominent, Ptilodon capucinus (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {242}, pmid = {38779054}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Ptilodon capucinus (the Coxcomb Prominent; Arthropoda; Insecta; Lepidoptera; Notodontidae). The genome sequence is 348.7 megabases in span. The assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.38 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,968 protein coding genes.}, }
@article {pmid38779050, year = {2023}, author = {Boyes, D and Hammond, J and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Grey Poplar Bell, Epinotia nisella (Clerck, 1759).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {281}, pmid = {38779050}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Epinotia nisella (the Grey Poplar Bell; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 585.0 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.44 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,952 protein coding genes.}, }
@article {pmid38779048, year = {2023}, author = {Boyes, D and Mulley, JF and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Six-striped Rustic, Xestia sexstrigata (Haworth, 1809).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {399}, pmid = {38779048}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Xestia sexstrigata (the Six-striped Rustic; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 638.3 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.36 kilobases in length. Gene annotation of this assembly on Ensembl identified 15,104 protein coding genes.}, }
@article {pmid38779046, year = {2023}, author = {Boyes, D and Holland, PWH and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Red-green Carpet, Chloroclysta siterata (Hufnagel, 1767).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {206}, pmid = {38779046}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Chloroclysta siterata (the Red-green Carpet; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 437.9 megabases in span. Most of the assembly is scaffolded into 21 chromosomal pseudomolecules including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.7 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,814 protein coding genes.}, }
@article {pmid38778011, year = {2024}, author = {Mercuri, AM and Clò, E and Zappa, J and Bosi, G and Furia, E and Ricucci, C and Di Lena, M and Camerini, F and Florenzano, A}, title = {BRAIN - Holocene archaeo-data for assessing plant-cultural diversity in Italy and other Mediterranean regions.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {520}, pmid = {38778011}, issn = {2052-4463}, mesh = {*Archaeology ; Botany/history ; Italy ; Mediterranean Region ; *Plants ; *Pollen ; Databases as Topic ; }, abstract = {In the field of botany applied to archaeological and palaeoecological studies, the multi- and inter-disciplinary nature of this research produces a lack of data sharing and scattered articles in the specialty literature or in national and international journals. The vast production of archaeobotany and palynology data makes it necessary to develop a tool for the availability, accessibility, and dissemination of existing research. Many databases exist on palaeoecology, archaeobotany or pollen data. There are no collections focused on archaeological sites and human-induced environments and centred on Southern Europe and the Mediterranean. BRAIN - Botanical Records of Archaeobotany Italian Network is the first database listing sites from which all types of plant records are available in Italy and nearby Mediterranean regions. BRAIN represents the largest integrated collection of archaeo/palaeo-botanical data and a range of descriptive information that makes data recovery FAIR ready. This unique network hosts data on the availability of anthropogenic pollen, palynomorphs and plant macroremains in the same database, and experts of different research fields may contribute to it.}, }
@article {pmid38777192, year = {2024}, author = {Aggarwal, R and Peters, G}, title = {Freshwater ecotoxicity characterization factors for PMT/vPvM substances.}, journal = {Chemosphere}, volume = {360}, number = {}, pages = {142391}, doi = {10.1016/j.chemosphere.2024.142391}, pmid = {38777192}, issn = {1879-1298}, mesh = {*Water Pollutants, Chemical/toxicity ; *Ecotoxicology ; *Fresh Water/chemistry ; Environmental Monitoring/methods ; Risk Assessment ; Germany ; Databases, Factual ; }, abstract = {This study addresses the gap in freshwater ecotoxicological characterization factors (CFs) for Persistent, Mobile, and Toxic (PMT) and Very Persistent and Very Mobile (vPvM) substances. These CFs are vital for integrating the ecotoxicity impacts of these chemicals into life cycle assessments. Our goals are twofold: first, to calculate experimental freshwater CFs for PMT/vPvM substances listed by the German Environment Agency (UBA); second, to compare these CFs with those from the USEtox database. The expanded UBA list includes 343 PMT/vPvM substances, each representing a unique chemical structure, and linked to 474 REACH-registered substances. This study successfully computed CFs for 244 substances, with 107 overlapping the USEtox database and 137 being new. However, ecotoxicity data limitations prevented CF determination for 97 substances. This research enhances our understanding of freshwater CFs for PMT/vPvM substances, covering 72% of UBA's 343 PMT/vPvM substances. Data scarcity remains a significant challenge, which invariably impedes CF calculations. Notably, the disparities observed between CF values in the USEtox database and those derived in this research largely stem from variations in ecotoxicity data. Consequently, this research underscores the dynamic nature of CFs for substances, emphasizing the need for regular updates to ensure their accuracy and relevance.}, }
@article {pmid38776304, year = {2024}, author = {Karlgren, K and Andersson Franko, M and Kilström, D}, title = {'Experiencing one thing and saying another'-Ecological Momentary Assessment (EMA) of nursing students' competence and challenge during clinical placements compared with retrospective interviews.}, journal = {PloS one}, volume = {19}, number = {5}, pages = {e0302866}, pmid = {38776304}, issn = {1932-6203}, mesh = {Humans ; *Students, Nursing/psychology ; Female ; Retrospective Studies ; *Clinical Competence ; Male ; *Ecological Momentary Assessment ; Adult ; Young Adult ; Interviews as Topic ; Smartphone ; }, abstract = {UNLABELLED: Clinical placements are essential to nursing education and understanding students' challenges in the clinical context is important for educators. Nevertheless, few studies have investigated students' experiences in the clinical context itself but rely on methods which ask participants to generalize their clinical experiences retrospectively.<br><br>OBJECTIVES: This study aimed to explore nursing students' experiences of clinical activities during and after clinical placements with a focus on feelings of competence and challenge. A particular interest was on comparing momentary assessments in the clinical context with retrospective interview data.<br><br>METHODS: Smartphones were used for ecological momentary assessment of students' experiences of clinical activities during five-week placements at 21 nursing homes. Both quantitative and qualitative data were collected. Interviews were conducted after the placements.<br><br>RESULTS: 575 responses were obtained showing final-year nursing students rated their competence significantly higher and challenge significantly lower than first-year students. An analysis of the quantitative data using the four-channel flow model showed that first-year students' activities were to a significantly higher extent associated with flow and anxiety, compared to those of final-year students. Conversely, the final-year students' activities were to a significantly higher extent associated with boredom than those of first-year students. The analysis of the students' reflections resulted in five themes: Specific activities are challenging, Lack of challenge, Learning and developing, Reflects critically on competence, and Arrangement of the clinical placement.<br><br>DISCUSSION: Final-year nursing students were significantly less challenged during the placements compared to first-year students. There was overlap in how students described their clinical experiences during and after placements, but there were also striking differences. The first-year students were overwhelmed by the challenges during the placements but viewed these experiences as valuable learning experiences afterwards. The final-year students also described several challenging clinical activities during the placements but none of these challenges were brought up afterwards in the interviews and instead a lack of challenge was emphasized. Momentary assessment thus enabled capturing data about clinical activities which may be overlooked by retrospective methods.}, }
@article {pmid38776282, year = {2024}, author = {MacPhail, VJ and Hatfield, R and Colla, SR}, title = {Bumble Bee Watch community science program increases scientific understanding of an important pollinator group across Canada and the USA.}, journal = {PloS one}, volume = {19}, number = {5}, pages = {e0303335}, pmid = {38776282}, issn = {1932-6203}, mesh = {Animals ; Bees/physiology ; United States ; *Pollination ; Canada ; Databases, Factual ; }, abstract = {In a time of increasing threats to bumble bees (Hymenoptera: Apidae: Bombus), it is important to understand their ecology and distribution. As experts are limited in resources to conduct field surveys, there is potential for community scientists to help. The Bumble Bee Watch (BBW) community science program involves volunteers taking photos of bumble bees in Canada and the USA and submitting them, along with geographic and optional plant information, to a website or through an app. Taxon experts then verify the bee species identification. The Bumble Bees of North America database (BBNA) stores data (no photographs) collected and identified by more traditional scientific methods over the same range. Here we compared BBW data to BBNA data over all years and just 2010-2020 to understand the scientific contribution of community scientists to the state of the knowledge about native bumble bees. We found that BBW had similar geographic and species coverage as BBNA. It had records from all 63 provinces, states, and territories where bumble bees occur (including four more than BBNA in 2010-2020), and represented 41 of the 48 species in BBNA (with ten more species than BBNA in 2010-2020). While BBW contributed only 8.50% of records overall, it contributed 25.06% of all records over 2010-2020. BBW confirmed the persistence of species and identified new locations of species, both inside and outside of the previously known extent of occurrences. BBW also contributed a wealth of ecological information, such as unique plant genera and species data for almost all the bee species. Thus, while BBW had fewer bee records than the BBNA database overall, it helped to fill in data gaps and provided novel information, complementing the traditional methods. This community science program is valuable in helping to inform conservation management for bumble bee species.}, }
@article {pmid38775247, year = {2024}, author = {Oliveira, S and Marchi, N and Excoffier, L}, title = {Assessing the limits of local ancestry inference from small reference panels.}, journal = {Molecular ecology resources}, volume = {24}, number = {6}, pages = {e13981}, doi = {10.1111/1755-0998.13981}, pmid = {38775247}, issn = {1755-0998}, support = {310030_188883//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; }, mesh = {*Genetics, Population/methods ; Humans ; Computational Biology/methods ; }, abstract = {Admixture is a common biological phenomenon among populations of the same or different species. Identifying admixed tracts within individual genomes can provide valuable information to date admixture events, reconstruct ancestry-specific demographic histories, or detect adaptive introgression, genetic incompatibilities, as well as regions of the genomes affected by (associative-) overdominance. Although many local ancestry inference (LAI) methods have been developed in the last decade, their performance was accessed using large reference panels, which are rarely available for non-model organisms or ancient samples. Moreover, the demographic conditions for which LAI becomes unreliable have not been explicitly outlined. Here, we identify the demographic conditions for which local ancestries can be best estimated using very small reference panels. Furthermore, we compare the performance of two LAI methods (RFMix and MOSAIC) with the performance of a newly developed approach (simpLAI) that can be used even when reference populations consist of single individuals. Based on simulations of various demographic models, we also determine the limits of these LAI tools and propose post-painting filtering steps to reduce false-positive rates and improve the precision and accuracy of the inferred admixed tracts. Besides providing a guide for using LAI, our work shows that reasonable inferences can be obtained from a single diploid genome per reference under demographic conditions that are not uncommon among past human groups and non-model organisms.}, }
@article {pmid38775206, year = {2024}, author = {Veglia, AJ and Rivera-Vicéns, RE and Grupstra, CGB and Howe-Kerr, LI and Correa, AMS}, title = {vAMPirus: A versatile amplicon processing and analysis program for studying viruses.}, journal = {Molecular ecology resources}, volume = {24}, number = {6}, pages = {e13978}, doi = {10.1111/1755-0998.13978}, pmid = {38775206}, issn = {1755-0998}, support = {OCE 22-24354//Directorate for Biological Sciences/ ; OCE-2145472//Directorate for Biological Sciences/ ; //Wagoner Foreign Study Award/ ; //Kirk W. Dotson Endowed Graduate Fellowship in Ecology and Evolutionary Biology/ ; //Lewis and Clark Grants for Exploration/ ; 100009646//Gulf Research Program of the National Academies of Sciences/ ; }, mesh = {*Software ; Computational Biology/methods ; DNA Viruses/genetics/classification ; Viruses/genetics/classification/isolation &amp; purification ; RNA Viruses/genetics/classification/isolation &amp; purification ; Phylogeny ; }, abstract = {Amplicon sequencing is an effective and increasingly applied method for studying viral communities in the environment. Here, we present vAMPirus, a user-friendly, comprehensive, and versatile DNA and RNA virus amplicon sequence analysis program, designed to support investigators in exploring virus amplicon sequencing data and running informed, reproducible analyses. vAMPirus intakes raw virus amplicon libraries and, by default, performs nucleotide- and amino acid-based analyses to produce results such as sequence abundance information, taxonomic classifications, phylogenies and community diversity metrics. The vAMPirus analytical framework leverages 16 different opensource tools and provides optional approaches that can increase the ratio of biological signal-to-noise and thereby reveal patterns that would have otherwise been masked. Here, we validate the vAMPirus analytical framework and illustrate its implementation as a general virus amplicon sequencing workflow by recapitulating findings from two previously published double-stranded DNA virus datasets. As a case study, we also apply the program to explore the diversity and distribution of a coral reef-associated RNA virus. vAMPirus is streamlined within Nextflow, offering straightforward scalability, standardization and communication of virus lineage-specific analyses. The vAMPirus framework is designed to be adaptable; community-driven analytical standards will continue to be incorporated as the field advances. vAMPirus supports researchers in revealing patterns of virus diversity and population dynamics in nature, while promoting study reproducibility and comparability.}, }
@article {pmid38774958, year = {2024}, author = {Huson, D and Xavier, JC and Steel, M}, title = {Self-generating autocatalytic networks: structural results, algorithms and their relevance to early biochemistry.}, journal = {Journal of the Royal Society, Interface}, volume = {21}, number = {214}, pages = {20230732}, pmid = {38774958}, issn = {1742-5662}, mesh = {*Algorithms ; Catalysis ; Models, Biological ; Biochemistry ; Origin of Life ; }, abstract = {The concept of an autocatalytic network of reactions that can form and persist, starting from just an available food source, has been formalized by the notion of a reflexively autocatalytic and food-generated (RAF) set. The theory and algorithmic results concerning RAFs have been applied to a range of settings, from metabolic questions arising at the origin of life, to ecological networks, and cognitive models in cultural evolution. In this article, we present new structural and algorithmic results concerning RAF sets, by studying more complex modes of catalysis that allow certain reactions to require multiple catalysts (or to not require catalysis at all), and discuss the differing ways catalysis has been viewed in the literature. We also focus on the structure and analysis of minimal RAFs and derive structural results and polynomial-time algorithms. We then apply these new methods to a large metabolic network to gain insights into possible biochemical scenarios near the origin of life.}, }
@article {pmid38772433, year = {2024}, author = {Chagas, &#xc9;CDS and Ferreira, FADS and Mwangi, VI and Terrazas, WCM and Becker, JN and Simões, RC and Pacífico, EMSS and Silva, ASD and Marques, CDS and Chagas, ECDS and Machado, MB and Figueira, EAG and Castro, DB and Ramos, TCA and Oliveira, JH}, title = {Spatio-temporal analysis of American Tegumentary Leishmaniasis incidences in the Brazilian state of Amazonas: 2011 to 2022.}, journal = {Acta tropica}, volume = {256}, number = {}, pages = {107266}, doi = {10.1016/j.actatropica.2024.107266}, pmid = {38772433}, issn = {1873-6254}, mesh = {Brazil/epidemiology ; Humans ; Incidence ; *Leishmaniasis, Cutaneous/epidemiology ; *Spatio-Temporal Analysis ; *Seasons ; Climate ; Female ; Male ; Adult ; Adolescent ; Young Adult ; Child ; }, abstract = {This study aimed to conduct a spatio-temporal analysis of tegumentary leishmaniasis occurrences in the Amazonas state, Brazil. An ecological study encompassing time series and spatial analysis was performed, exploring the geographic distribution and temporal trends of American Tegumentary Leishmaniasis (ATL) in Amazonas between 2011 and 2022. Secondary data extracted from the Department of Informatics of the Unified Health System (DATASUS) were utilized for this analysis. The study evaluated the relationship between disease cases and environmental/climatic variables (deforestation, temperature, precipitation, and relative humidity). Over the study period, 19,730 cases of tegumentary leishmaniasis were recorded, averaging an incidence of 41.4/100,000 inhabitants across the 62 municipalities of Amazonas state. Disease intensity varied with seasons. Generally, Amazonas state displayed a declining trend in ATL cases. However, certain municipalities, notably Rio Preto da Eva and Presidente Figueiredo, exhibited high incidence rates, while Canutama, Envira, Eirunepé, and Pauini municipalities demand closer attention due to their demonstrated increasing temporal trend of ATL cases. The analysis indicated a correlation between the number of ATL cases reported and relative humidity as well as precipitation. These findings underscore the significance of tegumentary leishmaniasis as a public health issue in the region and emphasize the necessity for public initiatives aimed at preventing this endemic illness.}, }
@article {pmid38771704, year = {2024}, author = {Warren, WC and Rice, ES and X, M and Roback, E and Keene, A and Martin, F and Ogeh, D and Haggerty, L and Carroll, RA and McGaugh, S and Rohner, N}, title = {Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery.}, journal = {G3 (Bethesda, Md.)}, volume = {14}, number = {8}, pages = {}, pmid = {38771704}, issn = {2160-1836}, support = {//University of Missouri/ ; 1923372//National Science Foundation/ ; /WT_/Wellcome Trust/United Kingdom ; R24 OD011198/OD/NIH HHS/United States ; 1R01GM127872-01/GF/NIH HHS/United States ; R01 GM127872/GM/NIGMS NIH HHS/United States ; WT222155/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Characidae/genetics ; *Chromosomes/genetics ; *Caves ; Phylogeny ; Genome ; Genomics/methods ; Genetic Variation ; Quantitative Trait Loci ; Synteny ; Phenotype ; }, abstract = {The ability of organisms to adapt to sudden extreme environmental changes produces some of the most drastic examples of rapid phenotypic evolution. The Mexican Tetra, Astyanax mexicanus, is abundant in the surface waters of northeastern Mexico, but repeated colonizations of cave environments have resulted in the independent evolution of troglomorphic phenotypes in several populations. Here, we present three chromosome-scale assemblies of this species, for one surface and two cave populations, enabling the first whole-genome comparisons between independently evolved cave populations to evaluate the genetic basis for the evolution of adaptation to the cave environment. Our assemblies represent the highest quality of sequence completeness with predicted protein-coding and noncoding gene metrics far surpassing prior resources and, to our knowledge, all long-read assembled teleost genomes, including zebrafish. Whole-genome synteny alignments show highly conserved gene order among cave forms in contrast to a higher number of chromosomal rearrangements when compared with other phylogenetically close or distant teleost species. By phylogenetically assessing gene orthology across distant branches of amniotes, we discover gene orthogroups unique to A. mexicanus. When compared with a representative surface fish genome, we find a rich amount of structural sequence diversity, defined here as the number and size of insertions and deletions as well as expanding and contracting repeats across cave forms. These new more complete genomic resources ensure higher trait resolution for comparative, functional, developmental, and genetic studies of drastic trait differences within a species.}, }
@article {pmid38770718, year = {2024}, author = {Schwarzerova, J and Hurta, M and Barton, V and Lexa, M and Walther, D and Provaznik, V and Weckwerth, W}, title = {A perspective on genetic and polygenic risk scores-advances and limitations and overview of associated tools.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {3}, pages = {}, pmid = {38770718}, issn = {1477-4054}, support = {FEKT/FIT-J-23-8274//Brno University of Technology intra-university junior project/ ; }, mesh = {Humans ; *Multifactorial Inheritance ; *Genetic Predisposition to Disease ; *Software ; Computational Biology/methods ; Genome-Wide Association Study/methods ; Risk Factors ; Risk Assessment/methods ; Genetic Risk Score ; }, abstract = {Polygenetic Risk Scores are used to evaluate an individual's vulnerability to developing specific diseases or conditions based on their genetic composition, by taking into account numerous genetic variations. This article provides an overview of the concept of Polygenic Risk Scores (PRS). We elucidate the historical advancements of PRS, their advantages and shortcomings in comparison with other predictive methods, and discuss their conceptual limitations in light of the complexity of biological systems. Furthermore, we provide a survey of published tools for computing PRS and associated resources. The various tools and software packages are categorized based on their technical utility for users or prospective developers. Understanding the array of available tools and their limitations is crucial for accurately assessing and predicting disease risks, facilitating early interventions, and guiding personalized healthcare decisions. Additionally, we also identify potential new avenues for future bioinformatic analyzes and advancements related to PRS.}, }
@article {pmid38767676, year = {2024}, author = {Geng, A and Zhang, C and Wang, J and Zhang, X and Qiu, W and Wang, L and Xi, J and Yang, B}, title = {Current advances of chlorinated organics degradation by bioelectrochemical systems: a review.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {40}, number = {7}, pages = {208}, pmid = {38767676}, issn = {1573-0972}, support = {2022YFC3702000//National Key Research and Development Program of China/ ; BE2020773//Social Development Project/ ; 23KJA610008//the Natural Science Foundation of Jiangsu Higher Education Institutions of China/ ; }, mesh = {*Biodegradation, Environmental ; *Electrochemical Techniques ; Wastewater/chemistry ; Hydrocarbons, Chlorinated/metabolism ; Water Pollutants, Chemical/metabolism ; Groundwater/chemistry ; Organic Chemicals/metabolism ; }, abstract = {Chlorinated organic compounds (COCs) are typical refractory organic compounds, having high biological toxicity. These compounds are a type of pervasive pollutants that can be present in polluted soil, air, and various types of waterways, such as groundwater, rivers, and lakes, posing a significant threat to the ecological environment and human health. Bioelectrochemical systems (BESs) are an effective strategy for the degradation of bio-refractory compounds. BESs improve the waste treatment efficiency through the application of weak electrical stimulation. This review discusses the processes of BESs configurations and degradation performances in different environmental media including wastewater, soil, waste gas and groundwater. In addition, the degradation mechanisms and performance-enhancing additives are summarized. The future challenges and perspectives on the development of BES for COCs removal are briefly discussed.}, }
@article {pmid38767452, year = {2024}, author = {Rashidi, A and Ebadi, M and Rehman, TU and Elhusseini, H and Kazadi, D and Halaweish, H and Khan, MH and Hoeschen, A and Cao, Q and Luo, X and Kabage, AJ and Lopez, S and Ramamoorthy, S and Holtan, SG and Weisdorf, DJ and Khoruts, A and Staley, C}, title = {Multi-omics Analysis of a Fecal Microbiota Transplantation Trial Identifies Novel Aspects of Acute GVHD Pathogenesis.}, journal = {Cancer research communications}, volume = {4}, number = {6}, pages = {1454-1466}, pmid = {38767452}, issn = {2767-9764}, support = {KL2 TR002492/TR/NCATS NIH HHS/United States ; UL1 TR002494/TR/NCATS NIH HHS/United States ; KL2TR002492//Foundation for the National Institutes of Health (FNIH)/ ; UL1TR002494//Foundation for the National Institutes of Health (FNIH)/ ; P30CA07759//HHS | NIH | National Cancer Institute (NCI)/ ; Chainbreaker grant//UMN | Clinical and Translational Science Institute, University of Minnesota (CTSI)/ ; n/a//Achieving Cures Together/ ; }, mesh = {Humans ; *Graft vs Host Disease/microbiology/immunology ; *Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; *Hematopoietic Stem Cell Transplantation/methods/adverse effects ; Adult ; Leukemia, Myeloid, Acute/therapy/microbiology/immunology ; Transplantation, Homologous/methods/adverse effects ; Faecalibacterium ; Aged ; Acute Disease ; Feces/microbiology ; Metabolome ; Multiomics ; }, abstract = {UNLABELLED: Acute GVHD (aGVHD) is a major complication of allogeneic hematopoietic cell transplantation (alloHCT) associated with gut microbiota disruptions. However, whether therapeutic microbiota modulation prevents aGVHD is unknown. We conducted a randomized, placebo-controlled trial of third-party fecal microbiota transplantation (FMT) administered at the peak of microbiota injury in 100 patients with acute myeloid leukemia receiving induction chemotherapy and alloHCT recipients. Despite improvements in microbiome diversity, expansion of commensals, and shrinkage of potential pathogens, aGVHD occurred more frequently after FMT than placebo. Although this unexpected finding could be explained by clinical differences between the two arms, we asked whether a microbiota explanation might be also present. To this end, we performed multi-omics analysis of preintervention and postintervention gut microbiome and serum metabolome. We found that postintervention expansion of Faecalibacterium, a commensal genus with gut-protective and anti-inflammatory properties under homeostatic conditions, predicted a higher risk for aGVHD. Faecalibacterium expansion occurred predominantly after FMT and was due to engraftment of unique donor taxa, suggesting that donor Faecalibacterium-derived antigens might have stimulated allogeneic immune cells. Faecalibacterium and ursodeoxycholic acid (an anti-inflammatory secondary bile acid) were negatively correlated, offering an alternative mechanistic explanation. In conclusion, we demonstrate context dependence of microbiota effects where a normally beneficial bacteria may become detrimental in disease. While FMT is a broad, community-level intervention, it may need precision engineering in ecologically complex settings where multiple perturbations (e.g., antibiotics, intestinal damage, alloimmunity) are concurrently in effect.<br><br>SIGNIFICANCE: Post-FMT expansion of Faecalibacterium, associated with donor microbiota engraftment, predicted a higher risk for aGVHD in alloHCT recipients. Although Faecalibacterium is a commensal genus with gut-protective and anti-inflammatory properties under homeostatic conditions, our findings suggest that it may become pathogenic in the setting of FMT after alloHCT. Our results support a future trial with precision engineering of the FMT product used as GVHD prophylaxis after alloHCT.}, }
@article {pmid38764972, year = {2023}, author = {Boyes, D and Holland, PWH and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Common Emerald, Hemithea aestivaria (Hübner, 1789).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {243}, pmid = {38764972}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Hemithea aestivaria (the Common Emerald; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 501.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 17.05 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,477 protein coding genes.}, }
@article {pmid38764970, year = {2023}, author = {Boyes, D and Lewis, OT and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Pebble Hook-tip, Drepana falcataria (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {207}, pmid = {38764970}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Drepana falcataria (the Pebble Hook-tip; Arthropoda; Insecta; Lepidoptera; Drepanidae). The genome sequence is 326.7 megabases in span. The whole assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length.}, }
@article {pmid38764134, year = {2024}, author = {Wang, J and Li, Y and Rahman, MM and Li, B and Yan, Z and Song, G and Zhao, Y and Wu, J and Chu, C}, title = {Unraveling the drivers and impacts of leaf phenological diversity in a subtropical forest: A fine-scale analysis using PlanetScope CubeSats.}, journal = {The New phytologist}, volume = {243}, number = {2}, pages = {607-619}, doi = {10.1111/nph.19850}, pmid = {38764134}, issn = {1469-8137}, support = {20220816162849005//Shenzhen Science and Technology Program/ ; 32301350//National Natural Science Foundation of China/ ; 31925027//National Natural Science Foundation of China/ ; 31922090//National Natural Science Foundation of China/ ; 32271595//National Natural Science Foundation of China/ ; 17305321//Hong Kong Research Grant Council General Research Fund/ ; //HKU Seed Funding for Strategic Interdisciplinary Research Scheme, the Hung Ying Physical Science Research Fund 2021-22/ ; //Innovation and Technology Fund (funding support to State Key Laboratories in Hong Kong of Agrobiotechnology) of the HKSAR, China/ ; LVEC-2023rc01//Key Talent Project of the State Key Laboratory of Vegetation and Environmental Change/ ; }, mesh = {*Plant Leaves/physiology ; *Forests ; *Biodiversity ; *Tropical Climate ; Biomass ; Soil ; China ; }, abstract = {Leaf phenology variations within plant communities shape community assemblages and influence ecosystem properties and services. However, questions remain regarding quantification, drivers, and productivity impacts of intra-site leaf phenological diversity. With a 50-ha subtropical forest plot in China's Heishiding Provincial Nature Reserve (part of the global ForestGEO network) as a testbed, we gathered a unique dataset combining ground-derived abiotic (topography, soil) and biotic (taxonomic diversity, functional diversity, functional traits) factors. We investigated drivers underlying leaf phenological diversity extracted from high-resolution PlanetScope data, and its influence on aboveground biomass (AGB) using structural equation modeling (SEM). Our results reveal considerable fine-scale leaf phenological diversity across the subtropical forest landscape. This diversity is directly and indirectly influenced by abiotic and biotic factors (e.g. slope, soil, traits, taxonomic diversity; r[2] = 0.43). While a notable bivariate relationship between AGB and leaf phenological diversity was identified (r = -0.24, P < 0.05), this relationship did not hold in SEM analysis after considering interactions with other biotic and abiotic factors (P > 0.05). These findings unveil the underlying mechanism regulating intra-site leaf phenological diversity. While leaf phenology is known to be associated with ecosystem properties, our findings confirm that AGB is primarily influenced by functional trait composition and taxonomic diversity rather than leaf phenological diversity.}, }
@article {pmid38764024, year = {2024}, author = {Trujillano, F and Jimenez, G and Manrique, E and Kahamba, NF and Okumu, F and Apollinaire, N and Carrasco-Escobar, G and Barrett, B and Fornace, K}, title = {Using image segmentation models to analyse high-resolution earth observation data: new tools to monitor disease risks in changing environments.}, journal = {International journal of health geographics}, volume = {23}, number = {1}, pages = {13}, pmid = {38764024}, issn = {1476-072X}, support = {/WT_/Wellcome Trust/United Kingdom ; 221963/Z/20/Z//Wellcome Trust and Royal Society/ ; BB/X511110/1//BBSRC and EPSRC Impact Accelerator Accounts/ ; }, mesh = {Humans ; Animals ; *Climate Change ; Malaria/epidemiology ; Mosquito Vectors ; Remote Sensing Technology/methods ; Geographic Information Systems ; Image Processing, Computer-Assisted/methods ; }, abstract = {BACKGROUND: In the near future, the incidence of mosquito-borne diseases may expand to new sites due to changes in temperature and rainfall patterns caused by climate change. Therefore, there is a need to use recent technological advances to improve vector surveillance methodologies. Unoccupied Aerial Vehicles (UAVs), often called drones, have been used to collect high-resolution imagery to map detailed information on mosquito habitats and direct control measures to specific areas. Supervised classification approaches have been largely used to automatically detect vector habitats. However, manual data labelling for model training limits their use for rapid responses. Open-source foundation models such as the Meta AI Segment Anything Model (SAM) can facilitate the manual digitalization of high-resolution images. This pre-trained model can assist in extracting features of interest in a diverse range of images. Here, we evaluated the performance of SAM through the Samgeo package, a Python-based wrapper for geospatial data, as it has not been applied to analyse remote sensing images for epidemiological studies.<br><br>RESULTS: We tested the identification of two land cover classes of interest: water bodies and human settlements, using different UAV acquired imagery across five malaria-endemic areas in Africa, South America, and Southeast Asia. We employed manually placed point prompts and text prompts associated with specific classes of interest to guide the image segmentation and assessed the performance in the different geographic contexts. An average Dice coefficient value of 0.67 was obtained for buildings segmentation and 0.73 for water bodies using point prompts. Regarding the use of text prompts, the highest Dice coefficient value reached 0.72 for buildings and 0.70 for water bodies. Nevertheless, the performance was closely dependent on each object, landscape characteristics and selected words, resulting in varying performance.<br><br>CONCLUSIONS: Recent models such as SAM can potentially assist manual digitalization of imagery by vector control programs, quickly identifying key features when surveying an area of interest. However, accurate segmentation still requires user-provided manual prompts and corrections to obtain precise segmentation. Further evaluations are necessary, especially for applications in rural areas.}, }
@article {pmid38762947, year = {2024}, author = {Liu, D and Zhou, M and Tan, H and Xiong, G and Wang, L and Shi, L and Li, C and Wu, W and Qiao, Y}, title = {Metabolomics, volatolomics, and bioinformatics analyses of the effects of ultra-high pressure pretreatment on taste and flavour parameters of cured Culter alburnus.}, journal = {Food chemistry}, volume = {453}, number = {}, pages = {139649}, doi = {10.1016/j.foodchem.2024.139649}, pmid = {38762947}, issn = {1873-7072}, mesh = {Animals ; *Taste ; *Flavoring Agents/chemistry/metabolism ; *Metabolomics ; *Computational Biology ; Fish Products/analysis/microbiology ; Pressure ; Cyprinidae/metabolism/microbiology ; Volatile Organic Compounds/chemistry/metabolism/analysis ; Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Humans ; Food Handling ; Amino Acids/metabolism/analysis ; }, abstract = {The effects of ultra-high pressure (UHP) pretreatment (50-250 MPa) on the fish curing were studied. UHP increased the overall volatile compound concentration of cured fish. Among 50-250 MPa five treatment groups, 150 MPa UHP group exhibited the highest total free amino acid content (294.34 mg/100 g) with that of the control group being 92.39 mg/100 g. The activity of cathepsin L was increased under 50-200 MPa UHP treatment (62.28-58.15 U/L), compared with that in the control group (53.80 U/L). UHP treatment resulted in a significant increase in small molecule compounds, especially the amino acid dipeptides and ATP metabolic products. Under UHP treatments, the bacterial phyla Actinobacteriota (1.04-5.25 %), Bacteroidota (0.20-4.47 %), and Deinococcota (0.00-0.05 %) exhibited an increased abundance, and they promoted taste and flavor formation. Our results indicated that UHP is a promising pretreatment method to improve taste and flavour in cured fish by affecting the microorganisms, cathepsin, and proteins.}, }
@article {pmid38760814, year = {2024}, author = {Sakai, K and Igarashi, Y and Tounai, S and Shirai, C and Tsurugi, Y and Kakuno, F and Komasa, Y and Fujimura, M and Uruha, M and Mori, K and Tateishi, S}, title = {Key issues in Japan's public health centers to prepare for future pandemics: a text mining study using a topic model.}, journal = {BMC health services research}, volume = {24}, number = {1}, pages = {636}, pmid = {38760814}, issn = {1472-6963}, mesh = {Humans ; Japan ; *COVID-19/epidemiology ; Cross-Sectional Studies ; *Pandemics ; Surveys and Questionnaires ; Data Mining/methods ; Public Health ; SARS-CoV-2 ; Male ; }, abstract = {BACKGROUND: In Japan, over 450 public health centers played a central role in the operation of the local public health system in response to the COVID-19 pandemic. This study aimed to identify key issues for improving the system for public health centers for future pandemics.<br><br>METHODS: We conducted a cross-sectional study using an online questionnaire. The respondents were first line workers in public health centers or local governments during the pandemic. We solicited open-ended responses concerning improvements needed for future pandemics. Issues were identified from these descriptions using morphological analysis and a topic model with KHcoder3.0. The number of topics was estimated using Perplexity as a measure, and Latent Dirichlet Allocation for meaning identification.<br><br>RESULTS: We received open-ended responses from 784 (48.6%) of the 1,612 survey respondents, which included 111 physicians, 330 nurses, and 172 administrative staff. Morphological analysis processed these descriptions into 36,632 words. The topic model summarized them into eight issues: 1) establishment of a crisis management system, 2) division of functions among public health centers, prefectures, and medical institutions, 3) clear role distribution in public health center staff, 4) training of specialists, 5) information sharing system (information about infectious diseases and government policies), 6) response to excessive workload (support from other local governments, cooperation within public health centers, and outsourcing), 7) streamlining operations, and 8) balance with regular duties.<br><br>CONCLUSIONS: This study identified key issues that need to be addressed to prepare Japan's public health centers for future pandemics. These findings are vital for discussions aimed at strengthening the public health system based on experiences from the COVID-19 pandemic.}, }
@article {pmid38758962, year = {2024}, author = {Massey, A and Boennec, C and Restrepo-Ortiz, CX and Blanchet, C and Alizon, S and Sofonea, MT}, title = {Real-time forecasting of COVID-19-related hospital strain in France using a non-Markovian mechanistic model.}, journal = {PLoS computational biology}, volume = {20}, number = {5}, pages = {e1012124}, pmid = {38758962}, issn = {1553-7358}, mesh = {*COVID-19/epidemiology ; Humans ; France/epidemiology ; *Forecasting/methods ; *SARS-CoV-2 ; Computational Biology/methods ; Retrospective Studies ; Models, Statistical ; Pandemics/statistics &amp; numerical data ; Hospitals/statistics &amp; numerical data ; Hospitalization/statistics &amp; numerical data ; Bed Occupancy/statistics &amp; numerical data ; }, abstract = {Projects such as the European Covid-19 Forecast Hub publish forecasts on the national level for new deaths, new cases, and hospital admissions, but not direct measurements of hospital strain like critical care bed occupancy at the sub-national level, which is of particular interest to health professionals for planning purposes. We present a sub-national French framework for forecasting hospital strain based on a non-Markovian compartmental model, its associated online visualisation tool and a retrospective evaluation of the real-time forecasts it provided from January to December 2021 by comparing to three baselines derived from standard statistical forecasting methods (a naive model, auto-regression, and an ensemble of exponential smoothing and ARIMA). In terms of median absolute error for forecasting critical care unit occupancy at the two-week horizon, our model only outperformed the naive baseline for 4 out of 14 geographical units and underperformed compared to the ensemble baseline for 5 of them at the 90% confidence level (n = 38). However, for the same level at the 4 week horizon, our model was never statistically outperformed for any unit despite outperforming the baselines 10 times spanning 7 out of 14 geographical units. This implies modest forecasting utility for longer horizons which may justify the application of non-Markovian compartmental models in the context of hospital-strain surveillance for future pandemics.}, }
@article {pmid38752675, year = {2024}, author = {Schaupp, CM and Byrne, G and Chan, M and Haggard, DE and Hazemi, M and Jankowski, MD and LaLone, CA and LaTier, A and Mattingly, KZ and Olker, JH and Renner, J and Sharma, B and Villeneuve, DL}, title = {An automated computational data pipeline to rapidly acquire, score, and rank toxicological data for ecological hazard assessment.}, journal = {Integrated environmental assessment and management}, volume = {20}, number = {6}, pages = {2203-2217}, doi = {10.1002/ieam.4945}, pmid = {38752675}, issn = {1551-3793}, support = {//USEPA Office of Research and Development, Chemical Safety for Sustainability National Research Program/ ; }, mesh = {Risk Assessment/methods ; *Environmental Monitoring/methods ; Animals ; Endangered Species ; Water Pollutants, Chemical/toxicity/analysis ; Ecotoxicology/methods ; United States ; Quantitative Structure-Activity Relationship ; }, abstract = {Biological Evaluations support Endangered Species Act (ESA) consultation with the US Fish and Wildlife Service and National Marine Fisheries Service by federal action agencies, such as the USEPA, regarding impacts of federal activities on threatened or endangered species. However, they are often time-consuming and challenging to conduct. The identification of pollutant benchmarks or guidance to protect taxa for states and tribes when USEPA has not yet developed criteria recommendations is also of importance to ensure a streamlined approach to Clean Water Act program implementation. Due to substantial workloads, tight regulatory timelines, and the often-protracted length of ESA consultations, there is a need to streamline the development of biological evaluation toxicity assessments for determining the impact of chemical pollutants on ESA-listed species. Moreover, there is limited availability of species-specific toxicity data for many contaminants, further complicating the consultation process. New approach methodologies are being increasingly used in toxicology and chemical safety assessment to rapidly and cost-effectively provide data that can fill gaps in hazard and/or exposure characterization. Here, we present the development of an automated computational pipeline-RASRTox (Rapidly Acquire, Score, and Rank Toxicological data)-to rapidly extract and categorize ecological toxicity benchmark values from curated data sources (ECOTOX, ToxCast) and well-established quantitative structure-activity relationships (TEST, ECOSAR). As a proof of concept, points-of-departure (PODs) generated in RASRTox for 13 chemicals were compared against benchmark values derived using traditional methods-toxicity reference values (TRVs) and water quality criteria (WQC). The RASRTox PODs were generally within an order of magnitude of corresponding TRVs, though less concordant compared with WQC. The greatest utility of RASRTox, however, lies in its ability to quickly and systematically identify critical studies that may serve as a basis for screening value derivation by toxicologists as part of an ecological hazard assessment. As such, the strategy described in this case study can potentially be adapted for other risk assessment contexts and stakeholder needs. Integr Environ Assess Manag 2024;20:2203-2217. © 2024 Society of Environmental Toxicology &amp; Chemistry (SETAC). This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.}, }
@article {pmid38746391, year = {2024}, author = {Acheampong, DA and Jenjaroenpun, P and Wongsurawat, T and Krulilung, A and Pomyen, Y and Kandel, S and Kunadirek, P and Chuaypen, N and Kusonmano, K and Nookaew, I}, title = {CAIM: Coverage-based Analysis for Identification of Microbiome.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38746391}, issn = {2692-8205}, support = {P20 GM125503/GM/NIGMS NIH HHS/United States ; R01 CA143130/CA/NCI NIH HHS/United States ; }, abstract = {Accurate taxonomic profiling of microbial taxa in a metagenomic sample is vital to gain insights into microbial ecology. Recent advancements in sequencing technologies have contributed tremendously toward understanding these microbes at species resolution through a whole shotgun metagenomic (WMS) approach. In this study, we developed a new bioinformatics tool, CAIM, for accurate taxonomic classification and quantification within both long- and short-read metagenomic samples using an alignment-based method. CAIM depends on two different containment techniques to identify species in metagenomic samples using their genome coverage information to filter out false positives rather than the traditional approach of relative abundance. In addition, we propose a nucleotide-count based abundance estimation, which yield lesser root mean square error than the traditional read-count approach. We evaluated the performance of CAIM on 28 metagenomic mock communities and 2 synthetic datasets by comparing it with other top-performing tools. CAIM maintained a consitently good performance across datasets in identifying microbial taxa and in estimating relative abundances than other tools. CAIM was then applied to a real dataset sequenced on both Nanopore (with and without amplification) and Illumina sequencing platforms and found high similality of taxonomic profiles between the sequencing platforms. Lastly, CAIM was applied to fecal shotgun metagenomic datasets of 232 colorectal cancer patients and 229 controls obtained from 4 different countries and primary 44 liver cancer patients and 76 controls. The predictive performance of models using the genome-coverage cutoff was better than those using the relative-abundance cutoffs in discriminating colorectal cancer and primary liver cancer patients from healthy controls with a highly confident species markers.}, }
@article {pmid38741754, year = {2024}, author = {Klatt, S and Otte, FW and Beavan, A and Schumacher, T and Millar, SK}, title = {How did you perform? Investigating football players' perception of self-regulated passing performances under auditory noise environments.}, journal = {Frontiers in psychology}, volume = {15}, number = {}, pages = {1390487}, pmid = {38741754}, issn = {1664-1078}, abstract = {INTRODUCTION: This paper deals with the question on how sport performances may be influenced by internal, emotional processes, which stem from outside feedback.<br><br>METHODS: In terms of methods, players' subjective performance ratings for four experimental auditory cue conditions were examined; these included both 'positive' and 'negative' stadium noise, 'no (auditory) conditions,' and a control/'baseline' condition. This resulted in a qualitative-analytic data set that was obtained succeeding each auditory cue condition using a unique football training machine (i.e., known as 'Footbonaut'). Without having received any coaching/performance feedback, players were asked to rate and individually comment on their perceived performance ratings for each experimental auditory condition.<br><br>RESULTS: Findings indicate stronger and more significant correlations between auditory conditions and subjective ratings compared to the non-auditory condition and its subjective rating. Furthermore, data provides initial insight into players' emotional experiences during each of the practice conditions.<br><br>DISCUSSION: These noteworthy findings on players' abilities to accurately judge their performances based on selfmonitoring and intrinsic feedback are discussed from an Ecological Dynamics perspective, linked to a Nonlinear Pedagogy for coaching. Here, representative and affective learning designs for skill learning and performance preparation are presented. Finally, a hypothetical catalyst effect of auditory stadium noise on subjective performance rating is proposed.}, }
@article {pmid38741150, year = {2024}, author = {Sõukand, R}, title = {Dark local knowledge: the yet-to-be scientifically discovered and locally acknowledged aspects of local knowledge systems.}, journal = {Journal of ethnobiology and ethnomedicine}, volume = {20}, number = {1}, pages = {50}, pmid = {38741150}, issn = {1746-4269}, mesh = {*Knowledge ; Humans ; Science ; }, abstract = {This essay brings forward the idea that there is more than meets the eye in local knowledge systems than what science can show us now. To comprehend this, we need to make a conceptual jump and look for the "dark matter" (the notion borrowed from astronomy that refers to a hypothetical form of matter that does not interact with light or electromagnetic fields) that can potentially sustain local knowledge. Considering that it is a complex of knowledge, practices, and beliefs contained in TEK, knowledge in LEK does not correspond to the notion of knowledge in science. Therefore, in order to map LEK-science interactions, we will refer to the concept of peoples' knowledge of LEK as acknowledgement and the scientific recognition and awareness of information, facts, and principles as knowledge. Applying this to a Johari Window, we can observe four categories of LEK in a known-unknown/acknowledged-unacknowledged matrix. We can refer to unknown and unacknowledged as dark local knowledge. Indeed, local knowledge systems contain many aspects that modern science cannot yet explain, as a major part of its components are not even considered in scholarly research. Dark local knowledge can potentially provide us with the invaluable touch of experience of countless generations, opening different ways of seeing reality.}, }
@article {pmid38739654, year = {2024}, author = {Bloxham, B and Lee, H and Gore, J}, title = {Biodiversity is enhanced by sequential resource utilization and environmental fluctuations via emergent temporal niches.}, journal = {PLoS computational biology}, volume = {20}, number = {5}, pages = {e1012049}, pmid = {38739654}, issn = {1553-7358}, mesh = {*Biodiversity ; *Models, Biological ; *Ecosystem ; Computational Biology ; Animals ; }, abstract = {How natural communities maintain their remarkable biodiversity and which species survive in complex communities are central questions in ecology. Resource competition models successfully explain many phenomena but typically predict only as many species as resources can coexist. Here, we demonstrate that sequential resource utilization, or diauxie, with periodic growth cycles can support many more species than resources. We explore how communities modify their own environments by sequentially depleting resources to form sequences of temporal niches, or intermediately depleted environments. Biodiversity is enhanced when community-driven or environmental fluctuations modulate the resource depletion order and produce different temporal niches on each growth cycle. Community-driven fluctuations under constant environmental conditions are rare, but exploring them illuminates the temporal niche structure that emerges from sequential resource utilization. With environmental fluctuations, we find most communities have more stably coexisting species than resources with survivors accurately predicted by the same temporal niche structure and each following a distinct optimal strategy. Our results thus present a new niche-based approach to understanding highly diverse fluctuating communities.}, }
@article {pmid38729378, year = {2024}, author = {Yu, H and Yin, D and Yang, B and Yang, Y and Chen, F}, title = {Challenges for sustainable development goal of land degradation neutrality in drylands: Evidence from the Northern Slope of the Tianshan Mountains, China.}, journal = {The Science of the total environment}, volume = {932}, number = {}, pages = {173094}, doi = {10.1016/j.scitotenv.2024.173094}, pmid = {38729378}, issn = {1879-1026}, abstract = {The SDG 15.3.1 target of Land Degradation Neutrality (LDN) only has 15 years from conception (in 2015) to realization (in 2030). Therefore, investigating the effectiveness and challenges of LDN has become a priority, especially in drylands, where fragile ecosystems intersect with multiple disturbances. In this study, solutions are proposed and validated based on the challenges of LDN. We chose the Northern Slope of the Tianshan Mountains as a case study and set baselines in 2005 and 2010. The region and degree of land change (including degraded, stable, and improved) were depicted at the pixel scale (100 × 100 m), and LDN realization was assessed at the regional scale (including administrative districts and 5000 × 5000 m grids). The results showed a significant disparity between the two baselines. The number of areas that realized the LDN target was rare, regardless of the scale of the administrative districts or grids. Chord plots, Spearman's correlation, and curve estimation were employed to reveal the relationship between LDN and seven natural or socioeconomic factors. We found that substantial degradation was closely related to the expansion of unused, urban, and mining land and reduction in water, glaciers, and forests. Further evidence suggests that agricultural development both positively and negatively affects LDN, whereas urbanization and mining activities are undesirable for LDN. Notably, the adverse effects of glacier melting require additional attention. Therefore, we consider the easy-to-achieve and hard-to-achieve baselines as the mandatory and desirable targets of LDN, respectively, and focus further efforts in three aspects: preventing agricultural exploitation from occupying ecological resources, defining reasonable zones for urbanization and mining, and reducing greenhouse gas emissions to mitigate warming. Overall, this study is expected to be a beneficial addition to existing LDN theoretical systems and serve as a case validation of the challenges of LDN in drylands.}, }
@article {pmid38729197, year = {2024}, author = {Caini, S and Meijer, A and Nunes, MC and Henaff, L and Zounon, M and Boudewijns, B and Del Riccio, M and Paget, J}, title = {Probable extinction of influenza B/Yamagata and its public health implications: a systematic literature review and assessment of global surveillance databases.}, journal = {The Lancet. Microbe}, volume = {5}, number = {8}, pages = {100851}, doi = {10.1016/S2666-5247(24)00066-1}, pmid = {38729197}, issn = {2666-5247}, mesh = {Humans ; COVID-19/epidemiology/prevention &amp; control ; Databases, Factual/statistics &amp; numerical data ; *Global Health/statistics &amp; numerical data ; *Influenza B virus/genetics/isolation &amp; purification ; *Influenza, Human/epidemiology/virology ; Pandemics ; *Public Health ; }, abstract = {Early after the start of the COVID-19 pandemic, the detection of influenza B/Yamagata cases decreased globally. Given the potential public health implications of this decline, in this Review, we systematically analysed data on influenza B/Yamagata virus circulation (for 2020-23) from multiple complementary sources of information. We identified relevant articles published in PubMed and Embase, and data from the FluNet, Global Initiative on Sharing All Influenza Data, and GenBank databases, webpages of respiratory virus surveillance systems from countries worldwide, and the Global Influenza Hospital Surveillance Network. A progressive decline of influenza B/Yamagata detections was reported across all sources, in absolute terms (total number of cases), as positivity rate, and as a proportion of influenza B detections. Sporadically reported influenza B/Yamagata cases since March, 2020 were mostly vaccine-derived, attributed to data entry errors, or have yet to be definitively confirmed. The likelihood of extinction necessitates a rapid response in terms of reassessing the composition of influenza vaccines, enhanced surveillance for B/Yamagata, and a possible change in the biosafety level when handling B/Yamagata viruses in laboratories.}, }
@article {pmid38724591, year = {2024}, author = {Bhandari, N and Bald, L and Wraase, L and Zeuss, D}, title = {Multispectral analysis-ready satellite data for three East African mountain ecosystems.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {473}, pmid = {38724591}, issn = {2052-4463}, support = {5064//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 2358//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {Climate Change ; *Ecosystem ; Environmental Monitoring/methods ; Ethiopia ; Remote Sensing Technology ; *Satellite Imagery ; Tanzania ; }, abstract = {The East African mountain ecosystems are facing increasing threats due to global change, putting their unique socio-ecological systems at risk. To monitor and understand these changes, researchers and stakeholders require accessible analysis-ready remote sensing data. Although satellite data is available for many applications, it often lacks accurate geometric orientation and has extensive cloud cover. This can generate misleading results and make it unreliable for time-series analysis. Therefore, it needs comprehensive processing before usage, which encompasses multi-step operations, requiring large computational and storage capacities, as well as expert knowledge. Here, we provide high-quality, atmospherically corrected, and cloud-free analysis-ready Sentinel-2 imagery for the Bale Mountains (Ethiopia), Mounts Kilimanjaro and Meru (Tanzania) ecosystems in East Africa. Our dataset ranges from 2017 to 2021 and is provided as monthly and annual aggregated products together with 24 spectral indices. Our dataset enables researchers and stakeholders to conduct immediate and impactful analyses. These applications can include vegetation mapping, wildlife habitat assessment, land cover change detection, ecosystem monitoring, and climate change research.}, }
@article {pmid38724027, year = {2024}, author = {Dar, FA and Hamid, M and Malik, RA and Wani, SA and Singh, CP and Shah, MA and Khuroo, AA}, title = {ToTE: A global database on trees of the treeline ecotone.}, journal = {Ecology}, volume = {105}, number = {6}, pages = {e4309}, doi = {10.1002/ecy.4309}, pmid = {38724027}, issn = {1939-9170}, support = {923/CSIR-UGC NET JUNE 2019//University Grants Commission/ ; SR/FST/LS-II/2017/103(C)//Department of Science &amp; Technology, Govt. of India, New Delhi/ ; SAC/EPSA/ALPINE/SHRESTI/10/2019//Space Applications Centre (SAC) ISRO, Ahmedabad/ ; }, mesh = {*Trees ; *Databases, Factual ; Biodiversity ; Forests ; Ecosystem ; }, abstract = {Globally, treelines form a transition zone between tree-dominated forest downslope and treeless alpine vegetation upslope. Treelines represent the highest boundary of "tree" life form in high-elevation mountains and at high latitudes. Recently, treelines have been shifting upslope in response to climate warming, so it has become important to understand global tree diversity and treeline distributions. However, to the best of our knowledge, no global database on tree flora of treelines exists, which limits our capacity to undertake macroecological analyses. Here, for the first time, we present a global data set on the trees of the treeline ecotone, supported by an online ToTE database. We synthesized the database from 1202 studies published over the last 60 years (1962 to 2022) following the Preferred Reporting Items in Systematic Reviews and Meta-Analysis (PRISMA) protocol. We classified the tree species in the database into three categories: treeline tree (TL) species, near to treeline (NTL) tree species, and tree species with an upper montane range limit (TUMR). The ToTE Version-1 presents a total of 208 tree taxa, including 189 species, five subspecies, and 14 varieties, belonging to 54 genera and 26 families distributed across 34 mountain regions worldwide that either grow exactly at the treeline or have a range limit below the treeline. Of the total taxa, 155, 14, and 39 belong to TL, NTL, and TUMR, respectively. Genera such as Abies, Picea, Pinus, Larix, and Juniperus are more represented in the treeline tree category. On the other hand, Acer, Prunus, Populus, and Quercus have more representatives in the near to treeline category, whereas Erica, Nothofagus, and Polylepis contribute more tree species with an upper montane range limit. Furthermore, families such as Rosaceae and Pinaceae include trees that occur both at the treeline and with an upper montane range limit, whereas Sapindaceae includes trees that occur exclusively near to treeline. Our database also includes information on the global distribution patterns of treeline tree species richness across mountains and biomes. The mountains with the highest number of tree species are the Andes (39) followed by the Himalaya (37). Close to 67% of tree species show restricted distributions in different mountains, with the highest endemism in the Andes and the Himalaya. In terms of tree species distribution, Pinus sylvestris was widespread, with a distribution across nine mountain regions, followed by Picea glauca and Fagus sylvatica, both distributed across five mountain regions. In terms of species' distribution across biomes, the temperate biome harbors the highest treeline tree species richness (152 species), which may reflect the fact that the majority of studies are available from the temperate regions of the world. The remaining 56 species are distributed within five other biomes, with the least in dry tropical and subarctic (four species each). Furthermore, currently 40 treeline tree species fall under different International Union for Conservation of Nature threat categories. We anticipate that our database will help advance research on macroecological, biogeographic, evolutionary, climate-change, and conservation aspects of the treeline on a global scale. The data are released under a Creative Commons Attribution 4.0 international license. Please cite this data paper when the data are reused.}, }
@article {pmid38723067, year = {2024}, author = {Holstad, A and Voje, KL and Opedal, &#xd8;H and Bolstad, GH and Bourg, S and Hansen, TF and Pélabon, C}, title = {Evolvability predicts macroevolution under fluctuating selection.}, journal = {Science (New York, N.Y.)}, volume = {384}, number = {6696}, pages = {688-693}, doi = {10.1126/science.adi8722}, pmid = {38723067}, issn = {1095-9203}, mesh = {Animals ; *Biological Evolution ; *Fossils ; Genetic Variation ; *Selection, Genetic ; Datasets as Topic ; }, abstract = {Heritable variation is a prerequisite for evolutionary change, but the relevance of genetic constraints on macroevolutionary timescales is debated. By using two datasets on fossil and contemporary taxa, we show that evolutionary divergence among populations, and to a lesser extent among species, increases with microevolutionary evolvability. We evaluate and reject several hypotheses to explain this relationship and propose that an effect of evolvability on population and species divergence can be explained by the influence of genetic constraints on the ability of populations to track rapid, stationary environmental fluctuations.}, }
@article {pmid38721834, year = {2025}, author = {Freedman, AH and Sackton, TB}, title = {Rethinking eco-evo studies of gene expression for non-model organisms in the genomic era.}, journal = {Molecular ecology}, volume = {34}, number = {15}, pages = {e17378}, doi = {10.1111/mec.17378}, pmid = {38721834}, issn = {1365-294X}, mesh = {*Genomics/methods ; Single-Cell Analysis/methods ; Sequence Analysis, RNA/methods ; Transcriptome ; Animals ; *Ecology/methods ; Gene Expression Regulation ; RNA-Seq ; *Gene Expression Profiling/methods ; *Gene Expression ; }, abstract = {Recent advances in genomic technology, including the rapid development of long-read sequencing technology and single-cell RNA-sequencing methods, are poised to significantly expand the kinds of studies that are feasible in ecological genomics. In this perspective, we review these new technologies and discuss their potential impact on gene expression studies in non-model organisms. Although traditional RNA-sequencing methods have been an extraordinarily powerful tool to apply functional genomics in an ecological context, bulk RNA-seq approaches often rely on de novo transcriptome assembly, and cannot capture expression changes in rare cell populations or distinguish shifts in cell type abundance. Advancements in genome assembly technology, particularly long-read sequencing, and improvements in the scalability of single-cell RNA-sequencing (scRNA-seq) offer unprecedented resolution in understanding cellular heterogeneity and gene regulation. We discuss the potential of these technologies to enable disentangling differential gene regulation from cell type composition differences and uncovering subtle expression patterns masked by bulk RNA-seq. The integration of these approaches provides a more nuanced understanding of the ecological and evolutionary dynamics of gene expression, paving the way for refined models and deeper insights into the generation of biodiversity.}, }
@article {pmid38721398, year = {2024}, author = {Ross, KE and Bastian, FB and Buys, M and Cook, CE and D'Eustachio, P and Harrison, M and Hermjakob, H and Li, D and Lord, P and Natale, DA and Peters, B and Sternberg, PW and Su, AI and Thakur, M and Thomas, PD and Bateman, A and , }, title = {Perspectives on tracking data reuse across biodata resources.}, journal = {Bioinformatics advances}, volume = {4}, number = {1}, pages = {vbae057}, pmid = {38721398}, issn = {2635-0041}, support = {U24 HG012212/HG/NHGRI NIH HHS/United States ; U24 HG007822/HG/NHGRI NIH HHS/United States ; U41 HG007822/HG/NHGRI NIH HHS/United States ; U24 HG011851/HG/NHGRI NIH HHS/United States ; R35 GM141873/GM/NIGMS NIH HHS/United States ; }, abstract = {MOTIVATION: Data reuse is a common and vital practice in molecular biology and enables the knowledge gathered over recent decades to drive discovery and innovation in the life sciences. Much of this knowledge has been collated into molecular biology databases, such as UniProtKB, and these resources derive enormous value from sharing data among themselves. However, quantifying and documenting this kind of data reuse remains a challenge.<br><br>RESULTS: The article reports on a one-day virtual workshop hosted by the UniProt Consortium in March 2023, attended by representatives from biodata resources, experts in data management, and NIH program managers. Workshop discussions focused on strategies for tracking data reuse, best practices for reusing data, and the challenges associated with data reuse and tracking. Surveys and discussions showed that data reuse is widespread, but critical information for reproducibility is sometimes lacking. Challenges include costs of tracking data reuse, tensions between tracking data and open sharing, restrictive licenses, and difficulties in tracking commercial data use.&#xa0;Recommendations that emerged from the discussion include: development of standardized formats for documenting data reuse, education about the obstacles posed by restrictive licenses, and continued recognition by funding agencies that data management is a critical activity that requires dedicated resources.<br><br>Summaries of survey results are available at: https://docs.google.com/forms/d/1j-VU2ifEKb9C-sW6l3ATB79dgHdRk5v_lESv2hawnso/viewanalytics (survey of data providers) and https://docs.google.com/forms/d/18WbJFutUd7qiZoEzbOytFYXSfWFT61hVce0vjvIwIjk/viewanalytics (survey of users).}, }
@article {pmid38720068, year = {2024}, author = {Mahon, MB and Sack, A and Aleuy, OA and Barbera, C and Brown, E and Buelow, H and Civitello, DJ and Cohen, JM and de Wit, LA and Forstchen, M and Halliday, FW and Heffernan, P and Knutie, SA and Korotasz, A and Larson, JG and Rumschlag, SL and Selland, E and Shepack, A and Vincent, N and Rohr, JR}, title = {A meta-analysis on global change drivers and the risk of infectious disease.}, journal = {Nature}, volume = {629}, number = {8013}, pages = {830-836}, pmid = {38720068}, issn = {1476-4687}, mesh = {Animals ; Humans ; Anthropogenic Effects ; *Biodiversity ; *Climate Change/statistics &amp; numerical data ; *Communicable Diseases/epidemiology/etiology ; Conservation of Natural Resources/trends ; Datasets as Topic ; *Environmental Pollution/adverse effects ; Forestry ; Forests ; *Introduced Species/statistics &amp; numerical data ; Plant Diseases/etiology ; Risk Assessment ; Urbanization ; }, abstract = {Anthropogenic change is contributing to the rise in emerging infectious diseases, which are significantly correlated with socioeconomic, environmental and ecological factors[1]. Studies have shown that infectious disease risk is modified by changes to biodiversity[2-6], climate change[7-11], chemical pollution[12-14], landscape transformations[15-20] and species introductions[21]. However, it remains unclear which global change drivers most increase disease and under what contexts. Here we amassed a dataset from the literature that contains 2,938 observations of infectious disease responses to global change drivers across 1,497 host-parasite combinations, including plant, animal and human hosts. We found that biodiversity loss, chemical pollution, climate change and introduced species are associated with increases in disease-related end points or harm, whereas urbanization is associated with decreases in disease end points. Natural biodiversity gradients, deforestation and forest fragmentation are comparatively unimportant or idiosyncratic as drivers of disease. Overall, these results are consistent across human and non-human diseases. Nevertheless, context-dependent effects of the global change drivers on disease were found to be common. The findings uncovered by this meta-analysis should help target disease management and surveillance efforts towards global change drivers that increase disease. Specifically, reducing greenhouse gas emissions, managing ecosystem health, and preventing biological invasions and biodiversity loss could help to reduce the burden of plant, animal and human diseases, especially when coupled with improvements to social and economic determinants of health.}, }
@article {pmid38718196, year = {2024}, author = {Leroux, A and Crainiceanu, C and Zeger, S and Taub, M and Ansari, B and Wager, TD and Bayman, E and Coffey, C and Langefeld, C and McCarthy, R and Tsodikov, A and Brummet, C and Clauw, DJ and Edwards, RR and Lindquist, MA and , }, title = {Statistical modeling of acute and chronic pain patient-reported outcomes obtained from ecological momentary assessment.}, journal = {Pain}, volume = {165}, number = {9}, pages = {1955-1965}, pmid = {38718196}, issn = {1872-6623}, support = {U54 DA049113/DA/NIDA NIH HHS/United States ; U54 DA049115/DA/NIDA NIH HHS/United States ; U54 DA049116/DA/NIDA NIH HHS/United States ; UM1 NS112874/NS/NINDS NIH HHS/United States ; U54 DA049110/DA/NIDA NIH HHS/United States ; U24 NS112873/NS/NINDS NIH HHS/United States ; R01 NS060910/NS/NINDS NIH HHS/United States ; UM1 NS118922/NS/NINDS NIH HHS/United States ; R01 AG075883/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; *Chronic Pain/diagnosis ; *Patient Reported Outcome Measures ; *Ecological Momentary Assessment ; *Models, Statistical ; *Pain Measurement/methods ; *Acute Pain/diagnosis ; Male ; Female ; }, abstract = {Ecological momentary assessment (EMA) allows for the collection of participant-reported outcomes (PROs), including pain, in the normal environment at high resolution and with reduced recall bias. Ecological momentary assessment is an important component in studies of pain, providing detailed information about the frequency, intensity, and degree of interference of individuals' pain. However, there is no universally agreed on standard for summarizing pain measures from repeated PRO assessment using EMA into a single, clinically meaningful measure of pain. Here, we quantify the accuracy of summaries (eg, mean and median) of pain outcomes obtained from EMA and the effect of thresholding these summaries to obtain binary clinical end points of chronic pain status (yes/no). Data applications and simulations indicate that binarizing empirical estimators (eg, sample mean, random intercept linear mixed model) can perform well. However, linear mixed-effect modeling estimators that account for the nonlinear relationship between average and variability of pain scores perform better for quantifying the true average pain and reduce estimation error by up to 50%, with larger improvements for individuals with more variable pain scores. We also show that binarizing pain scores (eg, <3 and ≥3) can lead to a substantial loss of statistical power (40%-50%). Thus, when examining pain outcomes using EMA, the use of linear mixed models using the entire scale (0-10) is superior to splitting the outcomes into 2 groups (<3 and ≥3) providing greater statistical power and sensitivity.}, }
@article {pmid38717702, year = {2024}, author = {Zhou, Q and Song, Y and Zhang, Y and Ping, Z and Zheng, Y and Chen, H and Liu, P and Hong, P and Zheng, Z}, title = {Land use transition and its effect on ecosystem service value with introducing "three wastes" factor in the industrial county, China.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {24}, pages = {34962-34980}, pmid = {38717702}, issn = {1614-7499}, support = {ZR2023MD033//Natural Science Foundation of Shandong Province/ ; LJNY202103//Key Technology Research and Development Program of Shandong Province/ ; }, mesh = {China ; *Ecosystem ; Conservation of Natural Resources ; Urbanization ; Forests ; Environmental Monitoring ; }, abstract = {Land use transition and its impact on ecosystem service value (ESV) are the foundation for optimizing the layout of territorial space and ecological civilization construction. With the acceleration of industrialization and urbanization, the area of construction land expands in China. To accurately estimate the ESV in industrial counties, the impact of construction land on the ecological environment should be fully considered. This paper took Gangcheng District, Jinan City, a steel base in the Shandong Province of China as an example, then the value coefficients of "three wastes" factors (waste gas, wastewater, and waste) were introduced, and an improved calculation method of ESV was put forward for industrial counties in combination with remote sensing and land use data. Finally, the land use transition and its ESV effect in typical industrial counties were analyzed using geo-informatic Tupu and grid method. The results showed that the most important land use transitions were from grassland and forestland to cultivated land, from cultivated land and forestland to construction land in 1990-2010, and from cultivated land transformed to forestland in 2010-2021. The types of land use transition were mainly repetitive and continuous. The ESV first decreased and then increased, with a slight overall decline for more than 30 years, showing a spatial distribution characteristic of "low in the south-central and high around." Land use transition had the impact on ESV with the negative contribution rate of 68.28% in 1990-2000 and 73.16% in 2000-2010, mainly caused by the transition from forestland and grassland to cultivated land and construction land, and the positive contribution rate of 81.72% in 2010-2021, mainly caused by the transition from cultivated land to forestland. Compared with the ESV calculation method without introducing the "three wastes" factor and Xie Gaodi's method, the improved method in this paper considered the inevitable impact of construction land on ESV in industrial counties and made the ESV calculated more accurate according to the regional nature. This paper cannot only enrich the theories and technical methods of land use transition and its effects, and provide a case reference for similar industrial counties, but also provide data and decision-making support for the spatial layout and ecological protection in the study area.}, }
@article {pmid38716048, year = {2023}, author = {Boyes, D and Hammond, J and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Ruddy Flat-body, Agonopterix subpropinquella (Stainton, 1849).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {487}, pmid = {38716048}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Agonopterix subpropinquella (the Ruddy Flat-body; Arthropoda; Insecta; Lepidoptera; Depressariidae). The genome sequence is 667.9 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.5 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,796 protein coding genes.}, }
@article {pmid38714914, year = {2024}, author = {Zhang, L and Zhang, Y and Liu, Y and Miao, W and Ai, J and Li, J and Peng, S and Li, S and Ye, L and Zeng, R and Shi, X and Ma, J and Lin, Y and Kuang, W and Cui, R}, title = {Multi-omics analysis revealed that the protein kinase MoKin1 affected the cellular response to endoplasmic reticulum stress in the rice blast fungus, Magnaporthe oryzae.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {449}, pmid = {38714914}, issn = {1471-2164}, mesh = {*Endoplasmic Reticulum Stress ; *Oryza/microbiology/genetics ; *Fungal Proteins/metabolism/genetics ; *Proteomics ; Plant Diseases/microbiology ; Gene Expression Regulation, Fungal ; Protein Kinases/metabolism/genetics ; Mutation ; Multiomics ; Ascomycota ; }, abstract = {BACKGROUND: Previous studies have shown that protein kinase MoKin1 played an important role in the growth, conidiation, germination and pathogenicity in rice blast fungus, Magnaporthe oryzae. ΔMokin1 mutant showed significant phenotypic defects and significantly reduced pathogenicity. However, the internal mechanism of how MoKin1 affected the development of physiology and biochemistry remained unclear in M. oryzae.<br><br>RESULT: This study adopted a multi-omics approach to comprehensively analyze MoKin1 function, and the results showed that MoKin1 affected the cellular response to endoplasmic reticulum stress (ER stress). Proteomic analysis revealed that the downregulated proteins in &#x394;Mokin1 mutant were enriched mainly in the response to ER stress triggered by the unfolded protein. Loss of MoKin1 prevented the ER stress signal from reaching the nucleus. Therefore, the phosphorylation of various proteins regulating the transcription of ER stress-related genes and mRNA translation was significantly downregulated. The insensitivity to ER stress led to metabolic disorders, resulting in a significant shortage of carbohydrates and a low energy supply, which also resulted in severe phenotypic defects in &#x394;Mokin1 mutant. Analysis of MoKin1-interacting proteins indicated that MoKin1 really took participate in the response to ER stress.<br><br>CONCLUSION: Our results showed the important role of protein kinase MoKin1 in regulating cellular response to ER stress, providing a new research direction to reveal the mechanism of MoKin1 affecting pathogenic formation, and to provide theoretical support for the new biological target sites searching and bio-pesticides developing.}, }
@article {pmid38714759, year = {2024}, author = {Lee, KS and Landry, Z and Athar, A and Alcolombri, U and Pramoj Na Ayutthaya, P and Berry, D and de Bettignies, P and Cheng, JX and Csucs, G and Cui, L and Deckert, V and Dieing, T and Dionne, J and Doskocil, O and D'Souza, G and García-Timermans, C and Gierlinger, N and Goda, K and Hatzenpichler, R and Henshaw, RJ and Huang, WE and Iermak, I and Ivleva, NP and Kneipp, J and Kubryk, P and Küsel, K and Lee, TK and Lee, SS and Ma, B and Martínez-Pérez, C and Matousek, P and Meckenstock, RU and Min, W and Mojzeš, P and Müller, O and Kumar, N and Nielsen, PH and Notingher, I and Palatinszky, M and Pereira, FC and Pezzotti, G and Pilat, Z and Plesinger, F and Popp, J and Probst, AJ and Riva, A and Saleh, AAE and Samek, O and Sapers, HM and Schubert, OT and Stubbusch, AKM and Tadesse, LF and Taylor, GT and Wagner, M and Wang, J and Yin, H and Yue, Y and Zenobi, R and Zini, J and Sarkans, U and Stocker, R}, title = {MicrobioRaman: an open-access web repository for microbiological Raman spectroscopy data.}, journal = {Nature microbiology}, volume = {9}, number = {5}, pages = {1152-1156}, pmid = {38714759}, issn = {2058-5276}, support = {GBMF9197//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 542395//Simons Foundation/ ; }, mesh = {*Spectrum Analysis, Raman/methods ; *Internet ; Humans ; Databases, Factual ; }, }
@article {pmid38714055, year = {2024}, author = {Li, Z and Wang, J and Yue, H and Rehman, A and Yousaf, M and Du, M and Zhang, X}, title = {Applying metabolic modeling and multi-omics to elucidate the biotransformation mechanisms of marine algal toxin domoic acid (DA) in sediments.}, journal = {Journal of hazardous materials}, volume = {472}, number = {}, pages = {134541}, doi = {10.1016/j.jhazmat.2024.134541}, pmid = {38714055}, issn = {1873-3336}, mesh = {*Kainic Acid/analogs &amp; derivatives/metabolism ; *Geologic Sediments/microbiology ; *Biotransformation ; *Marine Toxins/metabolism ; Microbiota ; Metabolome ; Biodegradation, Environmental ; Metagenome ; Water Pollutants, Chemical/metabolism ; Multiomics ; }, abstract = {Domoic acid (DA)-producing algal blooms are a global marine environmental issue. However, there has been no previous research addressing the question regarding the fate of DA in marine benthic environments. In this work, we investigated the DA fate in the water-sediment microcosm via the integrative analysis of a top-down metabolic model, metagenome, and metabolome. Results demonstrated that biodegradation is the leading mechanism for the nonconservative attenuation of DA. Specifically, DA degradation was prominently completed by the sediment aerobic community, with a degradation rate of 0.0681 ± 0.00954 d[-1]. The DA degradation pathway included hydration, dehydrogenation, hydrolysis, decarboxylation, automatic ring opening of hydration, and β oxidation reactions. Moreover, the reverse ecological analysis demonstrated that the microbial community transitioned from nutrient competition to metabolic cross-feeding during DA degradation, further enhancing the cooperation between DA degraders and other taxa. Finally, we reconstructed the metabolic process of microbial communities during DA degradation and confirmed that the metabolism of amino acid and organic acid drove the degradation of DA. Overall, our work not only elucidated the fate of DA in marine environments but also provided crucial insights for applying metabolic models and multi-omics to investigate the biotransformation of other contaminants.}, }
@article {pmid38713735, year = {2024}, author = {Oszoli, I and Zachar, I}, title = {Group-selection via aggregative propagule-formation enables cooperative multicellularity in an individual based, spatial model.}, journal = {PLoS computational biology}, volume = {20}, number = {5}, pages = {e1012107}, pmid = {38713735}, issn = {1553-7358}, mesh = {*Models, Biological ; *Biological Evolution ; Computational Biology ; Ecosystem ; Animals ; Predatory Behavior/physiology ; Selection, Genetic ; Computer Simulation ; }, abstract = {The emergence of multicellularity is one of the major transitions in evolution that happened multiple times independently. During aggregative multicellularity, genetically potentially unrelated lineages cooperate to form transient multicellular groups. Unlike clonal multicellularity, aggregative multicellular organisms do not rely on kin selection instead other mechanisms maintain cooperation against cheater phenotypes that benefit from cooperators but do not contribute to groups. Spatiality with limited diffusion can facilitate group selection, as interactions among individuals are restricted to local neighbourhoods only. Selection for larger size (e.g. avoiding predation) may facilitate the emergence of aggregation, though it is unknown, whether and how much role such selection played during the evolution of aggregative multicellularity. We have investigated the effect of spatiality and the necessity of predation on the stability of aggregative multicellularity via individual-based modelling on the ecological timescale. We have examined whether aggregation facilitates the survival of cooperators in a temporally heterogeneous environment against cheaters, where only a subset of the population is allowed to periodically colonize a new, resource-rich habitat. Cooperators constitutively produce adhesive molecules to promote aggregation and propagule-formation while cheaters spare this expense to grow faster but cannot aggregate on their own, hence depending on cooperators for long-term survival. We have compared different population-level reproduction modes with and without individual selection (predation) to evaluate the different hypotheses. In a temporally homogeneous environment without propagule-based colonization, cheaters always win. Predation can benefit cooperators, but it is not enough to maintain the necessary cooperator amount in successive dispersals, either randomly or by fragmentation. Aggregation-based propagation however can ensure the adequate ratio of cooperators-to-cheaters in the propagule and is sufficient to do so even without predation. Spatiality combined with temporal heterogeneity helps cooperators via group selection, thus facilitating aggregative multicellularity. External stress selecting for larger size (e.g. predation) may facilitate aggregation, however, according to our results, it is neither necessary nor sufficient for aggregative multicellularity to be maintained when there is effective group-selection.}, }
@article {pmid38711355, year = {2024}, author = {Tsutsui, K and Tanaka, R and Takeda, K and Fujii, K}, title = {Collaborative hunting in artificial agents with deep reinforcement learning.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {38711355}, issn = {2050-084X}, support = {20H04075//Japan Society for the Promotion of Science/ ; 21H04892//Japan Society for the Promotion of Science/ ; 21H05300//Japan Society for the Promotion of Science/ ; 22K17673//Japan Society for the Promotion of Science/ ; JPMJPR20CA//Japan Science and Technology Agency/ ; }, mesh = {Animals ; *Deep Learning ; *Predatory Behavior ; *Reinforcement, Psychology ; Cooperative Behavior ; Humans ; Computer Simulation ; Decision Making ; }, abstract = {Collaborative hunting, in which predators play different and complementary roles to capture prey, has been traditionally believed to be an advanced hunting strategy requiring large brains that involve high-level cognition. However, recent findings that collaborative hunting has also been documented in smaller-brained vertebrates have placed this previous belief under strain. Here, using computational multi-agent simulations based on deep reinforcement learning, we demonstrate that decisions underlying collaborative hunts do not necessarily rely on sophisticated cognitive processes. We found that apparently elaborate coordination can be achieved through a relatively simple decision process of mapping between states and actions related to distance-dependent internal representations formed by prior experience. Furthermore, we confirmed that this decision rule of predators is robust against unknown prey controlled by humans. Our computational ecological results emphasize that collaborative hunting can emerge in various intra- and inter-specific interactions in nature, and provide insights into the evolution of sociality.}, }
@article {pmid38709778, year = {2024}, author = {Xu, N and Zeng, P and Guo, Y and Siddique, MA and Li, J and Ren, X and Tang, F and Zhang, R}, title = {The spatiotemporal evolution of rural landscape patterns in Chinese metropolises under rapid urbanization.}, journal = {PloS one}, volume = {19}, number = {5}, pages = {e0301754}, pmid = {38709778}, issn = {1932-6203}, mesh = {China ; Cities ; Conservation of Natural Resources ; Ecosystem ; Geographic Information Systems ; Rural Population ; Spatio-Temporal Analysis ; *Urbanization ; }, abstract = {Understanding the evolution of rural landscapes in metropolises during rapid urbanization is crucial for formulating policies to protect the rural ecological environment. In this study, remote sensing and geographical information system data, as well as applied landscape index analysis, are used to examine the spatiotemporal evolution of rural landscape patterns in the Beijing-Tianjin region of China, which has experienced rapid urbanization. The relationships between land use/land cover changes and changes in rural landscape patterns are explored. The results revealed significant spatial differences in the rural landscapes in the Beijing-Tianjin region; farmland and forestland were the main types of landscapes, creating a "mountain-field-sea" natural landscape pattern. The conversion of rural landscapes in the Beijing-Tianjin region involved mainly the conversion of farmland to urban areas, with few exchanges between other landscape types. The urban areas in the Beijing-Tianjin region increased by 3% per decade; farmland decreased at the same rate. Additionally, the rural landscape patterns in the Beijing-Tianjin region were dominated by fragmentation, dispersion, and heterogeneity and moved from complex to regular. Water bodies displayed the most fragmented natural landscape; their number of patches increased by 36%, though their network characteristics were maintained. Forestland was the most concentrated natural landscape. In this study, theoretical support and a scientific reference for the optimization of rural landscape patterns and the improvement in rural living environments in rapidly urbanizing areas are provided.}, }
@article {pmid38708866, year = {2024}, author = {Villarreal-Rosas, J and Brown, CJ and Andradi-Brown, DA and Domínguez, R and Jacobo, P and Martínez, A and Mascote, C and Najera, E and Paiz, Y and Vázquez Moran, VH and Villarreal, J and Adame, MF}, title = {Integrating socioeconomic and ecological data into restoration practice.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {38}, number = {4}, pages = {e14286}, doi = {10.1111/cobi.14286}, pmid = {38708866}, issn = {1523-1739}, support = {//Advance Queensland Industry Research Fellowship/ ; //Jeremy and Hannelore Grantham Environmental Trust/ ; FT210100792//Australian Research Council/ ; }, mesh = {*Conservation of Natural Resources/methods/economics ; Mexico ; *Socioeconomic Factors ; Environmental Restoration and Remediation/economics ; Ecosystem ; Decision Support Techniques ; }, abstract = {Driven by the United Nations Decade on Restoration and international funding initiatives, such as the Mangrove Breakthrough, investment in mangrove restoration is expected to increase. Yet, mangrove restoration efforts frequently fail, usually because of ad hoc site-selection processes that do not consider mangrove ecology and the socioeconomic context. Using decision analysis, we developed an approach that accounts for socioeconomic and ecological data to identify sites with the highest likelihood of mangrove restoration success. We applied our approach in the Biosphere Reserve Marismas Nacionales Nayarit, Mexico, an area that recently received funding for implementing mangrove restoration actions. We identified 468 potential restoration sites, assessed their restorability potential based on socioeconomic and ecological metrics, and ranked sites for implementation with spatial optimization. The metrics we used included favorable conditions for propagules to establish and survive under sea-level rise, provision of ecosystem services, and community dynamics. Sites that were selected based on socioeconomic or ecological metrics alone had lower likelihood of mangrove restoration success than sites that were selected based on integrated socioeconomic and ecological metrics. For example, selecting sites based on only socioeconomic metrics captured 16% of the maximum attainable value of functioning mangroves able to provide propagules to potential restoration sites, whereas selecting sites based on ecological and socioeconomic metrics captured 46% of functioning mangroves. Our approach was developed as part of a collaboration between nongovernmental organizations, local government, and academics under rapid delivery time lines given preexisting mangrove restoration implementation commitments. The systematic decision process we used integrated socioeconomic and ecological considerations even under short delivery deadlines, and our approach can be adapted to help mangrove restoration site-selection decisions elsewhere.}, }
@article {pmid38707490, year = {2023}, author = {Boyes, D and Phillips, D and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Early Thorn, Selenia dentaria (Fabricius, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {485}, pmid = {38707490}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Selenia dentaria (the Early Thorn; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 1,030.8 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.41 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,390 protein coding genes.}, }
@article {pmid38705187, year = {2024}, author = {Meier, R and Hartop, E and Pylatiuk, C and Srivathsan, A}, title = {Towards holistic insect monitoring: species discovery, description, identification and traits for all insects.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {379}, number = {1904}, pages = {20230120}, pmid = {38705187}, issn = {1471-2970}, mesh = {*Insecta/physiology/classification/genetics ; Animals ; *DNA Barcoding, Taxonomic/methods ; Biodiversity ; }, abstract = {Holistic insect monitoring needs scalable techniques to overcome taxon biases, determine species abundances, and gather functional traits for all species. This requires that we address taxonomic impediments and the paucity of data on abundance, biomass and functional traits. We here outline how these data deficiencies could be addressed at scale. The workflow starts with large-scale barcoding (megabarcoding) of all specimens from mass samples obtained at biomonitoring sites. The barcodes are then used to group the specimens into molecular operational taxonomic units that are subsequently tested/validated as species with a second data source (e.g. morphology). New species are described using barcodes, images and short diagnoses, and abundance data are collected for both new and described species. The specimen images used for species discovery then become the raw material for training artificial intelligence identification algorithms and collecting trait data such as body size, biomass and feeding modes. Additional trait data can be obtained from vouchers by using genomic tools developed by molecular ecologists. Applying this pipeline to a few samples per site will lead to greatly improved insect monitoring regardless of whether the species composition of a sample is determined with images, metabarcoding or megabarcoding. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.}, }
@article {pmid38704010, year = {2024}, author = {Song, X and Li, C and Qiu, Z and Wang, C and Zeng, Q}, title = {Ecotoxicological effects of polyethylene microplastics and lead (Pb) on the biomass, activity, and community diversity of soil microbes.}, journal = {Environmental research}, volume = {252}, number = {Pt 3}, pages = {119012}, doi = {10.1016/j.envres.2024.119012}, pmid = {38704010}, issn = {1096-0953}, mesh = {*Soil Microbiology ; *Lead/toxicity ; *Soil Pollutants/toxicity ; *Microplastics/toxicity ; *Biomass ; *Polyethylene/toxicity ; Soil/chemistry ; Ecotoxicology ; }, abstract = {Microplastics and heavy metals are ubiquitous and persistent contaminants that are widely distributed worldwide, yet little is known about the effects of their interaction on soil ecosystems. A soil incubation experiment was conducted to investigate the individual and combined effects of polyethylene microplastics (PE-MPs) and lead (Pb) on soil enzymatic activities, microbial biomass, respiration rate, and community diversity. The results indicate that the presence of PE-MPs notably reduced soil pH and elevated soil Pb bioavailability, potentially exacerbated the combined toxicity on the biogeochemical cycles of soil nutrients, microbial biomass carbon and nitrogen, and the activities of soil urease, sucrase, and alkaline phosphatase. Soil CO2 emissions increased by 7.9% with PE-MPs alone, decreased by 46.3% with single Pb, and reduced by 69.4% with PE-MPs and Pb co-exposure, compared to uncontaminated soils. Specifically, the presence of PE-MPs and Pb, individually and in combination, facilitated the soil metabolic quotient, leading to reduced microbial metabolic efficiency. Moreover, the addition of Pb and PE-MPs modified the composition of the microbial community, leading to the enrichment of specific taxa. Tax4Fun analysis showed the effects of Pb, PE-MPs and their combination on the biogeochemical processes and ecological functions of microbes were mainly by altering amino acid metabolism, carbohydrate metabolism, membrane transport, and signal transduction. These findings offer valuable insights into the ecotoxicological effects of combined PE-MPs and Pb on soil microbial dynamics, reveals key assembly mechanisms and environmental drivers, and highlights the potential threat of MPs and heavy metals to the multifunctionality of soil ecosystems.}, }
@article {pmid38703986, year = {2024}, author = {Li, JY and Yao, S and Mo, Z and Miao, Y and Chen, Y and He, W and Jin, L and Tang, W}, title = {Submerged plant-biochar composite system exhibits effective control over residual organic pollutants in the benthic organisms of aquaculture ponds.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {351}, number = {}, pages = {124078}, doi = {10.1016/j.envpol.2024.124078}, pmid = {38703986}, issn = {1873-6424}, mesh = {*Aquaculture ; *Water Pollutants, Chemical/analysis/metabolism ; *Charcoal/chemistry ; *Ponds/chemistry ; *Geologic Sediments/chemistry ; Corbicula ; Biodegradation, Environmental ; Hydrocharitaceae/metabolism ; Animals ; }, abstract = {As of now, submerged plants and biochar have demonstrated significant benefits in aquaculture pond sediment remediation. However, there is limited research on the synergistic effects of biochar and submerged plants in mitigating hydrophobic organic contaminant (HOC) accumulation in aquaculture benthic organisms and in controlling the nutrient (nitrogen and phosphorus) levels in aquaculture water. This study assesses a submerged plant-biochar system's efficacy in removing HOCs from simulated freshwater aquaculture ponds. Vallisneria natans was planted in sediment with varying levels of wheat straw biochar, while Corbicula fluminea served as the targeted benthic organism. The bioaccumulation experiment identified the optimal biochar ratio for the Vallisneria natans-biochar system in controlling HOCs in aquaculture products. Analyses included final accumulation concentrations in benthic organisms, changes in freely-dissolved concentrations in aquaculture sediment, and a mass balance calculation to explore key factors in their removal from the system. Results indicated that the Vallisneria natans-1.5% biochar composite system achieved optimal control of HOCs in sediment and aquaculture products. Biochar addition to the sediment in the composite system demonstrated a "promotion with low addition, inhibition with high addition" effect on Vallisneria natans growth. Notably, the addition of 1.5% biochar (VN1.5 group) significantly promoted the growth of Vallisneria natans leaves and roots. Comparing the final pollutant proportions in different environmental media, concentrations in water (0.20%-1.8%), clam accumulation (0.032%-0.11%), and plant absorption (0.10%-0.44%) constituted a minimal portion of the overall pollutant load in the system. The majority of pollutants (24%-65%) were degraded in the aquaculture environment, with microbial degradation likely playing a predominant role. Bacterial phyla, particularly Proteobacteria and Firmicutes, were identified as potential direct contributors to pollutant degradation in the Vallisneria natans-biochar system.}, }
@article {pmid38696025, year = {2024}, author = {Xiao, Y and Luan, H and Lu, S and Xing, M and Guo, C and Qian, R and Xiao, X}, title = {Correction: Toxic effects of atmospheric deposition in mining areas on wheat seedlings.}, journal = {Environmental geochemistry and health}, volume = {46}, number = {6}, pages = {199}, doi = {10.1007/s10653-024-01986-5}, pmid = {38696025}, issn = {1573-2983}, }
@article {pmid38695096, year = {2025}, author = {Liu, H and Zhao, X and Xu, S and Zhao, L and Han, X and Xu, X and Zhao, N and Hu, L and Luo, C and Wang, X and Zhang, Q and Guo, T}, title = {Multi-omics reveal the gut microbiota-mediated severe foraging environment adaption of small wild ruminants in the Three-River-Source National Park, China.}, journal = {Integrative zoology}, volume = {20}, number = {5}, pages = {916-935}, pmid = {38695096}, issn = {1749-4877}, support = {32100100//Youth Fund Project of National Natural Science Foundation of China/ ; 2022-ZJ-943Q//National Science Foundation of Qinghai Province/ ; LHZX-2022-02//Chinese Academy of Sciences-People's Government of Qinghai Province on Sanjiangyuan National Park/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; China ; *Antelopes/microbiology/physiology ; Sheep/physiology/microbiology ; RNA, Ribosomal, 16S/genetics ; *Ruminants/microbiology/physiology ; *Adaptation, Physiological ; Parks, Recreational ; Bacteria/classification/genetics ; Feeding Behavior ; Multiomics ; }, abstract = {The Tibetan antelope (Pantholops hodgsonii), blue sheep (Pseudois nayaur), and Tibetan sheep (Ovis aries) are the dominant small ruminants in the Three-River-Source National Park (TRSNP). However, knowledge about the association between gut microbiota and host adaptability remains poorly understood. Herein, multi-omics sequencing approaches were employed to investigate the gut microbiota-mediated forage adaption in these ruminants. The results revealed that although wild ruminants (WR) of P. hodgsoni and P. nayaur were faced with severe foraging environments with significantly low vegetation coverage and nutrition, the apparent forage digestibility of dry matter, crude protein, and acid detergent fiber was significantly higher than that of O. aries. The 16s rRNA sequencing showed that the gut microbiota in WR underwent convergent evolution, and alpha diversity in these two groups was significantly higher than that in O. aries. Moreover, indicator species, including Bacteroidetes and Firmicutes, exhibited positive relationships with apparent forage digestibility, and their relative abundances were enriched in the gut of WR. Enterotype analysis further revealed that enterotype 1 belonged to WR, and the abundance of fatty acid synthesis metabolic pathway-related enzyme genes was significantly higher than enterotype 2, represented by O. aries. Besides, the metagenomic analysis identified 14 pathogenic bacterial species, among which 10 potentially pathogenic bacteria were significantly enriched in the gut microbiota of O. aries. Furthermore, the cellulolytic strains and genes encoding cellulase and hemicellulase were significantly enriched in WR. In conclusion, our results provide new evidence of gut microbiota to facilitate wildlife adaption in severe foraging environments of the TRSNP, China.}, }
@article {pmid38689759, year = {2024}, author = {Falk, S and Poole, O and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of a conopid fly, Myopa testacea (Linnaeus, 1767).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {99}, pmid = {38689759}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Myopa testacea (conopid fly; Arthropoda; Insecta; Diptera; Conopidae). The genome sequence is 243.3 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 17.61 kilobases in length. Gene annotation of this assembly on Ensembl identified 25,472 protein coding genes.}, }
@article {pmid38688803, year = {2024}, author = {Binion, KE and Perreira, KM and Villa Torres, L and White, JT and Hernandez, GC and Kaefer, M and Misseri, R and Ross, S and Chan, KH}, title = {A multi-site cultural and linguistic adaptation of a hypospadias decision aid for Latinx communities.}, journal = {Journal of pediatric urology}, volume = {20}, number = {4}, pages = {674.e1-674.e9}, pmid = {38688803}, issn = {1873-4898}, support = {UL1 TR002489/TR/NCATS NIH HHS/United States ; UM1 TR004406/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; Male ; *Hispanic or Latino/psychology ; *Hypospadias/ethnology/surgery/psychology ; *Decision Support Techniques ; Focus Groups ; Parents/psychology ; Child, Preschool ; Female ; Language ; Linguistics ; Cultural Characteristics ; }, abstract = {INTRODUCTION: Latinx, Spanish-speaking (LSS) patients are more likely to experience decisional conflict and regret about healthcare decisions than non-Hispanic, white, English-speaking patients.<br><br>OBJECTIVE: To adapt the Hypospadias Hub (Hub), a rigorously developed and tested web-based decision aid (DA), for LSS parents.<br><br>METHODS: Guided by the Ecological Validity Model (EVM), a heuristic framework was followed to culturally adapt the Hub (see Extended Summary Figure). In stage 1, recommendations were obtained from a focus group with members of the institution's Latinx Community Review Board (Latinx CRB) and semi-structured interviews with pediatricians with Latinx-focused practices. In stage 2, preliminary cultural modifications were made, the Hub was translated into Spanish, and a second focus group with the Latinx CRB was convened to review the revised Hub. In stage 3, semi-structured interviews with LSS parents of healthy boys (i.e., without hypospadias)&#xa0;&#x2264;&#xa0;5 years old were conducted to identify any cultural adaptations and/or usability issues regarding the revised Hub. In stage 4, based on parents' feedback, final revisions to the Hub were made. The focus groups and parent interviews were conducted in Spanish; then, the recordings were professionally transcribed in Spanish and translated into English. Interviews with pediatricians were conducted in English; then, the recordings were professionally transcribed. Three coders conducted a qualitative content analysis to identify areas for revision. Changes were applied iteratively.<br><br>RESULTS: Participants included 3 Latinx CRB members (2 women, 1 did not disclose gender; mean age&#xa0;=&#xa0;48.3, SD&#xa0;=&#xa0;21.2), 3 non-Latinx pediatricians (2 women, 1 man; mean age&#xa0;=&#xa0;49.6, SD&#xa0;=&#xa0;9.1), and 5 Latinx mothers (mean age&#xa0;=&#xa0;34.0, SD&#xa0;=&#xa0;1.26). Participants recommended: 1) featuring video testimonials from Latinx families or including Spanish voice-overs/subtitles; 2) diversifying racial/ethnic/geographic representation and including extended families in photographs/illustrations; 3) adding information about health insurance coverage and circumcision, 4) reassuring parents that the condition is not their fault, 5) considering cultural values (e.g., reliance on expert advice), and 6) clarifying medical terminology. Feedback related to seven EVM dimensions: concepts, content, context, goals, language, metaphors, and methods.<br><br>DISCUSSION: Participants perceived the Hub to be informative in guiding parents' treatment decisions. Revisions were reasonable and acceptable for a linguistic and cultural adaptation for LSS parents.<br><br>CONCLUSIONS: We identified and implemented preliminary cultural modifications to the Hub and applied user-centered design methods to test and revise the website. The product is a culturally appropriate DA for LSS parents. Next, English and Spanish-versions of the Hub will be tested in a randomized controlled trial.}, }
@article {pmid38688387, year = {2024}, author = {Hu, YL and Liu, Y and Fu, W and Yang, H}, title = {Efficiency and mechanism of enhanced norfloxacin removal using amorphous TiO2-modified biochar.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {351}, number = {}, pages = {124027}, doi = {10.1016/j.envpol.2024.124027}, pmid = {38688387}, issn = {1873-6424}, mesh = {*Charcoal/chemistry ; *Titanium/chemistry ; *Norfloxacin/chemistry ; Adsorption ; *Water Pollutants, Chemical/chemistry ; Anti-Bacterial Agents/chemistry ; Wastewater/chemistry ; Waste Disposal, Fluid/methods ; }, abstract = {Inadequate treatment of antibiotic-contaminated wastewater, including compounds such as norfloxacin (NOR), poses a substantial treat to both ecological safety and human well-being. An innovative approach was devised to address NOR pollution using amorphous TiO2 modified biochar (A-TiO2/BC) prepared via sol-gel impregnation. The resultant had a commendably specific surface area of 131.8 m[2]/g[-1], which was 1.91 times more than the original surface area of unmodified BC. A-TiO2/BC also exhibited abundant hydroxyl and oxygen-containing functional groups, thereby provided adequately active sites for NOR adsorption. R[2] values obtained from NOR isotherm adsorption models descended in order of Freundlich < Temkin < Sips < Langmuir, which indicated that the NOR removal by A-TiO2/BC mainly complied with monolayer adsorption accompanied by heterogeneous surface adsorption. Under weakly acidic conditions, NOR adsorption benefits from the synergistic physicochemical interactions of A-TiO2 and BC. Notably, A-TiO2/BC demonstrated an impressive NOR adsorption capacity of up to 78.14 mg g[-1], with a dosage of 20 mg L[-1] at 25 °C under pH 6. Such A-TiO2 modified biochar thus presents a promising alternative for NOR removal.}, }
@article {pmid38688113, year = {2024}, author = {Ghani, MI and Yi, B and Rehmani, MS and Wei, X and Siddiqui, JA and Fan, R and Liu, Y and El-Sheikh, MA and Chen, X and Ahmad, P}, title = {Potential of melatonin and Trichoderma harzianum inoculation in ameliorating salt toxicity in watermelon: Insights into antioxidant system, leaf ultrastructure, and gene regulation.}, journal = {Plant physiology and biochemistry : PPB}, volume = {211}, number = {}, pages = {108639}, doi = {10.1016/j.plaphy.2024.108639}, pmid = {38688113}, issn = {1873-2690}, mesh = {*Citrullus/microbiology/drug effects/metabolism ; *Melatonin/pharmacology ; *Antioxidants/metabolism ; *Plant Leaves/drug effects/metabolism ; *Gene Expression Regulation, Plant/drug effects ; Salt Stress ; Hypocreales ; Photosynthesis/drug effects ; Oxidative Stress/drug effects ; }, abstract = {Melatonin (MT) is an extensively studied biomolecule with dual functions, serving as an antioxidant and a signaling molecule. Trichoderma Harzianum (TH) is widely recognized for its effectiveness as a biocontrol agent against many plant pathogens. However, the interplay between seed priming and MT (150 μm) in response to NaCl (100 mM) and its interaction with TH have rarely been investigated. This study aimed to evaluate the potential of MT and TH, alone and in combination, to mitigate salt stress (SS) in watermelon plants. The findings of this study revealed a significant decline in the morphological, physiological, and biochemical indices of watermelon seedlings exposed to SS. However, MT and TH treatments reduced the negative impact of salt stress. The combined application of MT and TH exerted a remarkable positive effect by increasing the growth, photosynthetic and gas exchange parameters, chlorophyll fluorescence indices, and ion balance (decreasing Na[+] and enhancing K[+]). MT and TH effectively alleviated oxidative injury by inhibiting hydrogen peroxide formation in saline and non-saline environments, as established by reduced lipid peroxidation and electrolyte leakage. Moreover, oxidative injury induced by SS on the cells was significantly mitigated by regulation of the antioxidant system, AsA-GSH-related enzymes, the glyoxalase system, augmentation of osmolytes, and activation of several genes involved in the defense system. Additionally, the reduction in oxidative damage was examined by chloroplast integrity via transmission electron microscopy (TEM). Overall, the results of this study provide a promising contribution of MT and TH in safeguarding the watermelon crop from oxidative damage induced by salt stress.}, }
@article {pmid38686023, year = {2024}, author = {Boyes, D and Blaxter, ML and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Tipped Oak Case-bearer, Coleophora flavipennella (Duponchel 1843).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {3}, pmid = {38686023}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Coleophora flavipennella (the Tipped Oak Case-bearer; Arthropoda; Insecta; Lepidoptera; Coleophoridae). The genome sequence is 989.3 megabases in span. Most of the assembly is scaffolded into 57 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.77 kilobases in length.}, }
@article {pmid39989610, year = {2024}, author = {Liu, C and Downey, RJ and Salminen, JS and Rojas, SA and Richer, N and Pliner, EM and Hwang, J and Cruz-Almeida, Y and Manini, TM and Hass, CJ and Seidler, RD and Clark, DJ and Ferris, DP}, title = {Electrical brain activity during human walking with parametric variations in terrain unevenness and walking speed.}, journal = {Imaging neuroscience (Cambridge, Mass.)}, volume = {2}, number = {}, pages = {}, pmid = {39989610}, issn = {2837-6056}, support = {R01 NS104772/NS/NINDS NIH HHS/United States ; F32 AG072808/AG/NIA NIH HHS/United States ; S10 OD021726/OD/NIH HHS/United States ; U01 AG061389/AG/NIA NIH HHS/United States ; T32 AG062728/AG/NIA NIH HHS/United States ; }, abstract = {Mobile brain imaging with high-density electroencephalography (EEG) can provide insight into the cortical processes involved in complex human walking tasks. While uneven terrain is common in the natural environment and poses challenges to human balance control, there is limited understanding of the supraspinal processes involved with traversing uneven terrain. The primary objective of this study was to quantify electrocortical activity related to parametric variations in terrain unevenness for neurotypical young adults. We used high-density EEG to measure brain activity when 32 young adults walked on a novel custom-made uneven terrain treadmill surface with four levels of difficulty at a walking speed tailored to each participant. We identified multiple brain regions associated with uneven terrain walking. Alpha (8 - 13 Hz) and beta (13 - 30 Hz) spectral power decreased in the sensorimotor and posterior parietal areas with increasing terrain unevenness while theta (4 - 8 Hz) power increased in the mid/posterior cingulate area with terrain unevenness. We also found that within stride spectral power fluctuations increased with terrain unevenness. Our secondary goal was to investigate the effect of parametric changes in walking speed (0.25 m/s, 0.5 m/s, 0.75 m/s, 1.0 m/s) to differentiate the effects of walking speed from uneven terrain. Our results revealed that electrocortical activities only changed substantially with speed within the sensorimotor area but not in other brain areas. Together, these results indicate there are distinct cortical processes contributing to the control of walking over uneven terrain versus modulation of walking speed on smooth, flat terrain. Our findings increase our understanding of cortical involvement in an ecologically valid walking task and could serve as a benchmark for identifying deficits in cortical dynamics that occur in people with mobility deficits.}, }
@article {pmid39866757, year = {2023}, author = {Gudelj Rakić, J and Maksimović, M and Vlajinac, H and Janković, J and Vukašinović, D and Marinković, J}, title = {TRENDS IN OVERWEIGHT AND OBESITY AMONG SERBIAN ADULT POPULATION 2000-2013.}, journal = {Acta clinica Croatica}, volume = {62}, number = {4}, pages = {605-614}, pmid = {39866757}, issn = {1333-9451}, mesh = {Humans ; Serbia/epidemiology ; Female ; Male ; Adult ; *Obesity/epidemiology ; Prevalence ; *Overweight/epidemiology ; Cross-Sectional Studies ; Middle Aged ; Body Mass Index ; Young Adult ; Health Surveys ; }, abstract = {The aim of the study was to determine changes in body mass index (BMI) and in the prevalence of overweight and obesity in Serbian adult population. Data for this study were obtained from three National Health Interview Surveys, carried out as cross-sectional, nationally representative surveys in 2000, 2006 and 2013. The values of p for trends of sociodemographic and health related behavioral characteristics, of BMI distribution, and of overweight and obesity prevalence were determined by univariate and multivariate linear and logistic regression analyses, with year of survey as a continuous variable. The mean values of BMI and standard deviations in surveys were 26.09±3.92, 26.28±4.02 and 26.87±4.33 in men, and 25.91±5.25, 25.77±5.22 and 26.35±5.58 in women, respectively (trend p<0.001 both). The prevalence of obesity was 14.3%, 16.5% and 21.4% in men, and 20.0%, 19.7% and 23.3% in women, respectively (trend p<0.001 both). The prevalence of overweight did not change significantly during the observed period. In conclusion, the prevalence of obesity showed an increasing trend in both men and women, demanding targeted public health interventions.}, }
@article {pmid39830091, year = {2023}, author = {Boyes, D and Eljounaidi, K and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Beautiful Golden Y, Autographa pulchrina (Haworth, 1809).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {375}, pmid = {39830091}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Autographa pulchrina (the Beautiful Golden Y; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 426.2 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.25 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,916 protein coding genes.}, }
@article {pmid39268176, year = {2023}, author = {Boyes, D and Holland, PWH and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the White Satin, Leucoma salicis (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {323}, pmid = {39268176}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Leucoma salicis (the White Satin; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 733.2 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.73 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,222 protein coding genes.}, }
@article {pmid39114813, year = {2023}, author = {Boyes, D and Hammond, J and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Thicket Knot-horn, Acrobasis suavella (Zincken, 1818).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {252}, pmid = {39114813}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Acrobasis suavella (the Thicket Knot-horn; Arthropoda; Insecta; Lepidoptera; Pyralidae). The genome sequence is 647.3 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.31 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,101 protein coding genes.}, }
@article {pmid39430045, year = {2023}, author = {Boyes, D and Holland, PWH and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Olive Pearl, Udea olivalis (Denis &amp; Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {238}, pmid = {39430045}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Udea olivalis (the Olive Pearl; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 624.4 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length.}, }
@article {pmid39242656, year = {2023}, author = {Hui, C and Pyšek, P and Richardson, DM}, title = {Disentangling the relationships among abundance, invasiveness and invasibility in trait space.}, journal = {npj biodiversity}, volume = {2}, number = {1}, pages = {13}, pmid = {39242656}, issn = {2731-4243}, support = {89967//National Research Foundation/ ; NE/V007548/1//Natural Environment Research Council/ ; DP200101680//Australian Research Council/ ; 101059592//HORIZON EUROPE European Research Council/ ; EXPRO 19-28807X//Czech Science Foundation/ ; RVO 67985939//Czech Academy of Sciences/ ; RVO 67985939//Czech Academy of Sciences/ ; CZ.02.2.69/0.0/0.0/18_053/0017850//Ministry of Education, Youth, and Sports of the Czech Republic/ ; }, abstract = {Identifying conditions and traits that allow an introduced species to grow and spread, from being initially rare to becoming abundant (defined as invasiveness), is the crux of invasion ecology. Invasiveness and abundance are related but not the same, and we need to differentiate these concepts. Predicting both species abundance and invasiveness and their relationship in an invaded community is highly contextual, being contingent on the community trait profile and its invasibility. We operationalised a three-pronged invasion framework that considers traits, environmental context, and propagule pressure. Specifically, we measure the invasiveness of an alien species by combining three components (performance reflecting environmental suitability, product of species richness and the covariance between interaction strength and species abundance, and community-level interaction pressure); the expected population growth rate of alien species simply reflects the total effect of propagule pressure and the product of their population size and invasiveness. The invasibility of a community reflects the size of opportunity niches (the integral of positive invasiveness in the trait space) under the given abiotic conditions of the environment. Both species abundance and the surface of invasiveness over the trait space can be dynamic and variable. Whether an introduced species with functional traits similar to those of an abundant species in the community exhibits high or low invasiveness depends largely on the kernel functions of performance and interaction strength with respect to traits and environmental conditions. Knowledge of the covariance between interaction strength and species abundance and these kernel functions, thus, holds the key to accurate prediction of invasion dynamics.}, }
@article {pmid38903245, year = {2023}, author = {Boyes, D and Goate, Z and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the White-backed Marble, Hedya salicella (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {219}, pmid = {38903245}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Hedya salicella (the White-backed Marble; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 742.3 megabases in span. Most of the assembly is scaffolded into 25 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,961 protein coding genes.}, }
@article {pmid39262678, year = {2023}, author = {Boyes, D and Holland, PWH and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Brindled Flat-body, Agonopterix arenella (Denis &amp; Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {214}, pmid = {39262678}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Agonopterix arenella (the Brindled Flat-body; Arthropoda; Insecta; Lepidoptera; Depressariidae). The genome sequence is 545.8 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length.}, }
@article {pmid39502585, year = {2023}, author = {Boyes, D and Lewis, OT and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Small Phoenix, Ecliptopera silaceata (Denis &amp; Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {209}, pmid = {39502585}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Ecliptopera silaceata (the Small Phoenix; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 316.5 megabases in span. Most of the assembly is scaffolded into 29 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 17.5 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,770 protein coding genes.}, }
@article {pmid39211527, year = {2023}, author = {Boyes, D and Holland, PWH and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Small Square-spot, Diarsia rubi (Vieweg, 1790).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {210}, pmid = {39211527}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Diarsia rubi (the Small Square-spot; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 624.9 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,173 protein coding genes.}, }
@article {pmid38817338, year = {2022}, author = {Cocker, D and Sammarro, M and Chidziwisano, K and Elviss, N and Jacob, ST and Kajumbula, H and Mugisha, L and Musoke, D and Musicha, P and Roberts, AP and Rowlingson, B and Singer, AC and Byrne, RL and Edwards, T and Lester, R and Wilson, CN and Hollihead, B and Thomson, NR and Jewell, CP and Morse, T and Feasey, NA}, title = {Drivers of Resistance in Uganda and Malawi (DRUM): a protocol for the evaluation of One-Health drivers of Extended Spectrum Beta Lactamase (ESBL) resistance in Low-Middle Income Countries (LMICs).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {55}, pmid = {38817338}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; MR/R015074/1/MRC_/Medical Research Council/United Kingdom ; MR/S004793/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {In sub-Saharan Africa (sSA), there is high morbidity and mortality from severe bacterial infection and this is compounded by antimicrobial resistance, in particular, resistance to 3rd-generation cephalosporins. This resistance is typically mediated by extended-spectrum beta lactamases (ESBLs). To interrupt ESBL transmission it will be important to investigate how human behaviour, water, sanitation, and hygiene (WASH) practices, environmental contamination, and antibiotic usage in both urban and rural settings interact to contribute to transmission of ESBL E. coli and ESBL K. pneumoniae between humans, animals, and the environment. Here we present the protocol for the Drivers of Resistance in Uganda and Malawi (DRUM) Consortium, in which we will collect demographic, geospatial, clinical, animal husbandry and WASH data from a total of 400 households in Uganda and Malawi. Longitudinal human, animal and environmental sampling at each household will be used to isolate ESBL E. coli and ESBL K. pneumoniae. This will be complimented by a Risks, Attitudes, Norms, Abilities and Self-Regulation (RANAS) survey and structured observations to understand the contextual and psychosocial drivers of regional WASH practices. Bacterial isolates and plate sweeps will be further characterised using a mixture of short-,long-read and metagenomic whole-genome sequencing. These datasets will be integrated into agent-based models to describe the transmission of EBSL resistance in Uganda and Malawi and allow us to inform the design of interventions for interrupting transmission of ESBL-bacteria.}, }
@article {pmid38779052, year = {2023}, author = {Lohse, K and Hayward, A and Laetsch, DR and Marques, V and Vila, R and Tyler-Smith, C and ,  and ,  and ,  and , }, title = {The genome sequence of the Mazarine Blue, Cyaniris semiargus (Rottemburg, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {181}, pmid = {38779052}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Cyaniris semiargus (the Mazarine Blue; Arthropoda; Insecta; Lepidoptera; Lycaenidae). The genome sequence is 441.5 megabases in span. Most of the assembly is scaffolded into 24 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,408 protein coding genes.}, }
@article {pmid38798993, year = {2023}, author = {Boyes, D and Lewis, OT and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Lilac Beauty, Apeira syringaria (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {159}, pmid = {38798993}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Apeira syringaria (the Lilac Beauty; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 544.4 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.5 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,426 protein coding genes.}, }
@article {pmid38770266, year = {2023}, author = {Vila, R and Lohse, K and Hayward, A and Laetsch, DR and Wright, C and ,  and ,  and ,  and , }, title = {The genome sequence of the Chalkhill Blue, Lysandra coridon (Poda, 1761).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {162}, pmid = {38770266}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Lysandra coridon (the Chalkhill Blue; Arthropoda; Insecta; Lepidoptera; Lycaenidae). The genome sequence is 541 megabases in span. Most of the assembly is scaffolded into 90 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,334 protein coding genes.}, }
@article {pmid38764974, year = {2023}, author = {Boyes, D and Hammond, J and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Sycamore Piercer, Pammene aurita (Razowski, 1991).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {160}, pmid = {38764974}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Pammene aurita (the Sycamore Piercer; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 1,041.8 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 16.7 kilobases in length.}, }
@article {pmid39219859, year = {2023}, author = {Boyes, D and Lewis, OT and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Ruby Tiger, Phragmatobia fuliginosa (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {124}, pmid = {39219859}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Phragmatobia fuliginosa (the Ruby Tiger; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 629.4 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,338 protein coding genes.}, }
@article {pmid38707488, year = {2023}, author = {Boyes, D and ,  and ,  and ,  and ,  and ,  and Boyes, C and , }, title = {The genome sequence of the Fulvous Clothes Moth, Tinea semifulvella (Haworth, 1828).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {104}, pmid = {38707488}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Tinea semifulvella (the Fulvous Clothes Moth; Arthropoda; Insecta; Lepidoptera; Tineidae). The genome sequence is 596.6 megabases in span. The whole assembly is scaffolded into 45 chromosomal pseudomolecules, with the Z sex chromosome assembled. The mitochondrial genome has also been assembled and is 16.8 kilobases in length. Gene annotation of this assembly on Ensembl has identified 11,516 protein coding genes.}, }
@article {pmid39949385, year = {2023}, author = {Lohse, K and ,  and ,  and ,  and Vila, R and , }, title = {The genome sequence of the Common Blue, Polyommatus icarus (Rottemburg, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {72}, pmid = {39949385}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Polyommatus icarus (the Common Blue; Arthropoda; Insecta; Lepidoptera; Lycaenidae). The genome sequence is 512 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomolecules, including the assembled Z chromosome. The mitochondrial genome has also been assembled and is 15.6 kilobases long. Gene annotation of this assembly on Ensembl identified 13,350 protein-coding genes.}, }
@article {pmid39129913, year = {2023}, author = {Boyes, D and ,  and ,  and ,  and ,  and ,  and Mulley, JF and , }, title = {The genome sequence of the Dark Arches Apamea monoglypha (Hufnagel, 1766).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {63}, pmid = {39129913}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Apamea monoglypha (the Dark Arches, Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 576 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 16.5 kilobases in length. Gene annotation of this assembly on Ensembl has identified 17,963 protein coding genes.}, }
@article {pmid39148947, year = {2023}, author = {Boyes, D and ,  and ,  and ,  and ,  and ,  and Holland, PWH and , }, title = {The genome sequence of the Green-brindled Crescent, Allophyes oxyacanthae (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {53}, pmid = {39148947}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Allophyes oxyacanthae (the Green-brindled Crescent; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 458 megabases in span. The whole assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl has identified 17,301 protein coding genes.}, }
@article {pmid38868331, year = {2023}, author = {Li, C and Jin, L and Zhang, C and Li, S and Zhou, T and Hua, Z and Wang, L and Ji, S and Wang, Y and Gan, Y and Liu, J}, title = {Destabilized microbial networks with distinct performances of abundant and rare biospheres in maintaining networks under increasing salinity stress.}, journal = {iMeta}, volume = {2}, number = {1}, pages = {e79}, pmid = {38868331}, issn = {2770-596X}, abstract = {Global changes such as seawater intrusion and freshwater resource salinization increase environmental stress imposed on the aquatic microbiome. A strong predictive understanding of the responses of the aquatic microbiome to environmental stress will help in coping with the "gray rhino" events in the environment, thereby contributing to an ecologically sustainable future. Considering that microbial ecological networks are tied to the stability of ecosystem functioning and that abundant and rare biospheres with different biogeographic patterns are important drivers of ecosystem functioning, the roles of abundant and rare biospheres in maintaining ecological networks need to be clarified. Here we showed that, with the increasing salinity stress induced by the freshwater-to-seawater transition, the microbial diversity reduced significantly and the taxonomic structure experienced a strong succession. The complexity and stability of microbial ecological networks were diminished by the increasing stress. The composition of the microorganisms supporting the networks underwent sharp turnovers during the freshwater-to-seawater transition, with the abundant biosphere behaving more robustly than the rare biosphere. Notably, the abundant biosphere played a much more important role than the rare biosphere in stabilizing ecological networks under low-stress environments, but the difference between their relative importance narrowed significantly with the increasing stress, suggesting that the environmental stress weakened the "Matthew effect" in the microbial world. With in-depth insights into the aquatic microbial ecology under stress, our findings highlight the importance of adjusting conservation strategies for the abundant and rare biospheres to maintain ecosystem functions and services in response to rising environmental stress.}, }
@article {pmid39328383, year = {2023}, author = {Catalàn, N and Campo, RD and Talluto, L and Mendoza-Lera, C and Grandi, G and Bernal, S and Schiller, DV and Singer, G and Bertuzzo, E}, title = {Pulse, Shunt and Storage: Hydrological Contraction Shapes Processing and Export of Particulate Organic Matter in River Networks.}, journal = {Ecosystems (New York, N.Y.)}, volume = {26}, number = {4}, pages = {873-892}, pmid = {39328383}, issn = {1432-9840}, abstract = {UNLABELLED: Streams and rivers act as landscape-scale bioreactors processing large quantities of terrestrial particulate organic matter (POM). This function is linked to their flow regime, which governs residence times, shapes organic matter reactivity and controls the amount of carbon (C) exported to the atmosphere and coastal oceans. Climate change impacts flow regimes by increasing both flash floods and droughts. Here, we used a modelling approach to explore the consequences of lateral hydrological contraction, that is, the reduction of the wet portion of the streambed, for POM decomposition and transport at the river network scale. Our model integrates seasonal leaf litter input as generator of POM, transient storage of POM on wet and dry streambed portions with associated decomposition and ensuing changes in reactivity, and transport dynamics through a dendritic river network. Simulations showed that the amount of POM exported from the river network and its average reactivity increased with lateral hydrological contraction, due to the combination of (1) low processing of POM while stored on dry streambeds, and (2) large shunting during flashy events. The sensitivity analysis further supported that high lateral hydrological contraction leads to higher export of higher reactivity POM, regardless of transport coefficient values, average reactivity of fresh leaf litter and differences between POM reactivity under wet and dry conditions. Our study incorporates storage in dry streambed areas into the pulse-shunt concept (Raymond and others in Ecology 97(1):5-16, 2016. 10.1890/14-1684.1), providing a mechanistic framework and testable predictions about leaf litter storage, transport and decomposition in fluvial networks.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10021-022-00802-4.}, }
@article {pmid38799509, year = {2022}, author = {Boyes, D and ,  and ,  and ,  and ,  and ,  and Parkerson, L and , }, title = {The genome sequence of the common grass-veneer, Agriphila tristella (Denis &amp; Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {304}, pmid = {38799509}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Agriphila tristella (the common grass-veneer; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 802 megabases in span. Most of the assembly (99.83%) is scaffolded into 23 chromosomal pseudomolecules with the Z sex chromosome assembled. The mitochondrial genome was also assembled and is 15.3 kilobases in length.}, }
@article {pmid38867895, year = {2022}, author = {Wu, D and Liu, L and Jiao, N and Zhang, Y and Yang, L and Tian, C and Lan, P and Zhu, L and Loomba, R and Zhu, R}, title = {Targeting keystone species helps restore the dysbiosis of butyrate-producing bacteria in nonalcoholic fatty liver disease.}, journal = {iMeta}, volume = {1}, number = {4}, pages = {e61}, pmid = {38867895}, issn = {2770-596X}, support = {P42 ES010337/ES/NIEHS NIH HHS/United States ; R01 DK106419/DK/NIDDK NIH HHS/United States ; UL1 TR001442/TR/NCATS NIH HHS/United States ; }, abstract = {The dysbiosis of the gut microbiome is one of the pathogenic factors of nonalcoholic fatty liver disease (NAFLD) and also affects the treatment and intervention of NAFLD. Among gut microbiomes, keystone species that regulate the integrity and stability of an ecological community have become the potential intervention targets for NAFLD. Here, we collected stool samples from 22 patients with nonalcoholic steatohepatitis (NASH), 25 obese patients, and 16 healthy individuals from New York for 16S rRNA gene sequencing. An algorithm was implemented to identify keystone species based on causal inference theories and dynamic intervention simulation. External validation was performed in an independent cohort from California. Eight keystone species in the gut of NAFLD, represented by Porphyromonas loveana, Alistipes indistinctus, and Dialister pneumosintes, were identified, which could efficiently restore the microbial composition of the NAFLD toward a normal gut microbiome with 92.3% recovery. These keystone species regulate intestinal amino acid metabolism and acid-base environment to promote the growth of the butyrate-producing Lachnospiraceae and Ruminococcaceae species that are significantly reduced in NAFLD patients. Our findings demonstrate the importance of keystone species in restoring the microbial composition toward a normal gut microbiome, suggesting a novel potential microbial treatment for NAFLD.}, }
@article {pmid39144291, year = {2022}, author = {Fitzhugh, B and Brown, WA and Misarti, N and Takase, K and Tremayne, AH}, title = {Human Paleodemography and Paleoecology of the North Pacific Rim from the Mid to Late Holocene.}, journal = {Quaternary research}, volume = {108}, number = {PESAS}, pages = {123-149}, pmid = {39144291}, issn = {0033-5894}, support = {P2C HD042828/HD/NICHD NIH HHS/United States ; }, abstract = {Using 14 proxy human population time series from around the North Pacific (Alaska, Hokkaido and the Kuril Islands), we evaluate the possibility that the North Pacific climate and marine ecosystem includes a millennial-scale regime shift cycle affecting subsistence and migration. We develop both visual and statistical methods for addressing questions about relative population growth and movement in the past. We introduce and explore the use of a Time Iterative Moran I (TIMI) spatial autocorrelation method to compare time series trends quantitatively - a method that could prove useful in other paleoecological analyses. Results reveal considerable population dynamism around the North Pacific in the last 5000 years and strengthen a previously reported inverse correlation between Northeast and Northwest Pacific proxy population indices. Visual and TIMI analyses suggest multiple, overlapping explanations for the variability, including the potential that oscillating ecological regime shifts affect the North Pacific basin. These results provide an opening for coordinated research to unpack the interrelated social, cultural and environmental dynamics around the subarctic and arctic North Pacific at different spatial and temporal scales by international teams of archaeologists, historians, paleoecologists, paleoceanographers, paleoclimatologists, modelers and data management specialists.}, }
@article {pmid38799510, year = {2022}, author = {Boyes, D and Holland, PWH and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the silver Y moth, Autographa gamma (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {100}, pmid = {38799510}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Autographa gamma (the silver Y; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 373 megabases in span. The majority of the assembly (99.65%) is scaffolded into 32 chromosomal pseudomolecules, with the W and Z sex chromosomes assembled. The mitochondrial genome was also assembled and is 15.2 kilobases in length.}, }
@article {pmid39175988, year = {2021}, author = {Boyes, D and Holland, PWH and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the bramble shoot moth, Notocelia uddmanniana (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {6}, number = {}, pages = {348}, pmid = {39175988}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Notocelia uddmanniana (the bramble shoot moth; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 794 megabases in span. The majority of the assembly, 99.96%, is scaffolded into 28 chromosomal pseudomolecules, with the Z sex chromosome assembled.}, }
@article {pmid38912275, year = {2021}, author = {Boyes, D and Holland, PWH and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the iron prominent, Notodonta dromedarius (Linnaeus, 1767).}, journal = {Wellcome open research}, volume = {6}, number = {}, pages = {341}, pmid = {38912275}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Notodonta dromedarius (iron prominent; Arthropoda; Insecta; Lepidoptera; Notodontidae). The genome sequence is 342 megabases in span. The majority of the assembly, 99.35%, is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled.}, }
@article {pmid39449730, year = {2021}, author = {Boyes, D and Crowley, LM and Holland, PWH and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of Svensson's copper underwing, Amphipyra berbera Rungs, 1949.}, journal = {Wellcome open research}, volume = {6}, number = {}, pages = {314}, pmid = {39449730}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Amphipyra berbera (Svensson's copper underwing; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 582 megabases in span. The majority (99.97%) of the assembly is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled.}, }
@article {pmid38684755, year = {2024}, author = {Yang, P and Huang, G and Li, Y and Yu, L and Yin, Z and Li, Q}, title = {Identification of PANoptosis-related biomarkers and analysis of prognostic values in head and neck squamous cell carcinoma.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {9824}, pmid = {38684755}, issn = {2045-2322}, mesh = {Humans ; *Squamous Cell Carcinoma of Head and Neck/genetics/pathology/metabolism/mortality ; *Biomarkers, Tumor/metabolism/genetics ; Prognosis ; *Head and Neck Neoplasms/genetics/pathology/metabolism ; *Gene Expression Regulation, Neoplastic ; Female ; Male ; Computational Biology/methods ; Gene Expression Profiling ; Fas-Associated Death Domain Protein/metabolism/genetics ; Lymphatic Metastasis ; }, abstract = {PANoptosis plays a crucial role in cancer initiation and progression. However, the roles of PANoptosis-related genes (PARGs) in the prognosis and immune landscape of head and neck squamous cell carcinoma (HNSCC) remain unclear. Integrated bioinformatics analyses based on the data of HNSCC patients in the TCGA database were conducted. We extracted 48 PARGs expression profile and then conducted differentially expressed analysis, following building a Cox model to predict the survival of HNSCC patients. Subsequently, the relationships between the risk score, immune landscape, chemo-, and immune-therapy responses were analyzed, respectively. Moreover, we investigated the prognostic value, and further predicted the pathways influenced by PARGs. Finally, we identified the biological function of crucial PARGs. A total of 18 differentially expressed PARGs were identified in HNSCC, and a Cox model including CASP8, FADD, NLRP1, TNF, and ZBP1 was constructed, which showed that the risk score was associated with the prognosis as well as immune infiltration of HNSCC patients, and the risk score could be regarded as an independent biomarker. Additionally, patients with high-risk score might be an indicator of lymph node metastasis and advanced clinical stage. High-risk scores also contributed to the chemotherapy resistance and immune escape of HNSCC patients. In addition, FADD and ZBP1 played a crucial role in various cancer-related pathways, such as the MAPK, WNT, and MTOR signaling pathways. On the other hand, we suggested that FADD facilitated the progression and 5-fluorouracil (5-FU) resistance of HNSCC cells. A signature based on PANoptosis showed great predictive power for lymph node metastasis and advanced stage, suggesting that the risk score might be an independent prognostic biomarker for HNSCC. Meanwhile, FADD, identified as a prognostic biomarker, may represent an effective therapeutic target for HNSCC.}, }
@article {pmid38684726, year = {2024}, author = {Poquérusse, J and Brown, CL and Gaillard, C and Doughty, C and Dalén, L and Gallagher, AJ and Wooller, M and Zimov, N and Church, GM and Lamm, B and Hysolli, E}, title = {Assessing contemporary Arctic habitat availability for a woolly mammoth proxy.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {9804}, pmid = {38684726}, issn = {2045-2322}, mesh = {Arctic Regions ; *Ecosystem ; Animals ; *Mammoths ; *Biomass ; Alaska ; Carbon/analysis/metabolism ; }, abstract = {Interest continues to grow in Arctic megafaunal ecological engineering, but, since the mass extinction of megafauna ~ 12-15 ka, key physiographic variables and available forage continue to change. Here we sought to assess the extent to which contemporary Arctic ecosystems are conducive to the rewilding of megaherbivores, using a woolly mammoth (M. primigenius) proxy as a model species. We first perform a literature review on woolly mammoth dietary habits. We then leverage Oak Ridge National Laboratories Distributive Active Archive Center Global Aboveground and Belowground Biomass Carbon Density Maps to generate aboveground biomass carbon density estimates in plant functional types consumed by the woolly mammoth at 300 m resolution on Alaska's North Slope. We supplement these analyses with a NASA Arctic Boreal Vulnerability Experiment dataset to downgrade overall biomass estimates to digestible levels. We further downgrade available forage by using a conversion factor representing the relationship between total biomass and net primary productivity (NPP) for arctic vegetation types. Integrating these estimates with the forage needs of woolly mammoths, we conservatively estimate Alaska's North Slope could support densities of 0.0-0.38 woolly mammoth km[-2] (mean 0.13) across a variety of habitats. These results may inform innovative rewilding strategies.}, }
@article {pmid38683839, year = {2024}, author = {Ma, R and Li, C and Gao, A and Jiang, N and Li, J and Hu, W and Feng, X}, title = {Tick species diversity and potential distribution alternation of dominant ticks under different climate scenarios in Xinjiang, China.}, journal = {PLoS neglected tropical diseases}, volume = {18}, number = {4}, pages = {e0012108}, pmid = {38683839}, issn = {1935-2735}, mesh = {*Ticks/classification ; *Tick-Borne Diseases/epidemiology/parasitology ; China/epidemiology ; *Datasets as Topic ; Biodiversity ; Animal Distribution ; Humans ; Animals ; Climate Change ; }, abstract = {Ticks are a hematophagous parasite and a vector of pathogens for numerous human and animal diseases of significant importance. The expansion of tick distribution and the increased risk of tick-borne diseases due to global climate change necessitates further study of the spatial distribution trend of ticks and their potential influencing factors. This study constructed a dataset of tick species distribution in Xinjiang for 60 years based on literature database retrieval and historical data collection (January 1963-January 2023). The distribution data were extracted, corrected, and deduplicated. The dominant tick species were selected for analysis using the MaxEnt model to assess their potential distribution in different periods under the current and BCC-CSM2.MR mode scenarios. The results indicated that there are eight genera and 48 species of ticks in 108 cities and counties of Xinjiang, with Hyalomma asiaticum, Rhipicephalus turanicus, Dermacentor marginatus, and Haemaphysalis punctatus being the top four dominant species. The MaxEnt model analysis revealed that the suitability areas of the four dominant ticks were mainly distributed in the north of Xinjiang, in areas such as Altay and Tacheng Prefecture. Over the next four periods, the medium and high suitable areas within the potential distribution range of the four tick species will expand towards the northwest. Additionally, new suitability areas will emerge in Altay, Changji Hui Autonomous Prefecture, and other local areas. The 60-year tick dataset in this study provides a map of preliminary tick distribution in Xinjiang, with a diverse array of tick species and distribution patterns throughout the area. In addition, the MaxEnt model revealed the spatial change characteristics and future distribution trend of ticks in Xinjiang, which can provide an instrumental data reference for tick monitoring and tick-borne disease risk prediction not only in the region but also in other countries participating in the Belt and Road Initiative.}, }
@article {pmid38683244, year = {2024}, author = {Bai, Y and Song, K and Gao, M and Ma, J and Zhou, Y and Liu, H and Zeng, H and Wang, J and Zheng, X}, title = {Using multi-omics to explore the effect of Bacillus velezensis SAAS-63 on resisting nutrient stress in lettuce.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {313}, pmid = {38683244}, issn = {1432-0614}, mesh = {*Bacillus/metabolism/genetics ; *Lactuca/microbiology/growth &amp; development ; *Rhizosphere ; *Soil Microbiology ; *Nutrients/metabolism ; *Stress, Physiological ; Plant Roots/microbiology ; Microbiota ; Multiomics ; }, abstract = {To avoid the unreasonable use of chemical fertilizer, an environmentally friendly means of improving soil fertility is required. This study explored the role of the plant growth-promoting rhizosphere bacteria (PGPR) strain Bacillus velezensis SAAS-63 in improving nutrient stress in lettuce. Compared with no inoculation, B. velezensis SAAS-63 inoculants exhibited significantly increased fresh weight, root length, and shoot height under nutrient deficiency, as well as improved antioxidant activities and proline contents. The exogenous addition of B. velezensis SAAS-63 also significantly increased the accumulation of macroelements and micronutrients in lettuce. To elucidate the resistance mechanisms induced by B. velezensis SAAS-63 under nutrient stress, high-throughput sequencing and multi-omics analysis were performed. Inoculation with B. velezensis SAAS-63 altered the microbial community of the rhizosphere and increased the relative abundances of Streptomyces, Actinoallomurus, Verrucomicrobia, and Chloroflexi. It is worth noting that the inoculant SAAS-63 can affect plant rhizosphere metabolism. The inoculant changed the metabolic flow of phenylpropanoid metabolic pathway under nutrient deficiency and promoted phenylalanine to participate more in the synthesis of lignin precursors and coumarin substances by inhibiting the synthesis of flavone and isoflavone, thus improving plant resistance. This study showed that the addition of inoculant SAAS-63 could help plants recruit microorganisms to decompose and utilize trehalose and re-established the carbon metabolism of the plant rhizosphere. Additionally, microbes were found to be closely related to the accumulation of metabolites based on correlation analysis. The results indicated that the addition of PGPRs has an important role in regulating soil rhizosphere microbes and metabolism, providing valuable information for understanding how PGPRs affect complex biological processes and enhance plant adaptation to nutrient deficiency. KEY POINTS: • Inoculation with SAAS-63 significantly promoted plant growth under nutrient-deficient conditions • Inoculation with SAAS-63 affected rhizosphere microbial diversity and community structure • Inoculation with SAAS-63 affected plant rhizosphere metabolism and induced plants to synthesize substances that resist stress.}, }
@article {pmid38680650, year = {2023}, author = {Boyes, D and Hammond, J and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Crescent Bell, Epinotia bilunana (Haworth, 1811).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {163}, pmid = {38680650}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Epinotia bilunana (the Crescent Bell; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 659.0 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length.}, }
@article {pmid38677227, year = {2024}, author = {Alves, RA and Santos, MMD and Rudke, AP and Francisquetti Venturin, PR and Martins, JA}, title = {Site selection for nature-based solutions for stormwater management in urban areas: An approach combining GIS and multi-criteria analysis.}, journal = {Journal of environmental management}, volume = {359}, number = {}, pages = {120999}, doi = {10.1016/j.jenvman.2024.120999}, pmid = {38677227}, issn = {1095-8630}, mesh = {*Geographic Information Systems ; Brazil ; *Conservation of Natural Resources/methods ; *Rain ; Ecosystem ; Sustainable Development ; }, abstract = {In recent years, particularly following the definition of the UN Sustainable Development Goals (SDGs) for 2030, Nature-Based Solutions (NBS) have gained considerable attention, capturing the interest of both the scientific community and policymakers committed to addressing urban environmental issues. However, the need for studies to guide decision-makers in identifying suitable locations for NBS implementation within urban stormwater management is evident. To address this gap, the present study employs a methodological approach grounded in multi-criteria analysis integrated with Geographic Information Systems (GIS) to identify areas with potential for NBS implementation. In this process, ten NBS were proposed and tested in the drainage area of a shallow tropical urban lake in Londrina, southern Brazil. Additionally, the study investigates areas hosting lower-income populations, a relevant aspect for public managers given the diverse economic subsidies required to implement NBS. Furthermore, the study incorporates a preliminary analysis that evaluates the potential ecosystem benefits to determine the most suitable NBS for a specific site. The result shows that all the ten analyzed NBS were deemed suitable for the study area. Rain barrels had the highest percentage coverage in the study area (37.1%), followed by tree pits (27.9%), and rain gardens (25.4%). Despite having the highest distribution in the basin area, rain barrels exhibited only moderate ecosystem benefits, prompting the prioritization of other NBS with more significant ecological advantages in the final integrated map. In summary, the methodology proposed showed to be a robust approach to selecting optimal solutions in densely populated urban areas.}, }
@article {pmid38672746, year = {2024}, author = {Bakacsy, L and Kardos, LV and Szepesi, &#xc1; and Nagy, KN and Vasas, A and Feigl, G}, title = {Investigation of the Allelopathic Effect of Two Invasive Plant Species in Rhizotron System.}, journal = {Life (Basel, Switzerland)}, volume = {14}, number = {4}, pages = {}, pmid = {38672746}, issn = {2075-1729}, support = {FK129061//National Research, Development and Innovation Office (Hungary)/ ; }, abstract = {A key question in plant invasion biology is why invasive plants are more competitive in their introduced habitat than in their native habitat. Studies show that invasive species exhibit allelopathy, influencing other plants by releasing chemicals. Research on allelopathy uses in vitro tests, investigating effects on seed germination and seedling development. Although soil plays a role in modifying allelopathic effects, observations with soil are rare and almost nothing is known about the root development of test plants developing in soil and the effects of allelopathic compounds on root architecture. Our study evaluates the allelopathic effects of false indigo-bush (Amorpha fruticosa L.) and common milkweed (Asclepias syriaca L.) on oilseed rape growth as a model plant. The rhizotron system was used to study the effect of morphology and root architecture. Leaf-soil mixtures at 0.5%, 1%, and 5% concentrations were used. Shoot and root development was strongly inhibited at 5%. But there was no difference between the allelopathy of the two species, and the application of lower concentrations did not show any effect, demonstrating that soil has a significant modifying effect on their allelopathy. Our results highlight that the development of roots growing in the soil is also worth investigating in connection with allelopathy, which can strengthen the ecological importance of allelochemicals during successful invasions.}, }
@article {pmid38670119, year = {2024}, author = {Atağ, G and Kaptan, D and Yüncü, E and Başak Vural, K and Mereu, P and Pirastru, M and Barbato, M and Leoni, GG and Güler, MN and Er, T and Eker, E and Yazıcı, TD and Kılıç, MS and Altınışık, NE and Çelik, EA and Morell Miranda, P and Dehasque, M and Floridia, V and Götherström, A and Bilgin, CC and Togan, &#x130; and Günther, T and Özer, F and Hadjisterkotis, E and Somel, M}, title = {Population Genomic History of the Endangered Anatolian and Cyprian Mouflons in Relation to Worldwide Wild, Feral, and Domestic Sheep Lineages.}, journal = {Genome biology and evolution}, volume = {16}, number = {5}, pages = {}, pmid = {38670119}, issn = {1759-6653}, support = {/ERC_/European Research Council/International ; 772390//European Union's Horizon 2020 research and innovation programme/ ; //Scientific and Technological Research Council of Turkey/ ; //National Scholarship Programme/ ; //Swedish Research Council Vetenskapsr&#xe5;det/ ; //Carl Tryggers Stiftelse f&#xf6;r Vetenskaplig Forskning/ ; 772390/ERC_/European Research Council/International ; }, mesh = {Animals ; *Endangered Species ; Sheep/genetics ; *Sheep, Domestic/genetics ; Genome ; Genetic Variation ; }, abstract = {Once widespread in their homelands, the Anatolian mouflon (Ovis gmelini anatolica) and the Cyprian mouflon (Ovis gmelini ophion) were driven to near extinction during the 20th century and are currently listed as endangered populations by the International Union for Conservation of Nature. While the exact origins of these lineages remain unclear, they have been suggested to be close relatives of domestic sheep or remnants of proto-domestic sheep. Here, we study whole genome sequences of n = 5 Anatolian mouflons and n = 10 Cyprian mouflons in terms of population history and diversity, comparing them with eight other extant sheep lineages. We find reciprocal genetic affinity between Anatolian and Cyprian mouflons and domestic sheep, higher than all other studied wild sheep genomes, including the Iranian mouflon (O. gmelini). Studying diversity indices, we detect a considerable load of short runs of homozygosity blocks (<2 Mb) in both Anatolian and Cyprian mouflons, reflecting small effective population size (Ne). Meanwhile, Ne and mutation load estimates are lower in Cyprian compared with Anatolian mouflons, suggesting the purging of recessive deleterious variants in Cyprian sheep under a small long-term Ne, possibly attributable to founder effects, island isolation, introgression from domestic lineages, or differences in their bottleneck dynamics. Expanding our analyses to worldwide wild and feral Ovis genomes, we observe varying viability metrics among different lineages and a limited consistency between viability metrics and International Union for Conservation of Nature conservation status. Factors such as recent inbreeding, introgression, and unique population dynamics may have contributed to the observed disparities.}, }
@article {pmid38668970, year = {2024}, author = {Muthye, V and Lavrov, DV}, title = {Characterization of the Mitochondrial Proteome in the Ctenophore Mnemiopsis leidyi Using MitoPredictor.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2757}, number = {}, pages = {239-257}, pmid = {38668970}, issn = {1940-6029}, mesh = {Animals ; *Ctenophora/metabolism/genetics ; *Proteome ; *Mitochondrial Proteins/metabolism/genetics ; Computational Biology/methods ; Mitochondria/metabolism ; Proteomics/methods ; Software ; }, abstract = {Mitochondrial proteomes have been experimentally characterized for only a handful of animal species. However, the increasing availability of genomic and transcriptomic data allows one to infer mitochondrial proteins using computational tools. MitoPredictor is a novel random forest classifier, which utilizes orthology search, mitochondrial targeting signal (MTS) identification, and protein domain content to infer mitochondrial proteins in animals. MitoPredictor's output also includes an easy-to-use R Shiny applet for the visualization and analysis of the results. In this article, we provide a guide for predicting and analyzing the mitochondrial proteome of the ctenophore Mnemiopsis leidyi using MitoPredictor.}, }
@article {pmid38668514, year = {2024}, author = {Li, Q and Yao, S and Wen, H and Li, W and Jin, L and Huang, X}, title = {Improving Lead Phytoremediation Using Endophytic Bacteria Isolated from the Pioneer Plant Ageratina adenophora (Spreng.) from a Mining Area.}, journal = {Toxics}, volume = {12}, number = {4}, pages = {}, pmid = {38668514}, issn = {2305-6304}, support = {2020KY15017//Project for Enhancing Young and Middle-aged Teacher's Research Basis Ability in Colleges of Guangxi/ ; }, abstract = {This study aimed to isolate and characterise endophytic bacteria from the pioneer plant Ageratina adenophora in a mining area. Seven strains of metal-resistant endophytic bacteria that belong to five genera were isolated from the roots of A. adenophora. These strains exhibited various plant growth-promoting (PGP) capabilities. Sphingomonas sp. ZYG-4, which exhibited the ability to secrete indoleacetic acid (IAA; 53.2 ± 8.3 mg·L[-1]), solubilize insoluble inorganic phosphates (Phosphate solubilization; 11.2 ± 2.9 mg·L[-1]), and regulate root ethylene levels (1-aminocyclopropane-1-carboxylic acid deaminase activity; 2.87 ± 0.19 µM α-KB·mg[-1]·h[-1]), had the highest PGP potential. Therefore, Sphingomonas sp. ZYG-4 was used in a pot experiment to study its effect on the biomass and Pb uptake of both host (Ageratina adenophora) and non-host (Dysphania ambrosioides) plants. Compared to the uninoculated control, Sphingomonas sp. ZYG-4 inoculation increased the biomass of shoots and roots by 59.4% and 144.4% for A. adenophora and by 56.2% and 57.1% for D. ambrosioides, respectively. In addition, Sphingomonas sp. ZYG-4 inoculation enhanced Pb accumulation in the shoot and root by 268.9% and 1187.3% for A. adenophora, and by 163.1% and 343.8% for D. ambrosioides, respectively, compared to plants without bacterial inoculation. Our research indicates that endophytic bacteria are promising candidates for enhancing plant growth and facilitating microbe-assisted phytoremediation in heavy metal-contaminated soil.}, }
@article {pmid38668506, year = {2024}, author = {Li, S and Yang, J and Zheng, K and He, S and Liu, Z and Song, S and Zeng, T}, title = {Effective Activation of Peroxymonosulfate by Oxygen Vacancy Induced Musa Basjoo Biochar to Degrade Sulfamethoxazole: Efficiency and Mechanism.}, journal = {Toxics}, volume = {12}, number = {4}, pages = {}, pmid = {38668506}, issn = {2305-6304}, support = {2023M743772//China Postdoctoral Science Foundation/ ; 22276172//National Natural Science Foundation of China/ ; 22076168//National Natural Science Foundation of China/ ; LR21E080001//Zhejiang Provincial Natural Science Foundation of China/ ; RF-B2022005//Fundamental Research Funds for the Provincial Universities of Zhejiang/ ; 2023C03132//"Leading Goose" R&amp;D Program of Zhejiang/ ; }, abstract = {Biochar materials have garnered attention as potential catalysts for peroxymonosulfate (PMS) activation due to their cost-effectiveness, notable specific surface area, and advantageous structural properties. In this study, a suite of plantain-derived biochar (MBB-400, MBB-600, and MBB-800), possessing a well-defined pore structure and a substantial number of uniformly distributed active sites (oxygen vacancy, OVs), was synthesized through a facile calcination process at varying temperatures (400, 600, and 800 °C). These materials were designed for the activation of PMS in the degradation of sulfamethoxazole (SMX). Experimental investigations revealed that OVs not only functioned as enriched sites for pollutants, enhancing the opportunities for free radicals ([•]OH/SO4[•-]) and surface-bound radicals (SBRs) to attack pollutants, but also served as channels for intramolecular charge transfer leaps. This role contributed to a reduction in interfacial charge transfer resistance, expediting electron transfer rates with PMS, thereby accelerating the decomposition of pollutants. Capitalizing on these merits, the MBB-800/PMS system displayed a 61-fold enhancement in the conversion rate for SMX degradation compared to inactivated MBB/PMS system. Furthermore, the MBB-800 exhibited less cytotoxicity towards rat pheochromocytoma (PC12) cells. Hence, the straightforward calcination synthesis of MBB-800 emerges as a promising biochar catalyst with vast potential for sustainable and efficient wastewater treatment and environmental remediation.}, }
@article {pmid38666081, year = {2024}, author = {Omar, KM and Kitundu, GL and Jimoh, AO and Namikelwa, DN and Lisso, FM and Babajide, AA and Olufemi, SE and Awe, OI}, title = {Investigating antimicrobial resistance genes in Kenya, Uganda and Tanzania cattle using metagenomics.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e17181}, pmid = {38666081}, issn = {2167-8359}, mesh = {Animals ; Cattle ; *Metagenomics ; Kenya/epidemiology ; Uganda/epidemiology ; Tanzania ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Genes, Bacterial/genetics ; }, abstract = {Antimicrobial resistance (AMR) is a growing problem in African cattle production systems, posing a threat to human and animal health and the associated economic value chain. However, there is a poor understanding of the resistomes in small-holder cattle breeds in East African countries. This study aims to examine the distribution of antimicrobial resistance genes (ARGs) in Kenya, Tanzania, and Uganda cattle using a metagenomics approach. We used the SqueezeMeta-Abricate (assembly-based) pipeline to detect ARGs and benchmarked this approach using the Centifuge-AMRplusplus (read-based) pipeline to evaluate its efficiency. Our findings reveal a significant number of ARGs of critical medical and economic importance in all three countries, including resistance to drugs of last resort such as carbapenems, suggesting the presence of highly virulent and antibiotic-resistant bacterial pathogens (ESKAPE) circulating in East Africa. Shared ARGs such as aph(6)-id (aminoglycoside phosphotransferase), tet (tetracycline resistance gene), sul2 (sulfonamide resistance gene) and cfxA_gen (betalactamase gene) were detected. Assembly-based methods revealed fewer ARGs compared to read-based methods, indicating the sensitivity and specificity of read-based methods in resistome characterization. Our findings call for further surveillance to estimate the intensity of the antibiotic resistance problem and wider resistome classification. Effective management of livestock and antibiotic consumption is crucial in minimizing antimicrobial resistance and maximizing productivity, making these findings relevant to stakeholders, agriculturists, and veterinarians in East Africa and Africa at large.}, }
@article {pmid38662943, year = {2024}, author = {Lu, XY and Wu, HP and Ma, H and Li, H and Li, J and Liu, YT and Pan, ZY and Xie, Y and Wang, L and Ren, B and Liu, GK}, title = {Deep Learning-Assisted Spectrum-Structure Correlation: State-of-the-Art and Perspectives.}, journal = {Analytical chemistry}, volume = {96}, number = {20}, pages = {7959-7975}, doi = {10.1021/acs.analchem.4c01639}, pmid = {38662943}, issn = {1520-6882}, abstract = {Spectrum-structure correlation is playing an increasingly crucial role in spectral analysis and has undergone significant development in recent decades. With the advancement of spectrometers, the high-throughput detection triggers the explosive growth of spectral data, and the research extension from small molecules to biomolecules accompanies massive chemical space. Facing the evolving landscape of spectrum-structure correlation, conventional chemometrics becomes ill-equipped, and deep learning assisted chemometrics rapidly emerges as a flourishing approach with superior ability of extracting latent features and making precise predictions. In this review, the molecular and spectral representations and fundamental knowledge of deep learning are first introduced. We then summarize the development of how deep learning assist to establish the correlation between spectrum and molecular structure in the recent 5 years, by empowering spectral prediction (i.e., forward structure-spectrum correlation) and further enabling library matching and de novo molecular generation (i.e., inverse spectrum-structure correlation). Finally, we highlight the most important open issues persisted with corresponding potential solutions. With the fast development of deep learning, it is expected to see ultimate solution of establishing spectrum-structure correlation soon, which would trigger substantial development of various disciplines.}, }
@article {pmid38658779, year = {2024}, author = {Andrianova, MA and Seplyarskiy, VB and Terradas, M and Sánchez-Heras, AB and Mur, P and Soto, JL and Aiza, G and Borràs, E and Kondrashov, FA and Kondrashov, AS and Bazykin, GA and Valle, L}, title = {Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells.}, journal = {European journal of human genetics : EJHG}, volume = {32}, number = {7}, pages = {837-845}, pmid = {38658779}, issn = {1476-5438}, support = {PID2020-112595RB-I00//Ministry of Economy and Competitiveness | Agencia Estatal de Investigaci&#xf3;n (Spanish Agencia Estatal de Investigaci&#xf3;n)/ ; AGAUR 2017SGR1282; CERCA Program//Government of Catalonia | Departament de Salut, Generalitat de Catalunya/ ; ISCIII-AES-2017 PI17/01082//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; I5127-B//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; 429960716//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; ERC Consolidator (771209)//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; }, mesh = {Humans ; *DNA Polymerase III/genetics/metabolism ; Female ; Male ; Pedigree ; Heterozygote ; Genes, Recessive ; Neoplasms/genetics/pathology ; Mutation ; Germ-Line Mutation ; Adult ; }, abstract = {Constitutional heterozygous pathogenic variants in the exonuclease domain of POLE and POLD1, which affect the proofreading activity of the corresponding polymerases, cause a cancer predisposition syndrome characterized by increased risk of gastrointestinal polyposis, colorectal cancer, endometrial cancer and other tumor types. The generally accepted explanation for the connection between the disruption of the proofreading activity of polymerases epsilon and delta and cancer development is through an increase in the somatic mutation rate. Here we studied an extended family with multiple members heterozygous for the pathogenic POLD1 variant c.1421T>C p.(Leu474Pro), which segregates with the polyposis and cancer phenotypes. Through the analysis of mutational patterns of patient-derived fibroblasts colonies and de novo mutations obtained by parent-offspring comparisons, we concluded that heterozygous POLD1 L474P just subtly increases the somatic and germline mutation burden. In contrast, tumors developed in individuals with a heterozygous mutation in the exonuclease domain of POLD1, including L474P, have an extremely high mutation rate (>100 mut/Mb) associated with signature SBS10d. We solved this contradiction through the observation that tumorigenesis involves somatic inactivation of the wildtype POLD1 allele. These results imply that exonuclease deficiency of polymerase delta has a recessive effect on mutation rate.}, }
@article {pmid38656485, year = {2024}, author = {Jiménez-Madrigal, JP and Till, BJ and Gatica-Arias, A}, title = {Genetic Diversity Assessment in Plants from Reduced Representation Sequencing Data.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2787}, number = {}, pages = {107-122}, pmid = {38656485}, issn = {1940-6029}, mesh = {*Genetic Variation ; *Plants/genetics ; *Genome, Plant ; Software ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; Genomics/methods ; }, abstract = {Genetic diversity refers to the variety of genetic traits within a population or a species. It is an essential aspect of both plant ecology and plant breeding because it contributes to the adaptability, survival, and resilience of populations in changing environments. This chapter outlines a pipeline for estimating genetic diversity statistics from reduced representation or whole genome sequencing data. The pipeline involves obtaining DNA sequence reads, mapping the corresponding reads to a reference genome, calling variants from the alignments, and generating an unbiased estimation of nucleotide diversity and divergence between populations. The pipeline is suitable for single-end Illumina reads and can be adjusted for paired-end reads. The resulting pipeline provides a comprehensive approach for aligning and analyzing sequencing data to estimate genetic diversity.}, }
@article {pmid38655208, year = {2023}, author = {Wu, SH and Ko, JC and Lin, RS and Chang-Yang, CH and Chang, HW}, title = {Evaluating community-wide temporal sampling in passive acoustic monitoring: A comprehensive study of avian vocal patterns in subtropical montane forests.}, journal = {F1000Research}, volume = {12}, number = {}, pages = {1299}, pmid = {38655208}, issn = {2046-1402}, mesh = {Animals ; *Vocalization, Animal/physiology ; *Acoustics ; *Birds/physiology ; *Forests ; Environmental Monitoring/methods ; }, abstract = {BACKGROUND: From passive acoustic monitoring (PAM) recordings, the vocal activity rate (VAR), vocalizations per unit of time, can be calculated and is essential for assessing bird population abundance. However, VAR is subject to influences from a range of factors, including species and environmental conditions. Identifying the optimal sampling design to obtain representative acoustic data for VAR estimation is crucial for research objectives. PAM commonly uses temporal sampling strategies to decrease the volume of recordings and the resources needed for audio data management. Yet, the comprehensive impact of this sampling approach on VAR estimation remains insufficiently explored.<br><br>METHODS: In this study, we used vocalizations extracted from recordings of 12 bird species, taken at 14 PAM stations situated in subtropical montane forests over a four-month period, to assess the impact of temporal sampling on VAR across three distinct scales: short-term periodic, diel, and hourly. For short-term periodic sampling analysis, we employed hierarchical clustering analysis (HCA) and the coefficient of variation (CV). Generalized additive models (GAMs) were utilized for diel sampling analysis, and we determined the average difference in VAR values per minute for the hourly sampling analysis.<br><br>RESULTS: We identified significant day and species-specific VAR fluctuations. The survey season was divided into five segments; the earliest two showed high variability and are best avoided for surveys. Data from days with heavy rain and strong winds showed reduced VAR values and should be excluded from analysis. Continuous recordings spanning at least seven days, extending to 14 days is optimal for minimizing sampling variance. Morning chorus recordings effectively capture the majority of bird vocalizations, and hourly sampling with frequent, shorter intervals aligns closely with continuous recording outcomes.<br><br>CONCLUSIONS: While our findings are context-specific, they highlight the significance of strategic sampling in avian monitoring, optimizing resource utilization and enhancing the breadth of monitoring efforts.}, }
@article {pmid38654647, year = {2024}, author = {Spake, L and Hassan, A and Schaffnit, SB and Alam, N and Amoah, AS and Badjie, J and Cerami, C and Crampin, A and Dube, A and Kaye, MP and Kotch, R and Liew, F and McLean, E and Munthali-Mkandawire, S and Mwalwanda, L and Petersen, AC and Prentice, AM and Zohora, FT and Watts, J and Sear, R and Shenk, MK and Sosis, R and Shaver, JH}, title = {A practical guide to cross-cultural and multi-sited data collection in the biological and behavioural sciences.}, journal = {Proceedings. Biological sciences}, volume = {291}, number = {2021}, pages = {20231422}, pmid = {38654647}, issn = {1471-2954}, mesh = {Humans ; *Behavioral Sciences ; *Data Collection/methods ; Cross-Cultural Comparison ; Research Design ; Ecology/methods ; }, abstract = {Researchers in the biological and behavioural sciences are increasingly conducting collaborative, multi-sited projects to address how phenomena vary across ecologies. These types of projects, however, pose additional workflow challenges beyond those typically encountered in single-sited projects. Through specific attention to cross-cultural research projects, we highlight four key aspects of multi-sited projects that must be considered during the design phase to ensure success: (1) project and team management; (2) protocol and instrument development; (3) data management and documentation; and (4) equitable and collaborative practices. Our recommendations are supported by examples from our experiences collaborating on the Evolutionary Demography of Religion project, a mixed-methods project collecting data across five countries in collaboration with research partners in each host country. To existing discourse, we contribute new recommendations around team and project management, introduce practical recommendations for exploring the validity of instruments through qualitative techniques during piloting, highlight the importance of good documentation at all steps of the project, and demonstrate how data management workflows can be strengthened through open science practices. While this project was rooted in cross-cultural human behavioural ecology and evolutionary anthropology, lessons learned from this project are applicable to multi-sited research across the biological and behavioural sciences.}, }
@article {pmid38649162, year = {2024}, author = {Niimura, Y and Biswa, BB and Kishida, T and Toyoda, A and Fujiwara, K and Ito, M and Touhara, K and Inoue-Murayama, M and Jenkins, SH and Adenyo, C and Kayang, BB and Koide, T}, title = {Synchronized Expansion and Contraction of Olfactory, Vomeronasal, and Taste Receptor Gene Families in Hystricomorph Rodents.}, journal = {Molecular biology and evolution}, volume = {41}, number = {4}, pages = {}, pmid = {38649162}, issn = {1537-1719}, support = {18K06359//JSPS KAKENHI/ ; JPMJAS2017//JST aXis/ ; 1B2020//National Institute of Genetics, NIG-Joint/ ; }, mesh = {Animals ; *Evolution, Molecular ; *Multigene Family ; *Phylogeny ; Receptors, G-Protein-Coupled/genetics ; *Receptors, Odorant/genetics ; Receptors, Pheromone/genetics/metabolism ; *Rodentia/genetics ; Smell/genetics ; Taste/genetics ; *Vomeronasal Organ/metabolism ; }, abstract = {Chemical senses, including olfaction, pheromones, and taste, are crucial for the survival of most animals. There has long been a debate about whether different types of senses might influence each other. For instance, primates with a strong sense of vision are thought to have weakened olfactory abilities, although the oversimplified trade-off theory is now being questioned. It is uncertain whether such interactions between different chemical senses occur during evolution. To address this question, we examined four receptor gene families related to olfaction, pheromones, and taste: olfactory receptor (OR), vomeronasal receptor type 1 and type 2 (V1R and V2R), and bitter taste receptor (T2R) genes in Hystricomorpha, which is morphologically and ecologically the most diverse group of rodents. We also sequenced and assembled the genome of the grasscutter, Thryonomys swinderianus. By examining 16 available genome assemblies alongside the grasscutter genome, we identified orthologous gene groups among hystricomorph rodents for these gene families to separate the gene gain and loss events in each phylogenetic branch of the Hystricomorpha evolutionary tree. Our analysis revealed that the expansion or contraction of the four gene families occurred synchronously, indicating that when one chemical sense develops or deteriorates, the others follow suit. The results also showed that V1R/V2R genes underwent the fastest evolution, followed by OR genes, and T2R genes were the most evolutionarily stable. This variation likely reflects the difference in ligands of V1R/V2Rs, ORs, and T2Rs: species-specific pheromones, environment-based scents, and toxic substances common to many animals, respectively.}, }
@article {pmid38648741, year = {2024}, author = {Crauwels, C and Heidig, SL and Díaz, A and Vranken, WF}, title = {Large-scale structure-informed multiple sequence alignment of proteins with SIMSApiper.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {5}, pages = {}, pmid = {38648741}, issn = {1367-4811}, support = {1SE5923N//Research Foundation Flanders/ ; }, mesh = {*Software ; *Proteins/chemistry ; *Sequence Alignment/methods ; *Sequence Analysis, Protein/methods ; Algorithms ; Amino Acid Sequence ; Computational Biology/methods ; Databases, Protein ; }, abstract = {SUMMARY: SIMSApiper is a Nextflow pipeline that creates reliable, structure-informed MSAs of thousands of protein sequences faster than standard structure-based alignment methods. Structural information can be provided by the user or collected by the pipeline from online resources. Parallelization with sequence identity-based subsets can be activated to significantly speed up the alignment process. Finally, the number of gaps in the final alignment can be reduced by leveraging the position of conserved secondary structure elements.<br><br>The pipeline is implemented using Nextflow, Python3, and Bash. It is publicly available on github.com/Bio2Byte/simsapiper.}, }
@article {pmid38648214, year = {2024}, author = {Lauber, C and Zhang, X and Vaas, J and Klingler, F and Mutz, P and Dubin, A and Pietschmann, T and Roth, O and Neuman, BW and Gorbalenya, AE and Bartenschlager, R and Seitz, S}, title = {Deep mining of the Sequence Read Archive reveals major genetic innovations in coronaviruses and other nidoviruses of aquatic vertebrates.}, journal = {PLoS pathogens}, volume = {20}, number = {4}, pages = {e1012163}, pmid = {38648214}, issn = {1553-7374}, mesh = {Animals ; *Nidovirales/genetics ; *Genome, Viral ; *Coronavirus/genetics/classification ; *Phylogeny ; Vertebrates/virology/genetics ; Fishes/virology ; Evolution, Molecular ; Data Mining ; Nidovirales Infections/virology/genetics ; }, abstract = {Virus discovery by genomics and metagenomics empowered studies of viromes, facilitated characterization of pathogen epidemiology, and redefined our understanding of the natural genetic diversity of viruses with profound functional and structural implications. Here we employed a data-driven virus discovery approach that directly queries unprocessed sequencing data in a highly parallelized way and involves a targeted viral genome assembly strategy in a wide range of sequence similarity. By screening more than 269,000 datasets of numerous authors from the Sequence Read Archive and using two metrics that quantitatively assess assembly quality, we discovered 40 nidoviruses from six virus families whose members infect vertebrate hosts. They form 13 and 32 putative viral subfamilies and genera, respectively, and include 11 coronaviruses with bisegmented genomes from fishes and amphibians, a giant 36.1 kilobase coronavirus genome with a duplicated spike glycoprotein (S) gene, 11 tobaniviruses and 17 additional corona-, arteri-, cremega-, nanhypo- and nangoshaviruses. Genome segmentation emerged in a single evolutionary event in the monophyletic lineage encompassing the subfamily Pitovirinae. We recovered the bisegmented genome sequences of two coronaviruses from RNA samples of 69 infected fishes and validated the presence of poly(A) tails at both segments using 3'RACE PCR and subsequent Sanger sequencing. We report a genetic linkage between accessory and structural proteins whose phylogenetic relationships and evolutionary distances are incongruent with the phylogeny of replicase proteins. We rationalize these observations in a model of inter-family S recombination involving at least five ancestral corona- and tobaniviruses of aquatic hosts. In support of this model, we describe an individual fish co-infected with members from the families Coronaviridae and Tobaniviridae. Our results expand the scale of the known extraordinary evolutionary plasticity in nidoviral genome architecture and call for revisiting fundamentals of genome expression, virus particle biology, host range and ecology of vertebrate nidoviruses.}, }
@article {pmid38646766, year = {2024}, author = {Hu, JY and Liu, LY and Dai, QL and Yang, B and Zhou, WJ}, title = {Evaluation of ecotourism suitability based on AHP-GIS: Taking Xiaoxiangling area of the Giant Panda National Park and the surrounding communities as an example.}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {35}, number = {3}, pages = {780-788}, doi = {10.13287/j.1001-9332.202403.020}, pmid = {38646766}, issn = {1001-9332}, mesh = {Animals ; *Conservation of Natural Resources ; China ; *Parks, Recreational ; *Ecosystem ; *Ursidae ; *Geographic Information Systems ; Recreation ; }, abstract = {The primary goal of national parks is to protect ecological environment, but also with the functions of scientific research, education, and recreation. Aiming for the realization of universal sharing, we used the analytic hierarchy process (AHP) to construct an ecotourism suitability evaluation system by selecting four factors, including landscape resources, ecological environment carrying capacity, recreation utilization capacity and social condition, taking Xiaoxiangling area of Giant Panda National Park and the surrounding communities as an example. We evaluated the ecotourism suitability based on GIS, and conducted a questionnaire survey of tourists, to propose suggestions on the functional zoning in terms of ecotourism suitability and subjective choice preferences of tourists. The results showed that the ecotourism suitability of the evaluation area could be classified into five levels. The most suitable areas were located nearby the natural landscape resources and far away from the core conservation area, and the least suitable areas distributed at the edge of the core conservation area. According to the results of suitability analysis, the evaluation area was divided into suitable development area, moderate development area, and restricted development area. Combined with the tourist preferences, we divided the recreational activities in the evaluation area into seven activities, namely, ecotourism, eco-camping, science education, leisure vacation, agricultural and animal husbandry culture experience, eco-education, and mountain adventure. These findings could help provide suitable services for different tourists and offer reference for the ecotourism developmental planning of the Xiaoxiangling area of the Giant Panda National Park.}, }
@article {pmid38646687, year = {2024}, author = {Filatov, DA}, title = {ProSeq4: A user-friendly multiplatform program for preparation and analysis of large-scale DNA polymorphism datasets.}, journal = {Molecular ecology resources}, volume = {24}, number = {5}, pages = {e13962}, pmid = {38646687}, issn = {1755-0998}, support = {BB/P009808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Software ; *Polymorphism, Genetic ; *Computational Biology/methods ; Sequence Analysis, DNA/methods ; }, abstract = {Preparation of DNA polymorphism datasets for analysis is an important step in evolutionary genetic and molecular ecology studies. Ever-growing dataset sizes make this step time consuming, but few convenient software tools are available to facilitate processing of large-scale datasets including thousands of sequence alignments. Here I report "processor of sequences v4" (proSeq4)-a user-friendly multiplatform software for preparation and evolutionary genetic analyses of genome- or transcriptome-scale sequence polymorphism datasets. The program has an easy-to-use graphic user interface and is designed to process and analyse many thousands of datasets. It supports over two dozen file formats, includes a flexible sequence editor and various tools for data visualization, quality control and most commonly used evolutionary genetic analyses, such as NJ-phylogeny reconstruction, DNA polymorphism analyses and coalescent simulations. Command line tools (e.g. vcf2fasta) are also provided for easier integration into bioinformatic pipelines. Apart of molecular ecology and evolution research, proSeq4 may be useful for teaching, e.g. for visual illustration of different shapes of phylogenies generated with coalescent simulations in different scenarios. ProSeq4 source code and binaries for Windows, MacOS and Ubuntu are available from https://sourceforge.net/projects/proseq/.}, }
@article {pmid38644930, year = {2023}, author = {Boyes, D and Boyes, C and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Scalloped Oak, Crocallis elinguaria (Linneas, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {426}, pmid = {38644930}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Crocallis elinguaria (the Scalloped Oak; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 430.4 megabases in span. Most of the assembly is scaffolded into 17 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 16.86 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,741 protein coding genes.}, }
@article {pmid38644519, year = {2024}, author = {Chen, J and Lin, JJ and Wang, W and Huang, H and Pan, Z and Ye, G and Dong, S and Lin, Y and Lin, C and Huang, Q}, title = {EV-COMM: A database of interspecies and intercellular interactions mediated by extracellular vesicles.}, journal = {Journal of extracellular vesicles}, volume = {13}, number = {4}, pages = {e12442}, pmid = {38644519}, issn = {2001-3078}, support = {2021J06037//Fujian Provincial Department of Science and Technology/ ; 2022T3063//Fujian Provincial Department of Science and Technology/ ; 32161143016//National Natural Science Foundation of China/ ; 42177362//National Natural Science Foundation of China/ ; 42250410328//National Natural Science Foundation of China/ ; CAS-WX2021SF-0302//Chinese Academy of Sciences/ ; NO. NBSDC-DB-21//National Basic Science Data Center "Environment Health DataBase"/ ; }, mesh = {Animals ; Humans ; *Cell Communication ; Databases, Factual ; *Extracellular Vesicles/metabolism ; MicroRNAs/metabolism/genetics ; }, abstract = {Intra- and inter-organismal interactions play a crucial role in the maintenance and function of individuals, as well as communities. Extracellular vesicles (EVs) have been identified as effective mediators for the communication both within and between species. They can carry and transport molecular cargoes to transmit biological messages. Several databases (ExoBCD, ExoCarta, EVpedia, EV-TRACK, Vesiclepedia) complied the cargoes information including DNA, RNA, protein, lipid and metabolite associated with EVs. Databases that refer to the complete records on both donor and recipient information are warranted to facilitate the understanding of the interaction across cells and species. In this study, we developed a database that compiled the records equipped with a structured process of EV-mediated interaction. The sources of donor and recipient were classified by cell type, tissues/organs and species, thus providing an extended knowledge of cell-cell, species-species interaction. The isolation and identification methods were presented for assessing the quality of EVs. Information on functional cargoes was included, where microRNA was linked to a prediction server to broaden its potential effects. Physiological and pathological context was marked to show the environment where EVs functioned. At present, a total of 1481 data records in our database, including 971 cell-cell interactions belonging to more than 40 different tissues/organs, and 510 cross-species records. The database provides a web interface to browse, search, visualize and download the interaction records. Users can search for interactions by selecting the context of interest or specific cells/species types, as well as functional cargoes. To the best of our knowledge, the database is the first comprehensive database focusing on interactions between donor and recipient cells or species mediated by EVs, serving as a convenient tool to explore and validate interactions. The Database, shorten as EV-COMM (EV mediated communication) is freely available at http://sdc.iue.ac.cn/evs/list/ and will be continuously updated.}, }
@article {pmid38643978, year = {2024}, author = {Rosbakh, S and Carta, A and Fernández-Pascual, E and Phartyal, SS and Dayrell, RLC and Mattana, E and Saatkamp, A and Vandelook, F and Baskin, JM and Baskin, CC}, title = {Large dataset analyses advance knowledge of seed ecology and evolutionary biology.}, journal = {The New phytologist}, volume = {242}, number = {6}, pages = {2399-2400}, doi = {10.1111/nph.19752}, pmid = {38643978}, issn = {1469-8137}, support = {//Novo Nordisk Foundation/ ; }, mesh = {*Biological Evolution ; *Seeds/physiology/genetics ; *Ecology ; Datasets as Topic ; }, }
@article {pmid38643126, year = {2024}, author = {Xiao, W and Chen, YL and Du, LY and Wu, J and Wang, Z and Mao, B and Wen, FQ and Gibson, PG and McDonald, VM and Yu, H and Fu, JJ}, title = {Bacterial interactome disturbance in chronic obstructive pulmonary disease clinical stability and exacerbations.}, journal = {Respiratory research}, volume = {25}, number = {1}, pages = {173}, pmid = {38643126}, issn = {1465-993X}, support = {No.82100046//National Natural Science Foundation of China/ ; No.81870014//National Natural Science Foundation of China/ ; 2023NSFSC1460//Sichuan Science and Technology Program of China/ ; 2020YFS0145//Sichuan Science and Technology Program of China/ ; }, mesh = {Humans ; *Dysbiosis ; *Pulmonary Disease, Chronic Obstructive/drug therapy ; Lung ; Haemophilus ; Sputum/microbiology ; Disease Progression ; }, abstract = {RATIONALE: Our understanding of airway dysbiosis in chronic obstructive pulmonary disease (COPD) remains incomplete, which may be improved by unraveling the complexity in microbial interactome.<br><br>OBJECTIVES: To characterize reproducible features of airway bacterial interactome in COPD at clinical stability and during exacerbation, and evaluate their associations with disease phenotypes.<br><br>METHODS: We performed weighted ensemble-based co-occurrence network analysis of 1742 sputum microbiomes from published and new microbiome datasets, comprising two case-control studies of stable COPD versus healthy control, two studies of COPD stability versus exacerbation, and one study with exacerbation-recovery time series data.<br><br>RESULTS: Patients with COPD had reproducibly lower degree of negative bacterial interactions, i.e. total number of negative interactions as a proportion of total interactions, in their airway microbiome compared with healthy controls. Evaluation of the Haemophilus interactome showed that the antagonistic interaction networks of this established pathogen rather than its abundance consistently changed in COPD. Interactome dynamic analysis revealed reproducibly reduced antagonistic interactions but not diversity loss during COPD exacerbation, which recovered after treatment. In phenotypic analysis, unsupervised network clustering showed that loss of antagonistic interactions was associated with worse clinical symptoms (dyspnea), poorer lung function, exaggerated neutrophilic inflammation, and higher exacerbation risk. Furthermore, the frequent exacerbators (&#x2265;&#x2009;2 exacerbations per year) had significantly reduced antagonistic bacterial interactions while exhibiting subtle compositional changes in their airway microbiota.<br><br>CONCLUSIONS: Bacterial interactome disturbance characterized by reduced antagonistic interactions, rather than change in pathogen abundance or diversity, is a reproducible feature of airway dysbiosis in COPD clinical stability and exacerbations, which suggests that we may target interactome rather than pathogen alone for disease treatment.}, }
@article {pmid38632407, year = {2024}, author = {Maes, SL and Dietrich, J and Midolo, G and Schwieger, S and Kummu, M and Vandvik, V and Aerts, R and Althuizen, IHJ and Biasi, C and Björk, RG and Böhner, H and Carbognani, M and Chiari, G and Christiansen, CT and Clemmensen, KE and Cooper, EJ and Cornelissen, JHC and Elberling, B and Faubert, P and Fetcher, N and Forte, TGW and Gaudard, J and Gavazov, K and Guan, Z and Guðmundsson, J and Gya, R and Hallin, S and Hansen, BB and Haugum, SV and He, JS and Hicks Pries, C and Hovenden, MJ and Jalava, M and Jónsdóttir, IS and Juhanson, J and Jung, JY and Kaarlejärvi, E and Kwon, MJ and Lamprecht, RE and Le Moullec, M and Lee, H and Marushchak, ME and Michelsen, A and Munir, TM and Myrsky, EM and Nielsen, CS and Nyberg, M and Olofsson, J and Óskarsson, H and Parker, TC and Pedersen, EP and Petit Bon, M and Petraglia, A and Raundrup, K and Ravn, NMR and Rinnan, R and Rodenhizer, H and Ryde, I and Schmidt, NM and Schuur, EAG and Sjögersten, S and Stark, S and Strack, M and Tang, J and Tolvanen, A and Töpper, JP and Väisänen, MK and van Logtestijn, RSP and Voigt, C and Walz, J and Weedon, JT and Yang, Y and Ylänne, H and Björkman, MP and Sarneel, JM and Dorrepaal, E}, title = {Environmental drivers of increased ecosystem respiration in a warming tundra.}, journal = {Nature}, volume = {629}, number = {8010}, pages = {105-113}, pmid = {38632407}, issn = {1476-4687}, mesh = {Arctic Regions ; Carbon/metabolism/analysis ; Carbon Cycle ; Datasets as Topic ; *Ecosystem ; *Global Warming ; Hydrogen-Ion Concentration ; Nitrogen/metabolism/analysis ; Plants/metabolism ; Seasons ; Soil/chemistry ; Soil Microbiology ; Temperature ; *Tundra ; Time Factors ; *Cell Respiration ; }, abstract = {Arctic and alpine tundra ecosystems are large reservoirs of organic carbon[1,2]. Climate warming may stimulate ecosystem respiration and release carbon into the atmosphere[3,4]. The magnitude and persistency of this stimulation and the environmental mechanisms that drive its variation remain uncertain[5-7]. This hampers the accuracy of global land carbon-climate feedback projections[7,8]. Here we synthesize 136 datasets from 56 open-top chamber in situ warming experiments located at 28 arctic and alpine tundra sites which have been running for less than 1 year up to 25 years. We show that a mean rise of 1.4 °C [confidence interval (CI) 0.9-2.0 °C] in air and 0.4 °C [CI 0.2-0.7 °C] in soil temperature results in an increase in growing season ecosystem respiration by 30% [CI 22-38%] (n = 136). Our findings indicate that the stimulation of ecosystem respiration was due to increases in both plant-related and microbial respiration (n = 9) and continued for at least 25 years (n = 136). The magnitude of the warming effects on respiration was driven by variation in warming-induced changes in local soil conditions, that is, changes in total nitrogen concentration and pH and by context-dependent spatial variation in these conditions, in particular total nitrogen concentration and the carbon:nitrogen ratio. Tundra sites with stronger nitrogen limitations and sites in which warming had stimulated plant and microbial nutrient turnover seemed particularly sensitive in their respiration response to warming. The results highlight the importance of local soil conditions and warming-induced changes therein for future climatic impacts on respiration.}, }
@article {pmid38632405, year = {2024}, author = {Swain, A and Woodhouse, A and Fagan, WF and Fraass, AJ and Lowery, CM}, title = {Biogeographic response of marine plankton to Cenozoic environmental changes.}, journal = {Nature}, volume = {629}, number = {8012}, pages = {616-623}, pmid = {38632405}, issn = {1476-4687}, mesh = {Animals ; *Aquatic Organisms/physiology/classification ; Biodiversity ; Biological Evolution ; *Climate Change/history ; Datasets as Topic ; Extinction, Biological ; *Foraminifera/classification/physiology ; History, Ancient ; *Phylogeography ; *Plankton/classification/physiology ; Spatio-Temporal Analysis ; }, abstract = {In palaeontological studies, groups with consistent ecological and morphological traits across a clade's history (functional groups)[1] afford different perspectives on biodiversity dynamics than do species and genera[2,3], which are evolutionarily ephemeral. Here we analyse Triton, a global dataset of Cenozoic macroperforate planktonic foraminiferal occurrences[4], to contextualize changes in latitudinal equitability gradients[1], functional diversity, palaeolatitudinal specialization and community equitability. We identify: global morphological communities becoming less specialized preceding the richness increase after the Cretaceous-Palaeogene extinction; ecological specialization during the Early Eocene Climatic Optimum, suggesting inhibitive equatorial temperatures during the peak of the Cenozoic hothouse; increased specialization due to circulation changes across the Eocene-Oligocene transition, preceding the loss of morphological diversity; changes in morphological specialization and richness about 19 million years ago, coeval with pelagic shark extinctions[5]; delayed onset of changing functional group richness and specialization between hemispheres during the mid-Miocene plankton diversification. The detailed nature of the Triton dataset permits a unique spatiotemporal view of Cenozoic pelagic macroevolution, in which global biogeographic responses of functional communities and richness are decoupled during Cenozoic climate events. The global response of functional groups to similar abiotic selection pressures may depend on the background climatic state (greenhouse or icehouse) to which a group is adapted.}, }
@article {pmid38632210, year = {2024}, author = {Griesberger, P and Kunz, F and Hackländer, K and Mattsson, B}, title = {Building a decision-support tool to inform sustainability approaches under complexity: Case study on managing wild ruminants.}, journal = {Ambio}, volume = {53}, number = {9}, pages = {1307-1322}, pmid = {38632210}, issn = {1654-7209}, mesh = {Animals ; *Conservation of Natural Resources/methods ; *Animals, Wild ; *Decision Support Techniques ; *Bayes Theorem ; *Ruminants ; Austria ; Decision Making ; }, abstract = {In wildlife management, differing perspectives among stakeholders generate conflicts about how to achieve disparate sustainability goals that include ecological, economic, and sociocultural dimensions. To mitigate such conflicts, decisions regarding wildlife management must be taken thoughtfully. To our knowledge, there exists no integrative modeling framework to inform these decisions, considering all dimensions of sustainability. We constructed a decision-support tool based on stakeholder workshops and a Bayesian decision network to inform management of wild ruminants in the federal state of Lower Austria. We use collaborative decision analysis to compare resource allocations while accounting for trade-offs among dimensions of sustainability. The tool is designed for application by non-technical users across diverse decision-making contexts with particular sets of wildlife management actions, objectives, and uncertainties. Our tool represents an important step toward developing and evaluating a transparent and replicable approach for mitigating wildlife-based conflicts in Europe and beyond.}, }
@article {pmid38630866, year = {2024}, author = {Ma, L and Hu, Z and Shen, W and Zhang, Y and Wang, G and Chang, B and Lu, J and Cui, Y and Xu, H and Feng, Y and Jin, B and Zhang, X and Wang, L and Lin, J}, title = {Three-dimensional reconstruction and multiomics analysis reveal a unique pattern of embryogenesis in Ginkgo biloba.}, journal = {Plant physiology}, volume = {196}, number = {1}, pages = {95-111}, doi = {10.1093/plphys/kiae219}, pmid = {38630866}, issn = {1532-2548}, support = {5232016//Beijing Municipal Natural Science Foundation/ ; 32000558//National Natural Science Foundation of China/ ; BLX202116//Fundamental Research Funds for the Central Universities/ ; B13007//Program of Introducing Talents of Discipline to Universities/ ; }, mesh = {*Ginkgo biloba/genetics/embryology ; *Seeds/genetics/growth &amp; development ; Imaging, Three-Dimensional/methods ; Gene Expression Regulation, Plant ; Plant Proteins/metabolism/genetics ; X-Ray Microtomography ; Cotyledon/genetics ; Multiomics ; }, abstract = {Ginkgo (Ginkgo biloba L.) is one of the earliest extant species in seed plant phylogeny. Embryo development patterns can provide fundamental evidence for the origin, evolution, and adaptation of seeds. However, the architectural and morphological dynamics during embryogenesis in G. biloba remain elusive. Herein, we obtained over 2,200 visual slices from 3 stages of embryo development using micro-computed tomography imaging with improved staining methods. Based on 3-dimensional (3D) spatiotemporal pattern analysis, we found that a shoot apical meristem with 7 highly differentiated leaf primordia, including apical and axillary leaf buds, is present in mature Ginkgo embryos. 3D rendering from the front, top, and side views showed 2 separate transport systems of tracheids located in the hypocotyl and cotyledon, representing a unique pattern of embryogenesis. Furthermore, the morphological dynamic analysis of secretory cavities indicated their strong association with cotyledons during development. In addition, we identified genes GbLBD25a (lateral organ boundaries domain 25a), GbCESA2a (cellulose synthase 2a), GbMYB74c (myeloblastosis 74c), GbPIN2 (PIN-FORMED 2) associated with vascular development regulation, and GbWRKY1 (WRKYGOK 1), GbbHLH12a (basic helix-loop-helix 12a), and GbJAZ4 (jasmonate zim-domain 4) potentially involved in the formation of secretory cavities. Moreover, we found that flavonoid accumulation in mature embryos could enhance postgerminative growth and seedling establishment in harsh environments. Our 3D spatial reconstruction technique combined with multiomics analysis opens avenues for investigating developmental architecture and molecular mechanisms during embryogenesis and lays the foundation for evolutionary studies of embryo development and maturation.}, }
@article {pmid38629556, year = {2024}, author = {Dai, WT and Zhang, H and Wu, X and Zhong, M and Duan, GL and Dong, JH and Zhang, PP and Fan, HM}, title = {[Pollution Characteristics and Source Analysis of Soil Heavy Metal in Coal Mine Area near the Yellow River in Shandong].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {45}, number = {5}, pages = {2952-2961}, doi = {10.13227/j.hjkx.202306029}, pmid = {38629556}, issn = {0250-3301}, abstract = {To explore the pollution characteristics and source of soil heavy metal in a coal mine area near the Yellow River in Shandong, the geo-accumulation index method and improved Nemerow pollution index method were used to evaluate the pollution characteristics of soil heavy metal. The absolute principal component-multiple linear regression model (APCS-MLR) was used to quantitatively analyze the source of soil heavy metal, and the spatial distribution of Hg and Cd were analyzed using the Kriging spatial difference method in ArcGIS. The result accuracy of the APCS-MLR model was further verified. The results showed that:The measured contents of soil heavy metal Cu, Zn, Pb, Cr, Cd, Ni, As, and Hg all exceeded the normal site, among which, Hg and Cd exceeded the background values of soil elements in Shandong. The coefficient of variation (CV) of Hg was higher than 0.500, indicating significant spatial heterogeneity. Moreover, the correlation between Hg and other heavy metals was generally low, and the possibility of the same pollution source was small. The results of the geo-accumulation index and improved Nemerow pollution index showed that the overall soil heavy metal pollution was at a moderate level, among which the Hg pollution level was the highest, and its maximum value was at a slanted-heavy pollution level; Cu, Cd, and As in soil caused local pollution, which were at a slanted-light pollution level. Soil heavy metal pollution was closely related to mining activities, rehabilitation, and engineering construction in the coal mine area. The two major pollution sources of soil heavy metal in the research area were the compound source of the parent material and industrial and mining transportation sources (known source 1) and the compound source of atmospheric sedimentation and coal production (known source 2), the contribution rates of which were 76.705% and 16.171%, respectively. The results of the APCS-MLR model were shown to be reliable by analyzing the content distribution of Hg and Cd using the Kriging space difference mode. This research can provide scientific basis for the precise control and improvement of soil heavy metal pollution, ensuring the safety of food and agricultural products and improving the quality of the ecological environment in the coal mine area in the Shandong section of the Yellow River Basin.}, }
@article {pmid38629131, year = {2024}, author = {Reginato, M and Ordónez-Parra, CA and Messeder, JVS and Brito, VLG and Dellinger, A and Kriebel, R and Marra, C and Melo, L and Cornelissen, T and Fuzessy, L and Sperotto, P and Calderón-Hernández, M and Guerra, TJ and Kopper, C and Mancipe-Murillo, C and Pizo, MA and Posada-Herrera, JM and Hasui, &#xc9; and Silva, WR and Silveira, FAO}, title = {MelastomaTRAITs 1.0: A database of functional traits in Melastomataceae, a large pantropical angiosperm family.}, journal = {Ecology}, volume = {105}, number = {6}, pages = {e4308}, doi = {10.1002/ecy.4308}, pmid = {38629131}, issn = {1939-9170}, support = {//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; FWF P-30669 T-1186//Austrian Science Fund/ ; //Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; //Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; //Fulbright Association/ ; }, mesh = {*Databases, Factual ; Ecosystem ; *Melastomataceae/physiology/genetics ; }, abstract = {The recent availability of open-access repositories of functional traits has revolutionized trait-based approaches in ecology and evolution. Nevertheless, the underrepresentation of tropical regions and lineages remains a pervasive bias in plant functional trait databases, which constrains large-scale assessments of plant ecology, evolution, and biogeography. Here, we present MelastomaTRAITs 1.0, a comprehensive and updatable database of functional traits for the pantropical Melastomataceae, the ninth-largest angiosperm family with 177 genera and more than 5800 species. Melastomataceae encompass species with a wide diversity of growth forms (herbs, shrubs, trees, epiphytes, and woody climbers), habitats (including tropical forests, savannas, grasslands, and wetlands from sea level to montane areas above the treeline), ecological strategies (from pioneer, edge-adapted and invasive species to shade-tolerant understory species), geographic distribution (from microendemic to continental-wide distribution), reproductive, pollination, and seed dispersal systems. MelastomaTRAITs builds on 581 references, such as taxonomic monographs, ecological research, and unpublished data, and includes four whole-plant traits, six leaf traits, 11 flower traits, 18 fruit traits, and 27 seed traits for 2520 species distributed in 144 genera across all 21 tribes. Most data come from the Neotropics where the family is most species-rich. Miconieae (the largest tribe) contains the highest number of trait records (49.6%) and species (41.1%) records. The trait types with the most information in the database were whole-plant traits, flowers, and leaf traits. With the breadth of functional traits recorded, our database helps to fill a gap in information for tropical plants and will significantly improve our capacity for large-scale trait-based syntheses across levels of organization, plant-animal interactions, regeneration ecology, and thereby support conservation and restoration programs. There are no copyright restrictions on the dataset; please cite this data paper when reusing the data.}, }
@article {pmid38627476, year = {2024}, author = {Ridley, RS and Conrad, RE and Lindner, BG and Woo, S and Konstantinidis, KT}, title = {Potential routes of plastics biotransformation involving novel plastizymes revealed by global multi-omic analysis of plastic associated microbes.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {8798}, pmid = {38627476}, issn = {2045-2322}, support = {2136146//National Science Foundation/ ; }, mesh = {Humans ; *Multiomics ; *Plastics ; Polymers ; Biotransformation ; Biodegradation, Environmental ; }, abstract = {Despite increasing efforts across various disciplines, the fate, transport, and impact of synthetic plastics on the environment and public health remain poorly understood. To better elucidate the microbial ecology of plastic waste and its potential for biotransformation, we conducted a large-scale analysis of all publicly available meta-omic studies investigating plastics (n = 27) in the environment. Notably, we observed low prevalence of known plastic degraders throughout most environments, except for substantial enrichment in riverine systems. This indicates rivers may be a highly promising environment for discovery of novel plastic bioremediation products. Ocean samples associated with degrading plastics showed clear differentiation from non-degrading polymers, showing enrichment of novel putative biodegrading taxa in the degraded samples. Regarding plastisphere pathogenicity, we observed significant enrichment of antimicrobial resistance genes on plastics but not of virulence factors. Additionally, we report a co-occurrence network analysis of 10 + million proteins associated with the plastisphere. This analysis revealed a localized sub-region enriched with known and putative plastizymes-these may be useful for deeper investigation of nature's ability to biodegrade man-made plastics. Finally, the combined data from our meta-analysis was used to construct a publicly available database, the Plastics Meta-omic Database (PMDB)-accessible at plasticmdb.org. These data should aid in the integrated exploration of the microbial plastisphere and facilitate research efforts investigating the fate and bioremediation potential of environmental plastic waste.}, }
@article {pmid38627422, year = {2024}, author = {Hammoud, R and Tognin, S and Smythe, M and Gibbons, J and Davidson, N and Bakolis, I and Mechelli, A}, title = {Smartphone-based ecological momentary assessment reveals an incremental association between natural diversity and mental wellbeing.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {7051}, pmid = {38627422}, issn = {2045-2322}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Smartphone ; *Ecological Momentary Assessment ; Mental Health ; Trees ; Biodiversity ; }, abstract = {Using smartphone-based ecological momentary assessment, this study investigated an association between natural diversity on mental wellbeing. A sample of 1,998 participants completed 41,448 assessments between April 2018 and September 2023. Environments which included a larger range of natural features, such as trees, plants and birdlife (high natural diversity) were associated with greater mental wellbeing than environments including a smaller range of natural features (low natural diversity). There was evidence of a mediating effect of natural diversity on the association between natural environments and mental wellbeing. These results highlight the importance of policies and practices that support richness of biodiversity for public mental health.}, }
@article {pmid38625737, year = {2024}, author = {Jonathan, J and Barakabitze, AA and Fast, CD and Cox, C}, title = {Machine Learning for Prediction of Tuberculosis Detection: Case Study of Trained African Giant Pouched Rats.}, journal = {Online journal of public health informatics}, volume = {16}, number = {}, pages = {e50771}, pmid = {38625737}, issn = {1947-2579}, abstract = {BACKGROUND: Technological advancement has led to the growth and rapid increase of tuberculosis (TB) medical data generated from different health care areas, including diagnosis. Prioritizing better adoption and acceptance of innovative diagnostic technology to reduce the spread of TB significantly benefits developing countries. Trained TB-detection rats are used in Tanzania and Ethiopia for operational research to complement other TB diagnostic tools. This technology has increased new TB case detection owing to its speed, cost-effectiveness, and sensitivity.<br><br>OBJECTIVE: During the TB detection process, rats produce vast amounts of data, providing an opportunity to identify interesting patterns that influence TB detection performance. This study aimed to develop models that predict if the rat will hit (indicate the presence of TB within) the sample or not using machine learning (ML) techniques. The goal was to improve the diagnostic accuracy and performance of TB detection involving rats.<br><br>METHODS: APOPO (Anti-Persoonsmijnen Ontmijnende Product Ontwikkeling) Center in Morogoro provided data for this study from 2012 to 2019, and 366,441 observations were used to build predictive models using ML techniques, including decision tree, random forest, na&#xef;ve Bayes, support vector machine, and k-nearest neighbor, by incorporating a variety of variables, such as the diagnostic results from partner health clinics using methods endorsed by the World Health Organization (WHO).<br><br>RESULTS: The support vector machine technique yielded the highest accuracy of 83.39% for prediction compared to other ML techniques used. Furthermore, this study found that the inclusion of variables related to whether the sample contained TB or not increased the performance accuracy of the predictive model.<br><br>CONCLUSIONS: The inclusion of variables related to the diagnostic results of TB samples may improve the detection performance of the trained rats. The study results may be of importance to TB-detection rat trainers and TB decision-makers as the results may prompt them to take action to maintain the usefulness of the technology and increase the TB detection performance of trained rats.}, }
@article {pmid38622188, year = {2024}, author = {Liu, X and Chen, J and Tang, BH and He, L and Xu, Y and Yang, C}, title = {Eco-environmental changes due to human activities in the Erhai Lake Basin from 1990 to 2020.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {8646}, pmid = {38622188}, issn = {2045-2322}, support = {42301454//National Natural Science Foundation of China/ ; 42230109//National Natural Science Foundation of China/ ; 42201319//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Lakes ; *Sustainable Development ; Human Activities ; China ; Environmental Monitoring/methods ; }, abstract = {Human activities have increased with urbanisation in the Erhai Lake Basin, considerably impacting its eco-environmental quality (EEQ). This study aims to reveal the evolution and driving forces of the EEQ using water benefit-based ecological index (WBEI) in response to human activities and policy variations in the Erhai Lake Basin from 1990 to 2020. Results show that (1) the EEQ exhibited a pattern of initial degradation, subsequent improvement, further degradation and a rebound from 1990 to 2020, and the areas with poor and fair EEQ levels mainly concentrated around the Erhai Lake Basin with a high level of urbanisation and relatively flat terrain; (2) the EEQ levels were not optimistic in 1990, 1995 and 2015, and areas with poor and fair EEQ levels accounted for 43.41%, 47.01% and 40.05% of the total area, respectively; and (3) an overall improvement in the EEQ was observed in 1995-2000, 2000-2005, 2005-2009 and 2015-2020, and the improvement was most significant in 1995-2000, covering an area of 823.95 km[2] and accounting for 31.79% of the total area. Results also confirmed that the EEQ changes in the Erhai Lake Basin were primarily influenced by human activities and policy variations. Moreover, these results can provide a scientific basis for the formulation and planning of sustainable development policy in the Erhai Lake Basin.}, }
@article {pmid38621404, year = {2024}, author = {Turtle, L and Elliot, S and Drake, TM and Thorpe, M and Khoury, EG and Greenhalf, W and Hardwick, HE and Leeming, G and Law, A and Oosthuyzen, W and Pius, R and Shaw, CA and Baillie, JK and Openshaw, PJM and Docherty, AB and Semple, MG and Harrison, EM and Palmieri, C and , }, title = {Changes in hospital mortality in patients with cancer during the COVID-19 pandemic (ISARIC-CCP-UK): a prospective, multicentre cohort study.}, journal = {The Lancet. Oncology}, volume = {25}, number = {5}, pages = {636-648}, doi = {10.1016/S1470-2045(24)00107-4}, pmid = {38621404}, issn = {1474-5488}, support = {MR/Y033736/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; *COVID-19/mortality/epidemiology ; *Neoplasms/mortality/therapy ; Male ; Female ; Prospective Studies ; Aged ; Middle Aged ; *Hospital Mortality ; United Kingdom/epidemiology ; *SARS-CoV-2 ; Adult ; Aged, 80 and over ; Pandemics ; }, abstract = {BACKGROUND: Patients with cancer are at greater risk of dying from COVID-19 than many other patient groups. However, how this risk evolved during the pandemic remains unclear. We aimed to determine, on the basis of the UK national pandemic protocol, how factors influencing hospital mortality from COVID-19 could differentially affect patients undergoing cancer treatment. We also examined changes in hospital mortality and escalation of care in patients on cancer treatment during the first 2 years of the COVID-19 pandemic in the UK.<br><br>METHODS: We conducted a prospective cohort study of patients aged older than 19 years and admitted to 306 health-care facilities in the UK with confirmed SARS-CoV-2 infection, who were enrolled in the International Severe Acute Respiratory and emerging Infections Consortium (ISARIC) WHO Clinical Characterisation Protocol (CCP) across the UK from April 23, 2020, to Feb 28, 2022; this analysis included all patients in the complete dataset when the study closed. The primary outcome was 30-day in-hospital mortality, comparing patients on cancer treatment and those without cancer. The study was approved by the South Central-Oxford C Research Ethics Committee in England (Ref: 13/SC/0149) and the Scotland A Research Ethics Committee (Ref 20/SS/0028), and is registered on the ISRCTN Registry (ISRCTN66726260).<br><br>FINDINGS: 177&#x2008;871 eligible adult patients either with no history of cancer (n=171&#x2008;303) or on cancer treatment (n=6568) were enrolled; 93&#x2008;205 (52&#xb7;4%) were male, 84&#x2008;418 (47&#xb7;5%) were female, and in 248 (13&#xb7;9%) sex or gender details were not specified or data were missing. Patients were followed up for a median of 13 (IQR 6-21) days. Of the 6568 patients receiving cancer treatment, 2080 (31&#xb7;7%) died at 30 days, compared with 30&#x2008;901 (18&#xb7;0%) of 171&#x2008;303 patients without cancer. Patients aged younger than 50 years on cancer treatment had the highest age-adjusted relative risk (hazard ratio [HR] 5&#xb7;2 [95% CI 4&#xb7;0-6&#xb7;6], p<0&#xb7;0001; vs 50-69 years 2&#xb7;4 [2&#xb7;2-2&#xb7;6], p<0&#xb7;0001; 70-79 years 1&#xb7;8 [1&#xb7;6-2&#xb7;0], p<0&#xb7;0001; and >80 years 1&#xb7;5 [1&#xb7;3-1&#xb7;6], p<0&#xb7;0001) but a lower absolute risk (51 [6&#xb7;7%] of 763 patients <50 years died compared with 459 [30&#xb7;2%] of 1522 patients aged >80 years). In-hospital mortality decreased for all patients during the pandemic but was higher for patients on cancer treatment than for those without cancer throughout the study period.<br><br>INTERPRETATION: People with cancer have a higher risk of mortality from COVID-19 than those without cancer. Patients younger than 50 years with cancer treatment have the highest relative risk of death. Continued action is needed to mitigate the poor outcomes in patients with cancer, such as through optimising vaccination, long-acting passive immunisation, and early access to therapeutics. These findings underscore the importance of the ISARIC-WHO pandemic preparedness initiative.<br><br>FUNDING: National Institute for Health Research and the Medical Research Council.}, }
@article {pmid38618197, year = {2023}, author = {Short, S and Green Etxabe, A and Robinson, A and Spurgeon, D and Kille, P and ,  and ,  and ,  and , }, title = {The genome sequence of the red compost earthworm, Lumbricus rubellus (Hoffmeister, 1843).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {354}, pmid = {38618197}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual Lumbricus rubellus (the red compost earthworm; Annelida; Clitellata; Haplotaxida; Lumbricidae). The genome sequence is 787.5 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.81 kilobases in length. Gene annotation of this assembly on Ensembl identified 33,426 protein coding genes.}, }
@article {pmid38617028, year = {2024}, author = {Liu, J and He, C and Si, Y and Li, B and Wu, Q and Ni, J and Zhao, Y and Hu, Q and Du, S and Lu, Z and Jin, J and Xu, C}, title = {Toward Better and Healthier Air Quality: Global PM2.5 and O3 Pollution Status and Risk Assessment Based on the New WHO Air Quality Guidelines for 2021.}, journal = {Global challenges (Hoboken, NJ)}, volume = {8}, number = {4}, pages = {2300258}, pmid = {38617028}, issn = {2056-6646}, abstract = {To reduce the high burden of disease caused by air pollution, the World Health Organization (WHO) released new Air Quality Guidelines (AQG) on September 22, 2021. In this study, the daily fine particulate matter (PM2.5) and surface ozone (O3) data of 618 cities around the world is collected from 2019 to 2022. Based on the new AQG, the number of attainment days for daily average concentrations of PM2.5 (≤ 15 µg m[-3]) and O3 (≤ 100 µg m[-3]) is approximately 10% and 90%, respectively. China and India exhibit a decreasing trend in the number of highly polluted days (> 75 µg m[-3]) for PM. Every year over 68% and 27% of cities in the world are exposed to harmful PM2.5 (> 35 µg m[-3]) and O3 (> 100 µg m[-3]) pollution, respectively. Combined with the United Nations Sustainable Development Goals (SDGs), it is found that more than 35% of the world's cities face PM2.5-O3 compound pollution. Furthermore, the exposure risks in these cities (China, India, etc.) are mainly categorized as "High Risk", "Risk", and "Stabilization". In contrast, economically developed cities are mainly categorized as "High Safety", "Safety", and "Deep Stabilization." These findings indicate that global implementation of the WHO's new AQG will minimize the inequitable exposure risk from air pollution.}, }
@article {pmid38616489, year = {2024}, author = {Bleker, C and Ramšak, &#x17d; and Bittner, A and Podpečan, V and Zagorščak, M and Wurzinger, B and Baebler, &#x160; and Petek, M and Križnik, M and van Dieren, A and Gruber, J and Afjehi-Sadat, L and Weckwerth, W and Županič, A and Teige, M and Vothknecht, UC and Gruden, K}, title = {Stress Knowledge Map: A knowledge graph resource for systems biology analysis of plant stress responses.}, journal = {Plant communications}, volume = {5}, number = {6}, pages = {100920}, pmid = {38616489}, issn = {2590-3462}, mesh = {*Systems Biology ; *Stress, Physiological ; *Plants/genetics/metabolism ; Plant Physiological Phenomena/genetics ; Signal Transduction/genetics ; Databases, Factual ; }, abstract = {Stress Knowledge Map (SKM; https://skm.nib.si) is a publicly available resource containing two complementary knowledge graphs that describe the current knowledge of biochemical, signaling, and regulatory molecular interactions in plants: a highly curated model of plant stress signaling (PSS; 543 reactions) and a large comprehensive knowledge network (488 390 interactions). Both were constructed by domain experts through systematic curation of diverse literature and database resources. SKM provides a single entry point for investigations of plant stress response and related growth trade-offs, as well as interactive explorations of current knowledge. PSS is also formulated as a qualitative and quantitative model for systems biology and thus represents a starting point for a plant digital twin. Here, we describe the features of SKM and show, through two case studies, how it can be used for complex analyses, including systematic hypothesis generation and design of validation experiments, or to gain new insights into experimental observations in plant biology.}, }
@article {pmid38616247, year = {2024}, author = {Kibet, CK and Entfellner, JD and Jjingo, D and de Villiers, EP and de Villiers, S and Wambui, K and Kinyanjui, S and Masiga, D}, title = {Designing and delivering bioinformatics project-based learning in East Africa.}, journal = {BMC bioinformatics}, volume = {25}, number = {1}, pages = {150}, pmid = {38616247}, issn = {1471-2105}, support = {U2R TW010677/TW/FIC NIH HHS/United States ; U2RTW010677/TW/FIC NIH HHS/United States ; }, mesh = {Humans ; *Learning ; Africa, Eastern ; *COVID-19/epidemiology ; Computational Biology ; Pandemics ; }, abstract = {BACKGROUND: The Eastern Africa Network for Bioinformatics Training (EANBiT) has matured through continuous evaluation, feedback, and codesign. We highlight how the program has evolved to meet challenges and achieve its goals and how experiential learning through mini projects enhances the acquisition of skills and collaboration. We continued to learn and grow through honest feedback and evaluation of the program, trainers, and modules, enabling us to provide robust training even during the Coronavirus disease 2019 (COVID-19) pandemic, when we had to redesign the program due to restricted travel and in person group meetings.<br><br>RESULTS: In response to the pandemic, we developed a program to maintain "residential" training experiences and benefits remotely. We had to answer the following questions: What must change to still achieve the RT goals? What optimal platforms should be used? How would we manage connectivity and data challenges? How could we avoid online fatigue? Going virtual presented an opportunity to reflect on the essence and uniqueness of the program and its ability to meet the objective of strengthening bioinformatics skills among the cohorts of students using different delivery approaches. It allowed an increase in the number of participants. Evaluating each program component is critical for improvement, primarily when feedback feeds into the program's continuous amendment. Initially, the participants noted that there were too many modules, insufficient time, and a lack of hands-on training as a result of too much focus on theory. In the subsequent iterations, we reduced the number of modules from 27 to five, created a harmonized repository for the materials on GitHub, and introduced project-based learning through the mini projects.<br><br>CONCLUSION: We demonstrate that implementing a program design through detailed monitoring and evaluation leads to success, especially when participants who are the best fit for the program are selected on an appropriate level of skills, motivation, and commitment.}, }
@article {pmid38614075, year = {2024}, author = {Breeyear, JH and Mautz, BS and Keaton, JM and Hellwege, JN and Torstenson, ES and Liang, J and Bray, MJ and Giri, A and Warren, HR and Munroe, PB and Velez Edwards, DR and Zhu, X and Li, C and Edwards, TL}, title = {A new test for trait mean and variance detects unreported loci for blood-pressure variation.}, journal = {American journal of human genetics}, volume = {111}, number = {5}, pages = {954-965}, pmid = {38614075}, issn = {1537-6605}, support = {U01 HG006378/HG/NHGRI NIH HHS/United States ; U19 HL065962/HL/NHLBI NIH HHS/United States ; S10 RR025141/RR/NCRR NIH HHS/United States ; R01 HG004517/HG/NHGRI NIH HHS/United States ; TL1 TR002244/TR/NCATS NIH HHS/United States ; U01 HG008672/HG/NHGRI NIH HHS/United States ; U01 HG008684/HG/NHGRI NIH HHS/United States ; U01 HG008679/HG/NHGRI NIH HHS/United States ; RC2 GM092618/GM/NIGMS NIH HHS/United States ; P50 GM115305/GM/NIGMS NIH HHS/United States ; U01 HG006379/HG/NHGRI NIH HHS/United States ; U01 HG008664/HG/NHGRI NIH HHS/United States ; U01 HG008701/HG/NHGRI NIH HHS/United States ; U01 HG008676/HG/NHGRI NIH HHS/United States ; UL1 TR000445/TR/NCATS NIH HHS/United States ; F31 EY033663/EY/NEI NIH HHS/United States ; K12 HD043483/HD/NICHD NIH HHS/United States ; R01 HD074711/HD/NICHD NIH HHS/United States ; U01 HG008657/HG/NHGRI NIH HHS/United States ; U19 HL065962/HL/NHLBI NIH HHS/United States ; R01 HG004517/HG/NHGRI NIH HHS/United States ; U01 HG008666/HG/NHGRI NIH HHS/United States ; R01 HD074711/HD/NICHD NIH HHS/United States ; U01 HG004798/HG/NHGRI NIH HHS/United States ; K12 HD043483/HD/NICHD NIH HHS/United States ; U01 HG008680/HG/NHGRI NIH HHS/United States ; U01 HG006378/HG/NHGRI NIH HHS/United States ; UL1 RR024975/RR/NCRR NIH HHS/United States ; R01 AI093234/AI/NIAID NIH HHS/United States ; U01 HG008673/HG/NHGRI NIH HHS/United States ; R01 NS032830/NS/NINDS NIH HHS/United States ; U01 HG004798/HG/NHGRI NIH HHS/United States ; R21 HL121429/HL/NHLBI NIH HHS/United States ; R21 HL121429/HL/NHLBI NIH HHS/United States ; R01 NS032830/NS/NINDS NIH HHS/United States ; UL1 TR002243/TR/NCATS NIH HHS/United States ; U01 HG008685/HG/NHGRI NIH HHS/United States ; RC2 GM092618/GM/NIGMS NIH HHS/United States ; F31 EY033663/EY/NEI NIH HHS/United States ; }, mesh = {Humans ; *Blood Pressure/genetics ; *Quantitative Trait Loci ; *Genome-Wide Association Study ; Polymorphism, Single Nucleotide ; Models, Genetic ; Genotype ; Genetic Variation ; Computer Simulation ; Phenotype ; }, abstract = {Variability in quantitative traits has clinical, ecological, and evolutionary significance. Most genetic variants identified for complex quantitative traits have only a detectable effect on the mean of trait. We have developed the mean-variance test (MVtest) to simultaneously model the mean and log-variance of a quantitative trait as functions of genotypes and covariates by using estimating equations. The advantages of MVtest include the facts that it can detect effect modification, that multiple testing can follow conventional thresholds, that it is robust to non-normal outcomes, and that association statistics can be meta-analyzed. In simulations, we show control of type I error of MVtest over several alternatives. We identified 51 and 37 previously unreported associations for effects on blood-pressure variance and mean, respectively, in the UK Biobank. Transcriptome-wide association studies revealed 633 significant unique gene associations with blood-pressure mean variance. MVtest is broadly applicable to studies of complex quantitative traits and provides an important opportunity to detect novel loci.}, }
@article {pmid38613584, year = {2024}, author = {Kredics, L and Büchner, R and Balázs, D and Allaga, H and Kedves, O and Racić, G and Varga, A and Nagy, VD and Vágvölgyi, C and Sipos, G}, title = {Recent advances in the use of Trichoderma-containing multicomponent microbial inoculants for pathogen control and plant growth promotion.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {40}, number = {5}, pages = {162}, pmid = {38613584}, issn = {1573-0972}, mesh = {Humans ; *Agricultural Inoculants ; *Trichoderma ; Fertilizers ; *Pesticides ; Soil ; }, abstract = {Chemical pesticides and fertilizers are used in agricultural production worldwide to prevent damage from plant pathogenic microorganisms, insects, and nematodes, to minimize crop losses and to preserve crop quality. However, the use of chemical pesticides and fertilizers can severely pollute soil, water, and air, posing risks to the environment and human health. Consequently, developing new, alternative, environment-friendly microbial soil treatment interventions for plant protection and crop yield increase has become indispensable. Members of the filamentous fungal genus Trichoderma (Ascomycota, Sordariomycetes, Hypocreales) have long been known as efficient antagonists of plant pathogenic microorganisms based on various beneficial traits and abilities of these fungi. This minireview aims to discuss the advances in the field of Trichoderma-containing multicomponent microbiological inoculants based on recent experimental updates. Trichoderma strains can be combined with each other, with other fungi and/or with beneficial bacteria. The development and field performance of such inoculants will be addressed, focusing on the complementarity, synergy, and compatibility of their microbial components.}, }
@article {pmid38613177, year = {2024}, author = {Wan, JSH and Bonser, SP and Pang, CK and Fazlioglu, F and Rutherford, S}, title = {Adaptive responses to living in stressful habitats: Do invasive and native plant populations use different strategies?.}, journal = {Ecology letters}, volume = {27}, number = {4}, pages = {e14419}, doi = {10.1111/ele.14419}, pmid = {38613177}, issn = {1461-0248}, mesh = {Reproduction ; *Plant Physiological Phenomena ; *Stress, Physiological ; }, abstract = {Plants inhabit stressful environments characterized by a variety of stressors, including mine sites, mountains, deserts, and high latitudes. Populations from stressful and reference (non-stressful) sites often have performance differences. However, while invasive and native species may respond differently to stressful environments, there is limited understanding of the patterns in reaction norms of populations from these sites. Here, we use phylogenetically controlled meta-analysis to assess the performance of populations under stress and non-stress conditions. We ask whether stress populations of natives and invasives differ in the magnitude of lowered performance under non-stress conditions and if they vary in the degree of performance advantage under stress. We also assessed whether these distinctions differ with stress intensity. Our findings revealed that natives not only have greater adaptive advantages but also more performance reductions than invasives. Populations from very stressful sites had more efficient adaptations, and performance costs increased with stress intensity in natives only. Overall, the results support the notion that adaptation is frequently costless. Reproductive output was most closely associated with adaptive costs and benefits. Our study characterized the adaptive strategies used by invasive and native plants under stressful conditions, thereby providing important insights into the limitations of adaptation to extreme sites.}, }
@article {pmid38613081, year = {2024}, author = {Jeong, S and Choi, YJ}, title = {Association between Socioecological Status, Nutrient Intake, and Cancer Screening Behaviors in Adults Aged 40 and Over: Insights from the Eighth Korea National Health and Nutrition Examination Survey (KNHANES, 2019).}, journal = {Nutrients}, volume = {16}, number = {7}, pages = {}, pmid = {38613081}, issn = {2072-6643}, mesh = {Adult ; Humans ; Middle Aged ; *Early Detection of Cancer ; Nutrition Surveys ; Eating ; Energy Intake ; Republic of Korea ; *Neoplasms ; }, abstract = {Cancer screening is pivotal for early detection and improved survival rates. While socio-ecological factors are known to influence screening uptake, the role of lifestyle, dietary habits, and general health in shaping these decisions remains underexplored. Utilizing the 2019 Korea National Health and Nutrition Examination Survey (KNHANES), this study examined the myriad of factors impacting cancer screening utilization. Data from 274,872 adults aged 40 years or older were scrutinized, highlighting demographics, income, lifestyle behaviors, health-related variables, nutrient intake, and dietary quality. A combination of descriptive statistics and logistic regression helped us ascertain influential determinants. Higher educational attainment and income quartiles were positively correlated with cancer screening rates. Regular walkers, those engaged in moderate physical activity, and individuals with a previous cancer diagnosis were more likely to get screened. High-risk drinkers and smokers were less inclined towards screening. Dietary habits also influenced screening decisions. Notably, participants with healthier eating behaviors, indicated by factors such as regular breakfasts and fewer meals out, were more likely to undergo screening. Additionally, nutrient intake analysis revealed that those who had undergone screening consumed greater quantities of most nutrients, bar a few exceptions. For individuals aged 50-64, nutritional assessment indicators highlighted a higher mean adequacy ratio (MAR) and index of nutritional quality (INQ) value among those who participated in screening, suggesting better nutritional quality. This study elucidates the complex socio-ecological and nutritional landscape influencing cancer screening decisions. The results underscore the importance of a holistic approach, emphasizing lifestyle, dietary habits, and socio-economic considerations. It provides a roadmap for policymakers to craft more inclusive screening programs, ensuring equal access and promoting early detection.}, }
@article {pmid38612552, year = {2024}, author = {Jankovic, M and Knezevic, T and Tomic, A and Milicevic, O and Jovanovic, T and Djunic, I and Mihaljevic, B and Knezevic, A and Todorovic-Balint, M}, title = {Human Cytomegalovirus Oncoprotection across Diverse Populations, Tumor Histologies, and Age Groups: The Relevance for Prospective Vaccinal Therapy.}, journal = {International journal of molecular sciences}, volume = {25}, number = {7}, pages = {}, pmid = {38612552}, issn = {1422-0067}, support = {200110/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; Cytomegalovirus ; Prospective Studies ; Seroepidemiologic Studies ; *Neoplasms/epidemiology ; *Cytomegalovirus Infections/epidemiology ; }, abstract = {The oncogenicity of the human cytomegalovirus (CMV) is currently being widely debated. Most recently, mounting clinical evidence suggests an anti-cancer effect via CMV-induced T cell-mediated tumor destruction. However, the data were mostly obtained from single-center studies and in vitro experiments. Broad geographic coverage is required to offer a global perspective. Our study examined the correlation between country-specific CMV seroprevalence (across 73 countries) and the age-standardized incidence rate (of 34 invasive tumors). The populations studied were stratified according to decadal age periods as the immunologic effects of CMV seropositivity may depend upon age at initial infection. The International Agency for Research on Cancer of the World Health Organization (IARC WHO) database was used. The multivariate linear regression analysis revealed a worldwide inverse correlation between CMV seroprevalence and the incidences of 62.8% tumors. Notably, this inverse link persists for all cancers combined (Spearman's ρ = -0.732, p < 0.001; β = -0.482, p < 0.001, adjusted R[2] = 0.737). An antithetical and significant correlation was also observed in particular age groups for the vast majority of tumors. Our results corroborate the conclusions of previous studies and indicate that this oncopreventive phenomenon holds true on a global scale. It applies to a wide spectrum of cancer histologies, additionally supporting the idea of a common underlying mechanism-CMV-stimulated T cell tumor targeting. Although these results further advance the notion of CMV-based therapies, in-depth investigation of host-virus interactions is still warranted.}, }
@article {pmid38611576, year = {2024}, author = {Sulaiman, N and Salehi, F and Prakofjewa, J and Cavalleri, SAE and Ahmed, HM and Mattalia, G and Rastegar, A and Maghsudi, M and Amin, HM and Rasti, A and Hosseini, SH and Ghorbani, A and Pieroni, A and Sõukand, R}, title = {Cultural vs. State Borders: Plant Foraging by Hawraman and Mukriyan Kurds in Western Iran.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {7}, pages = {}, pmid = {38611576}, issn = {2223-7747}, abstract = {Plant foraging is a millennia-old activity still practiced by many people in the Middle East, particularly in the Fertile Crescent region, where several socioeconomic, ecological, and cultural factors shape this practice. This study seeks to understand the drivers of plant foraging in this complex region characterized by highly diverse linguistic, religious, and cultural groups. Our study aims to document the wild plants used by Kurds in Western Iran, identify similarities and differences among Hawraman and Mukriyan Kurdish groups in Iran, and compare our findings with a previous study on the Hawramani in Iraq. Forty-three semi-structured in-depth interviews were conducted in Kurdish villages of Western Iran. The results revealed the use of 44 wild food plant taxa, their preparation, and culinary uses. Among the reported taxa, 28 plant taxa were used by Mukriyani, and 33 by Hawramani. The study revealed a significant difference between the Hawraman and Mukriyan regions in Iran, whereas there is a high similarity between Hawramani Kurds in Iran and Iraq. We found that the invisible cultural border carries more weight than political divisions, and this calls for a paradigm shift in how we perceive and map the distribution of ethnobotanical knowledge.}, }
@article {pmid38609485, year = {2024}, author = {Kazlou, A and Bornukova, K and Wickham, A and Slaykovskiy, V and Peven, K and Klepchukova, A and Ponzo, S and Garfinkel, S}, title = {Effects of stress on pain in females using a mobile health app in the Russia-Ukraine conflict.}, journal = {Npj mental health research}, volume = {3}, number = {1}, pages = {2}, pmid = {38609485}, issn = {2731-4251}, support = {MR/V037676/1/MRC_/Medical Research Council/United Kingdom ; MR/V037676/1//MRC/NIHR/ ; }, abstract = {The chronic and acute effects of stress can have divergent effects on health; long-term effects are associated with detrimental physical and mental health sequelae, while acute effects may be advantageous in the short-term. Stress-induced analgesia, the attenuation of pain perception due to stress, is a well-known phenomenon that has yet to be systematically investigated under ecological conditions. Using Flo, a women's health and wellbeing app and menstrual cycle tracker, with a world-wide monthly active usership of more than 57 million, women in Ukraine were monitored for their reporting of stress, pain and affective symptoms before, and immediately after, the onset of the Russian-Ukrainian conflict. To avoid potential selection (attrition) or collider bias, we rely on a sample of 87,315 users who were actively logging multiple symptoms before and after the start of the war. We found an inverse relationship between stress and pain, whereby higher reports of stress predicted lower rates of pain. Stress did not influence any other physiological symptoms with a similar magnitude, nor did any other symptom have a similar effect on pain. This relationship generally decreased in magnitude in countries neighbouring and surrounding Ukraine, with Ukraine serving as the epicentre. These findings help characterise the relationship between stress and health in a real-world setting.}, }
@article {pmid38605417, year = {2024}, author = {Roder, T and Pimentel, G and Fuchsmann, P and Stern, MT and von Ah, U and Vergères, G and Peischl, S and Brynildsrud, O and Bruggmann, R and Bär, C}, title = {Scoary2: rapid association of phenotypic multi-omics data with microbial pan-genomes.}, journal = {Genome biology}, volume = {25}, number = {1}, pages = {93}, pmid = {38605417}, issn = {1474-760X}, support = {GRS-070/17//Gebert R&#xfc;f Stiftung/ ; }, mesh = {*Genome-Wide Association Study ; *Multiomics ; Phenotype ; Genes, Bacterial ; Genomics ; }, abstract = {Unraveling bacterial gene function drives progress in various areas, such as food production, pharmacology, and ecology. While omics technologies capture high-dimensional phenotypic data, linking them to genomic data is challenging, leaving 40-60% of bacterial genes undescribed. To address this bottleneck, we introduce Scoary2, an ultra-fast microbial genome-wide association studies (mGWAS) software. With its data exploration app and improved performance, Scoary2 is the first tool to enable the study of large phenotypic datasets using mGWAS. As proof of concept, we explore the metabolome of yogurts, each produced with a different Propionibacterium reichii strain and discover two genes affecting carnitine metabolism.}, }
@article {pmid38604487, year = {2024}, author = {Zhang, Y and Huang, C and Zhao, J and Hu, L and Yang, L and Zhang, Y and Sang, W}, title = {Insights into tolerance mechanisms of earthworms (Eisenia fetida) in copper-contaminated soils by integrating multi-omics analyses.}, journal = {Environmental research}, volume = {252}, number = {Pt 2}, pages = {118910}, doi = {10.1016/j.envres.2024.118910}, pmid = {38604487}, issn = {1096-0953}, mesh = {*Oligochaeta/metabolism/drug effects ; Animals ; *Soil Pollutants/toxicity/metabolism ; *Copper/toxicity/metabolism ; Gastrointestinal Microbiome/drug effects ; Metabolomics ; Oxidative Stress/drug effects ; Multiomics ; }, abstract = {Earthworms can resist high levels of soil copper (Cu) contamination and play an essential role in absorbing them effectively. However, the molecular mechanisms underlying Cu tolerance in earthworms are poorly understood. To address this research gap, we studied alterations of Eisenia fetida in antioxidant enzymes, gut microbiota, metabolites, and genes under varying levels of Cu exposure soils (0, 67.58, 168.96, 337.92 mg/kg). Our results revealed a reduction in antioxidant enzyme activities across all treatment groups, indicating an adaptive response to alleviate Cu-induced oxidative stress. Analysis of gut microbiota revealed a significant increase in the abundance of bacteria associated with nutrient uptake and Cu[2+] excretion under Cu stress. Furthermore, metabolomic analysis discovered an increase in certain metabolites associated with energy metabolism, such as pyruvic acid, L-malic acid, and fumaric acid, as Cu concentration escalated. These results suggested that enhanced energy supply contributes to the elevated tolerance of E. fetida towards Cu. Additionally, transcriptome analysis not only identified crucial detoxification genes (Hsp70, CTSL, GST, CHAC, and GCLC), but also confirmed the critical role of glutathione metabolism as a key pathway in E. fetida Cu detoxification processes. These findings provide a new perspective on the molecular mechanisms of Cu tolerance in earthworms.}, }
@article {pmid38602562, year = {2024}, author = {Nurkassimova, M and Omarova, N and Zinicovscaia, I and Yushin, N and Chaligava, O}, title = {Mosses as bioindicators of air pollution with potentially toxic elements in the Burabay State National Natural Park, Kazakhstan.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {5}, pages = {442}, pmid = {38602562}, issn = {1573-2959}, mesh = {Humans ; Environmental Biomarkers ; Parks, Recreational ; Kazakhstan ; Environmental Monitoring ; *Air Pollution ; *Bryophyta ; }, abstract = {The Burabay State National Natural Park is a national park of the great natural and historical values located in the north of Kazakhstan, which has been exposed in recent years to significant anthropogenic impact. The moss biomonitoring was performed in the Borovoye resort community, an important tourist destination in the national park, to identify the level of air pollution. Mosses collected at 29 locations were subjected to neutron activation analysis to determine 36 elements and additionally to ICP-OES to detect the level of Cu and Pb. Factor analysis was applied to check if there are any associations between identified elements and to link them with possible emission sources. According to contamination factor and pollution load indices the investigated area belongs to three classes of pollution: unpolluted, suspected and moderate. Potential ecological risk index calculated for selected elements revealed harmless risk to human health. The level of element obtained in Burabay State National Natural Park was compared with the data available for other national parks.}, }
@article {pmid38598963, year = {2024}, author = {Shen, C and Feng, G and Zhao, F and Huang, X and Li, X}, title = {The multi-omics analysis in the hepatopancreas of Eriocheir sinensis provides novel insights into the response mechanism of heat stress.}, journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics}, volume = {50}, number = {}, pages = {101232}, doi = {10.1016/j.cbd.2024.101232}, pmid = {38598963}, issn = {1878-0407}, mesh = {Animals ; *Hepatopancreas/metabolism ; *Brachyura/physiology/genetics/metabolism ; *Heat-Shock Response ; *Arthropod Proteins/genetics/metabolism ; *Proteomics ; Transcriptome ; Energy Metabolism ; Heat-Shock Proteins/genetics/metabolism ; Proteome ; Multiomics ; }, abstract = {Under global warming, heat stress can induce the excessive production of reactive oxygen species, causing irreversible damage to aquatic animals. It is essential to predict potentially harmful impacts on aquatic organisms under heat stress. Eriocheir sinensis, a typical crustacean crab, is widely distributed in China, American and Europe. Parent E. sinensis need migrate to the estuaries to reproduce in winter, and temperature is a key environmental factor. Herein, we performed a comprehensive transcriptomic and proteomic analysis in the hepatopancreas of E. sinensis under heat stress (20 °C and 30 °C), focusing on heat shock protein family, antioxidant system, energy metabolism and immune defense. The results revealed that parent E. sinensis generated adaptative responses to maintain physiological function under 20 °C stress via the transcriptional up-regulation of energy metabolism enzymes, mRNA synthesis and heat shock proteins. The transcriptional inhibition of key enzymes related to energy metabolism implied that 30 °C stress may lead to the dysfunction of energy metabolism in parent E. sinensis. Meanwhile, parent E. sinensis also enhanced the expression of ferritin and phospholipase D at translational level, and the glutathione s-transferase and heat shock protein 70 at both transcriptional and translational levels, speculating that parent E. sinensis can strengthen antioxidant and immune capacity to resist oxidative stress under 30 °C stress. This study elucidated the potential molecular mechanism in response to heat stress of parent E. sinensis hepatopancreas. The preliminary selection of heat tolerance genes or proteins in E. sinensis can provide a reference for the population prediction and the study of evolutionary mechanism under heat stress in crabs.}, }
@article {pmid38598334, year = {2024}, author = {Wei, X and Tsai, MS and Liang, L and Jiang, L and Hung, CJ and Jelliffe-Pawlowski, L and Rand, L and Snyder, M and Jiang, C}, title = {Vaginal microbiomes show ethnic evolutionary dynamics and positive selection of Lactobacillus adhesins driven by a long-term niche-specific process.}, journal = {Cell reports}, volume = {43}, number = {4}, pages = {114078}, doi = {10.1016/j.celrep.2024.114078}, pmid = {38598334}, issn = {2211-1247}, mesh = {Humans ; *Vagina/microbiology ; Female ; *Microbiota/genetics ; *Lactobacillus/genetics ; Adhesins, Bacterial/genetics ; Ethnicity/genetics ; Adult ; Evolution, Molecular ; Pregnancy ; Selection, Genetic ; Biological Evolution ; }, abstract = {The vaginal microbiome's composition varies among ethnicities. However, the evolutionary landscape of the vaginal microbiome in the multi-ethnic context remains understudied. We perform a systematic evolutionary analysis of 351 vaginal microbiome samples from 35 multi-ethnic pregnant women, in addition to two validation cohorts, totaling 462 samples from 90 women. Microbiome alpha diversity and community state dynamics show strong ethnic signatures. Lactobacillaceae have a higher ratio of non-synonymous to synonymous polymorphism and lower nucleotide diversity than non-Lactobacillaceae in all ethnicities, with a large repertoire of positively selected genes, including the mucin-binding and cell wall anchor genes. These evolutionary dynamics are driven by the long-term evolutionary process unique to the human vaginal niche. Finally, we propose an evolutionary model reflecting the environmental niches of microbes. Our study reveals the extensive ethnic signatures in vaginal microbial ecology and evolution, highlighting the importance of studying the host-microbiome ecosystem from an evolutionary perspective.}, }
@article {pmid38597343, year = {2024}, author = {Schwartz, LC and González, VL and Strong, EE and Truebano, M and Hilbish, TJ}, title = {Transgressive gene expression and expression plasticity under thermal stress in a stable hybrid zone.}, journal = {Molecular ecology}, volume = {33}, number = {9}, pages = {e17333}, doi = {10.1111/mec.17333}, pmid = {38597343}, issn = {1365-294X}, support = {//National Museum of Natural History/ ; //University of South Carolina/ ; }, mesh = {Animals ; *Hybridization, Genetic ; Temperature ; Climate Change ; Stress, Physiological/genetics ; Gene Expression/genetics ; Phenotype ; Mytilus/genetics ; Transcriptome ; }, abstract = {Interspecific hybridization can lead to myriad outcomes, including transgressive phenotypes in which the hybrids are more fit than either parent species. Such hybrids may display important traits in the context of climate change, able to respond to novel environmental conditions not previously experienced by the parent populations. While this has been evaluated in an agricultural context, the role of transgressive hybrids under changing conditions in the wild remains largely unexplored; this is especially true regarding transgressive gene expression. Using the blue mussel species complex (genus Mytilus) as a model system, we investigated the effects of hybridization on temperature induced gene expression plasticity by comparing expression profiles in parental species and their hybrids following a 2-week thermal challenge. Hybrid expression plasticity was most often like one parent or the other (50%). However, a large fraction of genes (26%) showed transgressive expression plasticity (i.e. the change in gene expression was either greater or lesser than that of both parent species), while only 2% were intermediately plastic in hybrids. Despite their close phylogenetic relationship, there was limited overlap in the differentially expressed genes responding to temperature, indicating interspecific differences in the responses to high temperature in which responses from hybrids are distinct from both parent species. We also identified differentially expressed long non-coding RNAs (lncRNAs), which we suggest may contribute to species-specific differences in thermal tolerance. Our findings provide important insight into the impact of hybridization on gene expression under warming. We propose transgressive hybrids may play an important role in population persistence under future warming conditions.}, }
@article {pmid38594342, year = {2024}, author = {Brodie, JF and Mohd-Azlan, J and Chen, C and Wearn, OR and Deith, MCM and Ball, JGC and Slade, EM and Burslem, DFRP and Teoh, SW and Williams, PJ and Nguyen, A and Moore, JH and Goetz, SJ and Burns, P and Jantz, P and Hakkenberg, CR and Kaszta, ZM and Cushman, S and Coomes, D and Helmy, OE and Reynolds, G and Rodríguez, JP and Jetz, W and Luskin, MS}, title = {Author Correction: Landscape-scale benefits of protected areas for tropical biodiversity.}, journal = {Nature}, volume = {628}, number = {8009}, pages = {E5}, doi = {10.1038/s41586-024-07333-z}, pmid = {38594342}, issn = {1476-4687}, }
@article {pmid38594221, year = {2024}, author = {Mujica, MI and Silva-Flores, P and Bueno, CG and Duchicela, J}, title = {Integrating perspectives in developing mycorrhizal trait databases: a call for inclusive and collaborative continental efforts.}, journal = {The New phytologist}, volume = {242}, number = {4}, pages = {1436-1440}, doi = {10.1111/nph.19754}, pmid = {38594221}, issn = {1469-8137}, support = {Ram&#xf3;n y Cajal fellowship #RYC2021-032533-I//Ministerio de Ciencia e Innovaci&#xf3;n/ ; 11230870//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; 3200774//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; }, mesh = {Biodiversity ; Databases, Factual ; *Mycorrhizae/physiology ; Quantitative Trait, Heritable ; *Symbiosis ; }, abstract = {Global assessments of mycorrhizal symbiosis present large sampling gaps in rich biodiversity regions. Filling these gaps is necessary to build large-scale, unbiased mycorrhizal databases to obtain reliable analyses and prevent misleading generalizations. Underrepresented regions in mycorrhizal research are mainly in Africa, Asia, and South America. Despite the high biodiversity and endemism in these regions, many groups of organisms remain understudied, especially mycorrhizal fungi. In this Viewpoint, we emphasize the importance of inclusive and collaborative continental efforts in integrating perspectives for comprehensive trait database development and propose a conceptual framework that can help build large mycorrhizal databases in underrepresented regions. Based on the four Vs of big data (volume, variety, veracity, and velocity), we identify the main challenges of constructing a large mycorrhizal dataset and propose solutions for each challenge. We share our collaborative methodology, which involves employing open calls and working groups to engage all mycorrhizal researchers in the region to build a South American Mycorrhizal Database. By fostering interdisciplinary collaborations and embracing a continental-scale approach, we can create robust mycorrhizal trait databases that provide valuable insights into the evolution, ecology, and functioning of mycorrhizal associations, reducing the geographical biases that are so common in large-scale ecological studies.}, }
@article {pmid38589621, year = {2024}, author = {Liew, F and Efstathiou, C and Fontanella, S and Richardson, M and Saunders, R and Swieboda, D and Sidhu, JK and Ascough, S and Moore, SC and Mohamed, N and Nunag, J and King, C and Leavy, OC and Elneima, O and McAuley, HJC and Shikotra, A and Singapuri, A and Sereno, M and Harris, VC and Houchen-Wolloff, L and Greening, NJ and Lone, NI and Thorpe, M and Thompson, AAR and Rowland-Jones, SL and Docherty, AB and Chalmers, JD and Ho, LP and Horsley, A and Raman, B and Poinasamy, K and Marks, M and Kon, OM and Howard, LS and Wootton, DG and Quint, JK and de Silva, TI and Ho, A and Chiu, C and Harrison, EM and Greenhalf, W and Baillie, JK and Semple, MG and Turtle, L and Evans, RA and Wain, LV and Brightling, C and Thwaites, RS and Openshaw, PJM and ,  and , }, title = {Large-scale phenotyping of patients with long COVID post-hospitalization reveals mechanistic subtypes of disease.}, journal = {Nature immunology}, volume = {25}, number = {4}, pages = {607-621}, pmid = {38589621}, issn = {1529-2916}, support = {MR/R502121/1/MRC_/Medical Research Council/United Kingdom ; MR/V027859/1/MRC_/Medical Research Council/United Kingdom ; MR/T50256X/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_20004/MRC_/Medical Research Council/United Kingdom ; MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; MC_PC_20029/MRC_/Medical Research Council/United Kingdom ; MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; MC_PC_20058/MRC_/Medical Research Council/United Kingdom ; MC_UU_12014/12/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MR/R005982/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; Post-Acute COVID-19 Syndrome ; *COVID-19 ; *Biomedical Research ; Hospitalization ; Immunoglobulin G ; }, abstract = {One in ten severe acute respiratory syndrome coronavirus 2 infections result in prolonged symptoms termed long coronavirus disease (COVID), yet disease phenotypes and mechanisms are poorly understood[1]. Here we profiled 368 plasma proteins in 657 participants ≥3 months following hospitalization. Of these, 426 had at least one long COVID symptom and 233 had fully recovered. Elevated markers of myeloid inflammation and complement activation were associated with long COVID. IL-1R2, MATN2 and COLEC12 were associated with cardiorespiratory symptoms, fatigue and anxiety/depression; MATN2, CSF3 and C1QA were elevated in gastrointestinal symptoms and C1QA was elevated in cognitive impairment. Additional markers of alterations in nerve tissue repair (SPON-1 and NFASC) were elevated in those with cognitive impairment and SCG3, suggestive of brain-gut axis disturbance, was elevated in gastrointestinal symptoms. Severe acute respiratory syndrome coronavirus 2-specific immunoglobulin G (IgG) was persistently elevated in some individuals with long COVID, but virus was not detected in sputum. Analysis of inflammatory markers in nasal fluids showed no association with symptoms. Our study aimed to understand inflammatory processes that underlie long COVID and was not designed for biomarker discovery. Our findings suggest that specific inflammatory pathways related to tissue damage are implicated in subtypes of long COVID, which might be targeted in future therapeutic trials.}, }
@article {pmid38587202, year = {2024}, author = {Montfort, J and Hervas-Sotomayor, F and Le Cam, A and Murat, F}, title = {FEVER: an interactive web-based resource for evolutionary transcriptomics across fishes.}, journal = {Nucleic acids research}, volume = {52}, number = {W1}, pages = {W65-W69}, pmid = {38587202}, issn = {1362-4962}, support = {ANR-23-CE13-0008//ANR/ ; }, mesh = {Animals ; *Fishes/genetics ; *Evolution, Molecular ; *Transcriptome/genetics ; *Internet ; Gene Expression Profiling/methods ; Databases, Genetic ; Phylogeny ; Genomics/methods ; Software ; Genome/genetics ; }, abstract = {Teleost fish represent one of the largest and most diverse clades of vertebrates, which makes them great models in various research areas such as ecology and evolution. Recent sequencing endeavors provided high-quality genomes for species covering the main fish evolutionary lineages, opening up large-scale comparative genomics studies. However, transcriptomic data across fish species and organs are heterogenous and have not been integrated with newly sequenced genomes making gene expression quantification and comparative analyses particularly challenging. Thus, resources integrating genomic and transcriptomic data across fish species and organs are still lacking. Here, we present FEVER, a web-based resource allowing evolutionary transcriptomics across species and tissues. First, based on query genes FEVER reconstructs gene trees providing orthologous and paralogous relationships as well as their evolutionary dynamics across 13 species covering the major fish lineages, and 4 model species as evolutionary outgroups. Second, it provides unbiased gene expression across 11 tissues using up-to-date fish genomes. Finally, genomic and transcriptomic data are combined together allowing the exploration of gene expression evolution following speciation and duplication events. FEVER is freely accessible at https://fever.sk8.inrae.fr/.}, }
@article {pmid38584951, year = {2024}, author = {Badiyal, A and Mahajan, R and Rana, RS and Sood, R and Walia, A and Rana, T and Manhas, S and Jayswal, DK}, title = {Synergizing biotechnology and natural farming: pioneering agricultural sustainability through innovative interventions.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1280846}, pmid = {38584951}, issn = {1664-462X}, abstract = {The world has undergone a remarkable transformation from the era of famines to an age of global food production that caters to an exponentially growing population. This transformation has been made possible by significant agricultural revolutions, marked by the intensification of agriculture through the infusion of mechanical, industrial, and economic inputs. However, this rapid advancement in agriculture has also brought about the proliferation of agricultural inputs such as pesticides, fertilizers, and irrigation, which have given rise to long-term environmental crises. Over the past two decades, we have witnessed a concerning plateau in crop production, the loss of arable land, and dramatic shifts in climatic conditions. These challenges have underscored the urgent need to protect our global commons, particularly the environment, through a participatory approach that involves countries worldwide, regardless of their developmental status. To achieve the goal of sustainability in agriculture, it is imperative to adopt multidisciplinary approaches that integrate fields such as biology, engineering, chemistry, economics, and community development. One noteworthy initiative in this regard is Zero Budget Natural Farming, which highlights the significance of leveraging the synergistic effects of both plant and animal products to enhance crop establishment, build soil fertility, and promote the proliferation of beneficial microorganisms. The ultimate aim is to create self-sustainable agro-ecosystems. This review advocates for the incorporation of biotechnological tools in natural farming to expedite the dynamism of such systems in an eco-friendly manner. By harnessing the power of biotechnology, we can increase the productivity of agro-ecology and generate abundant supplies of food, feed, fiber, and nutraceuticals to meet the needs of our ever-expanding global population.}, }
@article {pmid38583934, year = {2024}, author = {Swanson, SA and Miller, M}, title = {Toward a clearer understanding of what works to reduce gun violence: the role of falsification strategies.}, journal = {American journal of epidemiology}, volume = {193}, number = {8}, pages = {1061-1065}, doi = {10.1093/aje/kwae036}, pmid = {38583934}, issn = {1476-6256}, mesh = {Humans ; *Gun Violence/prevention &amp; control/statistics &amp; numerical data ; United States ; *Firearms/legislation &amp; jurisprudence ; Data Interpretation, Statistical ; Homicide/prevention &amp; control/statistics &amp; numerical data ; Wounds, Gunshot/prevention &amp; control/epidemiology ; }, abstract = {Strong epidemiologic evidence from ecological and individual-level studies in the United States supports the claim that access to firearms substantially increases the risk of dying by suicide, homicide, and firearm accidents. Less certain is how well particular interventions work to prevent these deaths and other firearm-related harms. Given the limits of existing data to study firearm violence and the infeasibility of conducting randomized trials of firearm access, it is important to do the best we can with the data we already have. We argue that falsification strategies are a critical-yet underutilized-component of any such analytical approach. The falsification strategies we focus on are versions of "negative controls" analyses in which we expect that an analysis should yield a null causal effect, and thus where not obtaining a null effect estimate raises questions about the assumptions underlying causal interpretation of a study's findings. We illustrate the saliency of this issue today with examples drawn from studies published in leading peer-reviewed journals within the last 5 years. Collecting rich, high-quality data always takes time, urgent as the need may be. On the other hand, doing better with the data we already have can start right now.}, }
@article {pmid38582819, year = {2025}, author = {Li, M and Wu, L and Shi, Y and Wu, L and Afzal, F and Jia, Y and Huang, Y and Hu, B and Chen, J and Huang, J}, title = {Bioinformatics and Functional Analysis of OsASMT1 Gene in Response to Abiotic Stress.}, journal = {Biochemical genetics}, volume = {63}, number = {2}, pages = {1527-1540}, pmid = {38582819}, issn = {1573-4927}, support = {2023NSFSC1270//The Sichuan Natural Science Foundation Project/ ; SKL-KF202316//The Open Project Program of State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China/ ; }, mesh = {*Oryza/genetics/drug effects/metabolism ; Computational Biology ; *Stress, Physiological/genetics ; *Plant Proteins/genetics/metabolism ; Gene Expression Regulation, Plant ; Copper/pharmacology ; Sodium Chloride/pharmacology ; Saccharomyces cerevisiae/genetics ; }, abstract = {The study aimed to elucidate the functional characteristics of OsASMT1 gene under copper (Cu) or sodium chloride (NaCl) stress. Bioinformatics scrutiny unveiled that OsASMT1 is situated on chromosome 9. Its protein architecture, comprising dimerization and methyltransferase domains, showed significant similarities to OsASMT2 and OsASMT3. High expression in roots and panicles, along with abiotic stress putative cis-regulatory elements in the promoter, indicated potential stress responsiveness. Real-time quantitative PCR confirmed OsASMT1 induction under Cu and NaCl stress in rice. Surprisingly, yeast expressing OsASMT1 did not exhibit enhanced resistance to abiotic stresses. The results of subcellular localization analysis indicated that OsASMT1 plays a role in the cytoplasm. While OsASMT1 responded to Cu and NaCl stress in rice, its heterologous expression in yeast failed to confer abiotic stress resistance, highlighting the need for further investigation of its functional implications.}, }
@article {pmid38581683, year = {2024}, author = {Loos, D and Filho, APDC and Dutilh, BE and Barber, AE and Panagiotou, G}, title = {A global survey of host, aquatic, and soil microbiomes reveals shared abundance and genomic features between bacterial and fungal generalists.}, journal = {Cell reports}, volume = {43}, number = {4}, pages = {114046}, doi = {10.1016/j.celrep.2024.114046}, pmid = {38581683}, issn = {2211-1247}, support = {/ERC_/European Research Council/International ; }, mesh = {*Soil Microbiology ; *Fungi/genetics/classification ; *Microbiota/genetics ; *Bacteria/genetics/classification ; Humans ; Biodiversity ; Genomics/methods ; Phylogeny ; }, abstract = {Environmental change, coupled with alteration in human lifestyles, is profoundly impacting the microbial communities critical to the health of the Earth and its inhabitants. To identify bacteria and fungi that are resistant and susceptible to habitat change, we analyze thousands of genera detected in 1,580 host, soil, and aquatic samples. This large-scale analysis identifies 48 bacterial and 4 fungal genera that are abundant across the three biomes, demonstrating fitness in diverse environmental conditions. Samples containing these generalists have significantly higher alpha diversity. These generalists play a significant role in shaping cross-kingdom community structure, boasting larger genomes with more secondary metabolism and antimicrobial resistance genes. Conversely, 30 bacterial and 19 fungal genera are only found in a single habitat, suggesting a limited ability to adapt to different and changing environments. These findings contribute to our understanding of microbial niche breadth and its consequences for global biodiversity loss.}, }
@article {pmid38581418, year = {2024}, author = {Chen, Z and Ain, NU and Zhao, Q and Zhang, X}, title = {From tradition to innovation: conventional and deep learning frameworks in genome annotation.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {3}, pages = {}, pmid = {38581418}, issn = {1477-4054}, support = {2021YFF1000900//National Key Research and Development Program of China/ ; RCYX20210706092103024//Shenzhen Science and Technology Program/ ; 32222019//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Deep Learning ; Genome ; Algorithms ; Software ; Computational Biology/methods ; Molecular Sequence Annotation ; }, abstract = {Following the milestone success of the Human Genome Project, the 'Encyclopedia of DNA Elements (ENCODE)' initiative was launched in 2003 to unearth information about the numerous functional elements within the genome. This endeavor coincided with the emergence of numerous novel technologies, accompanied by the provision of vast amounts of whole-genome sequences, high-throughput data such as ChIP-Seq and RNA-Seq. Extracting biologically meaningful information from this massive dataset has become a critical aspect of many recent studies, particularly in annotating and predicting the functions of unknown genes. The core idea behind genome annotation is to identify genes and various functional elements within the genome sequence and infer their biological functions. Traditional wet-lab experimental methods still rely on extensive efforts for functional verification. However, early bioinformatics algorithms and software primarily employed shallow learning techniques; thus, the ability to characterize data and features learning was limited. With the widespread adoption of RNA-Seq technology, scientists from the biological community began to harness the potential of machine learning and deep learning approaches for gene structure prediction and functional annotation. In this context, we reviewed both conventional methods and contemporary deep learning frameworks, and highlighted novel perspectives on the challenges arising during annotation underscoring the dynamic nature of this evolving scientific landscape.}, }
@article {pmid38578160, year = {2024}, author = {Zhang, T and Peng, W and Xiao, H and Cao, S and Chen, Z and Su, X and Luo, Y and Liu, Z and Peng, Y and Yang, X and Jiang, GF and Xu, X and Ma, Z and Zhou, Y}, title = {Population genomics highlights structural variations in local adaptation to saline coastal environments in woolly grape.}, journal = {Journal of integrative plant biology}, volume = {66}, number = {7}, pages = {1408-1426}, doi = {10.1111/jipb.13653}, pmid = {38578160}, issn = {1744-7909}, support = {20210020//Guangxi University, Bama Institute of Integration of Industry and Education, postgraduate joint training project/ ; 20210039//Guangxi University, Bama Institute of Integration of Industry and Education, postgraduate joint training project/ ; 2023YFF1000100//the National Key Research and Development Program of China/ ; 2023YFD2200700//the National Key Research and Development Program of China/ ; 32300191//National Natural Science Foundation of China/ ; 32372662//National Natural Science Foundation of China/ ; No.20210020;No.20210039//Guangxi University, Bama Institute of Integration of Industry and Education, postgraduate joint training project/ ; 2023YFF1000100;2023YFD2200700;//the National Key Research and Development Program of China/ ; No.32300191;No.32372662//National Natural Science Foundation of China/ ; }, mesh = {*Vitis/genetics ; Adaptation, Physiological/genetics ; Genome, Plant/genetics ; Genetics, Population ; Polymorphism, Single Nucleotide/genetics ; Salt Tolerance/genetics ; Genomic Structural Variation/genetics ; Genomics ; Genes, Plant ; }, abstract = {Structural variations (SVs) are a feature of plant genomes that has been largely unexplored despite their significant impact on plant phenotypic traits and local adaptation to abiotic and biotic stress. In this study, we employed woolly grape (Vitis retordii), a species native to the tropical and subtropical regions of East Asia with both coastal and inland habitats, as a valuable model for examining the impact of SVs on local adaptation. We assembled a haplotype-resolved chromosomal reference genome for woolly grape, and conducted population genetic analyses based on whole-genome sequencing (WGS) data from coastal and inland populations. The demographic analyses revealed recent bottlenecks in all populations and asymmetric gene flow from the inland to the coastal population. In total, 1,035 genes associated with plant adaptive regulation for salt stress, radiation, and environmental adaptation were detected underlying local selection by SVs and SNPs in the coastal population, of which 37.29% and 65.26% were detected by SVs and SNPs, respectively. Candidate genes such as FSD2, RGA1, and AAP8 associated with salt tolerance were found to be highly differentiated and selected during the process of local adaptation to coastal habitats in SV regions. Our study highlights the importance of SVs in local adaptation; candidate genes related to salt stress and climatic adaptation to tropical and subtropical environments are important genomic resources for future breeding programs of grapevine and its rootstocks.}, }
@article {pmid38577785, year = {2024}, author = {Baril, T and Galbraith, J and Hayward, A}, title = {Earl Grey: A Fully Automated User-Friendly Transposable Element Annotation and Analysis Pipeline.}, journal = {Molecular biology and evolution}, volume = {41}, number = {4}, pages = {}, pmid = {38577785}, issn = {1537-1719}, support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *DNA Transposable Elements/genetics ; Molecular Sequence Annotation ; *Drosophila melanogaster/genetics ; Genomics/methods ; Computational Biology ; }, abstract = {Transposable elements (TEs) are major components of eukaryotic genomes and are implicated in a range of evolutionary processes. Yet, TE annotation and characterization remain challenging, particularly for nonspecialists, since existing pipelines are typically complicated to install, run, and extract data from. Current methods of automated TE annotation are also subject to issues that reduce overall quality, particularly (i) fragmented and overlapping TE annotations, leading to erroneous estimates of TE count and coverage, and (ii) repeat models represented by short sections of total TE length, with poor capture of 5' and 3' ends. To address these issues, we present Earl Grey, a fully automated TE annotation pipeline designed for user-friendly curation and annotation of TEs in eukaryotic genome assemblies. Using nine simulated genomes and an annotation of Drosophila melanogaster, we show that Earl Grey outperforms current widely used TE annotation methodologies in ameliorating the issues mentioned above while scoring highly in benchmarking for TE annotation and classification and being robust across genomic contexts. Earl Grey provides a comprehensive and fully automated TE annotation toolkit that provides researchers with paper-ready summary figures and outputs in standard formats compatible with other bioinformatics tools. Earl Grey has a modular format, with great scope for the inclusion of additional modules focused on further quality control and tailored analyses in future releases.}, }
@article {pmid38569653, year = {2024}, author = {Augustijn, HE and Roseboom, AM and Medema, MH and van Wezel, GP}, title = {Harnessing regulatory networks in Actinobacteria for natural product discovery.}, journal = {Journal of industrial microbiology &amp; biotechnology}, volume = {51}, number = {}, pages = {}, pmid = {38569653}, issn = {1476-5535}, support = {948770/ERC_/European Research Council/International ; }, mesh = {*Actinobacteria/metabolism/genetics ; *Biological Products/metabolism ; Biosynthetic Pathways ; Computational Biology/methods ; *Drug Discovery ; Gene Expression Regulation, Bacterial ; *Gene Regulatory Networks ; Multigene Family ; Transcription Factors/metabolism/genetics ; }, abstract = {UNLABELLED: Microbes typically live in complex habitats where they need to rapidly adapt to continuously changing growth conditions. To do so, they produce an astonishing array of natural products with diverse structures and functions. Actinobacteria stand out for their prolific production of bioactive molecules, including antibiotics, anticancer agents, antifungals, and immunosuppressants. Attention has been directed especially towards the identification of the compounds they produce and the mining of the large diversity of biosynthetic gene clusters (BGCs) in their genomes. However, the current return on investment in random screening for bioactive compounds is low, while it is hard to predict which of the millions of BGCs should be prioritized. Moreover, many of the BGCs for yet undiscovered natural products are silent or cryptic under laboratory growth conditions. To identify ways to prioritize and activate these BGCs, knowledge regarding the way their expression is controlled is crucial. Intricate regulatory networks control global gene expression in Actinobacteria, governed by a staggering number of up to 1000 transcription factors per strain. This review highlights recent advances in experimental and computational methods for characterizing and predicting transcription factor binding sites and their applications to guide natural product discovery. We propose that regulation-guided genome mining approaches will open new avenues toward eliciting the expression of BGCs, as well as prioritizing subsets of BGCs for expression using synthetic biology approaches.<br><br>ONE-SENTENCE SUMMARY: This review provides insights into advances in experimental and computational methods aimed at predicting transcription factor binding sites and their applications to guide natural product discovery.}, }
@article {pmid38560995, year = {2024}, author = {Stiller, J and Feng, S and Chowdhury, AA and Rivas-González, I and Duchêne, DA and Fang, Q and Deng, Y and Kozlov, A and Stamatakis, A and Claramunt, S and Nguyen, JMT and Ho, SYW and Faircloth, BC and Haag, J and Houde, P and Cracraft, J and Balaban, M and Mai, U and Chen, G and Gao, R and Zhou, C and Xie, Y and Huang, Z and Cao, Z and Yan, Z and Ogilvie, HA and Nakhleh, L and Lindow, B and Morel, B and Fjeldså, J and Hosner, PA and da Fonseca, RR and Petersen, B and Tobias, JA and Székely, T and Kennedy, JD and Reeve, AH and Liker, A and Stervander, M and Antunes, A and Tietze, DT and Bertelsen, MF and Lei, F and Rahbek, C and Graves, GR and Schierup, MH and Warnow, T and Braun, EL and Gilbert, MTP and Jarvis, ED and Mirarab, S and Zhang, G}, title = {Complexity of avian evolution revealed by family-level genomes.}, journal = {Nature}, volume = {629}, number = {8013}, pages = {851-860}, pmid = {38560995}, issn = {1476-4687}, mesh = {Animals ; *Birds/genetics/classification/anatomy &amp; histology ; Brain/anatomy &amp; histology ; *Evolution, Molecular ; Extinction, Biological ; *Genome/genetics ; Genomics ; *Phylogeny ; Population Density ; Male ; Female ; }, abstract = {Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and the choice of genomic regions[1-3]. Here we address these issues by analysing the genomes of 363 bird species[4] (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a marked degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous-Palaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that are a challenge to model due to either extreme DNA composition, variable substitution rates, incomplete lineage sorting or complex evolutionary events such as ancient hybridization. Assessment of the effects of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates and relative brain size following the Cretaceous-Palaeogene extinction event, supporting the hypothesis that emerging ecological opportunities catalysed the diversification of modern birds. The resulting phylogenetic estimate offers fresh insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies.}, }
@article {pmid38560613, year = {2024}, author = {Boyes, D and Gibbs, M and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Brown Oak Tortrix, Archips crataeganus (Hübner, 1796).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {9}, pmid = {38560613}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Archips crataeganus (the Brown Oak Tortrix; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 626.9 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 16.64 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,596 protein coding genes.}, }
@article {pmid38554963, year = {2024}, author = {Li, W and Feng, Q and Li, Z and Jin, T and Zhang, Y and Southam, G}, title = {Inhibition of iron oxidation in Acidithiobacillus ferrooxidans by low-molecular-weight organic acids: Evaluation of performance and elucidation of mechanisms.}, journal = {The Science of the total environment}, volume = {927}, number = {}, pages = {171919}, doi = {10.1016/j.scitotenv.2024.171919}, pmid = {38554963}, issn = {1879-1026}, mesh = {*Acidithiobacillus/metabolism/drug effects ; *Iron/metabolism ; *Oxidation-Reduction ; Mining ; Formates/metabolism ; Acetic Acid/metabolism ; *Propionates ; }, abstract = {The catalytic role of Acidithiobacillus ferrooxidans (A. ferrooxidans) in iron biooxidation is pivotal in the formation of Acid Mine Drainage (AMD), which poses a significant threat to the environment. To control AMD generation, treatments with low-molecular-weight organic acids are being studied, yet their exact mechanisms are unclear. In this study, AMD materials, organic acids, and molecular methods were employed to gain a deeper understanding of the inhibitory effects of low-molecular-weight organic acids on the biooxidation of iron by A. ferrooxidans. The inhibition experiments of A. ferrooxidans on the oxidation of Fe[2+] showed that to attain a 90 % inhibition efficacy within 72 h, the minimum concentrations required for formic acid, acetic acid, propionic acid, and lactic acid are 0.5, 6, 4, and 10 mmol/L, respectively. Bacterial imaging illustrated the detrimental effects of these organic acids on the cell envelope structure. This includes severe damage to the outer membrane, particularly from formic and acetic acids, which also caused cell wall damage. Coupled with alterations in the types and quantities of protein, carbohydrate, and nucleic acid content in extracellular polymeric substances (EPS), indicate the mechanisms underlying these inhibitory treatments. Transcriptomic analysis revealed interference of these organic acids with crucial metabolic pathways, particularly those related to energy metabolism. These findings establish a comprehensive theoretical basis for understanding the inhibition of A. ferrooxidans' biooxidation by low-molecular-weight organic acids, offering a novel opportunity to effectively mitigate the generation of AMD at its source.}, }
@article {pmid38554685, year = {2024}, author = {Sfriso, AA and Juhmani, AS and Tomio, Y and Sfriso, A and Rizzolio, F and Adeel, M and Wahsha, M and Munari, C and Mistri, M}, title = {Microplastic accumulation and ecological impacts on benthic invertebrates: Insights from a microcosm experiment.}, journal = {Marine pollution bulletin}, volume = {202}, number = {}, pages = {116231}, doi = {10.1016/j.marpolbul.2024.116231}, pmid = {38554685}, issn = {1879-3363}, mesh = {Animals ; *Water Pollutants, Chemical/analysis ; *Invertebrates ; *Environmental Monitoring ; *Microplastics ; Aquatic Organisms ; Ecosystem ; }, abstract = {Microplastic (MP) pollution poses a global concern, especially for benthic invertebrates. This one-month study investigated the accumulation of small MP polymers (polypropylene and polyester resin, 3-500 μm, 250 μg L[-1]) in benthic invertebrates and on one alga species. Results revealed species-specific preferences for MP size and type, driven by ingestion, adhesion, or avoidance behaviours. Polyester resin accumulated in Mytilus galloprovincialis, Chamelea gallina, Hexaplex trunculus, and Paranemonia cinerea, while polypropylene accumulated on Ulva rigida. Over time, MP accumulation decreased in count but not size, averaging 6.2 ± 5.0 particles per individual after a month. MP were mainly found inside of the organisms, especially in the gut, gills, and gonads and externally adherent MP ranged from 11 to 35 % of the total. Biochemical energy assessments after two weeks of MP exposure indicated energy gains for water column species but energy loss for sediment-associated species, highlighting the susceptibility of infaunal benthic communities to MP contamination.}, }
@article {pmid38552719, year = {2024}, author = {Martin, NG and Defres, S and Willis, L and Beckley, R and Hardwick, H and Coxon, A and Kadambari, S and Yu, LM and Liu, X and Galal, U and Conlin, K and Griffiths, MJ and Kneen, R and Nadel, S and Heath, PT and Kelly, DE and Solomon, T and Sadarangani, M and Pollard, AJ and , }, title = {Paediatric meningitis in the conjugate vaccine era and a novel clinical decision model to predict bacterial aetiology.}, journal = {The Journal of infection}, volume = {88}, number = {5}, pages = {106145}, doi = {10.1016/j.jinf.2024.106145}, pmid = {38552719}, issn = {1532-2742}, mesh = {Humans ; Child ; Infant ; *Meningitis, Bacterial/diagnosis/cerebrospinal fluid/microbiology ; Child, Preschool ; Adolescent ; Female ; Male ; Prospective Studies ; *Vaccines, Conjugate ; *Meningitis, Viral/diagnosis/cerebrospinal fluid ; Clinical Decision Rules ; United Kingdom/epidemiology ; Neisseria meningitidis/isolation &amp; purification ; Streptococcus pneumoniae/isolation &amp; purification ; Decision Support Techniques ; }, abstract = {OBJECTIVES: The aims of this study were to assess aetiology and clinical characteristics in childhood meningitis, and develop clinical decision rules to distinguish bacterial meningitis from other similar clinical syndromes.<br><br>METHODS: Children aged <16 years hospitalised with suspected meningitis/encephalitis were included, and prospectively recruited at 31 UK hospitals. Meningitis was defined as identification of bacteria/viruses from cerebrospinal fluid (CSF) and/or a raised CSF white blood cell count. New clinical decision rules were developed to distinguish bacterial from viral meningitis and those of alternative aetiology.<br><br>RESULTS: The cohort included 3002 children (median age 2&#xb7;4 months); 1101/3002 (36&#xb7;7%) had meningitis, including 180 bacterial, 423 viral and 280 with no pathogen identified. Enterovirus was the most common pathogen in those aged <6 months and 10-16 years, with Neisseria meningitidis and/or Streptococcus pneumoniae commonest at age 6 months to 9 years. The Bacterial Meningitis Score had a negative predictive value of 95&#xb7;3%. We developed two clinical decision rules, that could be used either before (sensitivity 82%, specificity 71%) or after lumbar puncture (sensitivity 84%, specificity 93%), to determine risk of bacterial meningitis.<br><br>CONCLUSIONS: Bacterial meningitis comprised 6% of children with suspected meningitis/encephalitis. Our clinical decision rules provide potential novel approaches to assist with identifying children with bacterial meningitis.<br><br>FUNDING: This study was funded by the Meningitis Research Foundation, Pfizer and the NIHR Programme Grants for Applied Research.}, }
@article {pmid38552245, year = {2024}, author = {Han, B and Tian, D and Li, X and Liu, S and Tian, F and Liu, D and Wang, S and Zhao, K}, title = {Multiomics Analyses Provide New Insight into Genetic Variation of Reproductive Adaptability in Tibetan Sheep.}, journal = {Molecular biology and evolution}, volume = {41}, number = {3}, pages = {}, pmid = {38552245}, issn = {1537-1719}, support = {No. 2022-ZJ-901//Natural Science Foundation of Qinghai Province/ ; }, mesh = {Humans ; Female ; Sheep/genetics ; Animals ; Tibet ; *Genome-Wide Association Study ; *Multiomics ; Proteomics ; Reproduction ; Mutation ; }, abstract = {Domestication and artificial selection during production-oriented breeding have greatly shaped the level of genomic variability in sheep. However, the genetic variation associated with increased reproduction remains elusive. Here, two groups of samples from consecutively monotocous and polytocous sheep were collected for genome-wide association, transcriptomic, proteomic, and metabolomic analyses to explore the genetic variation in fecundity in Tibetan sheep. Genome-wide association study revealed strong associations between BMPR1B (p.Q249R) and litter size, as well as between PAPPA and lambing interval; these findings were validated in 1,130 individuals. Furthermore, we constructed the first single-cell atlas of Tibetan sheep ovary tissues and identified a specific mural granulosa cell subtype with PAPPA-specific expression and differential expression of BMPR1B between the two groups. Bulk RNA-seq indicated that BMPR1B and PAPPA expressions were similar between the two groups of sheep. 3D protein structure prediction and coimmunoprecipitation analysis indicated that mutation and mutually exclusive exons of BMPR1B are the main mechanisms for prolific Tibetan sheep. We propose that PAPPA is a key gene for stimulating ovarian follicular growth and development, and steroidogenesis. Our work reveals the genetic variation in reproductive performance in Tibetan sheep, providing insights and valuable genetic resources for the discovery of genes and regulatory mechanisms that improve reproductive success.}, }
@article {pmid38552150, year = {2024}, author = {Howard-Varona, C and Lindback, MM and Fudyma, JD and Krongauz, A and Solonenko, NE and Zayed, AA and Andreopoulos, WB and Olson, HM and Kim, YM and Kyle, JE and Glavina Del Rio, T and Adkins, JN and Tfaily, MM and Paul, S and Sullivan, MB and Duhaime, MB}, title = {Environment-specific virocell metabolic reprogramming.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38552150}, issn = {1751-7370}, support = {2149505//NSF Advances in Biological Informatics/ ; DE-AC05-76RL0-1830//U.S. Department of Energy/ ; //Joint Genome Institute/ ; //U.S. Department of Energy/ ; 1536989//National Science Foundation/ ; //University of Michigan/ ; 034//C-CoMP/ ; //Department of Energy/ ; T32 AI112542/AI/NIAID NIH HHS/United States ; 2055455//NSF Polar Programs/ ; 1-T32-AI-112542//National Institutes of Health (NIH)/National Institute of Allergy and Infectious Diseases (NIAID)/ ; //Facilities Integrating Collaborations for User Science/ ; 3790//Gordon and Betty Moore Foundation/ ; //EMSL/ ; //Office of Science/ ; DGE1256260//NSF Graduate Research Fellowship/ ; DE-AC02-05CH11231//Biological and Environmental Research/ ; C-CoMP NSF-STC 2019589//NSF Center for Chemical Currencies of a Microbial Planet/ ; //Environmental Molecular Sciences Laboratory/ ; DE-SC0020173//Office of Biological and Environmental Research/ ; }, mesh = {*Bacteriophages/genetics/physiology ; Proteomics ; Phosphates/metabolism ; Metabolomics ; Systems Biology ; Transcriptome ; Metabolic Reprogramming ; }, abstract = {Viruses impact microbial systems through killing hosts, horizontal gene transfer, and altering cellular metabolism, consequently impacting nutrient cycles. A virus-infected cell, a "virocell," is distinct from its uninfected sister cell as the virus commandeers cellular machinery to produce viruses rather than replicate cells. Problematically, virocell responses to the nutrient-limited conditions that abound in nature are poorly understood. Here we used a systems biology approach to investigate virocell metabolic reprogramming under nutrient limitation. Using transcriptomics, proteomics, lipidomics, and endo- and exo-metabolomics, we assessed how low phosphate (low-P) conditions impacted virocells of a marine Pseudoalteromonas host when independently infected by two unrelated phages (HP1 and HS2). With the combined stresses of infection and nutrient limitation, a set of nested responses were observed. First, low-P imposed common cellular responses on all cells (virocells and uninfected cells), including activating the canonical P-stress response, and decreasing transcription, translation, and extracellular organic matter consumption. Second, low-P imposed infection-specific responses (for both virocells), including enhancing nitrogen assimilation and fatty acid degradation, and decreasing extracellular lipid relative abundance. Third, low-P suggested virocell-specific strategies. Specifically, HS2-virocells regulated gene expression by increasing transcription and ribosomal protein production, whereas HP1-virocells accumulated host proteins, decreased extracellular peptide relative abundance, and invested in broader energy and resource acquisition. These results suggest that although environmental conditions shape metabolism in common ways regardless of infection, virocell-specific strategies exist to support viral replication during nutrient limitation, and a framework now exists for identifying metabolic strategies of nutrient-limited virocells in nature.}, }
@article {pmid38551211, year = {2024}, author = {Groote-Woortmann, W and Korbel, K and Hose, GC}, title = {STYGOTOX: A Quality-Assessed Database of (Eco)Toxicological Data on Stygofauna and Other Aquatic Subterranean Organisms.}, journal = {Environmental toxicology and chemistry}, volume = {43}, number = {12}, pages = {2492-2500}, pmid = {38551211}, issn = {1552-8618}, support = {LP190100927//Australian Research Council/ ; }, mesh = {Animals ; *Water Pollutants, Chemical/toxicity ; *Aquatic Organisms/drug effects ; *Databases, Factual ; Environmental Monitoring ; Risk Assessment ; }, abstract = {We have compiled the toxicity data on stygofauna and other aquatic subterranean organisms in one (eco)toxicological database. A total of 46 studies were found, containing 472 toxic endpoints covering 43 different stressors. These compounds were tested on subterranean organisms from four phyla, 12 orders, 24 genera, and 55 species. The studies included were published between 1976 and December 2023 using fauna collected in 13 different countries. The suitability of the studies was assessed to indicate the completeness of reporting and their suitability for use in hazard and risk assessment. This compilation provides a valuable source of data for future development of toxicity testing protocols for groundwater organisms, and to support decision-making, ecological risk assessments and the derivation of water quality criteria for the protection of groundwater ecosystems. Environ Toxicol Chem 2024;43:2492-2500. © 2024 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.}, }
@article {pmid38547306, year = {2024}, author = {Milić, D and Rat, M and Bokić, B and Mudri-Stojnić, S and Milošević, N and Sukur, N and Jakovetić, D and Radak, B and Tot, T and Vujanović, D and Anačkov, G and Radišić, D}, title = {Exploring the effects of habitat management on grassland biodiversity: A case study from northern Serbia.}, journal = {PloS one}, volume = {19}, number = {3}, pages = {e0301391}, pmid = {38547306}, issn = {1932-6203}, mesh = {Animals ; *Grassland ; Serbia ; *Ecosystem ; Biodiversity ; Agriculture ; Insecta ; Plants ; Birds/physiology ; }, abstract = {Grasslands represent a biodiversity hotspot in the European agricultural landscape, their restoration is necessary and offers a great opportunity to mitigate or halt harmful processes. These measures require a comprehensive knowledge of historical landscape changes, but also adequate management strategies. The required data was gathered from the sand grasslands of northern Serbia, as this habitat is of high conservation priority. This area also has a long history of different habitat management approaches (grazing and mowing versus unmanaged), which has been documented over of the last two decades. This dataset enabled us to quantify the effects of different measures across multiple taxa (plants, insect pollinators, and birds). We linked the gathered data on plants, pollinators, and birds with habitat management measures. Our results show that, at the taxon level, the adopted management strategies were beneficial for species richness, abundance, and composition, as the highest diversity of plant, insect pollinator, and bird species was found in managed areas. Thus, an innovative modelling approach was adopted in this work to identify and explain the effects of management practices on changes in habitat communities. The findings yielded can be used in the decision making as well as development of new management programmes. We thus posit that, when restoring and establishing particular communities, priority needs to be given to species with a broad ecological response. We recommend using the decision tree as a suitable machine learning model for this purpose.}, }
@article {pmid38540697, year = {2024}, author = {Giordano, D and Bonora, S and D'Orsi, I and D'Alelio, D and Facchiano, A}, title = {Structural and Functional Characterization of Lipoxygenases from Diatoms by Bioinformatics and Modelling Studies.}, journal = {Biomolecules}, volume = {14}, number = {3}, pages = {}, pmid = {38540697}, issn = {2218-273X}, mesh = {*Lipoxygenases/chemistry/genetics ; *Diatoms/genetics ; Oxylipins ; Phylogeny ; Molecular Docking Simulation ; Ecosystem ; Computational Biology ; }, abstract = {Lipoxygenases make several biological functions in cells, based on the products of the catalyzed reactions. In diatoms, microalgae ubiquitous in aquatic ecosystems, lipoxygenases have been noted for the oxygenation of fatty acids with the production of oxylipins, which are involved in many physiological and pathological processes in marine organisms. The interest in diatoms' lipoxygenases and oxylipins has increased due to their possible biotechnological applications, ranging from ecology to medicine. We investigated using bioinformatics and molecular docking tools the lipoxygenases of diatoms and the possible interaction with substrates. A large-scale analysis of sequence resources allowed us to retrieve 45 sequences of lipoxygenases from diatoms. We compared and analyzed the sequences by multiple alignments and phylogenetic trees, suggesting the possible clustering in phylogenetic groups. Then, we modelled the 3D structure of representative enzymes from the different groups and investigated in detail the structural and functional properties by docking simulations with possible substrates. The results allowed us to propose a classification of the lipoxygenases from diatoms based on their sequence features, which may be reflected in specific structural differences and possible substrate specificity.}, }
@article {pmid38540627, year = {2024}, author = {Santric-Milicevic, M and Pavlekic, K and Bukumiric, Z and Stevanovic, A and Nikolic, D and Matejic, B and Matanovic, D and Backovic, D and Tulic, G and Lukic, R and Zivanovic, D and Radosavljevic, S and Milovanovic, V and Zdujic, M and Stankovic, S and Asanin, M and Zdravkovic, M and Tomasevic, R}, title = {Nurses' Perception of Tension, Stress, and Pressure before and during the COVID-19 Pandemic: A Multicenter Serbian Study.}, journal = {Healthcare (Basel, Switzerland)}, volume = {12}, number = {6}, pages = {}, pmid = {38540627}, issn = {2227-9032}, abstract = {The mental health of healthcare workers, especially the nursing staff in intensive care units, is crucial for the optimal functioning of healthcare systems during medical emergencies. This study implements a cross-sectional design to investigate the associations between nurses' personal characteristics, workplace challenges, and job satisfaction with the increased perception of tension, stress, and pressure at the workplace (TSPW) before and during the COVID-19 pandemic. In 2021, we surveyed 4210 nurses from 19 intensive healthcare facilities in the capital of Serbia, Belgrade, and, at that time, collected data about their perceived TSPW before and during the COVID-19 pandemic. Our study identified six predictors of the increase in TSPW, as perceived by nurses: their work in COVID-19 infectious zones (OR = 1.446), exhaustion due to work under protective equipment (OR = 1.413), uncertainty and fear of infection (OR = 1.481), a high degree of superiors' appreciation and respect (OR = 1.147), a high degree of patients' attitudes (OR = 1.111), and a low degree of work autonomy (OR = 0.889). The study's findings suggest that a solution to this issue is necessary to ensure that nurses are safe and able to alleviate the physical and mental strain that comes with prolonged use of protective equipment. Nurses on the frontline of the pandemic require better health protection, better conditions, and respect for their role. Strategies to promote mental health would help reduce nurses' stress and increase job satisfaction.}, }
@article {pmid38538788, year = {2024}, author = {Johnson, TF and Beckerman, AP and Childs, DZ and Webb, TJ and Evans, KL and Griffiths, CA and Capdevila, P and Clements, CF and Besson, M and Gregory, RD and Thomas, GH and Delmas, E and Freckleton, RP}, title = {Revealing uncertainty in the status of biodiversity change.}, journal = {Nature}, volume = {628}, number = {8009}, pages = {788-794}, pmid = {38538788}, issn = {1476-4687}, mesh = {Animals ; *Biodiversity ; Conservation of Natural Resources/methods/trends ; Datasets as Topic ; Phylogeny ; Spatio-Temporal Analysis ; Time Factors ; *Uncertainty ; }, abstract = {Biodiversity faces unprecedented threats from rapid global change[1]. Signals of biodiversity change come from time-series abundance datasets for thousands of species over large geographic and temporal scales. Analyses of these biodiversity datasets have pointed to varied trends in abundance, including increases and decreases. However, these analyses have not fully accounted for spatial, temporal and phylogenetic structures in the data. Here, using a new statistical framework, we show across ten high-profile biodiversity datasets[2-11] that increases and decreases under existing approaches vanish once spatial, temporal and phylogenetic structures are accounted for. This is a consequence of existing approaches severely underestimating trend uncertainty and sometimes misestimating the trend direction. Under our revised average abundance trends that appropriately recognize uncertainty, we failed to observe a single increasing or decreasing trend at 95% credible intervals in our ten datasets. This emphasizes how little is known about biodiversity change across vast spatial and taxonomic scales. Despite this uncertainty at vast scales, we reveal improved local-scale prediction accuracy by accounting for spatial, temporal and phylogenetic structures. Improved prediction offers hope of estimating biodiversity change at policy-relevant scales, guiding adaptive conservation responses.}, }
@article {pmid38532952, year = {2024}, author = {Feutz, E and Biswas, PK and Ndeketa, L and Ogwel, B and Onwuchekwa, U and Sarwar, G and Sultana, S and Peñataro Yori, P and Acebedo, A and Ahmed, N and Ahmed, I and Atlas, HE and Awuor, AO and Bhuiyan, MAI and Conteh, B and Diawara, O and Elwood, S and Fane, M and Hossen, MI and Ireen, M and Jallow, AF and Karim, M and Kosek, MN and Kotloff, KL and Lefu, C and Liu, J and Maguire, R and Qamar, FN and Ndalama, M and Ochieng, JB and Okonji, C and Paredes, LFZ and Pavlinac, PB and Perez, K and Qureshi, S and Schiaffino, F and Traore, M and Tickell, KD and Wachepa, R and Witte, D and Cornick, J and Jahangir Hossain, M and Khanam, F and Olortegui, MP and Omore, R and Sow, SO and Yousafzai, MT and Galagan, SR}, title = {Data Management in Multicountry Consortium Studies: The Enterics For Global Health (EFGH) Shigella Surveillance Study Example.}, journal = {Open forum infectious diseases}, volume = {11}, number = {Suppl 1}, pages = {S48-S57}, pmid = {38532952}, issn = {2328-8957}, support = {D43 TW010913/TW/FIC NIH HHS/United States ; K43 TW012298/TW/FIC NIH HHS/United States ; UL1 TR002319/TR/NCATS NIH HHS/United States ; }, abstract = {BACKGROUND: Rigorous data management systems and planning are essential to successful research projects, especially for large, multicountry consortium studies involving partnerships across multiple institutions. Here we describe the development and implementation of data management systems and procedures for the Enterics For Global Health (EFGH) Shigella surveillance study-a 7-country diarrhea surveillance study that will conduct facility-based surveillance concurrent with population-based enumeration and a health care utilization survey to estimate the incidence of Shigella--associated diarrhea in children 6 to 35 months old.<br><br>METHODS: The goals of EFGH data management are to utilize the knowledge and experience of consortium members to collect high-quality data and ensure equity in access and decision-making. During the planning phase before study initiation, a working group of representatives from each EFGH country site, the coordination team, and other partners met regularly to develop the data management systems for the study.<br><br>RESULTS: This resulted in the Data Management Plan, which included selecting REDCap and SurveyCTO as the primary database systems. Consequently, we laid out procedures for data processing and storage, study monitoring and reporting, data quality control and assurance activities, and data access. The data management system and associated real-time visualizations allow for rapid data cleaning activities and progress monitoring and will enable quicker time to analysis.<br><br>CONCLUSIONS: Experiences from this study will contribute toward enriching the sparse landscape of data management methods publications and serve as a case study for future studies seeking to collect and manage data consistently and rigorously while maintaining equitable access to and control of data.}, }
@article {pmid38531865, year = {2024}, author = {Corponi, F and Li, BM and Anmella, G and Mas, A and Pacchiarotti, I and Valentí, M and Grande, I and Benabarre, A and Garriga, M and Vieta, E and Lawrie, SM and Whalley, HC and Hidalgo-Mazzei, D and Vergari, A}, title = {Automated mood disorder symptoms monitoring from multivariate time-series sensory data: getting the full picture beyond a single number.}, journal = {Translational psychiatry}, volume = {14}, number = {1}, pages = {161}, pmid = {38531865}, issn = {2158-3188}, mesh = {Humans ; *Mood Disorders/diagnosis ; *Affect ; Machine Learning ; Sleep ; }, abstract = {Mood disorders (MDs) are among the leading causes of disease burden worldwide. Limited specialized care availability remains a major bottleneck thus hindering pre-emptive interventions. MDs manifest with changes in mood, sleep, and motor activity, observable in ecological physiological recordings thanks to recent advances in wearable technology. Therefore, near-continuous and passive collection of physiological data from wearables in daily life, analyzable with machine learning (ML), could mitigate this problem, bringing MDs monitoring outside the clinician's office. Previous works predict a single label, either the disease state or a psychometric scale total score. However, clinical practice suggests that the same label may underlie different symptom profiles, requiring specific treatments. Here we bridge this gap by proposing a new task: inferring all items in HDRS and YMRS, the two most widely used standardized scales for assessing MDs symptoms, using physiological data from wearables. To that end, we develop a deep learning pipeline to score the symptoms of a large cohort of MD patients and show that agreement between predictions and assessments by an expert clinician is clinically significant (quadratic Cohen's κ and macro-average F1 score both of 0.609). While doing so, we investigate several solutions to the ML challenges associated with this task, including multi-task learning, class imbalance, ordinal target variables, and subject-invariant representations. Lastly, we illustrate the importance of testing on out-of-distribution samples.}, }
@article {pmid38531495, year = {2025}, author = {Yuan, Q and Yao, LF and Tang, JW and Ma, ZW and Mou, JY and Wen, XR and Usman, M and Wu, X and Wang, L}, title = {Rapid discrimination and ratio quantification of mixed antibiotics in aqueous solution through integrative analysis of SERS spectra via CNN combined with NN-EN model.}, journal = {Journal of advanced research}, volume = {69}, number = {}, pages = {61-74}, pmid = {38531495}, issn = {2090-1224}, mesh = {*Spectrum Analysis, Raman/methods ; *Anti-Bacterial Agents/analysis/chemistry ; *Neural Networks, Computer ; *Water Pollutants, Chemical/analysis ; Water/chemistry ; Algorithms ; Ciprofloxacin/analysis ; Deep Learning ; Levofloxacin/analysis ; Doxycycline/analysis ; }, abstract = {INTRODUCTION: Abusing antibiotic residues in the natural environment has become a severe public health and ecological environmental problem. The side effects of its biochemical and physiological consequences are severe. To avoid antibiotic contamination in water, implementing universal and rapid antibiotic residue detection technology is critical to maintaining antibiotic safety in aquatic environments. Surface-enhanced Raman spectroscopy (SERS) provides a powerful tool for identifying small molecular components with high sensitivity and selectivity. However, it remains a challenge to identify pure antibiotics from SERS spectra due to coexisting components in the mixture.<br><br>OBJECTIVES: In this study, an intelligent analysis model for the SERS spectrum based on a deep learning algorithm was proposed for rapid identification of the antibiotic components in the mixture and quantitative determination of the ratios of these components.<br><br>METHODS: We established a water environment system containing three antibiotic residues of ciprofloxacin, doxycycline, and levofloxacin. To facilitate qualitative and quantitative analysis of the SERS spectra antibiotic mixture datasets, we developed a computational framework integrating a convolutional neural network (CNN) and a non-negative elastic network (NN-EN) method.<br><br>RESULTS: The experimental results demonstrate that the CNN model has a recognition accuracy of 98.68%, and the interpretation analysis of Shapley Additive exPlanations (SHAP) shows that our model can specifically focus on the characteristic peak distribution. In contrast, the NN-EN model can accurately quantify each component's ratio in the mixture.<br><br>CONCLUSION: Integrating the SERS technique assisted by the CNN combined with the NN-EN model exhibits great potential for rapid identification and high-precision quantification of antibiotic residues in aquatic environments.}, }
@article {pmid38531460, year = {2024}, author = {Enjavinejad, SM and Zahedifar, M and Moosavi, AA and Khosravani, P}, title = {Integrated application of multiple indicators and geographic information system-based approaches for comprehensive assessment of environmental impacts of toxic metals-contaminated agricultural soils and vegetables.}, journal = {The Science of the total environment}, volume = {926}, number = {}, pages = {171747}, doi = {10.1016/j.scitotenv.2024.171747}, pmid = {38531460}, issn = {1879-1026}, mesh = {Adult ; Child ; Humans ; Vegetables ; Geographic Information Systems ; Environmental Monitoring ; Cadmium/analysis ; Copper/analysis ; Lead/analysis ; Risk Assessment ; *Metals, Heavy/analysis ; Soil/chemistry ; Carcinogens/analysis ; Receptors, Antigen, T-Cell ; *Soil Pollutants/analysis ; China ; }, abstract = {Conventional monitoring and mapping approaches are laborious, expensive, and time-consuming because they need a large number of data and consequently extensive sampling and experimental operations. Therefore, due to the growing concern about the potential of contamination of soils and agricultural products with heavy metals (HMs), a field experiment was conducted on 77 farm lands in an area of 2300 ha in the southeast of Shiraz (Iran) to investigate the source of metal contamination in the soils and vegetables and to model spatial distribution of HMs (iron, Fe; manganese, Mn; copper, Cu; zinc, Zn; cadmium, Cd; nickel, Ni, and lead, Pb) over the region using geographic information system (GIS) and geostatistical (Ordinary Kriging, OK) approaches and compare the results with deterministic approaches (Inverse Distance Weighting, IDW with different weighting power). Furthermore, some ecological and health risks indices including Pollution index (PI), Nemerow integrated pollution index (NIPI), pollution load index (PLI), degree of contamination (Cdeg), modified contamination degree (mCd), PIaverage and PIvector for soil quality, multi-element contamination (MEC), the probability of toxicity (MERMQ), the potential ecological index (RI), total hazard index (THI) and total carcinogenic risk index (TCR) based on ingestion, inhalation, and dermal exposure pathways for adults and children respectively for analyzing the noncarcinogenic and carcinogenic risks were calculated. Experimental semivariogram of the mentioned HMs were calculated and theoretical models (i.e., exponential, spherical, Gaussian, and linear models) were fitted in order to model their spatial structures and to investigate the most representative models. Moreover, principal component analysis (PCA) and cluster analysis (CA) were used to identify sources of HMs in the soils. Results showed that IDW method was more efficient than the OK approach to estimate the properties and HMs contents in the soils and plants. The estimated daily intake of metals (DIM) values of Pb and Ni exceeded their safe limits. In addition, Cd was the main element responsible for ecological risk. The PIave and PIvector indices showed that soil quality in the study area is not suitable. According to mCd values, the soils classified as ultra-high contaminated for Cu and Cd, extremely high for Zn and Pb, very high, high, and very low degree of contamination for Ni, Mn, and Fe, respectively. 36, 60, and 4 % of the sampling sites had high, medium, and low risk levels with 49, 21, and 9 % probability of toxicity, respectively. The maximum health risk index (HRI) value of 20.42 with extremely high risk for children was obtained for Ni and the HI for adults and children were 0.22 and 1.55, respectively. The THI values of Pb and Cd were the highest compared to the other HMs studied, revealing a possible non-cancer risk in children associated with exposure to these metals. The routes of exposure with the greatest influence on the THI and TCR indices were in the order of ingestion > inhalation > dermal. Therefore, ingestion, as the main route of exposure, is the route of greatest contribution to health risks. PCA analysis revealed that Fe, Mn, Cu, and Ni may originate from natural sources, while Fe was appeared to be controlled by fertilizer, and Cu primarily coming from pesticide, while Cd and Pb were mainly associated with the anthropogenic contamination, atmospheric depositions, and terrific in the urban soils. While, Zn mainly originated from fertilization. Findings are vital for developing remediation approaches for controlling the contaminants distribution as well as for monitoring and mapping the quality and health of soil resources.}, }
@article {pmid38528816, year = {2024}, author = {Del Bianco, T and Haartsen, R and Mason, L and Leno, VC and Springer, C and Potter, M and Mackay, W and Smit, P and Plessis, CD and Brink, L and Johnson, MH and Murphy, D and Loth, E and Odendaal, H and Jones, EJH}, title = {The importance of decomposing periodic and aperiodic EEG signals for assessment of brain function in a global context.}, journal = {Developmental psychobiology}, volume = {66}, number = {4}, pages = {e22484}, doi = {10.1002/dev.22484}, pmid = {38528816}, issn = {1098-2302}, support = {777394//EU/EFPIA/SFARI/Autistica/AUTISM SPEAKS Innovative Medicines Initiative 2 Joint Undertaking (AIMS-2-TRIALS)/ ; 115300//Innovative Medicines Initiative 1 Joint Undertaking (AIMS-2-TRIALS)/ ; MR/K021389/1//the Medical Research Council for the projects "The Development of Social Attention and Perception Abilities in Typical and At-risk Infants"/ ; MR/T003057/1//"Human neurocognitive development: Early-stage processing, modifiers, and outcomes"/ ; 213608/Z/18/Z//Sir Henry Wellcome Postdoctoral Fellowship/ ; MR/S036423/1//UK&#xa0;Research&#xa0;and Innovation/ ; }, mesh = {Child ; Humans ; Female ; *Electroencephalography ; *Brain ; Brain Mapping ; Cognition ; }, abstract = {Measures of early neuro-cognitive development that are suitable for use in low-resource settings are needed to enable studies of the effects of early adversity on the developing brain in a global context. These measures should have high acquisition rates and good face and construct validity. Here, we investigated the feasibility of a naturalistic electroencephalography (EEG) paradigm in a low-resource context during childhood. Additionally, we examined the sensitivity of periodic and aperiodic EEG metrics to social and non-social stimuli. We recorded simultaneous 20-channel EEG and eye-tracking in 72 children aged 4-12 years (45 females) while they watched videos of women singing nursery rhymes and moving toys, selected to represent familiar childhood experiences. These measures were part of a feasibility study that assessed the feasibility and acceptability of a follow-up data collection of the South African Safe Passage Study, which tracks environmental adversity and brain and cognitive development from before birth up until childhood. We examined whether data quantity and quality varied with child characteristics and the sensitivity of varying EEG metrics (canonical band power in the theta and alpha band and periodic and aperiodic features of the power spectra). We found that children who completed the EEG and eye-tracking assessment were, in general, representative of the full cohort. Data quantity was higher in children with greater visual attention to the stimuli. Out of the tested EEG metrics, periodic measures in the theta frequency range were most sensitive to condition differences, compared to alpha range measures and canonical and aperiodic EEG measures. Our results show that measuring EEG during ecologically valid social and non-social stimuli is feasible in low-resource settings, is feasible for most children, and produces robust indices of social brain function. This work provides preliminary support for testing longitudinal links between social brain function, environmental factors, and emerging behaviors.}, }
@article {pmid38527064, year = {2024}, author = {Barrett, C and Chiphwanya, J and Mkwanda, S and Matipula, DE and Ndhlovu, P and Chaponda, L and Turner, JD and Giorgi, E and Betts, H and Martindale, S and Taylor, MJ and Read, JM and Kelly-Hope, LA}, title = {The national distribution of lymphatic filariasis cases in Malawi using patient mapping and geostatistical modelling.}, journal = {PLoS neglected tropical diseases}, volume = {18}, number = {3}, pages = {e0012056}, pmid = {38527064}, issn = {1935-2735}, mesh = {Humans ; *Elephantiasis, Filarial/epidemiology ; Malawi/epidemiology ; Prevalence ; Data Management ; Surveys and Questionnaires ; }, abstract = {BACKGROUND: In 2020 the World Health Organization (WHO) declared that Malawi had successfully eliminated lymphatic filariasis (LF) as a public health problem. Understanding clinical case distributions at a national and sub-national level is important, so essential care packages can be provided to individuals living with LF symptoms. This study aimed to develop a national database and map of LF clinical cases across Malawi using geostatistical modelling approaches, programme-identified clinical cases, antigenaemia prevalence and climate information.<br><br>METHODOLOGY: LF clinical cases identified through programme house-to-house surveys across 90 sub-district administrative boundaries (Traditional Authority (TA)) and antigenaemia prevalence from 57 sampled villages in Malawi were used in a two-step geostatistical modelling process to predict LF clinical cases across all TAs of the country. First, we modelled antigenaemia prevalence in relation to climate covariates to predict nationwide antigenaemia prevalence. Second, we modelled clinical cases for unmapped TAs based on our antigenaemia prevalence spatial estimates.<br><br>PRINCIPLE FINDINGS: The models estimated 20,938 (95% CrI 18,091 to 24,071) clinical cases in unmapped TAs (70.3%) in addition to the 8,856 (29.7%), programme-identified cases in mapped TAs. In total, the overall national number of LF clinical cases was estimated to be 29,794 (95% CrI 26,957 to 32,927). The antigenaemia prevalence and clinical case mapping and modelling found the highest burden of disease in Chikwawa and Nsanje districts in the Southern Region and Karonga district in the Northern Region of the country.<br><br>CONCLUSIONS: The models presented in this study have facilitated the development of the first national LF clinical case database and map in Malawi, the first endemic country in sub-Saharan Africa. It highlights the value of using existing LF antigenaemia prevalence and clinical case data together with modelling approaches to produce estimates that may be used for the WHO dossier requirements, to help target limited resources and implement long-term health strategies.}, }
@article {pmid38523092, year = {2024}, author = {Ouyang, YY and Su, ZW and Li, CH and Zeng, AC and Guo, FT}, title = {Forest fire risk zoning based on fuzzy logic and analytical network process.}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {35}, number = {2}, pages = {354-362}, doi = {10.13287/j.1001-9332.202402.024}, pmid = {38523092}, issn = {1001-9332}, mesh = {Humans ; Fires/prevention &amp; control ; Forests ; *Fuzzy Logic ; Geographic Information Systems ; Trees ; *Wildfires/statistics &amp; numerical data ; }, abstract = {Forest fires have a significant impact on human life, property safety, and ecological environment. Deve-loping high-quality forest fire risk maps is beneficial for preventing forest fires, guiding resource allocation for firefighting, assisting in fire suppression efforts, and supporting decision-making. With a multi-criteria decision analysis (MCDA) method based on geographic information systems (GIS) and literature review, we assessed the main factors influencing the occurrences of forest fires in Youxi County, Fujian Province. We analyzed the importance of each fire risk factor using the analytic network process (ANP) and assigned weights, and evaluated the sub-standard weights using fuzzy logic assessment. Using ArcGIS aggregation functions, we generated a forest fire risk map and validated it with satellite fire points. The results showed that the areas classified as level 4 or higher fire risk accounted for a considerable proportion in Youxi County, and that the central and northern regions were at higher risk. The overall fire risk situation in the county was severe. The fuzzy ANP model demonstrated a high accuracy of 85.8%. The introduction of this novel MCDA method could effectively improve the accuracy of forest fire risk mapping at a small scale, providing a basis for early fire warning and the planning and allocation of firefighting resources.}, }
@article {pmid38521905, year = {2024}, author = {Wu, J and Lv, Y and Hao, P and Zhang, Z and Zheng, Y and Chen, E and Fan, Y}, title = {Immunological profile of lactylation-related genes in Crohn's disease: a comprehensive analysis based on bulk and single-cell RNA sequencing data.}, journal = {Journal of translational medicine}, volume = {22}, number = {1}, pages = {300}, pmid = {38521905}, issn = {1479-5876}, support = {82300630//National Natural Science Foundation of China/ ; 2022GGB011//Project of Young and Middle-aged Backbone Talents Cultivation/ ; 2021J011329//Fujian Provincial Natural Science Foundation/ ; 2021QNB017//Health Science Foundation of Fujian Youth Program/ ; }, mesh = {Humans ; *Crohn Disease/genetics ; Databases, Factual ; Lactic Acid ; Sequence Analysis, RNA ; }, abstract = {BACKGROUND: Crohn's disease (CD) is a disease characterized by intestinal immune dysfunction, often accompanied by metabolic abnormalities. Disturbances in lactate metabolism have been found in the intestine of patients with CD, but studies on the role of lactate and related Lactylation in the pathogenesis of CD are still unknown.<br><br>METHODS: We identified the core genes associated with Lactylation by downloading and merging three CD-related datasets (GSE16879, GSE75214, and GSE112366) from the GEO database, and analyzed the functions associated with the hub genes and the correlation between their expression levels and immune infiltration through comprehensive analysis. We explored the Lactylation levels of different immune cells using single-cell data and further analyzed the differences in Lactylation levels between inflammatory and non-inflammatory sites.<br><br>RESULTS: We identified six Lactylation-related hub genes that are highly associated with CD. Further analysis revealed that these six hub genes were highly correlated with the level of immune cell infiltration. To further clarify the effect of Lactylation on immune cells, we analyzed single-cell sequencing data of immune cells from inflammatory and non-inflammatory sites in CD patients and found that there were significant differences in the levels of Lactylation between different types of immune cells, and that the levels of Lactylation were significantly higher in immune cells from inflammatory sites.<br><br>CONCLUSIONS: These results suggest that Lactylation-related genes and their functions are closely associated with changes in inflammatory cells in CD patients.}, }
@article {pmid38514998, year = {2024}, author = {Alari, A and Ranzani, O and Olmos, S and Milà, C and Rico, A and Ballester, J and Basagaña, X and Dadvand, P and Duarte-Salles, T and Nieuwenhuijsen, M and Vivanco-Hidalgo, RM and Tonne, C}, title = {Short-term exposure to air pollution and hospital admission after COVID-19 in Catalonia: the COVAIR-CAT study.}, journal = {International journal of epidemiology}, volume = {53}, number = {2}, pages = {}, doi = {10.1093/ije/dyae041}, pmid = {38514998}, issn = {1464-3685}, support = {//Health Effects Institute/ ; }, mesh = {Humans ; Spain/epidemiology ; Cohort Studies ; Nitrogen Dioxide/adverse effects/analysis ; COVID-19 Testing ; *COVID-19/epidemiology ; *Air Pollution/adverse effects/analysis ; *Air Pollutants/adverse effects/analysis ; Particulate Matter/adverse effects/analysis ; *Ozone/adverse effects/analysis ; Hospitalization ; Hospitals ; Environmental Exposure/adverse effects/analysis ; }, abstract = {BACKGROUND: A growing body of evidence has reported positive associations between long-term exposure to air pollution and poor COVID-19 outcomes. Inconsistent findings have been reported for short-term air pollution, mostly from ecological study designs. Using individual-level data, we studied the association between short-term variation in air pollutants [nitrogen dioxide (NO2), particulate matter with a diameter of <2.5 µm (PM2.5) and a diameter of <10 µm (PM10) and ozone (O3)] and hospital admission among individuals diagnosed with COVID-19.<br><br>METHODS: The COVAIR-CAT (Air pollution in relation to COVID-19 morbidity and mortality: a large population-based cohort study in Catalonia, Spain) cohort is a large population-based cohort in Catalonia, Spain including 240&#xa0;902 individuals diagnosed with COVID-19 in the primary care system from 1 March until 31 December 2020. Our outcome was hospitalization within 30&#x2009;days of COVID-19 diagnosis. We used individual residential address to assign daily air-pollution exposure, estimated using machine-learning methods for spatiotemporal prediction. For each pandemic wave, we fitted Cox proportional-hazards models accounting for non-linear-distributed lagged exposure over the previous 7&#xa0;days.<br><br>RESULTS: Results differed considerably by pandemic wave. During the second wave, an interquartile-range increase in cumulative weekly exposure to air pollution (lag0_7) was associated with a 12% increase (95% CI: 4% to 20%) in COVID-19 hospitalizations for NO2, 8% (95% CI: 1% to 16%) for PM2.5 and 9% (95% CI: 3% to 15%) for PM10. We observed consistent positive associations for same-day (lag0) exposure, whereas lag-specific associations beyond lag0 were generally not statistically significant.<br><br>CONCLUSIONS: Our study suggests positive associations between NO2, PM2.5 and PM10 and hospitalization risk among individuals diagnosed with COVID-19 during the second wave. Cumulative hazard ratios were largely driven by exposure on the same day as hospitalization.}, }
@article {pmid38514747, year = {2024}, author = {Chanda, MM and Purse, BV and Hemadri, D and Patil, SS and Yogisharadhya, R and Prajapati, A and Shivachandra, SB}, title = {Spatial and temporal analysis of haemorrhagic septicaemia outbreaks in India over three decades (1987-2016).}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {6773}, pmid = {38514747}, issn = {2045-2322}, mesh = {Animals ; Cattle ; *Hemorrhagic Septicemia/epidemiology/veterinary/microbiology ; *Pasteurella multocida ; Buffaloes/microbiology ; Disease Outbreaks ; India/epidemiology ; *Cattle Diseases/microbiology ; }, abstract = {Haemorrhagic septicaemia (HS) is an economically important disease affecting cattle and buffaloes and the livelihoods of small-holder farmers that depend upon them. The disease is caused by Gram-negative bacterium, Pasteurella multocida, and is considered to be endemic in many states of India with more than 25,000 outbreaks in the past three decades. Currently, there is no national policy for control of HS in India. In this study, we analysed thirty year (1987-2016) monthly data on HS outbreaks using different statistical and mathematical methods to identify spatial variability and temporal patterns (seasonality, periodicity). There was zonal variation in the trend and seasonality of HS outbreaks. Overall, South zone reported maximum proportion of the outbreaks (70.2%), followed by East zone (7.2%), Central zone (6.4%), North zone (5.6%), West zone (5.5%) and North-East zone (4.9%). Annual state level analysis indicated that the reporting of HS outbreaks started at different years independently and there was no apparent transmission between the states. The results of the current study are useful for the policy makers to design national control programme on HS in India and implement state specific strategies. Further, our study and strategies could aid in implementation of similar approaches in HS endemic tropical countries around the world.}, }
@article {pmid38514421, year = {2024}, author = {Morel, B and Williams, TA and Stamatakis, A and Szöllősi, GJ}, title = {AleRax: a tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer, and loss.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {4}, pages = {}, pmid = {38514421}, issn = {1367-4811}, support = {//Klaus Tschira Foundation/ ; /ERC_/European Research Council/International ; }, mesh = {Phylogeny ; *Gene Duplication ; *Algorithms ; Software ; Models, Statistical ; Evolution, Molecular ; }, abstract = {MOTIVATION: Genomes are a rich source of information on the pattern and process of evolution across biological scales. How best to make use of that information is an active area of research in phylogenetics. Ideally, phylogenetic methods should not only model substitutions along gene trees, which explain differences between homologous gene sequences, but also the processes that generate the gene trees themselves along a shared species tree. To conduct accurate inferences, one needs to account for uncertainty at both levels, that is, in gene trees estimated from inherently short sequences and in their diverse evolutionary histories along a shared species tree.<br><br>RESULTS: We present AleRax, a software that can infer reconciled gene trees together with a shared species tree using a simple, yet powerful, probabilistic model of gene duplication, transfer, and loss. A key feature of AleRax is its ability to account for uncertainty in the gene tree and its reconciliation by using an efficient approximation to calculate the joint phylogenetic-reconciliation likelihood and sample reconciled gene trees accordingly. Simulations and analyses of empirical data show that AleRax is one order of magnitude faster than competing gene tree inference tools while attaining the same accuracy. It is consistently more robust than species tree inference methods such as SpeciesRax and ASTRAL-Pro 2 under gene tree uncertainty. Finally, AleRax can process multiple gene families in parallel thereby allowing users to compare competing phylogenetic hypotheses and estimate model parameters, such as duplication, transfer, and loss probabilities for genome-scale datasets with hundreds of taxa.<br><br>GNU GPL at https://github.com/BenoitMorel/AleRax and data are made available at https://cme.h-its.org/exelixis/material/alerax_data.tar.gz.}, }
@article {pmid38512945, year = {2024}, author = {Scalabrin, E and Radaelli, M and Capodaglio, G and Pierobon, M and Del Vecchio, S and Buffa, G}, title = {Hemp cultivation opportunities for marginal lands development.}, journal = {PloS one}, volume = {19}, number = {3}, pages = {e0299981}, pmid = {38512945}, issn = {1932-6203}, mesh = {*Cannabis ; Flowers ; Inflorescence ; Dietary Supplements ; Plant Leaves ; }, abstract = {Agricultural diversification and high-quality products deriving from sustainable crops such as hemp can represent a solution to revitalize marginal areas and reverse land abandonment. This study aimed at comparing four different hemp cultivars (Carmagnola Selezionata, "CS"; Futura 75, "FUT"; Felina 32, "FEL"; Secuieni Jubileu, "JUB") to provide information to select the best suited cultivar for cultivation in mountain marginal areas and for specific end-use applications. Hemp cultivars were cultivated in a single experimental field to compare their ecological and agronomic behavior (duration of life cycle phases, plant size and biomass allocation, and plant resource-use strategies). Through metabolomic analysis of both vegetative and reproductive parts of the plants we tested the presence of substances of nutraceutical interest and traced seed nutritional profile. The four cultivars had different ecological and agronomic behavior, and nutritional profile. We found several compounds with potential pharmaceutical and nutraceutical values in all parts of the plant (leaves, inflorescences, and stems). JUB resulted the most suitable for seed production while CS showed the highest content of bioactive compounds in flowers and leaves. FUT, showed the best suitability for multi-purpose cultivation, while FEL seemed to be not appropriate for the cultivation in mountain area. The multi-disciplinary approach we adopted was effective in distinguish across hemp cultivars and provided information to farmers for the selection of the best hemp cultivar to select. Hemp had a high potential for cultivation in marginal lands, demonstrating to be an economic resource due to its multi-purpose use and to the possibility to generate high-added values products. Our results could serve as a stimulus for the reintroduction of this culture in the study area and in other similar environments.}, }
@article {pmid38509110, year = {2024}, author = {Berner, LT and Orndahl, KM and Rose, M and Tamstorf, M and Arndal, MF and Alexander, HD and Humphreys, ER and Loranty, MM and Ludwig, SM and Nyman, J and Juutinen, S and Aurela, M and Happonen, K and Mikola, J and Mack, MC and Vankoughnett, MR and Iversen, CM and Salmon, VG and Yang, D and Kumar, J and Grogan, P and Danby, RK and Scott, NA and Olofsson, J and Siewert, MB and Deschamps, L and Lévesque, E and Maire, V and Morneault, A and Gauthier, G and Gignac, C and Boudreau, S and Gaspard, A and Kholodov, A and Bret-Harte, MS and Greaves, HE and Walker, D and Gregory, FM and Michelsen, A and Kumpula, T and Villoslada, M and Ylänne, H and Luoto, M and Virtanen, T and Forbes, BC and Hölzel, N and Epstein, H and Heim, RJ and Bunn, A and Holmes, RM and Hung, JKY and Natali, SM and Virkkala, AM and Goetz, SJ}, title = {The Arctic Plant Aboveground Biomass Synthesis Dataset.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {305}, pmid = {38509110}, issn = {2052-4463}, support = {80NSSC21K1364//National Aeronautics and Space Administration (NASA)/ ; 80NSSC22K1247//National Aeronautics and Space Administration (NASA)/ ; 80NSSC22K1247//National Aeronautics and Space Administration (NASA)/ ; NNX12AK83G//National Aeronautics and Space Administration (NASA)/ ; NNX15AP04H//National Aeronautics and Space Administration (NASA)/ ; 2127273//National Science Foundation (NSF)/ ; 1417745//National Science Foundation (NSF)/ ; 1636476//National Science Foundation (NSF)/ ; 2224776//National Science Foundation (NSF)/ ; 2127273//National Science Foundation (NSF)/ ; 330319//Academy of Finland (Suomen Akatemia)/ ; 330319//Academy of Finland (Suomen Akatemia)/ ; 330845//Academy of Finland (Suomen Akatemia)/ ; 1342890//Academy of Finland (Suomen Akatemia)/ ; 256991//Academy of Finland (Suomen Akatemia)/ ; 2021-05767//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; FRQNT-2018-PR-208107//Fonds de Recherche du Qu&#xe9;bec - Nature et Technologies (Quebec Fund for Research in Nature and Technology)/ ; FRQNT-2018-PR-208107//Fonds de Recherche du Qu&#xe9;bec - Nature et Technologies (Quebec Fund for Research in Nature and Technology)/ ; }, mesh = {Arctic Regions ; Biomass ; *Ecosystem ; *Trees ; *Plants ; }, abstract = {Plant biomass is a fundamental ecosystem attribute that is sensitive to rapid climatic changes occurring in the Arctic. Nevertheless, measuring plant biomass in the Arctic is logistically challenging and resource intensive. Lack of accessible field data hinders efforts to understand the amount, composition, distribution, and changes in plant biomass in these northern ecosystems. Here, we present The Arctic plant aboveground biomass synthesis dataset, which includes field measurements of lichen, bryophyte, herb, shrub, and/or tree aboveground biomass (g m[-2]) on 2,327 sample plots from 636 field sites in seven countries. We created the synthesis dataset by assembling and harmonizing 32 individual datasets. Aboveground biomass was primarily quantified by harvesting sample plots during mid- to late-summer, though tree and often tall shrub biomass were quantified using surveys and allometric models. Each biomass measurement is associated with metadata including sample date, location, method, data source, and other information. This unique dataset can be leveraged to monitor, map, and model plant biomass across the rapidly warming Arctic.}, }
@article {pmid38507308, year = {2024}, author = {Sánchez Reyes, LL and McTavish, EJ and O'Meara, B}, title = {DateLife: Leveraging Databases and Analytical Tools to Reveal the Dated Tree of Life.}, journal = {Systematic biology}, volume = {73}, number = {2}, pages = {470-485}, pmid = {38507308}, issn = {1076-836X}, support = {ABI-1458603//National Science Foundation/ ; DBI-0905606//National Evolutionary Synthesis Center/ ; ABI-1759846//Open Tree of Life project/ ; ABI-1458572//Phylotastic project/ ; }, mesh = {*Phylogeny ; *Classification/methods ; *Software ; Databases, Factual ; }, abstract = {Chronograms-phylogenies with branch lengths proportional to time-represent key data on timing of evolutionary events, allowing us to study natural processes in many areas of biological research. Chronograms also provide valuable information that can be used for education, science communication, and conservation policy decisions. Yet, achieving a high-quality reconstruction of a chronogram is a difficult and resource-consuming task. Here we present DateLife, a phylogenetic software implemented as an R package and an R Shiny web application available at www.datelife.org, that provides services for efficient and easy discovery, summary, reuse, and reanalysis of node age data mined from a curated database of expert, peer-reviewed, and openly available chronograms. The main DateLife workflow starts with one or more scientific taxon names provided by a user. Names are processed and standardized to a unified taxonomy, allowing DateLife to run a name match across its local chronogram database that is curated from Open Tree of Life's phylogenetic repository, and extract all chronograms that contain at least two queried taxon names, along with their metadata. Finally, node ages from matching chronograms are mapped using the congruification algorithm to corresponding nodes on a tree topology, either extracted from Open Tree of Life's synthetic phylogeny or one provided by the user. Congruified node ages are used as secondary calibrations to date the chosen topology, with or without initial branch lengths, using different phylogenetic dating methods such as BLADJ, treePL, PATHd8, and MrBayes. We performed a cross-validation test to compare node ages resulting from a DateLife analysis (i.e, phylogenetic dating using secondary calibrations) to those from the original chronograms (i.e, obtained with primary calibrations), and found that DateLife's node age estimates are consistent with the age estimates from the original chronograms, with the largest variation in ages occurring around topologically deeper nodes. Because the results from any software for scientific analysis can only be as good as the data used as input, we highlight the importance of considering the results of a DateLife analysis in the context of the input chronograms. DateLife can help to increase awareness of the existing disparities among alternative hypotheses of dates for the same diversification events, and to support exploration of the effect of alternative chronogram hypotheses on downstream analyses, providing a framework for a more informed interpretation of evolutionary results.}, }
@article {pmid38506735, year = {2024}, author = {Stefanovic, M and Takano, K and Wittekind, CE and Ehring, T}, title = {Dynamic symptom associations in posttraumatic stress disorder: a network approach.}, journal = {European journal of psychotraumatology}, volume = {15}, number = {1}, pages = {2317675}, pmid = {38506735}, issn = {2000-8066}, mesh = {Humans ; *Stress Disorders, Post-Traumatic/diagnosis ; Anxiety ; Checklist ; Diagnostic and Statistical Manual of Mental Disorders ; Ecological Momentary Assessment ; }, abstract = {Background and objective: The current study aimed to investigate the within-day symptom dynamics in PTSD patients, specifically focusing on symptoms that most predict changes in other symptoms. The study included a baseline diagnostic assessment, followed by an assessment using the experience sampling method (ESM) via a smartphone.Method: Participants answered questions related to their PTSD symptoms four times per day for 15 consecutive days (compliance rate 75%). The clinical sample consisted of 48 treatment-seeking individuals: 44 with PTSD as a primary diagnosis, and four patients with subsyndromal PTSD, all of whom had not yet begun trauma-focused treatment. The ESM assessment included the 20 items from the PTSD Checklist for DSM-5, five items from the International Trauma Questionnaire (ITQ) assessing disturbances in relationships and functional impairment, and two items from the Clinician-Administered PTSD Scale for DSM-5 assessing symptoms of depersonalization and derealization.Results: Temporal networks (prospective associations between symptoms) showed that changes in hypervigilance predicted changes in the greatest number of symptoms at the next time point. Furthermore, hypervigilance showed temporal connections with at least one additional symptom from each of the DSM-5 PTSD symptom clusters.Conclusions: Results show that the contemporaneous network (representing the relationship between given symptoms within the same assessment occasion) and the temporal network (representing prospective associations between symptoms) differ and that it is important to estimate both. Some findings from earlier research are replicated, but heterogeneity across studies remains. Future studies should include potential moderators.}, }
@article {pmid38505831, year = {2023}, author = {Clifton-Brown, J and Hastings, A and von Cossel, M and Murphy-Bokern, D and McCalmont, J and Whitaker, J and Alexopoulou, E and Amaducci, S and Andronic, L and Ashman, C and Awty-Carroll, D and Bhatia, R and Breuer, L and Cosentino, S and Cracroft-Eley, W and Donnison, I and Elbersen, B and Ferrarini, A and Ford, J and Greef, J and Ingram, J and Lewandowski, I and Magenau, E and Mos, M and Petrick, M and Pogrzeba, M and Robson, P and Rowe, RL and Sandu, A and Schwarz, KU and Scordia, D and Scurlock, J and Shepherd, A and Thornton, J and Trindade, LM and Vetter, S and Wagner, M and Wu, PC and Yamada, T and Kiesel, A}, title = {Perennial biomass cropping and use: Shaping the policy ecosystem in European countries.}, journal = {Global change biology. Bioenergy}, volume = {15}, number = {5}, pages = {538-558}, pmid = {38505831}, issn = {1757-1693}, abstract = {Demand for sustainably produced biomass is expected to increase with the need to provide renewable commodities, improve resource security and reduce greenhouse gas emissions in line with COP26 commitments. Studies have demonstrated additional environmental benefits of using perennial biomass crops (PBCs), when produced appropriately, as a feedstock for the growing bioeconomy, including utilisation for bioenergy (with or without carbon capture and storage). PBCs can potentially contribute to Common Agricultural Policy (CAP) (2023-27) objectives provided they are carefully integrated into farming systems and landscapes. Despite significant research and development (R&amp;D) investment over decades in herbaceous and coppiced woody PBCs, deployment has largely stagnated due to social, economic and policy uncertainties. This paper identifies the challenges in creating policies that are acceptable to all actors. Development will need to be informed by measurement, reporting and verification (MRV) of greenhouse gas emissions reductions and other environmental, economic and social metrics. It discusses interlinked issues that must be considered in the expansion of PBC production: (i) available land; (ii) yield potential; (iii) integration into farming systems; (iv) R&amp;D requirements; (v) utilisation options; and (vi) market systems and the socio-economic environment. It makes policy recommendations that would enable greater PBC deployment: (1) incentivise farmers and land managers through specific policy measures, including carbon pricing, to allocate their less productive and less profitable land for uses which deliver demonstrable greenhouse gas reductions; (2) enable greenhouse gas mitigation markets to develop and offer secure contracts for commercial developers of verifiable low-carbon bioenergy and bioproducts; (3) support innovation in biomass utilisation value chains; and (4) continue long-term, strategic R&amp;D and education for positive environmental, economic and social sustainability impacts.}, }
@article {pmid38493394, year = {2024}, author = {Ketterer, T and Sieke, E and Min, J and Quidgley-Martin, M and Barral, RL and Akers, A and Adams, A and Miller, E and Miller, MK and Mollen, C}, title = {Contraception Initiation in the Emergency Department: Adolescent Perspectives.}, journal = {The Journal of adolescent health : official publication of the Society for Adolescent Medicine}, volume = {75}, number = {1}, pages = {147-154}, pmid = {38493394}, issn = {1879-1972}, support = {K23 HD109464/HD/NICHD NIH HHS/United States ; R21 HD095096/HD/NICHD NIH HHS/United States ; }, mesh = {Humans ; Adolescent ; Female ; *Emergency Service, Hospital ; Pregnancy ; *Pregnancy in Adolescence/prevention &amp; control ; *Contraception Behavior/psychology ; Health Knowledge, Attitudes, Practice ; Qualitative Research ; Prospective Studies ; Adolescent Behavior/psychology ; Interviews as Topic ; Contraception/psychology ; Counseling ; }, abstract = {PURPOSE: The purpose of this study was to identify factors affecting contraceptive intention and behavior among adolescent females in the pediatric Emergency Department.<br><br>METHODS: We conducted a qualitative interview study nested within a larger prospective cohort study examining adolescent contraceptive counseling for females ages 15-18&#xa0;years at-risk of unintended pregnancy presenting to the pediatric Emergency Department. Interviews were conducted in a subset of participants. The ecologically expanded Theory of Planned Behavior, expert opinion, and literature review informed the interview guide. Interviews were recorded, transcribed, coded and monitored for thematic saturation.<br><br>RESULTS: Twenty-eight interviews were analyzed. Mean age was 17.1&#xa0;years. Themes were mapped to ecologically expanded Theory of Planned Behavior constructs. Within health system influences, prior contraceptive experiences and patient-clinician interactions were described. Within community influences, contraceptive education, knowledge and misinformation, teen pregnancy norms, and social media impacts were described. Within attitudes influences, side-effect and safety concerns, contraceptive motivations and teen pregnancy beliefs were described. Within subjective norm influences, peer and family impacts were described. Within perceived behavioral control, Emergency Department (ED) counseling intervention impacts were described.<br><br>DISCUSSION: We identified factors affecting contraceptive initiation/behavior among an ED adolescent population that otherwise may not have received contraceptive education in similar detail as provided by study clinicians. Adolescents' prior contraceptive and clinician interactions, limited access to contraceptive education, knowledge and misinformation, and side-effect and safety concerns affected initiation. Peer/family sharing and social media were leading contraceptive information sources. Future studies should incorporate insights into adolescent ED intervention design to make optimal use of resources while maximizing potential benefit.}, }
@article {pmid38493360, year = {2024}, author = {Wen, F and Liu, R and Garcia Y Garcia, A and Ye, H and Lu, L and Qimuge, E and Sun, Z and Nie, C and Han, X and Zhang, Y}, title = {Study on the prediction method of grasshopper occurrence risk in Inner Mongolia based on the maximum entropy model during the growing period.}, journal = {Journal of economic entomology}, volume = {117}, number = {3}, pages = {843-857}, doi = {10.1093/jee/toae036}, pmid = {38493360}, issn = {1938-291X}, support = {CBAS2022 DF001//Director of the International Research Center for Big Data for Sustainable SDG/ ; 420QN293//Hainan Provincial Natural Science Foundation of China/ ; 2021119//Youth Innovation Promotion Association CAS/ ; 2020 KTYWLZX08//Future Star Talent Program of Aerospace Information Research Institute, Chinese Academy of Sciences/ ; }, mesh = {*Grasshoppers/growth &amp; development/physiology ; Animals ; Entropy ; *Models, Statistical ; Animal Husbandry ; Herbivory ; Population Dynamics ; Animal Migration ; Ecosystem ; Agriculture ; Ecological Momentary Assessment ; Geographic Information Systems ; Surveys and Questionnaires ; Remote Sensing Technology ; }, abstract = {Grasshoppers represent a significant biological challenge in Inner Mongolia's grasslands, severely affecting the region's animal husbandry. Thus, dynamic monitoring of grasshopper infestation risk is crucial for sustainable livestock farming. This study employed the Maxent model, along with remote sensing data, to forecast Oedaleus decorus asiaticus occurrence during the growing season, using grasshopper suitability habitats as a base. The Maxent model's predictive accuracy was high, with an AUC of 0.966. The most influential environmental variables for grasshopper distribution were suitable habitat data (34.27%), the temperature-vegetation dryness index during the spawning period (18.81%), and various other meteorological and vegetation factors. The risk index model was applied to calculate the grasshopper distribution across different risk levels for the years 2019-2022. The data indicated that the level 1 risk area primarily spans central, eastern, and southwestern Inner Mongolia. By examining the variable weights, the primary drivers of risk level fluctuation from 2019 to 2022 were identified as accumulated precipitation and land surface temperature anomalies during the overwintering period. This study offers valuable insights for future O. decorus asiaticus monitoring in Inner Mongolia.}, }
@article {pmid38486028, year = {2024}, author = {Arslan, D and Akdağ, B and Yaşar, &#xc7; and Olivier, A and Benedetti, Y and Morelli, F and Çiçek, K}, title = {An extensive database on the traits and occurrences of amphibian species in Turkey.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {292}, pmid = {38486028}, issn = {2052-4463}, mesh = {Animals ; *Amphibians ; Biodiversity ; *Ecosystem ; Turkey ; Databases, Factual ; }, abstract = {Amphibians are the most endangered taxa among vertebrates, and they face many threats during their complex life cycles. The species' life history traits and occurrence database help understand species responses against ecological factors. Consequently, the species-level-trait database has gained more prominence in recent years as a useful tool for understanding the dimensions of communities, assembly processes of communities, and conserving biodiversity at the ecosystem level against environmental changes. However, in Turkey, there are deficiencies in the knowledge of the ecological traits of amphibians compared to other vertebrate taxa, as most studies have focused on their distribution or taxonomic status. Consequently, there is a need to create such a database for future research on all known extant amphibians in Turkey. We compiled a species-level data set of species traits and occurrences for all amphibians in Turkey using 436 literature sources. We completed 36 trait categories with 5611 occurrence data for 37 amphibian species in Turkey. This study provides an open, useful, and comprehensive database for macroecological and conservation studies on amphibians in Turkey.}, }
@article {pmid38483685, year = {2024}, author = {Guo, Y and Li, X and Li, Q and Hu, Z}, title = {Environmental impact assessment of acidic coal gangue leaching solution on groundwater: a coal gangue pile in Shanxi, China.}, journal = {Environmental geochemistry and health}, volume = {46}, number = {4}, pages = {120}, pmid = {38483685}, issn = {1573-2983}, mesh = {Coal/analysis ; Environmental Pollution ; Soil ; *Environmental Pollutants ; Ions ; China ; *Soil Pollutants/analysis ; *Coal Mining ; }, abstract = {With the continual advancement of coal resource development, the comprehensive utilization of coal gangue as a by-product encounters certain constraints. A substantial amount of untreated coal gangue is openly stored, particularly acidic gangue exposed to rainfall. The leaching effect of acidic solutions, containing heavy metal ions and other pollutants, results in environmental challenges such as local soil or groundwater pollution, presenting a significant concern in the current ecological landscape of mining areas. Investigating the migration patterns of pollutants in the soil-groundwater system and elucidating the characteristics of polluted solute migration are imperative. To understand the migration dynamics of pollutants and unveil the features of solute migration, this study focuses on a coal gangue dump in a mining area in Shanxi. Utilizing indoor leaching experiments and soil column migration experiments, a two-dimensional soil-groundwater model is established using the finite element method of COMSOL. This model quantitatively delineates the migration patterns of key pollutant components leached from coal gangue into the groundwater. The findings reveal that sulfate ions can migrate and infiltrate groundwater within a mere 7 years in the vadose zone of aeration. Moreover, the average concentration of iron ions in groundwater can reach approximately 58.3 mg/L. Convection, hydrodynamic dispersion, and adsorption emerge as the primary factors influencing pollution transport. Understanding the leaching patterns and environmental impacts of major pollutants in acidic coal gangue is crucial for predicting soil-groundwater pollution and implementing effective protective measures.}, }
@article {pmid38483497, year = {2024}, author = {Yang, R and Feng, J and Tang, J and Sun, Y}, title = {Risk assessment and classification prediction for water environment treatment PPP projects.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {89}, number = {5}, pages = {1264-1281}, doi = {10.2166/wst.2024.052}, pmid = {38483497}, issn = {0273-1223}, mesh = {*Environment ; Risk Assessment ; *Risk Management ; }, abstract = {Water treatment public-private partnership (PPP) projects are pivotal for sustainable water management but are often challenged by complex risk factors. Efficient risk management in these projects is crucial, yet traditional methodologies often fall short of addressing the dynamic and intricate nature of these risks. Addressing this gap, this comprehensive study introduces an advanced risk classification prediction model tailored for water treatment PPP projects, aimed at enhancing risk management capabilities. The proposed model encompasses an intricate evaluation of crucial risk areas: the natural and ecological environments, socio-economic factors, and engineering entities. It delves into the complex relationships between these risk elements and the overall risk profile of projects. Grounded in a sophisticated ensemble learning framework employing stacking, our model is further refined through a weighted voting mechanism, significantly elevating its predictive accuracy. Rigorous validation using data from the Jiujiang City water environment system project Phase I confirms the model's superiority over standard machine learning models. The development of this model marks a significant stride in risk classification for water treatment PPP projects, offering a powerful tool for enhancing risk management practices. Beyond accurately predicting project risks, this model also aids in developing effective government risk management strategies.}, }
@article {pmid38483377, year = {2024}, author = {Browning, CR and Pinchak, NP and Calder, CA and Boettner, B}, title = {Racial Differences in Activity Space Exposures and Everyday Perceptions of Safety Among Urban Youth.}, journal = {The Journal of adolescent health : official publication of the Society for Adolescent Medicine}, volume = {74}, number = {6}, pages = {1156-1163}, pmid = {38483377}, issn = {1879-1972}, support = {P2C HD042849/HD/NICHD NIH HHS/United States ; P2C HD058484/HD/NICHD NIH HHS/United States ; R01 DA032371/DA/NIDA NIH HHS/United States ; R01 HD088545/HD/NICHD NIH HHS/United States ; }, mesh = {Adolescent ; Child ; Female ; Humans ; Male ; *Black or African American/psychology ; Geographic Information Systems ; Ohio ; Perception ; *Residence Characteristics ; *Safety ; *Urban Population ; Violence/ethnology ; *White ; }, abstract = {PURPOSE: The everyday experience of safety promotes health and successful development during adolescence. To date, few studies have examined racial variation in the spatial determinants of in-the-moment perceived safety.<br><br>METHODS: Drawing on data from the Columbus, Ohio-based Adolescent Health and Development in Context study (N&#xa0;= 1,405), we consider the influence of intraindividual variability in Global Positioning System-based exposure to both high-proportion White urban neighborhoods and neighborhood violence for the everyday location-based safety perceptions of Black and White youth (ages 11-17) as captured by ecological momentary assessment.<br><br>RESULTS: Exposure to higher area-level violence reduces youths' safety perceptions. Momentary exposure to residentially White-dominated neighborhoods also reduces perceived safety, but only for Black youth who spend more time, on average, in White areas. In contrast, we observe some limited evidence that White youth perceive greater safety when in White neighborhoods if they spend more time in white neighborhoods on average.<br><br>DISCUSSION: These findings point to the need for greater attention to in situ experiences in understanding the origins of racial disparities in health and wellbeing. For Black youth, a restricted focus on the consequences of residing in Black segregated neighborhoods may obscure potentially health consequential exposures beyond these areas.}, }
@article {pmid38482998, year = {2024}, author = {Furuya, S and Zheng, F and Lu, Q and Fletcher, JM}, title = {Separating Scarring Effect and Selection of Early-Life Exposures With Genetic Data.}, journal = {Demography}, volume = {61}, number = {2}, pages = {363-392}, doi = {10.1215/00703370-11239766}, pmid = {38482998}, issn = {1533-7790}, mesh = {Humans ; Infant ; Educational Status ; *Environmental Exposure ; Infant Mortality ; Life Change Events ; Prenatal Exposure Delayed Effects ; Gene-Environment Interaction ; }, abstract = {Causal life course research examining consequences of early-life exposures has largely relied on associations between early-life environments and later-life outcomes using exogenous environmental shocks. Nonetheless, even with (quasi-)randomized early-life exposures, these associations may reflect not only causation ("scarring") but also selection (i.e., which members are included in data assessing later life). Investigating this selection and its impacts on estimated effects of early-life conditions has, however, often been ignored because of a lack of pre-exposure data. This study proposes an approach for assessing and correcting selection, separately from scarring, using genetic measurements. Because genetic measurements are determined at the time of conception, any associations with early-life exposures should be interpreted as selection. Using data from the UK Biobank, we find that in utero exposure to a higher area-level infant mortality rate is associated with genetic predispositions correlated with better educational attainment and health. These findings point to the direction and magnitude of selection from this exposure. Corrections for this selection in examinations of effects of exposure on later educational attainment suggest underestimates of 26-74%; effects on other life course outcomes also vary across selection correction methods.}, }
@article {pmid38479865, year = {2024}, author = {Kekalih, A and Adi, NP and Soemarko, DS}, title = {Preparation and Challenges in Developing a Big Data Analysis Framework in Occupational Medicine in Indonesia.}, journal = {Journal of UOEH}, volume = {46}, number = {1}, pages = {113-118}, doi = {10.7888/juoeh.46.113}, pmid = {38479865}, issn = {0387-821X}, mesh = {Humans ; *Artificial Intelligence ; *Occupational Medicine ; Big Data ; Indonesia ; Pandemics ; }, abstract = {This mini review explores the transformative potential of big data analysis and artificial intelligence (AI) in reforming occupational medicine in Indonesia. Emphasizing the preconditions, case studies, and benefits, it underscores the role of big data in enhancing worker well-being. The review highlights the importance of informative health big data, especially in high-risk industries, with examples of case studies of AI implementation in occupational medicine during the COVID-19 pandemic and other relevant scenarios. While acknowledging the challenges of AI implementation, the essay identifies the role of academic and professional organizations as pioneers in big data utilization. Six potential benefits that are identified, including improved patient care and efficient resource allocation, demonstrate the transformative impact of big data analysis. The proposed pathway of preparation underscores the need for awareness, skill enhancement, and collaboration, addressing challenges in data management and stakeholder engagement. The conclusion emphasizes continuous assessment, feasibility studies, and commitment as essential steps in advancing occupational medicine through big data analysis.}, }
@article {pmid38476212, year = {2024}, author = {Kearsley, E and Verbeeck, H and Stoffelen, P and Janssens, SB and Yakusu, EK and Kosmala, M and De Mil, T and Bauters, M and Kitima, ER and Ndiapo, JM and Chuda, AL and Richardson, AD and Wingate, L and Ilondea, BA and Beeckman, H and van den Bulcke, J and Boeckx, P and Hufkens, K}, title = {Historical tree phenology data reveal the seasonal rhythms of the Congo Basin rainforest.}, journal = {Plant-environment interactions (Hoboken, N.J.)}, volume = {5}, number = {2}, pages = {e10136}, pmid = {38476212}, issn = {2575-6265}, abstract = {Tropical forest phenology directly affects regional carbon cycles, but the relation between species-specific and whole-canopy phenology remains largely uncharacterized. We present a unique analysis of historical tropical tree phenology collected in the central Congo Basin, before large-scale impacts of human-induced climate change. Ground-based long-term (1937-1956) phenological observations of 140 tropical tree species are recovered, species-specific phenological patterns analyzed and related to historical meteorological records, and scaled to characterize stand-level canopy dynamics. High phenological variability within and across species and in climate-phenology relationships is observed. The onset of leaf phenophases in deciduous species was triggered by drought and light availability for a subset of species and showed a species-specific decoupling in time along a bi-modal seasonality. The majority of the species remain evergreen, although central African forests experience relatively low rainfall. Annually a maximum of 1.5% of the canopy is in leaf senescence or leaf turnover, with overall phenological variability dominated by a few deciduous species, while substantial variability is attributed to asynchronous events of large and/or abundant trees. Our results underscore the importance of accounting for constituent signals in canopy-wide scaling and the interpretation of remotely sensed phenology signals.}, }
@article {pmid38474911, year = {2024}, author = {Omega, RL and Ishigaki, Y and Permana, S and Matsumoto, Y and Yamamoto, K and Shozugawa, K and Hori, M}, title = {Low-Cost Sensor Deployment on a Public Minibus in Fukushima Prefecture.}, journal = {Sensors (Basel, Switzerland)}, volume = {24}, number = {5}, pages = {}, pmid = {38474911}, issn = {1424-8220}, support = {20KK0231//JSPS KAKENHI/ ; }, mesh = {*Radiation Monitoring ; *Fukushima Nuclear Accident ; Motor Vehicles ; Geographic Information Systems ; Electrocardiography ; Japan ; Radiation Dosage ; }, abstract = {This study analyzed radiation dose data to observe the annual decline in ambient radiation doses and assess the factors contributing to fluctuations in reconstructed areas of the Fukushima prefecture. Utilizing a novel mobile monitoring system installed on a community minibus, the study employed a cost-effective sensor, namely, Pocket Geiger which was integrated with a microcontroller and telecommunication system for data transfer, access, visualization, and accumulation. The study area included the region between Okuma and Tomioka towns. The ambient dose rate recorded along the minibus route was depicted on a map, averaged within a 1 × 1 km mesh created with the Quantum Geographic Information System. To ensure accuracy, the shielding factor of the minibus material is determined to adjust the dose readings. A significant decrease (p < 0.001) in the radiation dose ranges from 2022 to 2023 was observed. The land use classification by the Advanced Land Observation Satellite revealed an ecological half-life ranging from 2.41 years to 1 year, suggesting a rapid radiation decay across all land types. This underscores the close connection between radiation attenuation and environmental factors, as well as decontamination efforts across diverse land categories.}, }
@article {pmid38474163, year = {2024}, author = {Kozicki, M and Sąsiadek-Andrzejczak, E and Wach, R and Maras, P}, title = {Flexible Cotton Fabric-Based Ionizing Radiation Dosimeter for 2D Dose Distribution Measurements over a Wide Dose Range at High Dose Rates.}, journal = {International journal of molecular sciences}, volume = {25}, number = {5}, pages = {}, pmid = {38474163}, issn = {1422-0067}, mesh = {*Radiation Dosimeters ; *Radiation, Ionizing ; Cellulose ; Radiometry/methods ; }, abstract = {This work presents an ecological, flexible 2D radiochromic dosimeter for measuring ionizing radiation in the kilogray dose range. Cotton woven fabric made of cellulose was volume-modified with nitrotetrazolium blue chloride as a radiation-sensitive compound. Its features include a color change during exposure from yellowish to purple-brown and flexibility that allows it to adapt to various shapes. It was found that (i) the dose response is up to ~80 kGy, (ii) it is independent of the dose rate for 1.1-73.1 kGy/min, (iii) it can be measured in 2D using a flatbed scanner, (iv) the acquired images can be filtered using a mean filter, which improves its dose resolution, (v) the dose resolution is -0.07 to -0.4 kGy for ~0.6 to ~75.7 kGy for filtered images, and (vi) two linear dose subranges can be distinguished: ~0.6 to ~7.6 kGy and ~9.9 to ~62.0 kGy. The dosimeter combined with flatbed scanner reading and data processing using dedicated software packages constitutes a comprehensive system for measuring dose distributions for objects with complex shapes.}, }
@article {pmid38473771, year = {2024}, author = {Li, Z and Fan, H and Yang, L and Wang, S and Hong, D and Cui, W and Wang, T and Wei, C and Sun, Y and Wang, K and Liu, Y}, title = {Multi-Omics Analysis of the Effects of Soil Amendment on Rapeseed (Brassica napus L.) Photosynthesis under Drip Irrigation with Brackish Water.}, journal = {International journal of molecular sciences}, volume = {25}, number = {5}, pages = {}, pmid = {38473771}, issn = {1422-0067}, support = {2022B02021-3-1//The research was funded by the Major Science and Technology Project and Key Research and Development of Autonomous region, Xinjiang, China/ ; (Title: Research and demonstration on the key technologies of soil improvement and ecological prevention and control in the desert desert belt of Southern Xinjiang)//The Central Government Guides Local Science and Technology Development Fund Projects/ ; CXFZ202207//Shihezi University Innovative Development Special Projectand, China/ ; }, mesh = {*Brassica napus ; Antioxidants ; Multiomics ; *Brassica rapa ; Photosynthesis ; Crops, Agricultural ; Water ; }, abstract = {Drip irrigation with brackish water increases the risk of soil salinization while alleviating water shortage in arid areas. In order to alleviate soil salinity stress on crops, polymer soil amendments are increasingly used. But the regulation mechanism of a polymer soil amendment composed of polyacrylamide polyvinyl alcohol, and manganese sulfate (PPM) on rapeseed photosynthesis under drip irrigation with different types of brackish water is still unclear. In this field study, PPM was applied to study the responses of the rapeseed (Brassica napus L.) phenotype, photosynthetic physiology, transcriptomics, and metabolomics at the peak flowering stage under drip irrigation with water containing 6 g·L[-1] NaCl (S) and Na2CO3 (A). The results showed that the inhibitory effect of the A treatment on rapeseed photosynthesis was greater than that of the S treatment, which was reflected in the higher Na[+] content (73.30%) and lower photosynthetic-fluorescence parameters (6.30-61.54%) and antioxidant enzyme activity (53.13-77.10%) of the A-treated plants. The application of PPM increased the biomass (63.03-75.91%), photosynthetic parameters (10.55-34.06%), chlorophyll fluorescence parameters (33.83-62.52%), leaf pigment content (10.30-187.73%), and antioxidant enzyme activity (28.37-198.57%) under S and A treatments. However, the difference is that under the S treatment, PPM regulated the sulfur metabolism, carbon fixation and carbon metabolism pathways in rapeseed leaves. And it also regulated the photosynthesis-, oxidative phosphorylation-, and TCA cycle-related metabolic pathways in rapeseed leaves under A treatment. This study will provide new insights for the application of polymer materials to tackle the salinity stress on crops caused by drip irrigation with brackish water, and solve the difficulty in brackish water utilization.}, }
@article {pmid38467837, year = {2024}, author = {Bhosle, A and Bae, S and Zhang, Y and Chun, E and Avila-Pacheco, J and Geistlinger, L and Pishchany, G and Glickman, JN and Michaud, M and Waldron, L and Clish, CB and Xavier, RJ and Vlamakis, H and Franzosa, EA and Garrett, WS and Huttenhower, C}, title = {Integrated annotation prioritizes metabolites with bioactivity in inflammatory bowel disease.}, journal = {Molecular systems biology}, volume = {20}, number = {4}, pages = {338-361}, pmid = {38467837}, issn = {1744-4292}, support = {P30 DK040561/DK/NIDDK NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 CA230551/CA/NCI NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; Animals ; Mice ; *Inflammatory Bowel Diseases/drug therapy/metabolism ; *Colitis ; Metabolome ; Bile Acids and Salts ; }, abstract = {Microbial biochemistry is central to the pathophysiology of inflammatory bowel diseases (IBD). Improved knowledge of microbial metabolites and their immunomodulatory roles is thus necessary for diagnosis and management. Here, we systematically analyzed the chemical, ecological, and epidemiological properties of ~82k metabolic features in 546 Integrative Human Microbiome Project (iHMP/HMP2) metabolomes, using a newly developed methodology for bioactive compound prioritization from microbial communities. This suggested >1000 metabolic features as potentially bioactive in IBD and associated ~43% of prevalent, unannotated features with at least one well-characterized metabolite, thereby providing initial information for further characterization of a significant portion of the fecal metabolome. Prioritized features included known IBD-linked chemical families such as bile acids and short-chain fatty acids, and less-explored bilirubin, polyamine, and vitamin derivatives, and other microbial products. One of these, nicotinamide riboside, reduced colitis scores in DSS-treated mice. The method, MACARRoN, is generalizable with the potential to improve microbial community characterization and provide therapeutic candidates.}, }
@article {pmid38465958, year = {2024}, author = {Rivero-Marcos, M and Lasa, B and Neves, T and Zamarreño, &#xc1;M and García-Mina, JM and García-Olaverri, C and Aparicio-Tejo, PM and Cruz, C and Ariz, I}, title = {Plant ammonium sensitivity is associated with external pH adaptation, repertoire of nitrogen transporters, and nitrogen requirement.}, journal = {Journal of experimental botany}, volume = {75}, number = {11}, pages = {3557-3578}, pmid = {38465958}, issn = {1460-2431}, support = {RYC2021-032345-I//European Union Next Generation EU/PRTR/ ; }, mesh = {*Nitrogen/metabolism ; Hydrogen-Ion Concentration ; *Ammonium Compounds/metabolism ; Nitrates/metabolism ; Plant Proteins/metabolism/genetics ; Plants/metabolism ; Adaptation, Physiological ; }, abstract = {Modern crops exhibit diverse sensitivities to ammonium as the primary nitrogen source, influenced by environmental factors such as external pH and nutrient availability. Despite its significance, there is currently no systematic classification of plant species based on their ammonium sensitivity. We conducted a meta-analysis of 50 plant species and present a new classification method based on the comparison of fresh biomass obtained under ammonium and nitrate nutrition. The classification uses the natural logarithm of the biomass ratio as the size effect indicator of ammonium sensitivity. This numerical parameter is associated with critical factors for nitrogen demand and form preference, such as Ellenberg indicators and the repertoire of nitrogen transporters for ammonium and nitrate uptake. Finally, a comparative analysis of the developmental and metabolic responses, including hormonal balance, is conducted in two species with divergent ammonium sensitivity values in the classification. Results indicate that nitrate has a key role in counteracting ammonium toxicity in species with a higher abundance of genes encoding NRT2-type proteins and fewer of those encoding the AMT2-type proteins. Additionally, the study demonstrates the reliability of the phytohormone balance and methylglyoxal content as indicators for anticipating ammonium toxicity.}, }
@article {pmid38461307, year = {2024}, author = {Zhang, L and Li, H and Shi, M and Ren, K and Zhang, W and Cheng, Y and Wang, Y and Xia, XQ}, title = {FishSNP: a high quality cross-species SNP database of fishes.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {286}, pmid = {38461307}, issn = {2052-4463}, mesh = {Animals ; *Fishes/genetics ; Genome ; *Genomics ; *Polymorphism, Single Nucleotide ; Reproducibility of Results ; *Databases, Genetic ; }, abstract = {The progress of aquaculture heavily depends on the efficient utilization of diverse genetic resources to enhance production efficiency and maximize profitability. Single nucleotide polymorphisms (SNPs) have been widely used in the study of aquaculture genomics, genetics, and breeding research since they are the most prevalent molecular markers on the genome. Currently, a large number of SNP markers from cultured fish species are scattered in individual studies, making querying complicated and data reuse problematic. We compiled relevant SNP data from literature and public databases to create a fish SNP database, FishSNP (http://bioinfo.ihb.ac.cn/fishsnp), and also used a unified analysis pipeline to process raw data that the author of the literature did not perform SNP calling on to obtain SNPs with high reliability. This database presently contains 45,690,243 (45 million) nonredundant SNP data for 13 fish species, with 30,288,958 (30 million) of those being high-quality SNPs. The main function of FishSNP is to search, browse, annotate and download SNPs, which provide researchers various and comprehensive associated information.}, }
@article {pmid38452667, year = {2024}, author = {Chen, X and Zhu, Y and Zheng, W and Yan, S and Li, Y and Xie, S}, title = {Elucidating doxycycline biotransformation mechanism by Chryseobacterium sp. WX1: Multi-omics insights.}, journal = {Journal of hazardous materials}, volume = {469}, number = {}, pages = {133975}, doi = {10.1016/j.jhazmat.2024.133975}, pmid = {38452667}, issn = {1873-3336}, mesh = {*Doxycycline ; *Chryseobacterium/genetics ; Multiomics ; Proteomics ; Biotransformation ; }, abstract = {Doxycycline (DOX) represents a second-generation tetracycline antibiotic that persists as a challenging-to-degrade contaminant in environmental compartments. Despite its ubiquity, scant literature exists on bacteria proficient in DOX degradation. This study marked a substantial advancement in this field by isolating Chryseobacterium sp. WX1 from an activated sludge enrichment culture, showcasing its unprecedented ability to completely degrade 50 mg/L of DOX within 44 h. Throughout the degradation process, seven biotransformation products were identified, revealing a complex pathway that began with the hydroxylation of DOX, followed by a series of transformations. Employing an integrated multi-omics approach alongside in vitro heterologous expression assays, our study distinctly identified the tetX gene as a critical facilitator of DOX hydroxylation. Proteomic analyses further pinpointed the enzymes postulated to mediate the downstream modifications of DOX hydroxylation derivatives. The elucidated degradation pathway encompassed several key biological processes, such as the microbial transmembrane transport of DOX and its intermediates, the orchestration of enzyme synthesis for transformation, energy metabolism, and other gene-regulated biological directives. This study provides the first insight into the adaptive biotransformation strategies of Chryseobacterium under DOX-induced stress, highlighting the potential applications of this strain to augment DOX removal in wastewater treatment systems containing high concentrations of DOX.}, }
@article {pmid38452336, year = {2024}, author = {Vacchi, L and Zirone, E and Strina, V and Cavaletti, G and Ferrarese, C}, title = {Mobile Applications to Support Multiple Sclerosis Communities: The Post-COVID-19 Scenario.}, journal = {Telemedicine journal and e-health : the official journal of the American Telemedicine Association}, volume = {30}, number = {6}, pages = {e1615-e1628}, doi = {10.1089/tmj.2023.0515}, pmid = {38452336}, issn = {1556-3669}, mesh = {Humans ; Access to Information ; COVID-19/epidemiology/prevention &amp; control ; *Digital Health/trends ; Health Knowledge, Attitudes, Practice ; Italy/epidemiology ; *Mobile Applications/trends ; *Multiple Sclerosis/diagnosis/therapy ; Social Networking ; *Telemedicine/trends ; }, abstract = {Introduction: The increase in the use of mobile apps since the COVID-19 pandemic, even among people with multiple sclerosis (PwMS) and health care providers (HCPs), has enabled access to reliable information, symptoms monitoring and management, and social connections. The pandemic has undoubtedly contributed to the acceleration of the "digital revolution." But how far has it progressed for the MS communities? Methods: Italian Google Play and App Store were queried, selecting MS-specific apps in English or Italian language and usable by a wide public. Results: Fifty-four (n = 54) MS-specific apps were identified; most were PwMS-oriented (83%), free of charge (94%), and in English language (76%). The 45 PwMS-oriented apps focused on increasing MS knowledge (71%), tracking symptoms (33%), and promoting networking with peers or HCPs (38%). The 13 HCPs-oriented tools addressed education and updates on MS (62%), disease assessment and management (54%), and research (15%). Google Search tool was also queried to find non-MS-specific apps to fulfill some unmet domains (as sleep, pain, sexual or mental health). Twenty-four additional apps were listed to provide a valuable contribution. Conclusion: The "digital revolution" led to increasingly customized tools for PwMS, especially as m-health or social-networking apps. However, apps to support other specific MS-relevant domains, appealing HCPs-oriented apps, and specific mobile tools for MS caregivers are still lacking. The absence of data assessing the usability and quality of MS apps in ecologically contexts leads to not reliable conclusions about potential benefits. A strong dialogue between MS communities and the digital industry is encouraged to fill this gap.}, }
@article {pmid38451645, year = {2024}, author = {Souza, IM and Araújo, EM and Silva Filho, AMD}, title = {Incomplete recording of race/colour in health information systems in Brazil: time trend, 2009-2018.}, journal = {Ciencia &amp; saude coletiva}, volume = {29}, number = {3}, pages = {e05092023}, doi = {10.1590/1413-81232024293.05092023}, pmid = {38451645}, issn = {1678-4561}, mesh = {Humans ; Black People ; Brazil/epidemiology ; *Health Information Systems ; *Hospital Information Systems ; Racial Groups ; Ethnicity ; }, abstract = {This ecological study of time trends and multiple groups evaluated incompleteness in the race/colour field of Brazilian health information system records and the related time trend, 2009-2018, for the diseases and disorders most prevalent in the black population. The Romero and Cunha (2006) classification was applied in order to examine incompleteness using secondary data from Brazil's National Notifiable Diseases System, Hospital Information System and Mortality Information System, by administrative regions of Brazil, while percentage underreporting and time trend were calculated using simple linear regression models with Prais-Winsten correction (p-value<0.05). All records scored poorly except those for mortality from external causes (excellent), tuberculosis (good) and infant mortality (fair). An overall downward trend was observed in percentage incompleteness. Analysis by region found highest mean incompleteness in the North (30.5%), Northeast (33.3%) and Midwest (33.0%) regions. The Southeast and Northeast regions showed the strongest downward trends. The findings intended to increase visibility on the implications of the race/color field for health equity.}, }
@article {pmid38448699, year = {2024}, author = {Tao, F and Houlton, BZ and Frey, SD and Lehmann, J and Manzoni, S and Huang, Y and Jiang, L and Mishra, U and Hungate, BA and Schmidt, MWI and Reichstein, M and Carvalhais, N and Ciais, P and Wang, YP and Ahrens, B and Hugelius, G and Hocking, TD and Lu, X and Shi, Z and Viatkin, K and Vargas, R and Yigini, Y and Omuto, C and Malik, AA and Peralta, G and Cuevas-Corona, R and Di Paolo, LE and Luotto, I and Liao, C and Liang, YS and Saynes, VS and Huang, X and Luo, Y}, title = {Reply to: Model uncertainty obscures major driver of soil carbon.}, journal = {Nature}, volume = {627}, number = {8002}, pages = {E4-E6}, pmid = {38448699}, issn = {1476-4687}, mesh = {*Uncertainty ; }, }
@article {pmid38447714, year = {2024}, author = {Liu, Y and You, S and Ding, L and Yuan, F and Sun, Y}, title = {Hepatotoxic effects of chronic exposure to environmentally relevant concentrations of Di-(2-ethylhexyl) phthalate (DEHP) on crucian carp: Insights from multi-omics analyses.}, journal = {The Science of the total environment}, volume = {923}, number = {}, pages = {171447}, doi = {10.1016/j.scitotenv.2024.171447}, pmid = {38447714}, issn = {1879-1026}, mesh = {Animals ; *Diethylhexyl Phthalate/metabolism ; Ecosystem ; *Carps/metabolism ; Multiomics ; *Phthalic Acids/toxicity/analysis ; }, abstract = {Di-(2-ethylhexyl) phthalate (DEHP) is an extensively used phthalate esters (PAEs) that raise growing ecotoxicological concerns due to detrimental effects on living organisms and ecosystems. This study performed hepatotoxic investigations on crucian carp under chronic low-dosage (CLD) exposure to DEHP at environmentally relevant concentrations (20-500 μg/L). The results demonstrated that the CLD exposure induced irreversible damage to the liver tissue. Multi-omics (transcriptomics and metabolomics) analyses revealed the predominant toxicological mechanisms underlying DEHP-induced hepatotoxicity by inhibiting energy production pathways and the up-regulation of the purine metabolism. Disruption of metabolic pathways led to excessive reactive oxygen species (ROS) production and subsequent oxidative stress. The adverse metabolic effects were exacerbated by an interplay between oxidative stress and endoplasmic reticulum stress. This study not only provides new mechanistic insights into the ecotoxicological effects of DEHP under chronic low-dosage exposure, but also suggests a potential strategy for further ecological risk assessment of PAEs.}, }
@article {pmid38447388, year = {2024}, author = {van der Feltz-Cornelis, C and Turk, F and Sweetman, J and Khunti, K and Gabbay, M and Shepherd, J and Montgomery, H and Strain, WD and Lip, GYH and Wootton, D and Watkins, CL and Cuthbertson, DJ and Williams, N and Banerjee, A}, title = {Prevalence of mental health conditions and brain fog in people with long COVID: A systematic review and meta-analysis.}, journal = {General hospital psychiatry}, volume = {88}, number = {}, pages = {10-22}, doi = {10.1016/j.genhosppsych.2024.02.009}, pmid = {38447388}, issn = {1873-7714}, mesh = {Humans ; *COVID-19/epidemiology ; Prevalence ; *Post-Acute COVID-19 Syndrome ; Cognitive Dysfunction/epidemiology/etiology ; Mental Disorders/epidemiology ; }, abstract = {OBJECTIVE: Long COVID can include impaired cognition ('brain fog'; a term encompassing multiple symptoms) and mental health conditions. We performed a systematic review and meta-analysis to estimate their prevalence and to explore relevant factors associated with the incidence of impaired cognition and mental health conditions.<br><br>METHODS: Searches were conducted in Medline and PsycINFO to cover the start of the pandemic until August 2023. Included studies reported prevalence of mental health conditions and brain fog in adults with long COVID after clinically-diagnosed or PCR-confirmed SARS-CoV-2 infection.<br><br>FINDINGS: 17 studies were included, reporting 41,249 long COVID patients. Across all timepoints (3-24&#xa0;months), the combined prevalence of mental health conditions and brain fog was 20&#xb7;4% (95% CI 11&#xb7;1%-34&#xb7;4%), being lower among those previously hospitalised than in community-managed patients(19&#xb7;5 vs 29&#xb7;7% respectively; p&#xa0;=&#xa0;0&#xb7;047). The odds of mental health conditions and brain fog increased over time and when validated instruments were used. Odds of brain fog significantly decreased with increasing vaccination rates (p&#xa0;=&#xa0;&#xb7;000).<br><br>CONCLUSIONS: Given the increasing prevalence of mental health conditions and brain fog over time, preventive interventions and treatments are needed. Research is needed to explore underlying mechanisms that could inform further research in development of effective treatments. The reduced risk of brain fog associated with vaccination emphasizes the need for ongoing vaccination programs.}, }
@article {pmid38445504, year = {2024}, author = {Kudamba, A and Kasolo, JN and Bbosa, GS and Lugaajju, A and Wabinga, H and Kafeero, HM and Ssenku, JE and Alemu, SO and Walusansa, A and Niyonzima, N and Muwonge, H}, title = {Review of Herbal Medicinal Plants Used in the Management of Cancers in the East Africa Region from 2019 to 2023.}, journal = {Integrative cancer therapies}, volume = {23}, number = {}, pages = {15347354241235583}, pmid = {38445504}, issn = {1552-695X}, mesh = {Male ; Humans ; *Plants, Medicinal ; Africa, Eastern ; *Prostatic Neoplasms ; *Apocynaceae ; Databases, Factual ; }, abstract = {BACKGROUND: In the East African region, herbal plants are essential in the treatment and control of cancer. Given the diverse ecological and cultural makeup of the regional states, it is likely that different ethnic groups will use the same or different plants for the same or different diseases. However, since 2019, this has not been compiled into a single study.<br><br>PURPOSE: The study aimed to compile and record the medicinal plants utilized in East Africa from April 2019 to June 2023 to treat various cancer types.<br><br>MATERIALS AND METHODS: The study examined 13 original studies that included ethnobotanical research conducted in East Africa. They were retrieved from several internet databases, including Google Scholar, Scopus, PubMed/Medline, Science Direct, and Research for Life. The study retrieved databases on plant families and species, plant parts used, preparation methods and routes of administration, and the country where the ethnobotanical field surveys were conducted. Graphs were produced using the GraphPad Prism 8.125 program (GraphPad Software, Inc., San Diego, CA). Tables and figures were used to present the data, which had been condensed into percentages and frequencies.<br><br>RESULTS: A total of 105 different plant species from 45 different plant families were identified, including Asteraceae (14), Euphorbiaceae (12), Musaceae (8), and Apocynaceae (7). Uganda registered the highest proportion (46% of the medicinal plants used). The most commonly mentioned medicinal plant species in cancer management was Prunus africana. Herbs (32%), trees and shrubs (28%), and leaves (45%) constituted the majority of herbal remedies. Most herbal remedies were prepared by boiling (decoction) and taken orally (57%).<br><br>CONCLUSION: East Africa is home to a wide variety of medicinal plant species that local populations and herbalists, or TMP, frequently use in the treatment of various types of cancer. The most frequently used families are Asteraceae and Euphorbiaceae, with the majority of species being found in Uganda. The most frequently utilized plant species is Prunus africana. Studies on the effectiveness of Prunus africana against other malignancies besides prostate cancer are required.}, }
@article {pmid38444395, year = {2024}, author = {Liu, Y and Li, L and Feng, J and Wan, B and Tu, Q and Cai, W and Jin, F and Tang, G and Rodrigues, LR and Zhang, X and Yin, J and Zhang, Y}, title = {Modulation of chronic obstructive pulmonary disease progression by antioxidant metabolites from Pediococcus pentosaceus: enhancing gut probiotics abundance and the tryptophan-melatonin pathway.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2320283}, pmid = {38444395}, issn = {1949-0984}, mesh = {Animals ; Mice ; Antioxidants ; Pediococcus pentosaceus ; *Melatonin/pharmacology ; Tryptophan ; *Gastrointestinal Microbiome ; *Probiotics ; *Pulmonary Disease, Chronic Obstructive ; }, abstract = {Chronic obstructive pulmonary disease (COPD), a condition primarily linked to oxidative stress, poses significant health burdens worldwide. Recent evidence has shed light on the association between the dysbiosis of gut microbiota and COPD, and their metabolites have emerged as potential modulators of disease progression through the intricate gut-lung axis. Here, we demonstrate the efficacy of oral administration of the probiotic Pediococcus pentosaceus SMM914 (SMM914) in delaying the progression of COPD by attenuating pulmonary oxidative stress. Specially, SMM914 induces a notable shift in the gut microbiota toward a community structure characterized by an augmented abundance of probiotics producing short-chain fatty acids and antioxidant metabolisms. Concurrently, SMM914 synthesizes L-tryptophanamide, 5-hydroxy-L-tryptophan, and 3-sulfino-L-alanine, thereby enhancing the tryptophan-melatonin pathway and elevating 6-hydroxymelatonin and hypotaurine in the lung environment. This modulation amplifies the secretion of endogenous anti-inflammatory factors, diminishes macrophage polarization toward the M1 phenotype, and ultimately mitigates the oxidative stress in mice with COPD. The demonstrated efficacy of the probiotic intervention, specifically with SMM914, not only highlights the modulation of intestine microbiota but also emphasizes the consequential impact on the intricate interplay between the gastrointestinal system and respiratory health.}, }
@article {pmid38443441, year = {2024}, author = {Zhang, Z and Xu, H and Zhu, G}, title = {Incorporating high-frequency information into edge convolution for link prediction in complex networks.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {5437}, pmid = {38443441}, issn = {2045-2322}, support = {1908085QF283//Natural Science Foundation of Anhui Province/ ; 2019jb08//Doctoral Startup Research Fund of Suzhou University/ ; 2021bsk016//Doctoral Startup Research Fund of Suzhou University/ ; GXXT-2022-047//University Synergy Innovation Program of Anhui Province/ ; 2021XJPT50, 2022xhx004, 2022xhx099//Scientific Research Projects Funded by Suzhou University/ ; AE202201//Open Research Fund of National Engineering Research Center for Agro-Ecological Big Data Analysis &amp; Application, Anhui University/ ; }, abstract = {Link prediction in complex networks aims to mine hidden or to-be-generated links between network nodes, which plays a significant role in fields such as the cold start of recommendation systems, knowledge graph completion and biomedical experiments. The existing link prediction models based on graph neural networks, such as graph convolution neural networks, often only learn the low-frequency information reflecting the common characteristics of nodes while ignoring the high-frequency information reflecting the differences between nodes when learning node representation, which makes the corresponding link prediction models show over smoothness and poor performance. Focusing on links in complex networks, this paper proposes an edge convolutional graph neural network EdgeConvHiF that fuses high-frequency node information to achieve the representation learning of links so that link prediction can be realized by implementing the classification of links. EdgeConvHiF can also be employed as a baseline, and extensive experiments on real-world benchmarks validate that EdgeConvHiF not only has high stability but also has more advantages than the existing representative baselines.}, }
@article {pmid38443432, year = {2024}, author = {Ge, X and Peng, L and Deng, Z and Du, J and Sun, C and Wang, B}, title = {Chromosome-scale genome assemblies of Himalopsyche anomala and Eubasilissa splendida (Insecta: Trichoptera).}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {267}, pmid = {38443432}, issn = {2052-4463}, support = {32271631//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; Comparative Genomic Hybridization ; Ecology ; *Insecta/genetics ; *Genome, Insect ; *Databases, Genetic ; }, abstract = {Trichoptera is one of the most evolutionarily successful aquatic insect lineages and is highly valued value in adaptive evolution research. This study presents the chromosome-level genome assemblies of Himalopsyche anomala and Eubasilissa splendida achieved using PacBio, Illumina, and Hi-C sequencing. For H. anomala and E. splendida, assembly sizes were 663.43 and 859.28 Mb, with scaffold N50 lengths of 28.44 and 31.17 Mb, respectively. In H. anomala and E. splendida, we anchored 24 and 29 pseudochromosomes, and identified 11,469 and 10,554 protein-coding genes, respectively. The high-quality genomes of H. anomala and E. splendida provide critical genomic resources for understanding the evolution and ecology of Trichoptera and performing comparative genomics analyses.}, }
@article {pmid38443357, year = {2024}, author = {Zhou, H and Zhang, X and Liu, H and Ma, J and Hao, F and Ye, H and Wang, Y and Zhang, S and Yue, M and Zhao, P}, title = {Chromosome-level genome assembly of Platycarya strobilacea.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {269}, pmid = {38443357}, issn = {2052-4463}, support = {32370386, 32070372, and 32200295//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Asia, Eastern ; Biological Evolution ; Chromosomes ; *Juglandaceae/genetics ; Phylogeny ; *Genome, Plant ; *Databases, Genetic ; }, abstract = {Platycarya strobilacea belongs to the walnut family (Juglandaceae), is commonly known as species endemic to East Asia, and is an ecologically important, wind pollinated, woody deciduous tree. To facilitate this ancient tree for the ecological value and conservation of this ancient tree, we report a new high-quality genome assembly of P. strobilacea. The genome size was 677.30 Mb, with a scaffold N50 size of 45,791,698 bp, and 98.43% of the assembly was anchored to 15 chromosomes. We annotated 32,246 protein-coding genes in the genome, of which 96.30% were functionally annotated in six databases. This new high-quality assembly of P. strobilacea provide valuable resource for the phylogenetic and evolutionary analysis of the walnut family and angiosperm.}, }
@article {pmid38442095, year = {2024}, author = {Tamosiunaite, M and Tetzlaff, C and Wörgötter, F}, title = {Unsupervised learning of perceptual feature combinations.}, journal = {PLoS computational biology}, volume = {20}, number = {3}, pages = {e1011926}, pmid = {38442095}, issn = {1553-7358}, mesh = {Animals ; *Unsupervised Machine Learning ; *Models, Neurological ; Neurons/physiology ; }, abstract = {In many situations it is behaviorally relevant for an animal to respond to co-occurrences of perceptual, possibly polymodal features, while these features alone may have no importance. Thus, it is crucial for animals to learn such feature combinations in spite of the fact that they may occur with variable intensity and occurrence frequency. Here, we present a novel unsupervised learning mechanism that is largely independent of these contingencies and allows neurons in a network to achieve specificity for different feature combinations. This is achieved by a novel correlation-based (Hebbian) learning rule, which allows for linear weight growth and which is combined with a mechanism for gradually reducing the learning rate as soon as the neuron's response becomes feature combination specific. In a set of control experiments, we show that other existing advanced learning rules cannot satisfactorily form ordered multi-feature representations. In addition, we show that networks, which use this type of learning always stabilize and converge to subsets of neurons with different feature-combination specificity. Neurons with this property may, thus, serve as an initial stage for the processing of ecologically relevant real world situations for an animal.}, }
@article {pmid38441325, year = {2024}, author = {Davies, H and Blackwell, E and Fins, IS and Noble, PJM and Pinchbeck, G and Pirmohamed, M and Killick, DR}, title = {Recording of suspected adverse drug reaction reporting in veterinary free-text clinical narratives.}, journal = {The Journal of small animal practice}, volume = {65}, number = {6}, pages = {361-367}, doi = {10.1111/jsap.13721}, pmid = {38441325}, issn = {1748-5827}, support = {VM0541//Veterinary Medicines Directorate/ ; SRP 02.21//British Small Animal Veterinary Association/ ; 204822/z/16/z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Adverse Drug Reaction Reporting Systems/statistics &amp; numerical data ; Animals ; *Drug-Related Side Effects and Adverse Reactions/veterinary ; Data Mining ; Veterinary Drugs/adverse effects ; Electronic Health Records ; Veterinary Medicine ; Pharmacovigilance ; }, abstract = {OBJECTIVES: To use text mining approaches to identify instances of suspected adverse drug reactions recorded in first opinion veterinary free-text clinical narratives, and to evaluate whether these were also reported to either the Veterinary Medicines Directorate or the relevant Marketing Authorisation holder in order to derive an estimate of the suspected adverse drug reaction (sADR) minimum under-reporting rate. To characterise sADR reports and explore whether particular features are associated with report submission.<br><br>MATERIALS AND METHODS: Two regular expressions were developed to identify mentions of "adverse drug reactions" and "side effects" in the free-text clinical narratives of electronic health records contained within the Small Animal Veterinary Surveillance Network database. Consultations containing a match for the developed regular expressions were manually reviewed for inclusion and further classified to determine the suspected product, seriousness and expectedness of the event, and an indication of whether the event had been reported. The associations between event characteristics and reporting were explored using Fisher's exact tests.<br><br>RESULTS: A total of 10,565 records were manually reviewed from which 827 sADRs were identified. Approximately 90% of these sADRs were not recorded as reported. Suspected adverse drug reactions that were not considered "expected" were recorded as reported more frequently than "expected" sADRs. However, clinical severity did not appear to impact on whether there was a record of reporting.<br><br>CLINICAL SIGNIFICANCE: This is the first estimate of under reporting sADRs based on real world evidence from veterinary clinical records. The under-reporting rate implied by this study highlights that further interventions are required to improve reporting rate within the veterinary profession in order to support pharmacovigilance activities and improve drug safety.}, }
@article {pmid38438998, year = {2024}, author = {Wu, LF and Zhu, WG and Yu, EP and Cao, HL and Wang, ZF}, title = {Draft genome of Brasenia schreberi, a worldwide distributed and endangered aquatic plant.}, journal = {BMC genomic data}, volume = {25}, number = {1}, pages = {24}, pmid = {38438998}, issn = {2730-6844}, mesh = {*Seeds ; *Plant Weeds ; Allelopathy ; China ; Databases, Factual ; }, abstract = {OBJECTIVES: Brasenia is a monotypic genus in the family of Cabombaceae. The only species, B. schreberi, is a macrophyte distributed worldwide. Because it requires good water quality, it is endangered in China and other countries due to the deterioration of aquatic habitats. The young leaves and stems of B. schreberi are covered by thick mucilage, which has high medical value. As an allelopathic aquatic plant, it can also be used in the management of aquatic weeds. Here, we present its assembled and annotated genome to help shed light on medial and allelopathic substrates and facilitate their conservation.<br><br>DATA DESCRIPTION: Genomic DNA and RNA extracted from B. schreberi leaf tissues were used for whole genome and RNA sequencing using a Nanopore and/or MGI sequencer. The assembly was 1,055,148,839&#xa0;bp in length, with 92 contigs and an N50 of 22,379,495&#xa0;bp. The repetitive elements in the assembly were 555,442,205&#xa0;bp. A completeness assessment of the assembly with BUSCO and compleasm indicated 88.4 and 90.9% completeness in the Eudicots database and 95.4 and 96.6% completeness in the Embryphyta database. Gene annotation revealed 67,747 genes that coded for 73,344 proteins.}, }
@article {pmid38436579, year = {2024}, author = {Qian, J and Qian, L and Pu, N and Bi, Y and Wilhelms, A and Norra, S}, title = {An Intelligent Early Warning System for Harmful Algal Blooms: Harnessing the Power of Big Data and Deep Learning.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {35}, pages = {15607-15618}, doi = {10.1021/acs.est.3c03906}, pmid = {38436579}, issn = {1520-5851}, mesh = {*Deep Learning ; *Harmful Algal Bloom ; *Big Data ; *Environmental Monitoring/methods ; Lakes ; }, abstract = {Harmful algal blooms (HABs) pose a significant ecological threat and economic detriment to freshwater environments. In order to develop an intelligent early warning system for HABs, big data and deep learning models were harnessed in this study. Data collection was achieved utilizing the vertical aquatic monitoring system (VAMS). Subsequently, the analysis and stratification of the vertical aquatic layer were conducted employing the "DeepDPM-Spectral Clustering" method. This approach drastically reduced the number of predictive models and enhanced the adaptability of the system. The Bloomformer-2 model was developed to conduct both single-step and multistep predictions of Chl-a, integrating the " Alert Level Framework" issued by the World Health Organization to accomplish early warning for HABs. The case study conducted in Taihu Lake revealed that during the winter of 2018, the water column could be partitioned into four clusters (Groups W1-W4), while in the summer of 2019, the water column could be partitioned into five clusters (Groups S1-S5). Moreover, in a subsequent predictive task, Bloomformer-2 exhibited superiority in performance across all clusters for both the winter of 2018 and the summer of 2019 (MAE: 0.175-0.394, MSE: 0.042-0.305, and MAPE: 0.228-2.279 for single-step prediction; MAE: 0.184-0.505, MSE: 0.101-0.378, and MAPE: 0.243-4.011 for multistep prediction). The prediction for the 3 days indicated that Group W1 was in a Level I alert state at all times. Conversely, Group S1 was mainly under an Level I alert, with seven specific time points escalating to a Level II alert. Furthermore, the end-to-end architecture of this system, coupled with the automation of its various processes, minimized human intervention, endowing it with intelligent characteristics. This research highlights the transformative potential of integrating big data and artificial intelligence in environmental management and emphasizes the importance of model interpretability in machine learning applications.}, }
@article {pmid38436026, year = {2024}, author = {Specker, F and Paz, A and Crowther, TW and Maynard, DS}, title = {Treemendous: an R package for integrating taxonomic information across backbones.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e16896}, pmid = {38436026}, issn = {2167-8359}, mesh = {*Biodiversity ; Databases, Factual ; *Ecology ; Forests ; Software ; Trees ; }, abstract = {Standardizing and translating species names from different databases is key to the successful integration of data sources in biodiversity research. There are numerous taxonomic name-resolution applications that implement increasingly powerful name-cleaning and matching approaches, allowing the user to resolve species relative to multiple backbones simultaneously. Yet there remains no principled approach for combining information across these underlying taxonomic backbones, complicating efforts to combine and merge species lists with inconsistent and conflicting taxonomic information. Here, we present Treemendous, an open-source software package for the R programming environment that integrates taxonomic relationships across four publicly available backbones to improve the name resolution of tree species. By mapping relationships across the backbones, this package can be used to resolve datasets with conflicting and inconsistent taxonomic origins, while ensuring the resulting species are accepted and consistent with a single reference backbone. The user can chain together different functionalities ranging from simple matching to a single backbone, to graph-based iterative matching using synonym-accepted relations across all backbones in the database. In addition, the package allows users to 'translate' one tree species list into another, streamlining the assimilation of new data into preexisting datasets or models. The package provides a flexible workflow depending on the use case, and can either be used as a stand-alone name-resolution package or in conjunction with existing packages as a final step in the name-resolution pipeline. The Treemendous package is fast and easy to use, allowing users to quickly merge different data sources by standardizing their species names according to the regularly updated database. By combining taxonomic information across multiple backbones, the package increases matching rates and minimizes data loss, allowing for more efficient translation of tree species datasets to aid research into forest biodiversity and tree ecology.}, }
@article {pmid38434748, year = {2023}, author = {Boyes, D and Hammond, J and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Diamond-back Marble, Eudemis profundana (Denis &amp; Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {184}, pmid = {38434748}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Eudemis profundana (the Diamond-back Marble; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 691.3 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.5 kilobases in length.}, }
@article {pmid38434745, year = {2023}, author = {Boyes, D and Lees, DC and Hammond, J and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Ashy Button, Acleris sparsana (Denis &amp; Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {241}, pmid = {38434745}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Acleris sparsana (the Ashy Button; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 589.5 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,123 protein coding genes.}, }
@article {pmid38434742, year = {2023}, author = {Boyes, D and Boyes, C and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Minor Shoulder-knot, Brachylomia viminalis (Fabricius, 1777).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {245}, pmid = {38434742}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Brachylomia viminalis (the Minor Shoulder-knot; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 782.2 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.15 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,191 protein coding genes.}, }
@article {pmid38434736, year = {2023}, author = {Boyes, D and Lewis, OT and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Orange Footman, Eilema sororcula (Hufnagel, 1766).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {282}, pmid = {38434736}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Eilema sororcula (the Orange Footman; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 729.4 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.46 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,093 protein coding genes.}, }
@article {pmid38434623, year = {2023}, author = {Thiébaut, A and Altenhoff, AM and Campli, G and Glover, N and Dessimoz, C and Waterhouse, RM}, title = {DrosOMA: the Drosophila Orthologous Matrix browser.}, journal = {F1000Research}, volume = {12}, number = {}, pages = {936}, pmid = {38434623}, issn = {2046-1402}, mesh = {Animals ; *Drosophila/genetics ; Comparative Genomic Hybridization ; Databases, Factual ; *Evolution, Molecular ; Genomics ; }, abstract = {BACKGROUND: Comparative genomic analyses to delineate gene evolutionary histories inform the understanding of organismal biology by characterising gene and gene family origins, trajectories, and dynamics, as well as enabling the tracing of speciation, duplication, and loss events, and facilitating the transfer of gene functional information across species. Genomic data are available for an increasing number of species from the genus Drosophila, however, a dedicated resource exploiting these data to provide the research community with browsable results from genus-wide orthology delineation has been lacking.<br><br>METHODS: Using the OMA Orthologous Matrix orthology inference approach and browser deployment framework, we catalogued orthologues across a selected set of Drosophila species with high-quality annotated genomes. We developed and deployed a dedicated instance of the OMA browser to facilitate intuitive exploration, visualisation, and downloading of the genus-wide orthology delineation results.<br><br>RESULTS: DrosOMA - the Drosophila Orthologous Matrix browser, accessible from https://drosoma.dcsr.unil.ch/ - presents the results of orthology delineation for 36 drosophilids from across the genus and four outgroup dipterans. It enables querying and browsing of the orthology data through a feature-rich web interface, with gene-view, orthologous group-view, and genome-view pages, including comprehensive gene name and identifier cross-references together with available functional annotations and protein domain architectures, as well as tools to visualise local and global synteny conservation.<br><br>CONCLUSIONS: The DrosOMA browser demonstrates the deployability of the OMA browser framework for building user-friendly orthology databases with dense sampling of a selected taxonomic group. It provides the Drosophila research community with a tailored resource of browsable results from genus-wide orthology delineation.}, }
@article {pmid38433952, year = {2024}, author = {Mallinson, DC and Elwert, F and Ehrenthal, DB}, title = {Spillover effects of gestational age on sibling's literacy.}, journal = {Early child development and care}, volume = {194}, number = {2}, pages = {244-259}, pmid = {38433952}, issn = {0300-4430}, support = {R01 HD102125/HD/NICHD NIH HHS/United States ; T32 HD007014/HD/NICHD NIH HHS/United States ; }, abstract = {Adverse health events within families can harm children's development, including their early literacy. Using data from a longitudinal Wisconsin birth cohort, we estimated the spillover effect of younger siblings' gestational ages on older siblings' kindergarten-level literacy. We sampled 20,014 sibling pairs born during 2007-2010 who took Phonological Awareness Literacy Screening-Kindergarten tests during 2012-2016. Exposures were gestational age (completed weeks), preterm birth (gestational age <37 weeks), and very preterm birth (gestational age <32 weeks). We used gain-score regression-a fixed effects strategy-to estimate spillover effect. A one-week increase in younger siblings' gestational age improved the older siblings' test score by 0.011 SD (95% confidence interval: 0.001, 0.021 SD). The estimated spillover effect was larger among siblings whose mothers reported having a high school diploma/equivalent only (0.024 SD; 95% CI: 0.004, 0.044 SD). The finding underscores the networked effects of one individual's early-life health shocks on their family members.}, }
@article {pmid38432384, year = {2024}, author = {Baima Ferreira Freitas, I and Duarte-Neto, PJ and Sorigotto, LR and Cardoso Yoshii, MP and de Palma Lopes, LF and de Almeida Pereira, MM and Girotto, L and Badolato Athayde, D and Veloso Goulart, B and Montagner, CC and Schiesari, LC and Martinelli, LA and Gaeta Espíndola, EL}, title = {Effects of pasture intensification and sugarcane cultivation on non-target species: A realistic evaluation in pesticide-contaminated mesocosms.}, journal = {The Science of the total environment}, volume = {922}, number = {}, pages = {171425}, doi = {10.1016/j.scitotenv.2024.171425}, pmid = {38432384}, issn = {1879-1026}, mesh = {Female ; Animals ; Cattle ; *Pesticides/toxicity ; *Saccharum ; Environmental Biomarkers ; Soil ; Water/chemistry ; 2,4-Dichlorophenoxyacetic Acid/toxicity ; *Water Pollutants, Chemical/toxicity ; }, abstract = {Conventional soil management in agricultural areas may expose non-target organisms living nearby to several types of contaminants. In this study, the effects of soil management in extensive pasture (EP), intensive pasture (IP), and sugarcane crops (C) were evaluated in a realistic-field-scale study. Thirteen aquatic mesocosms embedded in EP, IP, and C treatments were monitored over 392 days. The recommended management for each of the areas was simulated, such as tillage, fertilizer, pesticides (i.e. 2,4-D, fipronil) and vinasse application, and cattle pasture. To access the potential toxic effects that the different steps of soil management in these areas may cause, the cladoceran Ceriophania silvestrii was used as aquatic bioindicator, the dicot Eruca sativa as phytotoxicity bioindicator in water, and the dipteran Chironomus sancticaroli as sediment bioindicator. Generalized linear mixed models were used to identify differences between the treatments. Low concentrations of 2,4-D (<97 μg L[-1]) and fipronil (<0.21 μg L[-1]) in water were able to alter fecundity, female survival, and the intrinsic rate of population increase of C. silvestrii in IP and C treatments. Similarly, the dicot E. sativa had germination, shoot and root growth affected mainly by 2,4-D concentrations in the water. For C. sancticarolli, larval development was affected by the presence of fipronil (<402.6 ng g[-1]). The acidic pH (below 5) reduced the fecundity and female survival of C. silvestrii and affected the germination and growth of E. sativa. Fecundity and female survival of C. silvestrii decrease in the presence of phosphorus-containing elements. The outcomes of this study may improve our understanding of the consequences of exposure of freshwater biota to complex stressors in an environment that is rapidly and constantly changing.}, }
@article {pmid38430051, year = {2024}, author = {Rillig, MC and Mansour, I and Hempel, S and Bi, M and König-Ries, B and Kasirzadeh, A}, title = {How widespread use of generative AI for images and video can affect the environment and the science of ecology.}, journal = {Ecology letters}, volume = {27}, number = {3}, pages = {e14397}, doi = {10.1111/ele.14397}, pmid = {38430051}, issn = {1461-0248}, mesh = {*Artificial Intelligence ; *Biodiversity ; }, abstract = {Generative artificial intelligence (AI) models will have broad impacts on society including the scientific enterprise; ecology and environmental science will be no exception. Here, we discuss the potential opportunities and risks of advanced generative AI for visual material (images and video) for the science of ecology and the environment itself. There are clearly opportunities for positive impacts, related to improved communication, for example; we also see possibilities for ecological research to benefit from generative AI (e.g., image gap filling, biodiversity surveys, and improved citizen science). However, there are also risks, threatening to undermine the credibility of our science, mostly related to actions of bad actors, for example in terms of spreading fake information or committing fraud. Risks need to be mitigated at the level of government regulatory measures, but we also highlight what can be done right now, including discussing issues with the next generation of ecologists and transforming towards radically open science workflows.}, }
@article {pmid38429902, year = {2024}, author = {Chen, C and He, Y and Ni, Y and Tang, Z and Zhang, W}, title = {Identification of crosstalk genes relating to ECM-receptor interaction genes in MASH and DN using bioinformatics and machine learning.}, journal = {Journal of cellular and molecular medicine}, volume = {28}, number = {6}, pages = {e18156}, pmid = {38429902}, issn = {1582-4934}, support = {81771152//National Nature Science Foundation of China/ ; }, mesh = {Humans ; *Interleukin-17 ; *Diabetic Nephropathies ; Phosphatidylinositol 3-Kinases ; Computational Biology ; Machine Learning ; }, abstract = {This study aimed to identify genes shared by metabolic dysfunction-associated fatty liver disease (MASH) and diabetic nephropathy (DN) and the effect of extracellular matrix (ECM) receptor interaction genes on them. Datasets with MASH and DN were downloaded from the Gene Expression Omnibus (GEO) database. Pearson's coefficients assessed the correlation between ECM-receptor interaction genes and cross talk genes. The coexpression network of co-expression pairs (CP) genes was integrated with its protein-protein interaction (PPI) network, and machine learning was employed to identify essential disease-representing genes. Finally, immuno-penetration analysis was performed on the MASH and DN gene datasets using the CIBERSORT algorithm to evaluate the plausibility of these genes in diseases. We found 19 key CP genes. Fos proto-oncogene (FOS), belonging to the IL-17 signalling pathway, showed greater centrality PPI network; Hyaluronan Mediated Motility Receptor (HMMR), belonging to ECM-receptor interaction genes, showed most critical in the co-expression network map of 19 CP genes; Forkhead Box C1 (FOXC1), like FOS, showed a high ability to predict disease in XGBoost analysis. Further immune infiltration showed a clear positive correlation between FOS/FOXC1 and mast cells that secrete IL-17 during inflammation. Combining the results of previous studies, we suggest a FOS/FOXC1/HMMR regulatory axis in MASH and DN may be associated with mast cells in the acting IL-17 signalling pathway. Extracellular HMMR may regulate the IL-17 pathway represented by FOS through the Mitogen-Activated Protein Kinase 1 (ERK) or PI3K-Akt-mTOR pathway. HMMR may serve as a signalling carrier between MASH and DN and could be targeted for therapeutic development.}, }
@article {pmid38426108, year = {2024}, author = {Huo, J and Li, X and Hu, X and Lv, A}, title = {Multi-omics analysis of miRNA-mediated intestinal microflora changes in crucian carp Carassius auratus infected with Rahnella aquatilis.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1335602}, pmid = {38426108}, issn = {1664-3224}, mesh = {Animals ; Goldfish/genetics ; *Carps/genetics ; *Rahnella/genetics ; NF-kappa B ; Multiomics ; *Gastrointestinal Microbiome ; Tumor Necrosis Factor-alpha ; Inflammation ; *Enteritis ; Transforming Growth Factor beta ; *MicroRNAs/genetics ; }, abstract = {Infection by an emerging bacterial pathogen Rahnella aquatilis caused enteritis and septicemia in fish. However, the molecular pathogenesis of enteritis induced by R. aquatilis infection and its interacting mechanism of the intestinal microflora associated with microRNA (miRNA) immune regulation in crucian carp Carassius auratus are still unclear. In this study, C. auratus intraperitoneally injected with R. aquatilis KCL-5 was used as an experimental animal model, and the intestinal pathological changes, microflora, and differentially expressed miRNAs (DEMs) were investigated by multi-omics analysis. The significant changes in histopathological features, apoptotic cells, and enzyme activities (e.g., lysozyme (LYS), alkaline phosphatase (AKP), alanine aminotransferase (ALT), aspartate transaminase (AST), and glutathione peroxidase (GSH-Px)) in the intestine were examined after infection. Diversity and composition analysis of the intestinal microflora clearly demonstrated four dominant bacteria: Proteobacteria, Fusobacteria, Bacteroidetes, and Firmicutes. A total of 87 DEMs were significantly screened, and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the potential target genes were mainly involved in the regulation of lipid, glutathione, cytosine, and purine metabolism, which participated in the local immune response through the intestinal immune network for IgA production, lysosome, and Toll-like receptor (TLR) pathways. Moreover, the expression levels of 11 target genes (e.g., TLR3, MyD88, NF-κB, TGF-β, TNF-α, MHC II, IL-22, LysC, F2, F5, and C3) related to inflammation and immunity were verified by qRT-PCR detection. The correlation analysis indicated that the abundance of intestinal Firmicutes and Proteobacteria was significantly associated with the high local expression of miR-203/NF-κB, miR-129/TNF-α, and miR-205/TGF-β. These findings will help to elucidate the molecular regulation mechanism of the intestinal microflora, inflammation, and immune response-mediated miRNA-target gene axis in cyprinid fish.}, }
@article {pmid38423780, year = {2024}, author = {Hitchings, L and Fleet, B and Smith, DT and Read, JM and Melville, C and Sedda, L}, title = {Determining the distance patterns in the movements of future doctors in UK between 2002 and 2015: a retrospective cohort study.}, journal = {BMJ open}, volume = {14}, number = {3}, pages = {e077635}, pmid = {38423780}, issn = {2044-6055}, mesh = {Humans ; Retrospective Studies ; *Career Choice ; Gender Identity ; Social Class ; *Students, Medical ; Schools, Medical ; United Kingdom ; }, abstract = {OBJECTIVE: To determine and identify distance patterns in the movements of medical students and junior doctors between their training locations.<br><br>DESIGN: A retrospective cohort study of UK medical students from 2002 to 2015 (UKMED data).<br><br>SETTING: All UK medical schools, foundations and specialty training organisation.<br><br>PARTICIPANTS: All UK medical students from 2002 to 2015, for a total of 97&#x2009;932 participants.<br><br>OUTCOME MEASURES: Individual movements and number of movements by county of students from family home to medical school training, from medical school to foundation training and from foundation to specialty training.<br><br>METHODS: Leslie matrix, principal components analysis, Gini coefficient, &#x3c7;[2] test, generalised linear models and variable selection methods were employed to explore the different facets of students' and junior doctors' movements from the family home to medical school and for the full pathway (from family home to specialty training).<br><br>RESULTS: The majority of the movements between the different stages of the full pathway were restricted to a distance of up to 50&#x2009;km; although the proportion of movements changed from year-to-year, with longer movements during 2007-2008. At the individual level, ethnicity, socioeconomic class of the parent(s) and the deprivation score of the family home region were found to be the most important factors associated with the length of the movements from the family home to medical school. Similar results were found when movements were aggregated at the county level, with the addition of factors such as gender and qualification at entry (to medical school) being statistically associated with the number of new entrant students moving between counties.<br><br>CONCLUSION: Our findings show that while future doctors do not move far from their family home or training location, this pattern is not homogeneous over time. Distances are influenced by demographics, socioeconomic status and deprivation. These results may contribute in designing interventions aimed at solving the chronic problems of maldistribution and underdoctoring in the UK.}, }
@article {pmid38422100, year = {2024}, author = {Barrenechea Angeles, I and Nguyen, NL and Greco, M and Tan, KS and Pawlowski, J}, title = {Assigning the unassigned: A signature-based classification of rDNA metabarcodes reveals new deep-sea diversity.}, journal = {PloS one}, volume = {19}, number = {2}, pages = {e0298440}, pmid = {38422100}, issn = {1932-6203}, mesh = {Phylogeny ; *DNA, Environmental ; DNA, Ribosomal ; Databases, Factual ; *Foraminifera/genetics ; Water ; }, abstract = {Environmental DNA metabarcoding reveals a vast genetic diversity of marine eukaryotes. Yet, most of the metabarcoding data remain unassigned due to the paucity of reference databases. This is particularly true for the deep-sea meiofauna and eukaryotic microbiota, whose hidden diversity is largely unexplored. Here, we tackle this issue by using unique DNA signatures to classify unknown metabarcodes assigned to deep-sea foraminifera. We analyzed metabarcoding data obtained from 311 deep-sea sediment samples collected in the Clarion-Clipperton Fracture Zone, an area of potential polymetallic nodule exploitation in the Eastern Pacific Ocean. Using the signatures designed in the 37F hypervariable region of the 18S rRNA gene, we were able to classify 802 unassigned metabarcodes into 61 novel lineages, which have been placed in 27 phylogenetic clades. The comparison of new lineages with other foraminiferal datasets shows that most novel lineages are widely distributed in the deep sea. Five lineages are also present in the shallow-water datasets; however, phylogenetic analysis of these lineages separates deep-sea and shallow-water metabarcodes except in one case. While the signature-based classification does not solve the problem of gaps in reference databases, this taxonomy-free approach provides insight into the distribution and ecology of deep-sea species represented by unassigned metabarcodes, which could be useful in future applications of metabarcoding for environmental monitoring.}, }
@article {pmid38418873, year = {2024}, author = {Delavaux, CS and Crowther, TW and Bever, JD and Weigelt, P and Gora, EM}, title = {Mutualisms weaken the latitudinal diversity gradient among oceanic islands.}, journal = {Nature}, volume = {627}, number = {8003}, pages = {335-339}, pmid = {38418873}, issn = {1476-4687}, mesh = {Animals ; *Biodiversity ; Datasets as Topic ; *Geographic Mapping ; *Islands ; Mycorrhizae/physiology ; *Plants/microbiology ; Pollination ; *Symbiosis ; Tropical Climate ; Oceans and Seas ; Phylogeography ; }, abstract = {The latitudinal diversity gradient (LDG) dominates global patterns of diversity[1,2], but the factors that underlie the LDG remain elusive. Here we use a unique global dataset[3] to show that vascular plants on oceanic islands exhibit a weakened LDG and explore potential mechanisms for this effect. Our results show that traditional physical drivers of island biogeography[4]-namely area and isolation-contribute to the difference between island and mainland diversity at a given latitude (that is, the island species deficit), as smaller and more distant islands experience reduced colonization. However, plant species with mutualists are underrepresented on islands, and we find that this plant mutualism filter explains more variation in the island species deficit than abiotic factors. In particular, plant species that require animal pollinators or microbial mutualists such as arbuscular mycorrhizal fungi contribute disproportionately to the island species deficit near the Equator, with contributions decreasing with distance from the Equator. Plant mutualist filters on species richness are particularly strong at low absolute latitudes where mainland richness is highest, weakening the LDG of oceanic islands. These results provide empirical evidence that mutualisms, habitat heterogeneity and dispersal are key to the maintenance of high tropical plant diversity and mediate the biogeographic patterns of plant diversity on Earth.}, }
@article {pmid38416313, year = {2024}, author = {Vigna-Taglianti, FD and Martorana, M and Viola, E and Renna, M and Vadrucci, S and Sciutto, A and Andrà, C and Mehanović, E and Ginechesi, M and Vullo, C and Ceccano, A and Casella, P and Faggiano, F and , }, title = {Evaluation of Effectiveness of the Unplugged Program on Gambling Behaviours among Adolescents: Study Protocol of the Experimental Controlled Study "GAPUnplugged".}, journal = {Journal of prevention (2022)}, volume = {45}, number = {3}, pages = {405-429}, pmid = {38416313}, issn = {2731-5541}, support = {0005406//ASLRoma1/ ; }, mesh = {Humans ; *Gambling/prevention &amp; control/psychology ; Adolescent ; Female ; Male ; Surveys and Questionnaires ; Adolescent Behavior/psychology ; Program Evaluation ; Risk-Taking ; Students/psychology ; Italy ; }, abstract = {Gambling risk behaviour is an emerging problem among adolescents. "Unplugged" is an effective Social Influence curriculum for preventing substance use among students. This study aims to develop and test a new component focused on gambling added to the Unplugged program. Schools of Piedmont region and Rome city were invited to participate in the study. A self-completed anonymous questionnaire including questions on socio-demographic characteristics, addictive behaviours, beliefs, attitudes and risk perceptions about gambling, normative perceptions, parental practices, school climate, refusal skills, impulsiveness, self-esteem, antisocial behaviours and sensation seeking was prepared for baseline and follow-up surveys. The protocol of the study was submitted and approved by the Novara Ethical Committee and registered in ClinicalTrials.gov (NCT05630157, Protocol ID: 080.742, 11/17/2022). Twenty-nine schools accepted to participate in the study. Sixty-three classes (1325 students) satisfied the eligibility criteria for intervention and were allocated to the intervention arm, and the other 61 (1269 students) were allocated to the control arm. Because of drop-out, absentees, refusals, and invalid questionnaires, data on 1874 students (998 in the intervention and 876 in the control arm), were available for the analysis at baseline. Data management of follow-up questionnaires is in progress. Results of the present study will be useful to clarify the effectiveness of prevention interventions in reducing gambling behaviours among adolescents. Moreover, this will be the first experience of evaluating a new component focused on a different risk behaviour, added to a curriculum previously shown as effective on other risk behaviours.}, }
@article {pmid38415798, year = {2024}, author = {Jager, T}, title = {Identifying and Predicting Delayed Mortality with Toxicokinetic-Toxicodynamic Models.}, journal = {Environmental toxicology and chemistry}, volume = {43}, number = {5}, pages = {1030-1035}, doi = {10.1002/etc.5833}, pmid = {38415798}, issn = {1552-8618}, mesh = {Animals ; Humans ; Daphnia magna/drug effects ; Datasets as Topic ; Death ; *Ecotoxicology/methods ; Fluoroquinolones/toxicity ; *Mortality ; Pesticides/toxicity ; *Pharmacokinetics ; Risk Assessment ; Stochastic Processes ; Time Factors ; *Toxicity Tests, Acute/methods/standards ; }, abstract = {The prevalence of standardized toxicity testing in ecotoxicology has largely obscured the notion that toxicity is a function of time as well. The necessity of considering time is vividly demonstrated by observations of delayed mortality, that is, deaths continue to occur even when animals are no longer exposed to a toxicant. In this contribution, I explore to what extent toxicokinetic-toxicodynamic (TKTD) models from the framework of the General Unified Threshold model for Survival (GUTS) can capture delayed mortality, and to what extent this phenomenon can be predicted from short-term standard tests. I use a previously published data set for fluoroquinolones in Daphnia magna that shows strongly delayed mortality (using immobilization as a proxy for death). The model analysis shows that the GUTS stochastic death models can capture delayed mortality in the complete data set with a long recovery phase, but that the delayed effects would not have been predicted from a 2-day standard test. The study underlines the limited information content of standard acute test designs. Toxicokinetic-toxicodynamic modeling offers a handle on the time aspects of toxicity but cannot always be relied on to provide accurate extrapolations based on severely limited standard tests. The phenomenon of delayed toxicity requires more structured study to clarify its prevalence and impact; I discuss several avenues for further investigation. Environ Toxicol Chem 2024;43:1030-1035. © 2024 SETAC.}, }
@article {pmid38413777, year = {2024}, author = {Lemane, T and Lezzoche, N and Lecubin, J and Pelletier, E and Lescot, M and Chikhi, R and Peterlongo, P}, title = {Indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets with kmindex and ORA.}, journal = {Nature computational science}, volume = {4}, number = {2}, pages = {104-109}, pmid = {38413777}, issn = {2662-8457}, support = {ANR-19-CE45-0008//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-19-CE45-0008//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-19-CE45-0008//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-19-CE45-0008//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-22-CE45-0007//Agence Nationale de la Recherche (French National Research Agency)/ ; PIA/ANR16-CONV-0005//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-19-P3IA-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-19-CE45-0008//Agence Nationale de la Recherche (French National Research Agency)/ ; 956229//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; 872539//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; }, mesh = {*Genomics ; Oceans and Seas ; *Seawater ; Metagenome/genetics ; Databases, Nucleic Acid ; }, abstract = {Public sequencing databases contain vast amounts of biological information, yet they are largely underutilized as it is challenging to efficiently search them for any sequence(s) of interest. We present kmindex, an approach that can index thousands of metagenomes and perform sequence searches in a fraction of a second. The index construction is an order of magnitude faster than previous methods, while search times are two orders of magnitude faster. With negligible false positive rates below 0.01%, kmindex outperforms the precision of existing approaches by four orders of magnitude. Here we demonstrate the scalability of kmindex by successfully indexing 1,393 marine seawater metagenome samples from the Tara Oceans project. Additionally, we introduce the publicly accessible web server Ocean Read Atlas, which enables real-time queries on the Tara Oceans dataset.}, }
@article {pmid38413616, year = {2024}, author = {Xu, W and Pan, Z and Wu, Y and An, XL and Wang, W and Adamovich, B and Zhu, YG and Su, JQ and Huang, Q}, title = {A database on the abundance of environmental antibiotic resistance genes.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {250}, pmid = {38413616}, issn = {2052-4463}, support = {32161143016//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42177362//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42250410328//National Natural Science Foundation of China (National Science Foundation of China)/ ; GPNI GR no. 20212317//Belarusian Republican Foundation for Fundamental Research (BRFFR)/ ; }, mesh = {*Anti-Bacterial Agents/pharmacology ; China ; *Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Microbiota ; *Databases, Genetic ; }, abstract = {Antimicrobial resistance (AMR) poses a severe threat to global health. The wide distribution of environmental antibiotic resistance genes (ARGs), which can be transferred between microbiota, especially clinical pathogens and human commensals, contributed significantly to AMR. However, few databases on the spatiotemporal distribution, abundance, and health risk of ARGs from multiple environments have been developed, especially on the absolute level. In this study, we compiled the ARG occurrence data generated by a high-throughput quantitative PCR platform from 1,403 samples in 653 sampling sites across 18 provinces in China. The database possessed 291,870 records from five types of habitats on the abundance of 290 ARGs, as well as 8,057 records on the abundance of 30 mobile genetic elements (MGEs) from 2013 to 2020. These ARGs conferred resistance to major common types of antibiotics (a total of 15 types) and represented five major resistance mechanisms, as well as four risk ranks. The database can provide information for studies on the dynamics of ARGs and is useful for the health risk assessment of AMR.}, }
@article {pmid38407293, year = {2024}, author = {Dai, Y and Chen, H and Yu, J and Cai, J and Lu, B and Dai, M and Zhu, L}, title = {Global and regional trends in the incidence and prevalence of uterine fibroids and attributable risk factors at the national level from 2010 to 2019: A worldwide database study.}, journal = {Chinese medical journal}, volume = {137}, number = {21}, pages = {2583-2589}, pmid = {38407293}, issn = {2542-5641}, mesh = {Humans ; Female ; *Leiomyoma/epidemiology ; Incidence ; Risk Factors ; Prevalence ; Adult ; Middle Aged ; Uterine Neoplasms/epidemiology ; Disability-Adjusted Life Years ; Databases, Factual ; }, abstract = {BACKGROUND: Uterine fibroids (UFs), the most common tumors in women worldwide, may reduce quality of life and daily activities and even lead to adverse fertility and general health events in patients, causing significant societal health and financial burdens. The objective of this study was to evaluate the global burden through epidemiological trends and examine the potential risk factors for UFs at the national level.<br><br>METHODS: Data on the incidence, prevalence, disability-adjusted life years (DALYs), age-standardized incidence rates (ASIRs), age-standardized prevalence rates (ASPRs), and age-standardized DALY rates for UFs were collected, and the associations with the Human Development Index (HDI) and fertility were evaluated. The age trends in the average annual percent change (AAPC) of the incidence and prevalence rates of UFs were evaluated by joinpoint regression analysis. The associations between lifestyle, metabolic, and socioeconomic factors and the ASIRs of UFs were examined using multivariable linear regression analysis.<br><br>RESULTS: The worldwide incidence and prevalence of UFs have been increasing in the past decade, with AAPCs of 0.27% in the incidence rate and 0.078% in the prevalence rate. During 2010-2019, significant increasing trends in UF ASIR were observed in 52 of 88 countries. The age-specific incidence and prevalence of UFs in most age groups showed increasing trends except for 45-54-year-old women which showed no significant trend. Ecological analysis demonstrated no relationship between the incidence of UFs and the HDI but an inverse association with fertility. The incidence of UFs was positively correlated with alcohol intake, hypertension, overweight, and obesity and negatively correlated with smoking.<br><br>CONCLUSION: With the increasing incidence and prevalence worldwide, effective targeted prevention and control of relevant risk factors at the national level should be encouraged to reduce the disease burden of UFs.}, }
@article {pmid38405013, year = {2024}, author = {Boyes, D and Sims, I and Lees, DC and Eagles, M and ,  and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Chequered Fruit-tree Tortrix, Pandemis corylana (Fabricius, 1794).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {6}, pmid = {38405013}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Pandemis corylana (the Chequered Fruit-tree Tortrix; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 441.6 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.53 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,608 protein coding genes.}, }
@article {pmid38404638, year = {2023}, author = {Boyes, D and Eagles, M and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Light Emerald, Campaea margaritaria (Linnaeus, 1761).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {476}, pmid = {38404638}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Campaea margaritaria (the Light Emerald; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 335.2 megabases in span. The whole assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.9 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,403 protein coding genes.}, }
@article {pmid38404637, year = {2023}, author = {Boyes, D and Holland, PWH and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Phoenix, Eulithis prunata (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {185}, pmid = {38404637}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Eulithis prunata (the Phoenix; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 263.1 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.9 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,023 protein coding genes.}, }
@article {pmid38404636, year = {2023}, author = {Boyes, D and Eagles, M and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Flame Shoulder, Ochropleura plecta (Linnaeus, 1761).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {506}, pmid = {38404636}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Ochropleura plecta (the Flame Shoulder; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 643.9 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.34 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,016 protein coding genes.}, }
@article {pmid38404635, year = {2023}, author = {Hayward, A and Lohse, K and Vila, R and Laetsch, DR and Hedlund, JSU and ,  and ,  and ,  and , }, title = {The genome sequence of the Brown Argus, Aricia agestis (Denis &amp; Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {336}, pmid = {38404635}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present genome assemblies from two male Aricia agestis specimens (the Brown Argus; Arthropoda; Insecta; Lepidoptera; Lycaenidae). The genome sequences are 435.3 and 437.4 megabases in span. Each assembly is scaffolded into 23 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genomes were assembled and are 15.47 and 15.45 kilobases in length. Gene annotation of these assemblies on Ensembl identified 12,688 and 12,654 protein coding genes.}, }
@article {pmid38402992, year = {2024}, author = {Zhu, Y and Wang, L and Ma, J and Hua, Z and Yang, Y and Chen, F}, title = {Assessment of carbon sequestration potential of mining areas under ecological restoration in China.}, journal = {The Science of the total environment}, volume = {921}, number = {}, pages = {171179}, doi = {10.1016/j.scitotenv.2024.171179}, pmid = {38402992}, issn = {1879-1026}, abstract = {Mining activities aggravate the ecological degradation and emission of greenhouse gases throughout the world, thereby affecting the global climate and posing a serious threat to the ecological safety. Vegetation restoration is considered to be an effective and sustainable strategy to improve the post-mining soil quality and functions. However, we still have a limited knowledge of the impact of vegetation restoration on carbon sequestration potential in mining areas. In this pursuit, the present study was envisaged to integrate the findings from studies on soil organic carbon (SOC) sequestration in mining areas under vegetation restoration with field monitoring data. The carbon sequestration potential under vegetation restoration in China's mining areas was estimated by using a machine learning model. The results showed that (1) Vegetation restoration exhibited a consistently positive impact on the changes in the SOC reserves. The carbon sequestration potential was the highest in mixed forests, followed by broad-leaved forests, coniferous forests, grassland, shrubland, and farmland; (2) The number of years of vegetation restoration and mean annual precipitation were found to be the important moderating variables affecting the SOC reserves in reclaimed soils in mining areas; (3) There were significant differences in the SOC sequestration potential under different vegetation restoration scenarios in mining areas in China. The SOC sequestration potential reached up to 9.86 million t C a[-1], when the soil was restored to the initial state. Based on the meta-analysis, the maximal attainable SOC sequestration potential was found to be 4.26 million t C a[-1]. The SOC sequestration potential reached the highest level of 12.86 million t C a[-1], when the optimal vegetation type in a given climate was restored. The results indicated the importance of vegetation restoration for improving the soil sequestration potential in mining areas. The time lag in carbon sequestration potential for different vegetation types in mining areas was also revealed. Our findings can assist the development of ecological restoration regimens in mining areas to mitigate the global climate change.}, }
@article {pmid38402941, year = {2024}, author = {Ulanova, A and Mansfeldt, C}, title = {EcoGenoRisk: Developing a computational ecological risk assessment tool for synthetic biology.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {346}, number = {}, pages = {123647}, doi = {10.1016/j.envpol.2024.123647}, pmid = {38402941}, issn = {1873-6424}, mesh = {*Synthetic Biology ; *Software ; Risk Assessment ; Computational Biology ; Genome, Bacterial ; }, abstract = {The expanding field of synthetic biology (synbio) supports new opportunities in the design of targeted bioproducts or modified microorganisms. However, this rapid development of synbio products raises concerns surrounding the potential risks of modified microorganisms contaminating unintended environments. These potential invasion risks require new bioinformatic tools to inform the design phase. EcoGenoRisk is a newly constructed computational risk assessment tool for invasiveness that aims to predict where synbio microorganisms may establish a population by screening for habitats of genetically similar microorganisms. The first module of the tool identifies genetically similar microorganisms and potential ecological relationships such as competition, mutualism, and inhibition. In total, 520 archaeal and 32,828 bacterial complete assembly genomes were analyzed to test the specificity and accuracy of the tool as well as to characterize the enzymatic profiles of different taxonomic lineages. Additionally, ecological relationships were analyzed to determine which would result in the greatest potential overlap between shared functional profiles. Notably, competition displayed the significantly highest overlap of shared functions between compared genomes. Overall, EcoGenoRisk is a flexible software pipeline that assists environmental risk assessors to query large databases of known microorganisms and prioritize follow-up bench scale studies.}, }
@article {pmid38402789, year = {2024}, author = {Gonyo, SB and Burkart, H and Regan, S}, title = {Leveraging big data for outdoor recreation management: A case study from the York river in Virginia.}, journal = {Journal of environmental management}, volume = {354}, number = {}, pages = {120482}, doi = {10.1016/j.jenvman.2024.120482}, pmid = {38402789}, issn = {1095-8630}, mesh = {Child ; Humans ; Child, Preschool ; Middle Aged ; *Recreation ; Virginia ; *Rivers ; Big Data ; Quality of Life ; }, abstract = {Outdoor recreation is important for improving quality of life, well-being, and local economies, but quantifying its value without direct monetary transactions can be challenging. This study explores combining non-market valuation techniques with emerging big data sources to estimate the value of recreation for the York River and surrounding parks in Virginia. By applying the travel cost method to anonymous human mobility data, we gain deeper insights into the significance of recreational experiences for visitors and the local economy. Results of a zero-inflated Negative Binomial model show a mean consumer surplus value of $26.91 per trip, totaling $15.5 million across nearly 600,000 trips observed in 2022. Further, weekends, holidays, and the summer and fall months are found to be peak visitation times, whereas those with young children and who are Hispanic or over 64 years old are less likely to visit. These findings shed light on various factors influencing visitation patterns and recreation values, including temporal effects and socio-demographics, revealing disparities that warrant targeted efforts for inclusivity and accessibility. Policymakers can use these insights to make informed and sustainable choices in outdoor recreation management, fostering the preservation of natural resources for the benefit of both visitors and the environment.}, }
@article {pmid38398847, year = {2024}, author = {Navratilova, HF and Lanham-New, S and Whetton, AD and Geifman, N}, title = {Associations of Diet with Health Outcomes in the UK Biobank: A Systematic Review.}, journal = {Nutrients}, volume = {16}, number = {4}, pages = {}, pmid = {38398847}, issn = {2072-6643}, mesh = {Female ; Humans ; Male ; Middle Aged ; *Cardiovascular Diseases/epidemiology/etiology ; Colorectal Neoplasms/epidemiology/etiology/prevention &amp; control ; *Diabetes Mellitus, Type 2/epidemiology/etiology ; *Diet/statistics &amp; numerical data/adverse effects ; Diet, Healthy/statistics &amp; numerical data ; Neoplasms/epidemiology/etiology ; Risk Factors ; UK Biobank/statistics &amp; numerical data ; United Kingdom/epidemiology ; }, abstract = {The UK Biobank is a cohort study that collects data on diet, lifestyle, biomarkers, and health to examine diet-disease associations. Based on the UK Biobank, we reviewed 36 studies on diet and three health conditions: type 2 diabetes (T2DM), cardiovascular disease (CVD), and cancer. Most studies used one-time dietary data instead of repeated 24 h recalls, which may lead to measurement errors and bias in estimating diet-disease associations. We also found that most studies focused on single food groups or macronutrients, while few studies adopted a dietary pattern approach. Several studies consistently showed that eating more red and processed meat led to a higher risk of lung and colorectal cancer. The results suggest that high adherence to "healthy" dietary patterns (consuming various food types, with at least three servings/day of whole grain, fruits, and vegetables, and meat and processed meat less than twice a week) slightly lowers the risk of T2DM, CVD, and colorectal cancer. Future research should use multi-omics data and machine learning models to account for the complexity and interactions of dietary components and their effects on disease risk.}, }
@article {pmid38396178, year = {2024}, author = {Wang, F and Sun, N and Zhang, C and Fan, C and Xiong, J and Wei, X and Hao, W}, title = {Experimental study on mine water purification mechanism for broken coal and rock masses in the underground reservoir of ecologically vulnerable mining area.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {14}, pages = {21442-21457}, pmid = {38396178}, issn = {1614-7499}, support = {52104155//National Natural Science Foundation of China/ ; 51974297//National Natural Science Foundation of China/ ; }, mesh = {*Coal ; *Mining ; Water Quality ; Minerals ; }, abstract = {Water-rock interaction mechanism and water purification capacity of broken coal and rock masses are very important for the efficient operation of the underground reservoir. In this paper, a water purification simulation device for an underground mine reservoir was designed. The experimental study on the dynamic interaction between broken coal and rock masses and mine water was carried out. The water purification mechanism is analyzed from the changes in rock mineral composition and mine water quality before and after the test. The results show that after the broken coal and rock mass purification, the water turbidity and the concentration of chlorides and suspended solids decreased obviously. The water purification capacities of mudstone and sandstone are stronger than that of coal samples. After 60 days of reaction between the working face sewage and the broken samples (mudstone, sandstone, and coal), the turbidity, chromaticity, and residual chlorine decreased by > 90%, 90%, and 60%, respectively; and COD decreased by 35.29%, 30.59%, and 28.99%, respectively. While the TDS and the total hardness increased by about 40%, 30%, and 10% for the mudstone, sandstone, and coal, respectively. It shows that coal also has the worst degradation performance. The water purification effect of broken coal and rock masses has a significant time effect. The early stage of water-rock interaction is dominated by mineral dissolution, and the middle stage is dominated by precipitation and adsorption. The pH value of the solution has a certain influence on the ion change. In the later stage, the water-rock interaction is weak in a dynamic equilibrium state, and the change in the mine water quality index is not obvious. Considering the influence of rock lithology on water quality and the law of water-rock interaction time, the construction site selection and water storage time optimization of underground reservoirs in Jinjie Coal Mine were carried out, respectively.}, }
@article {pmid38396055, year = {2024}, author = {Gauzens, B and Kalinkat, G and Antunes, AC and Boy, T and O'Gorman, EJ and Jacob, U and Jochum, M and Kortsch, S and Rosenbaum, B and Figueiredo, L and Brose, U}, title = {Quantitative description of six fish species' gut contents and prey abundances in the Baltic Sea (1968-1978).}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {236}, pmid = {38396055}, issn = {2052-4463}, support = {DFG-FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG-FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG-FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG-FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG-FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG-FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DAAD, 57070483//Deutscher Akademischer Austauschdienst (German Academic Exchange Service)/ ; }, mesh = {Animals ; Baltic States ; *Fishes ; *Gastrointestinal Contents ; Oceans and Seas ; }, abstract = {The dataset presents a compilation of stomach contents from six demersal fish species from two functional groups inhabiting the Baltic Sea. It includes detailed information on prey identities, body masses, and biomasses recovered from both the fish's digestive systems and their surrounding environment. Environmental parameters, such as salinity and temperature levels, have been integrated to enrich this dataset. The juxtaposition of information on prey found in stomachs and in the environment provides an opportunity to quantify trophic interactions across different environmental contexts and investigate how fish foraging behaviour adapts to changes in their environment, such as an increase in temperature. The compilation of body mass and taxonomic information for all species allows approaching these new questions using either a taxonomic (based on species identity) or functional trait (based on body mass) approach.}, }
@article {pmid38395906, year = {2024}, author = {Ou, AH and Rosenthal, SB and Adli, M and Akiyama, K and Akula, N and Alda, M and Amare, AT and Ardau, R and Arias, B and Aubry, JM and Backlund, L and Bauer, M and Baune, BT and Bellivier, F and Benabarre, A and Bengesser, S and Bhattacharjee, AK and Biernacka, JM and Cervantes, P and Chen, GB and Chen, HC and Chillotti, C and Cichon, S and Clark, SR and Colom, F and Cousins, DA and Cruceanu, C and Czerski, PM and Dantas, CR and Dayer, A and Del Zompo, M and Degenhardt, F and DePaulo, JR and Étain, B and Falkai, P and Fellendorf, FT and Ferensztajn-Rochowiak, E and Forstner, AJ and Frisén, L and Frye, MA and Fullerton, JM and Gard, S and Garnham, JS and Goes, FS and Grigoroiu-Serbanescu, M and Grof, P and Gruber, O and Hashimoto, R and Hauser, J and Heilbronner, U and Herms, S and Hoffmann, P and Hofmann, A and Hou, L and Jamain, S and Jiménez, E and Kahn, JP and Kassem, L and Kato, T and Kittel-Schneider, S and König, B and Kuo, PH and Kusumi, I and Lackner, N and Laje, G and Landén, M and Lavebratt, C and Leboyer, M and Leckband, SG and Jaramillo, CAL and MacQueen, G and Maj, M and Manchia, M and Marie-Claire, C and Martinsson, L and Mattheisen, M and McCarthy, MJ and McElroy, SL and McMahon, FJ and Mitchell, PB and Mitjans, M and Mondimore, FM and Monteleone, P and Nievergelt, CM and Nöthen, MM and Novák, T and Ösby, U and Ozaki, N and Papiol, S and Perlis, RH and Pisanu, C and Potash, JB and Pfennig, A and Reich-Erkelenz, D and Reif, A and Reininghaus, EZ and Rietschel, M and Rouleau, GA and Rybakowski, JK and Schalling, M and Schofield, PR and Schubert, KO and Schulze, TG and Schweizer, BW and Seemüller, F and Severino, G and Shekhtman, T and Shilling, PD and Shimoda, K and Simhandl, C and Slaney, CM and Squassina, A and Stamm, T and Stopkova, P and Tighe, SK and Tortorella, A and Turecki, G and Vieta, E and Volkert, J and Witt, S and Wray, NR and Wright, A and Young, LT and Zandi, PP and Kelsoe, JR}, title = {Lithium response in bipolar disorder is associated with focal adhesion and PI3K-Akt networks: a multi-omics replication study.}, journal = {Translational psychiatry}, volume = {14}, number = {1}, pages = {109}, pmid = {38395906}, issn = {2158-3188}, support = {R01 MH059556/MH/NIMH NIH HHS/United States ; R01 MH059535/MH/NIMH NIH HHS/United States ; R01 MH059567/MH/NIMH NIH HHS/United States ; R01 MH059545/MH/NIMH NIH HHS/United States ; P01 CA089392/CA/NCI NIH HHS/United States ; Z01 MH002810/ImNIH/Intramural NIH HHS/United States ; I01 BX003431/BX/BLRD VA/United States ; R01 MH059548/MH/NIMH NIH HHS/United States ; R01 MH059533/MH/NIMH NIH HHS/United States ; U01 MH092758/MH/NIMH NIH HHS/United States ; K02 DA021237/DA/NIDA NIH HHS/United States ; R01 MH059553/MH/NIMH NIH HHS/United States ; R01 MH060068/MH/NIMH NIH HHS/United States ; MR/L006642/1/MRC_/Medical Research Council/United Kingdom ; R01 MH059534/MH/NIMH NIH HHS/United States ; }, mesh = {Humans ; *Lithium/pharmacology/therapeutic use ; *Bipolar Disorder/drug therapy/genetics ; Proto-Oncogene Proteins c-akt/genetics ; Phosphatidylinositol 3-Kinases/genetics ; Genome-Wide Association Study ; Multiomics ; Focal Adhesions ; }, abstract = {Lithium is the gold standard treatment for bipolar disorder (BD). However, its mechanism of action is incompletely understood, and prediction of treatment outcomes is limited. In our previous multi-omics study of the Pharmacogenomics of Bipolar Disorder (PGBD) sample combining transcriptomic and genomic data, we found that focal adhesion, the extracellular matrix (ECM), and PI3K-Akt signaling networks were associated with response to lithium. In this study, we replicated the results of our previous study using network propagation methods in a genome-wide association study of an independent sample of 2039 patients from the International Consortium on Lithium Genetics (ConLiGen) study. We identified functional enrichment in focal adhesion and PI3K-Akt pathways, but we did not find an association with the ECM pathway. Our results suggest that deficits in the neuronal growth cone and PI3K-Akt signaling, but not in ECM proteins, may influence response to lithium in BD.}, }
@article {pmid38395161, year = {2024}, author = {Brunelli, A and Cazzagon, V and Faraggiana, E and Bettiol, C and Picone, M and Marcomini, A and Badetti, E}, title = {An overview on dispersion procedures and testing methods for the ecotoxicity testing of nanomaterials in the marine environment.}, journal = {The Science of the total environment}, volume = {921}, number = {}, pages = {171132}, doi = {10.1016/j.scitotenv.2024.171132}, pmid = {38395161}, issn = {1879-1026}, mesh = {*Nanostructures/toxicity/chemistry ; Oxides/chemistry ; Research Design ; Ecotoxicology ; }, abstract = {Considerable efforts have been devoted to develop or adapt existing guidelines and protocols, to obtain robust and reproducible results from (eco)toxicological assays on engineered nanomaterials (NMs). However, while many studies investigated adverse effects of NMs on freshwater species, less attention was posed to the marine environment, a major sink for these contaminants. This review discusses the procedures used to assess the ecotoxicity of NMs in the marine environment, focusing on the use of protocols and methods for preparing NMs dispersions and on the NMs physicochemical characterization in exposure media. To this purpose, a critical analysis of the literature since 2010 was carried out, based on the publication of the first NMs dispersion protocols. Among the 89 selected studies, only <5 % followed a standardized dispersion protocol combined with NMs characterization in ecotoxicological media, while more than half used a non-standardized dispersion method but performed NMs characterization. In the remaining studies, only partial or no information on dispersion procedures or on physicochemical characterization was provided. This literature review also highlighted that metal oxides NMs were the most studied (42 %), but with an increasing interest in last years towards nanoplastics (14 %) and multicomponent nanomaterials (MCNMs, 7 %), in line with the growing attention on these emerging contaminants. For all these NMs, primary producers as algae and bacteria were the most studied groups of marine species, in addition to mollusca, while organisms at higher trophic levels were less represented, likely due to challenges in evaluating adverse effects on more complex organisms. Thus, despite the wide use of NMs in different applications, standard dispersion protocols are not often used for ecotoxicity testing with marine species. However, the efforts to characterize NMs in ecotoxicological media recognize the importance of following conditions that are as standardized as possible to support the ecological hazard assessment of NMs.}, }
@article {pmid38390626, year = {2024}, author = {Kumar, A and Ojha, PK and Roy, K}, title = {First report on pesticide sub-chronic and chronic toxicities against dogs using QSAR and chemical read-across.}, journal = {SAR and QSAR in environmental research}, volume = {35}, number = {3}, pages = {241-263}, doi = {10.1080/1062936X.2024.2320143}, pmid = {38390626}, issn = {1029-046X}, mesh = {Dogs ; Animals ; *Pesticides/toxicity ; Quantitative Structure-Activity Relationship ; Reproducibility of Results ; Databases, Factual ; }, abstract = {Excessive use of chemicals is the outcome of the industrialization of agricultural sectors which leads to disturbance of ecological balance. Various agrochemicals are widely used in agricultural fields, urban green areas, and to protect from various pest-associated diseases. Due to their long-term health and environmental hazards, chronic toxicity assessment is crucial. Since in vivo and in vitro toxicity assessments are costly, lengthy, and require a large number of animal experiments, in silico toxicity approaches are better alternatives to save time, cost, and animal experimentation. We have developed the first regression-based 2D-QSAR models using different sub-chronic and chronic toxicity data of pesticides against dogs employing 2D descriptors. From the statistical results (ntrain=53-62, r2 = 0.614 to 0.754, QLOO2 = 0.501 to 0.703 and QF12 = 0.531 to 0.718, QF22=0.523-0.713), it was concluded that the models are robust, reliable, interpretable, and predictive. Similarity-based read-across algorithm was also used to improve the predictivity (QF12=0.595-0.813,QF22=0.573-0.809) of the models. 5132 chemicals obtained from the CPDat and 1694 pesticides obtained from the PPDB database were also screened using the developed models, and their predictivity and reliability were checked. Thus, these models will be helpful for eco-toxicological data-gap filling, toxicity prediction of untested pesticides, and development of novel, safer &amp; eco-friendly pesticides.}, }
@article {pmid38389111, year = {2024}, author = {Messer, LF and Lee, CE and Wattiez, R and Matallana-Surget, S}, title = {Novel functional insights into the microbiome inhabiting marine plastic debris: critical considerations to counteract the challenges of thin biofilms using multi-omics and comparative metaproteomics.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {36}, pmid = {38389111}, issn = {2049-2618}, support = {NE/V009621/1//Natural Environment Research Council/ ; NE/V009621/1//Natural Environment Research Council/ ; NE/V009621/1//Natural Environment Research Council/ ; NE/S007342/1//NERC Scottish Universities Partnership for Environmental Research (SUPER) Doctoral Training Partnership/ ; }, mesh = {*Plastics ; Bacteria/genetics ; Multiomics ; Biofilms ; Biodegradation, Environmental ; *Microbiota/genetics ; }, abstract = {BACKGROUND: Microbial functioning on marine plastic surfaces has been poorly documented, especially within cold climates where temperature likely impacts microbial activity and the presence of hydrocarbonoclastic microorganisms. To date, only two studies have used metaproteomics to unravel microbial genotype-phenotype linkages in the marine 'plastisphere', and these have revealed the dominance of photosynthetic microorganisms within warm climates. Advancing the functional representation of the marine plastisphere is vital for the development of specific databases cataloging the functional diversity of the associated microorganisms and their peptide and protein sequences, to fuel biotechnological discoveries. Here, we provide a comprehensive assessment for plastisphere metaproteomics, using multi-omics and data mining on thin plastic biofilms to provide unique insights into plastisphere metabolism. Our robust experimental design assessed DNA/protein co-extraction and cell lysis strategies, proteomics workflows, and diverse protein search databases, to resolve the active plastisphere taxa and their expressed functions from an understudied cold environment.<br><br>RESULTS: For the first time, we demonstrate the predominance and activity of hydrocarbonoclastic genera (Psychrobacter, Flavobacterium, Pseudomonas) within a primarily heterotrophic plastisphere. Correspondingly, oxidative phosphorylation, the citrate cycle, and carbohydrate metabolism were the dominant pathways expressed. Quorum sensing and toxin-associated proteins of Streptomyces were indicative of inter-community interactions. Stress response proteins expressed by Psychrobacter, Planococcus, and Pseudoalteromonas and proteins mediating xenobiotics degradation in Psychrobacter and Pseudoalteromonas suggested phenotypic adaptations to the toxic chemical microenvironment of the plastisphere. Interestingly, a targeted search strategy identified plastic biodegradation enzymes, including polyamidase, hydrolase, and depolymerase, expressed by rare taxa. The expression of virulence factors and mechanisms of antimicrobial resistance suggested pathogenic genera were active, despite representing a minor component of the plastisphere community.<br><br>CONCLUSION: Our study addresses a critical gap in understanding the functioning of the marine plastisphere, contributing new insights into the function and ecology of an emerging and important microbial niche. Our comprehensive multi-omics and comparative metaproteomics experimental design enhances biological interpretations to provide new perspectives on microorganisms of potential biotechnological significance beyond biodegradation and to improve the assessment of the risks associated with microorganisms colonizing marine plastic pollution. Video Abstract.}, }
@article {pmid38386279, year = {2024}, author = {Ambrosini, E and Giangregorio, C and Lomurno, E and Moccia, S and Milis, M and Loizou, C and Azzolino, D and Cesari, M and Cid Gala, M and Galán de Isla, C and Gomez-Raja, J and Borghese, NA and Matteucci, M and Ferrante, S}, title = {Automatic Spontaneous Speech Analysis for the Detection of Cognitive Functional Decline in Older Adults: Multilanguage Cross-Sectional Study.}, journal = {JMIR aging}, volume = {7}, number = {}, pages = {e50537}, pmid = {38386279}, issn = {2561-7605}, support = {001/WHO_/World Health Organization/International ; }, mesh = {Humans ; Aged ; Female ; Male ; *Cognitive Dysfunction/diagnosis ; Cross-Sectional Studies ; Italy/epidemiology ; Aged, 80 and over ; *Speech/physiology ; Spain/epidemiology ; Mental Status and Dementia Tests ; Machine Learning ; Algorithms ; }, abstract = {BACKGROUND: The rise in life expectancy is associated with an increase in long-term and gradual cognitive decline. Treatment effectiveness is enhanced at the early stage of the disease. Therefore, there is a need to find low-cost and ecological solutions for mass screening of community-dwelling older adults.<br><br>OBJECTIVE: This work aims to exploit automatic analysis of free speech to identify signs of cognitive function decline.<br><br>METHODS: A sample of 266 participants older than 65 years were recruited in Italy and Spain and were divided into 3 groups according to their Mini-Mental Status Examination (MMSE) scores. People were asked to tell a story and describe a picture, and voice recordings were used to extract high-level features on different time scales automatically. Based on these features, machine learning algorithms were trained to solve binary and multiclass classification problems by using both mono- and cross-lingual approaches. The algorithms were enriched using Shapley Additive Explanations for model explainability.<br><br>RESULTS: In the Italian data set, healthy participants (MMSE score&#x2265;27) were automatically discriminated from participants with mildly impaired cognitive function (20&#x2264;MMSE score&#x2264;26) and from those with moderate to severe impairment of cognitive function (11&#x2264;MMSE score&#x2264;19) with accuracy of 80% and 86%, respectively. Slightly lower performance was achieved in the Spanish and multilanguage data sets.<br><br>CONCLUSIONS: This work proposes a transparent and unobtrusive assessment method, which might be included in a mobile app for large-scale monitoring of cognitive functionality in older adults. Voice is confirmed to be an important biomarker of cognitive decline due to its noninvasive and easily accessible nature.}, }
@article {pmid38385125, year = {2023}, author = {Boyes, D and Turnbull, L and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Hornet Moth, Sesia apiformis (Clerck, 1759).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {499}, pmid = {38385125}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Sesia apiformis (the Hornet Moth; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 546.8 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,358 protein coding genes.}, }
@article {pmid38385124, year = {2023}, author = {Boyes, D and Broad, GR and ,  and ,  and ,  and ,  and ,  and ,  and Holland, PWH and , }, title = {The genome sequence of the Shuttle-shaped Dart, Agrotis puta (Hübner, 1803).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {84}, pmid = {38385124}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Agrotis puta (the Shuttle-shaped Dart; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 522 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl has identified 15,136 protein coding genes.}, }
@article {pmid38383691, year = {2024}, author = {Yu, D and Zhang, Y and Dang, H and Zhang, Q}, title = {Multiomics analyses reveal the mechanisms of the responses of subalpine treeline trees to phenology and winter low-temperature stress.}, journal = {Physiologia plantarum}, volume = {176}, number = {1}, pages = {e14218}, doi = {10.1111/ppl.14218}, pmid = {38383691}, issn = {1399-3054}, support = {31971491//National Natural Science Foundation of China/ ; 32201371//National Natural Science Foundation of China/ ; }, mesh = {*Trees/genetics ; Temperature ; *Multiomics ; Cold Temperature ; Seasons ; }, abstract = {Withstanding extreme cold stress is a prerequisite for alpine treeline trees to persist and survive. However, the underlying mechanism by which treeline trees sense phenological changes and survive hard winters has not been fully elucidated. Here, we investigated the physiology, transcriptome, and metabolome of the subalpine treeline species Larix chinensis to identify the molecular mechanism of phenological and cold resistance. Calcium and antioxidant enzyme activities (e.g., superoxide dismutase and glutathione peroxidase) are essential for coping with winter cold stress in L. chinensis. Transcriptome analysis revealed that circadian rhythm and phytohormone signalling transduction played important roles in regulating L. chinensis phenological changes and cold stress responses. The variations in the transcriptome identified were accompanied by the specific accumulation of flavones, flavonols, and monosaccharides. The flavonoid biosynthesis and phenylpropanoid biosynthesis pathways played important roles in the adaptation of L. chinensis to the extreme winter environment, and flavone and flavonol biosynthesis was an important pathway involved in bud burst. In addition, temperature and photoperiod had synergistic influences on the formation and release of bud dormancy. Thus, our findings provided new insights into the mechanism of subalpine treeline formation.}, }
@article {pmid38383603, year = {2025}, author = {Nevers, Y and Warwick Vesztrocy, A and Rossier, V and Train, CM and Altenhoff, A and Dessimoz, C and Glover, NM}, title = {Quality assessment of gene repertoire annotations with OMArk.}, journal = {Nature biotechnology}, volume = {43}, number = {1}, pages = {124-133}, pmid = {38383603}, issn = {1546-1696}, mesh = {*Molecular Sequence Annotation/methods ; Animals ; *Software ; *Proteome/genetics ; Genomics/methods ; Databases, Protein ; }, abstract = {In the era of biodiversity genomics, it is crucial to ensure that annotations of protein-coding gene repertoires are accurate. State-of-the-art tools to assess genome annotations measure the completeness of a gene repertoire but are blind to other errors, such as gene overprediction or contamination. We introduce OMArk, a software package that relies on fast, alignment-free sequence comparisons between a query proteome and precomputed gene families across the tree of life. OMArk assesses not only the completeness but also the consistency of the gene repertoire as a whole relative to closely related species and reports likely contamination events. Analysis of 1,805 UniProt Eukaryotic Reference Proteomes with OMArk demonstrated strong evidence of contamination in 73 proteomes and identified error propagation in avian gene annotation resulting from the use of a fragmented zebra finch proteome as a reference. This study illustrates the importance of comparing and prioritizing proteomes based on their quality measures.}, }
@article {pmid38379958, year = {2024}, author = {Tran, T and Xie, S}, title = {Mitigating Wildlife Spillover in the Clinical Setting: How Physicians and Veterinarians Can Help Prevent Future Disease Outbreaks.}, journal = {AJPM focus}, volume = {3}, number = {2}, pages = {100193}, pmid = {38379958}, issn = {2773-0654}, abstract = {INTRODUCTION: The transmission of pathogens from wildlife to humans is a major global health threat that has been highlighted by the proposed origins of the COVID-19 pandemic. Numerous barriers impede pathogen spillover events from ensuing widespread human transmission, but human activity has accelerated the frequency of spillovers and subsequent disease outbreaks, in part through a booming wildlife trade whose impacts on health are not well understood.<br><br>METHODS: A literature review was conducted to examine the risk that the wildlife trade poses to public health and the degree to which these risks are recognized and addressed in clinical practice and medical and veterinary education.<br><br>RESULTS: The illicit aspects of the wildlife trade challenge efforts to understand its impacts on health. The U.S. and Europe play a leading role in the global wildlife trade that often goes unacknowledged. In particular, the consumption of wild meat and ownership of exotic pets poses public health risks. The potential role of clinicians is underutilized, both in the clinical setting and in clinical education.<br><br>DISCUSSION: Physicians and veterinarians have the unique opportunity to utilize their clinical roles to address these knowledge gaps and mitigate future outbreaks. We outline a multifaceted approach that includes increasing clinical knowledge about the ecology of zoonotic diseases, leveraging opportunities for mitigation during patient/client-clinician interactions, and incorporating One Health core competencies into medical and veterinary school curricula.}, }
@article {pmid38379504, year = {2024}, author = {Castro-Alvarez, S and Sinharay, S and Bringmann, LF and Meijer, RR and Tendeiro, JN}, title = {Assessment of fit of the time-varying dynamic partial credit model using the posterior predictive model checking method.}, journal = {The British journal of mathematical and statistical psychology}, volume = {77}, number = {3}, pages = {532-552}, doi = {10.1111/bmsp.12339}, pmid = {38379504}, issn = {2044-8317}, mesh = {Humans ; *Psychometrics/methods/statistics &amp; numerical data ; *Models, Statistical ; *Computer Simulation ; Longitudinal Studies ; Time Factors ; Bayes Theorem ; Data Interpretation, Statistical ; Regression Analysis ; }, abstract = {Several new models based on item response theory have recently been suggested to analyse intensive longitudinal data. One of these new models is the time-varying dynamic partial credit model (TV-DPCM; Castro-Alvarez et al., Multivariate Behavioral Research, 2023, 1), which is a combination of the partial credit model and the time-varying autoregressive model. The model allows the study of the psychometric properties of the items and the modelling of nonlinear trends at the latent state level. However, there is a severe lack of tools to assess the fit of the TV-DPCM. In this paper, we propose and develop several test statistics and discrepancy measures based on the posterior predictive model checking (PPMC) method (PPMC; Rubin, The Annals of Statistics, 1984, 12, 1151) to assess the fit of the TV-DPCM. Simulated and empirical data are used to study the performance of and illustrate the effectiveness of the PPMC method.}, }
@article {pmid38376945, year = {2024}, author = {Townley, B and Akin, D and Dimaguila, GL and Sawires, R and Sepulveda Kattan, G and King, S and Bines, J and Wood, N and Lambert, S and Buttery, J}, title = {Exploring the Infectious Contribution to Intussusception Causality Using the Effects of COVID-19 Lockdowns in Australia: An Ecological Study.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {79}, number = {1}, pages = {255-262}, doi = {10.1093/cid/ciae084}, pmid = {38376945}, issn = {1537-6591}, support = {//Murdoch Children's/ ; //Research Institute/ ; //Child Health Analytics and Informatics Research/ ; }, mesh = {Humans ; *COVID-19/epidemiology/prevention &amp; control ; *Intussusception/epidemiology/etiology ; Infant ; Retrospective Studies ; Child, Preschool ; Child ; Male ; Female ; Australia/epidemiology ; Adolescent ; *SARS-CoV-2 ; Infant, Newborn ; Adult ; Hospitalization/statistics &amp; numerical data ; Middle Aged ; Young Adult ; Aged ; New South Wales/epidemiology ; Queensland/epidemiology ; Victoria/epidemiology ; }, abstract = {BACKGROUND: Intussusception is the primary cause of acute bowel obstruction in infants. The majority of cases <2 years of age are classed as idiopathic, with viral infection implicated as one of the causes. Coronavirus disease 2019 (COVID-19) public health measures led to significant decreases in communicable disease prevalence. During these times, reductions in intussusception frequency were greater than would be expected with our previous understanding of its infectious etiology.<br><br>METHODS: We conducted a retrospective, multistate, ecological study over a 12-year period. Monthly case numbers of "intussusception"-coded admissions (code K56.1; International Classification of Diseases and Related Health Problems, Tenth Revision, Australian Modification) were acquired from state-wide admissions data sets from New South Wales, Victoria, and Queensland, representing 77.62% of the eligible Australian population. These counts within differing jurisdictional lockdowns were compared with non-lockdown periods in order to investigate a correlation between intussusception frequency and lockdown periods.<br><br>RESULTS: We found a negative association between intussusception frequency and lockdown periods in both eligible states. The largest reductions were seen in the <2-year age groups, with Victoria experiencing a 62.7% reduction (rate ratio, 0.37; P < .001) and New South Wales a 40.1% reduction (0.599; P = .006) during lockdown times. Controls for variations in lockdown restrictions between both regional and metropolitan areas also showed expected decreases.<br><br>CONCLUSIONS: Our ecological study demonstrates significant decreases in the frequency of pediatric intussusception admissions during the COVID-19 lockdown periods. The unexpected magnitude of the reductions suggests that the true proportion of infectious disease-caused idiopathic intussusception is greatly underestimated.}, }
@article {pmid38376180, year = {2024}, author = {Schaan, AP and Vidal, A and Zhang, A-N and Poyet, M and Alm, EJ and Groussin, M and Ribeiro-Dos-Santos, &#xc2;}, title = {Temporal dynamics of gut microbiomes in non-industrialized urban Amazonia.}, journal = {mSystems}, volume = {9}, number = {3}, pages = {e0070723}, pmid = {38376180}, issn = {2379-5077}, support = {88882.160155/2017-01//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior (CAPES)/ ; 304413/2015-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Brazil ; *Microbiota ; Bacteria ; Urbanization ; }, abstract = {Increasing levels of industrialization have been associated with changes in gut microbiome structure and loss of features thought to be crucial for maintaining gut ecological balance. The stability of gut microbial communities over time within individuals seems to be largely affected by these changes but has been overlooked among transitioning populations from low- to middle-income countries. Here, we used metagenomic sequencing to characterize the temporal dynamics in gut microbiomes of 24 individuals living an urban non-industrialized lifestyle in the Brazilian Amazon. We further contextualized our data with 165 matching longitudinal samples from an urban industrialized and a rural non-industrialized population. We show that gut microbiome composition and diversity have greater variability over time among non-industrialized individuals when compared to industrialized counterparts and that taxa may present diverse temporal dynamics across human populations. Enterotype classifications show that community types are generally stable over time despite shifts in microbiome structure. Furthermore, by tracking genomes over time, we show that levels of bacterial population replacements are more frequent among Amazonian individuals and that non-synonymous variants accumulate in genes associated with degradation of host dietary polysaccharides. Taken together, our results suggest that the stability of gut microbiomes is influenced by levels of industrialization and that tracking microbial population dynamics is important to understand how the microbiome will adapt to these transitions.IMPORTANCEThe transition from a rural or non-industrialized lifestyle to urbanization and industrialization has been linked to changes in the structure and function of the human gut microbiome. Understanding how the gut microbiomes changes over time is crucial to define healthy states and to grasp how the gut microbiome interacts with the host environment. Here, we investigate the temporal dynamics of gut microbiomes from an urban and non-industrialized population in the Amazon, as well as metagenomic data sets from urban United States and rural Tanzania. We showed that healthy non-industrialized microbiomes experience greater compositional shifts over time compared to industrialized individuals. Furthermore, bacterial strain populations are more frequently replaced in non-industrialized microbiomes, and most non-synonymous mutations accumulate in genes associated with the degradation of host dietary components. This indicates that microbiome stability is affected by transitions to industrialization, and that strain tracking can elucidate the ecological dynamics behind such transitions.}, }
@article {pmid38376167, year = {2024}, author = {Hegarty, B and Riddell V, J and Bastien, E and Langenfeld, K and Lindback, M and Saini, JS and Wing, A and Zhang, J and Duhaime, M}, title = {Benchmarking informatics approaches for virus discovery: caution is needed when combining in silico identification methods.}, journal = {mSystems}, volume = {9}, number = {3}, pages = {e0110523}, pmid = {38376167}, issn = {2379-5077}, support = {DGE1256260, 2055455, DGE134012//National Science Foundation (NSF)/ ; NA17OAR4320152//DOC | National Oceanic and Atmospheric Administration (NOAA)/ ; Blue Sky Initiative//College of Engineering, University of Michigan/ ; }, mesh = {Ecosystem ; *Viruses ; Metagenomics/methods ; Databases, Nucleic Acid ; }, abstract = {UNLABELLED: Understanding the ecological impacts of viruses on natural and engineered ecosystems relies on the accurate identification of viral sequences from community sequencing data. To maximize viral recovery from metagenomes, researchers frequently combine viral identification tools. However, the effectiveness of this strategy is unknown. Here, we benchmarked combinations of six widely used informatics tools for viral identification and analysis (VirSorter, VirSorter2, VIBRANT, DeepVirFinder, CheckV, and Kaiju), called "rulesets." Rulesets were tested against mock metagenomes composed of taxonomically diverse sequence types and diverse aquatic metagenomes to assess the effects of the degree of viral enrichment and habitat on tool performance. We found that six rulesets achieved equivalent accuracy [Matthews Correlation Coefficient (MCC) = 0.77, Padj ≥ 0.05]. Each contained VirSorter2, and five used our "tuning removal" rule designed to remove non-viral contamination. While DeepVirFinder, VIBRANT, and VirSorter were each found once in these high-accuracy rulesets, they were not found in combination with each other: combining tools does not lead to optimal performance. Our validation suggests that the MCC plateau at 0.77 is partly caused by inaccurate labeling within reference sequence databases. In aquatic metagenomes, our highest MCC ruleset identified more viral sequences in virus-enriched (44%-46%) than in cellular metagenomes (7%-19%). While improved algorithms may lead to more accurate viral identification tools, this should be done in tandem with careful curation of sequence databases. We recommend using the VirSorter2 ruleset and our empirically derived tuning removal rule. Our analysis provides insight into methods for in silico viral identification and will enable more robust viral identification from metagenomic data sets.<br><br>IMPORTANCE: The identification of viruses from environmental metagenomes using informatics tools has offered critical insights in microbial ecology. However, it remains difficult for researchers to know which tools optimize viral recovery for their specific study. In an attempt to recover more viruses, studies are increasingly combining the outputs from multiple tools without validating this approach. After benchmarking combinations of six viral identification tools against mock metagenomes and environmental samples, we found that these tools should only be combined cautiously. Two to four tool combinations maximized viral recovery and minimized non-viral contamination compared with either the single-tool or the five- to six-tool ones. By providing a rigorous overview of the behavior of in silico viral identification strategies and a pipeline to replicate our process, our findings guide the use of existing viral identification tools and offer a blueprint for feature engineering of new tools that will lead to higher-confidence viral discovery in microbiome studies.}, }
@article {pmid38371853, year = {2024}, author = {Meyer, F and Sandbakk, &#xd8; and Millet, GP}, title = {Editorial: Sport performance analysis: from the laboratory to the field.}, journal = {Frontiers in sports and active living}, volume = {6}, number = {}, pages = {1372080}, pmid = {38371853}, issn = {2624-9367}, }
@article {pmid38368650, year = {2024}, author = {Shchepin, ON and López Villalba, &#xc1; and Inoue, M and Prikhodko, IS and Erastova, DA and Okun, MV and Woyzichovski, J and Yajima, Y and Gmoshinskiy, VI and Moreno, G and Novozhilov, YK and Schnittler, M}, title = {DNA barcodes reliably differentiate between nivicolous species of Diderma (Myxomycetes, Amoebozoa) and reveal regional differences within Eurasia.}, journal = {Protist}, volume = {175}, number = {2}, pages = {126023}, doi = {10.1016/j.protis.2024.126023}, pmid = {38368650}, issn = {1618-0941}, mesh = {*Myxomycetes ; DNA Barcoding, Taxonomic/methods ; Bayes Theorem ; Phylogeny ; DNA, Ribosomal/genetics ; }, abstract = {The nivicolous species of the genus Diderma are challenging to identify, and there are several competing views on their delimitation. We analyzed 102 accessions of nivicolous Diderma spp. that were sequenced for two or three unlinked genes to determine which of the current taxonomic treatments is better supported by molecular species delimitation methods. The results of a haplotype web analysis, Bayesian species delimitation under a multispecies coalescent model, and phylogenetic analyses on concatenated alignments support a splitting approach that distinguishes six taxa: Diderma alpinum, D. europaeum, D. kamchaticum, D. meyerae, D. microcarpum and D. niveum. The first two approaches also support the separation of Diderma alpinum into two species with allopatric distribution. An extended dataset of 800 specimens (mainly from Europe) that were barcoded with 18S rDNA revealed only barcode variants similar to those in the species characterized by the first data set, and showed an uneven distribution of these species in the Northern Hemisphere: Diderma microcarpum and D. alpinum were the only species found in all seven intensively sampled mountain regions. Partial 18S rDNA sequences serving as DNA barcodes provided clear signatures that allowed for unambiguous identification of the nivicolous Diderma spp., including two putative species in D. alpinum.}, }
@article {pmid38366261, year = {2024}, author = {Jensen, PM and Danielsen, F and Jacobsen, SK and Vikstrøm, T}, title = {Fair concordance between Google Trends and Danish ornithologists in the assessment of temporal trends in Danish bird populations highlights the informational value of big data.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {3}, pages = {276}, pmid = {38366261}, issn = {1573-2959}, support = {869673//CAPARDUS/ ; 862731//FRAMEwork/ ; 101058509//ECS/ ; 101096887//BestLife2030/ ; 5228-00001B//UArctic/ ; }, mesh = {Animals ; Humans ; *Ecosystem ; *Search Engine ; Big Data ; Environmental Monitoring ; Birds ; Denmark ; }, abstract = {The ongoing depletion of natural systems and associated biodiversity decline is of growing international concern. Climate change is expected to exacerbate anthropogenic impacts on wild populations. The scale of impact on ecosystems and ecosystem services will be determined by the impact on a multitude of species and functional groups, which due to their biology and numbers are difficult to monitor. The IPCC has argued that surveillance or monitoring is critical and proposed that monitoring systems should be developed, which not only track developments but also function as "early warning systems." Human populations are already generating large continuous datasets on multiple taxonomic groups through internet searches. These time series could in principle add substantially to current monitoring if they reflect true changes in the natural world. We here examined whether information on internet search frequencies delivered by the Danish population and captured by Google Trends (GT) appropriately informs on population trends in 106 common Danish bird species. We compared the internet search activity with independent equivalent population trend assessments from the Danish Ornithological Society (BirdLife Denmark/DOF). We find a fair concordance between the GT trends and the assessments by DOF. A substantial agreement can be obtained by omitting species without clear temporal trends. Our findings suggest that population trend proxies from internet search frequencies can be used to supplement existing wildlife population monitoring and to ask questions about an array of ecological phenomena, which potentially can be integrated into an early warning system for biodiversity under climate change.}, }
@article {pmid38365244, year = {2024}, author = {Yu, XA and McLean, C and Hehemann, JH and Angeles-Albores, D and Wu, F and Muszyński, A and Corzett, CH and Azadi, P and Kujawinski, EB and Alm, EJ and Polz, MF}, title = {Low-level resource partitioning supports coexistence among functionally redundant bacteria during successional dynamics.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38365244}, issn = {1751-7370}, support = {DE-SC0008743//United States Department of Energy/ ; DE-SC0015662//United States Department of Energy/ ; }, mesh = {Bacteria/genetics ; *Seaweed ; *Microbiota ; }, abstract = {Members of microbial communities can substantially overlap in substrate use. However, what enables functionally redundant microorganisms to coassemble or even stably coexist remains poorly understood. Here, we show that during unstable successional dynamics on complex, natural organic matter, functionally redundant bacteria can coexist by partitioning low-concentration substrates even though they compete for one simple, dominant substrate. We allowed ocean microbial communities to self-assemble on leachates of the brown seaweed Fucus vesiculosus and then analyzed the competition among 10 taxonomically diverse isolates representing two distinct stages of the succession. All, but two isolates, exhibited an average of 90% ± 6% pairwise overlap in resource use, and functional redundancy of isolates from the same assembly stage was higher than that from between assembly stages, leading us to construct a simpler four-isolate community with two isolates from each of the early and late stages. We found that, although the short-term dynamics of the four-isolate communities in F. vesiculosus leachate was dependent on initial isolate ratios, in the long term, the four isolates stably coexist in F. vesiculosus leachate, albeit with some strains at low abundance. We therefore explored the potential for nonredundant substrate use by genomic content analysis and RNA expression patterns. This analysis revealed that the four isolates mainly differed in peripheral metabolic pathways, such as the ability to degrade pyrimidine, leucine, and tyrosine, as well as aromatic substrates. These results highlight the importance of fine-scale differences in metabolic strategies for supporting the frequently observed coexistence of large numbers of rare organisms in natural microbiomes.}, }
@article {pmid38365075, year = {2024}, author = {Lyu, Y and Gao, Y and Pang, X and Sun, S and Luo, P and Cai, D and Qin, K and Wu, Z and Wang, B}, title = {Elucidating contributions of volatile organic compounds to ozone formation using random forest during COVID-19 pandemic: A case study in China.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {346}, number = {}, pages = {123532}, doi = {10.1016/j.envpol.2024.123532}, pmid = {38365075}, issn = {1873-6424}, mesh = {Humans ; *Air Pollutants/analysis ; *Volatile Organic Compounds/analysis ; Pandemics ; *Ozone/analysis ; Random Forest ; Nitrogen Dioxide ; *COVID-19 ; Toluene ; Alkenes ; China ; Environmental Monitoring ; *Xylenes ; }, abstract = {Ozone has been reported to increase despite nitrogen oxides reductions during the COVID-19 pandemic, and ozone formation needs to be revisited using volatile organic compounds (VOCs), which are rarely measured during the pandemic. Here, a total of 98 VOCs species were monitored in an economy-active city in China from January 2021 to August 2022 to assess contributions to ozone formation during the pandemic. Total VOCs concentrations were 35.55 ± 21.47 ppb during the entire period, among which alkanes account for the largest fraction (13.78 ppb, 38.0%), followed by aromatics (6.16 ppb, 16.8%) and oxygenated VOCs (OVOCs, 5.69 ppb, 15.7%). Most VOCs groups (e.g., alkenes, OVOCs) and individual species (e.g., isoprene, methyl vinyl ketone) display obvious seasonal and diurnal variations, which are related to their sources and reactivities. No weekend effects of VOCs suggest limited influences from traffic emissions during pandemic. Aromatics and alkenes are the major contributors (39% and 33%) to ozone formation potential, largely driven by o/m/p-xylene (21%), ethylene (15%), toluene (9%). Secondary organic aerosol formation potential is dominated by toluene (>50%) despite its low proportion (5%). Further inclusion of VOCs and meteorology in the Random Forest model shows good ozone prediction performance (R[2] = 0.77-0.86, RMSE = 11.95-19.91 μg/m[3], MAE = 8.89-14.58 μg/m[3]). VOCs and NO2 contribute >50% of total importance with the largest difference in importance ratio of VOCs/NO2 in the summer and winter, implying ozone formation regime may vary. No seasonal variations in importance of meteorology are observed, while importance of other variables (e.g., PM2.5) is highest in the summer. This work identifies critical VOCs groups and species for ozone formation during the pandemic, and demonstrates the feasibility of machine learning algorithms in elucidation of ozone formation mechanisms.}, }
@article {pmid38360168, year = {2024}, author = {Ko, CY and Lee, YC and Wang, YC and Hsu, HH and Chow, CH and Chen, RG and Liu, TH and Chen, CS and Chiu, TS and Chiang, DH and Wu, RF and Tseng, WL}, title = {Modulations of ocean-atmosphere interactions on squid abundance over Southwest Atlantic.}, journal = {Environmental research}, volume = {250}, number = {}, pages = {118444}, doi = {10.1016/j.envres.2024.118444}, pmid = {38360168}, issn = {1096-0953}, mesh = {*Decapodiformes/physiology ; Animals ; Atlantic Ocean ; *Atmosphere ; Temperature ; Seasons ; Climate Change ; }, abstract = {Anthropogenic shifts in seas are reshaping fishing trends, with significant implications for aquatic food sources throughout this century. Examining a 21-year abundance dataset of Argentine shortfin squids Illex argentinus paired with a regional oceanic analysis, we noted strong correlations between squid annual abundance and sea surface temperature (SST) in January and February and eddy kinetic energy (EKE) from March to May in the Southwest Atlantic. A deeper analysis revealed combined ocean-atmosphere interactions, pinpointed as the primary mode in a rotated empirical orthogonal function analysis of SST. This pattern produced colder SST and amplified EKE in the surrounding seas, factors crucial for the unique life stages of squids. Future projections from the CMIP6 archive indicated that this ocean-atmosphere pattern, referred to as the Atlantic symmetric pattern, would persist in its cold SST phase, promoting increased squid abundance. However, rising SSTs due to global warming might counteract the abundance gains. Our findings uncover a previously unrecognized link between squids and specific environmental conditions governed by broader ocean-atmosphere interactions in the Southwest Atlantic. Integrating these insights with seasonal and decadal projections can offer invaluable information to stakeholders in squid fisheries and marine conservation under a changing climate.}, }
@article {pmid38358627, year = {2024}, author = {Akar, AU and Sisman, S and Ulku, H and Yel, E and Yalpir, S}, title = {Evaluating lake water quality with a GIS-based MCDA integrated approach: a case in Konya/Karapınar.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {13}, pages = {19478-19499}, pmid = {38358627}, issn = {1614-7499}, mesh = {Humans ; *Water Quality ; *Geographic Information Systems ; Lakes ; Environmental Monitoring/methods ; Decision Support Techniques ; }, abstract = {Considering water quality is an essential requirement in terms of environmental planning and management. To protect and manage water resources effectively, it is necessary to develop an analytical decision-support system. In this study, a systematic approach was suggested to evaluate the lake water quality. The methodology includes the prediction of the values in different locations of the lakes from experimental data through inverse distance weighting (IDW) method, creation of maps by using Geographic Information System (GIS) integrated with analytic hierarchy process (AHP) from multi-criteria decision analysis (MCDA), reclassification into five class, combining the time-related spatial data into a single map to predict the whole lake water quality from the data of sampling points, and finally overlapping the final maps with topography/geology and land use. The proposed approach was verified and presented as case study for Meke and Acigol Lakes in Konya/Turkey which were affected by human and natural factors although they have ecological, hydromorphological, and socio-economic importance. In the proposed approach, categorizing water quality parameters as "hardness and minerals," "substrates and nutrients," "solids content," "metals," and "oil-grease" groups was helpful for AHP with the determined group weights of 0.484, 0.310, 0.029, and 0.046, respectively. Assigning weights within each group and then assigning weights between groups resulted in creating accurate final map. The proposed approach is flexible and applicable to any lake water quality data; even with a limited number of data, the whole lake water quality maps could be created for assessment.}, }
@article {pmid38358505, year = {2024}, author = {Zhang, J and Wu, Z and Dong, B and Ge, S and He, S}, title = {Effective degradation of quinoline by catalytic ozonation with MnCexOy catalysts: performance and mechanism.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {89}, number = {3}, pages = {823-837}, doi = {10.2166/wst.2024.027}, pmid = {38358505}, issn = {0273-1223}, mesh = {Humans ; Manganese Compounds ; Oxides ; Catalysis ; *Quinolines ; *Cocaine ; *Coke ; Oxygen ; *Ozone ; }, abstract = {Quinoline inevitably remains in the effluent of coking wastewater treatment plants due to its bio-refractory nature, which might cause unfavorable effects on human and ecological environments. In this study, MnCexOy was consciously synthesized by α-MnO2 doped with Ce[3+] (Ce:Mn = 1:10) and employed as the ozonation catalyst for quinoline degradation. After that, the removal efficiency and mechanism of quinoline were systematically analyzed by characterizing the physicochemical properties of MnCexOy, investigating free radicals and monitoring the solution pH. Results indicated that the removal rate of quinoline was greatly improved by the prepared MnCexOy catalyst. Specifically, the removal efficiencies of quinoline could be 93.73, 62.57 and 43.76%, corresponding to MnCexOy, α-MnO2 and single ozonation systems, respectively. The radical scavenging tests demonstrated that [•]OH and [•]O2[-] were the dominant reactive oxygen species in the MnCexOy ozonation system. Meanwhile, the contribution levels of [•]OH and [•]O2[-] to quinoline degradation were about 42 and 35%, respectively. The abundant surface hydroxyl groups and oxygen vacancies of the MnCexOy catalyst were two important factors for decomposing molecular O3 into more [•]OH and [•]O2[-]. This study could provide scientific support for the application of the MnCexOy/O3 system in degrading quinoline in bio-treated coking wastewater.}, }
@article {pmid38357349, year = {2024}, author = {Moore, LR and Caspi, R and Campbell, DA and Casey, JR and Crevecoeur, S and Lea-Smith, DJ and Long, B and Omar, NM and Paley, SM and Schmelling, NM and Torrado, A and Zehr, JP and Karp, PD}, title = {CyanoCyc cyanobacterial web portal.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1340413}, pmid = {38357349}, issn = {1664-302X}, abstract = {CyanoCyc is a web portal that integrates an exceptionally rich database collection of information about cyanobacterial genomes with an extensive suite of bioinformatics tools. It was developed to address the needs of the cyanobacterial research and biotechnology communities. The 277 annotated cyanobacterial genomes currently in CyanoCyc are supplemented with computational inferences including predicted metabolic pathways, operons, protein complexes, and orthologs; and with data imported from external databases, such as protein features and Gene Ontology (GO) terms imported from UniProt. Five of the genome databases have undergone manual curation with input from more than a dozen cyanobacteria experts to correct errors and integrate information from more than 1,765 published articles. CyanoCyc has bioinformatics tools that encompass genome, metabolic pathway and regulatory informatics; omics data analysis; and comparative analyses, including visualizations of multiple genomes aligned at orthologous genes, and comparisons of metabolic networks for multiple organisms. CyanoCyc is a high-quality, reliable knowledgebase that accelerates scientists' work by enabling users to quickly find accurate information using its powerful set of search tools, to understand gene function through expert mini-reviews with citations, to acquire information quickly using its interactive visualization tools, and to inform better decision-making for fundamental and applied research.}, }
@article {pmid38356288, year = {2024}, author = {Speyer, LG and Murray, AL and Kievit, R}, title = {Investigating Moderation Effects at the Within-Person Level Using Intensive Longitudinal Data: A Two-Level Dynamic Structural Equation Modelling Approach in Mplus.}, journal = {Multivariate behavioral research}, volume = {59}, number = {3}, pages = {620-637}, doi = {10.1080/00273171.2023.2288575}, pmid = {38356288}, issn = {1532-7906}, mesh = {Humans ; Longitudinal Studies ; *Latent Class Analysis ; Depression/psychology ; Social Media/statistics &amp; numerical data ; Software ; Loneliness/psychology ; Models, Statistical ; Female ; Male ; Data Interpretation, Statistical ; }, abstract = {Recent technological advances have provided new opportunities for the collection of intensive longitudinal data. Using methods such as dynamic structural equation modeling, these data can provide new insights into moment-to-moment dynamics of psychological and behavioral processes. In intensive longitudinal data (t > 20), researchers often have theories that imply that factors that change from moment to moment within individuals act as moderators. For instance, a person's level of sleep deprivation may affect how much an external stressor affects mood. Here, we describe how researchers can implement, test, and interpret dynamically changing within-person moderation effects using two-level dynamic structural equation modeling as implemented in the structural equation modeling software Mplus. We illustrate the analysis of within-person moderation effects using an empirical example investigating whether changes in spending time online using social media affect the moment-to-moment effect of loneliness on depressive symptoms, and highlight avenues for future methodological development. We provide annotated Mplus code, enabling researchers to better isolate, estimate, and interpret the complexities of within-person interaction effects.}, }
@article {pmid38355478, year = {2024}, author = {Zhang, M and Qiao, L and Sun, P and Jiang, H and Shi, Y and Zhang, W and Mei, Y and Yu, M and Wang, H}, title = {Spatiotemporal pattern of leprosy in southwest China from 2010 to 2020: an ecological study.}, journal = {BMC public health}, volume = {24}, number = {1}, pages = {465}, pmid = {38355478}, issn = {1471-2458}, support = {2019YFE0113300//The National Key R&amp;D Program of China/ ; 81972950, 82173431, 82103748//National Natural Science Foundation of China/ ; ZDXYS202204//Jiangsu Provincial Medical Key Laboratory, Jiangsu Province Capability Improvement Project through Science, Technology and Education/ ; 2019060001//The Nanjing Incubation Program for National Clinical Research Center/ ; 2022-I2M-C&amp;T-B-094//Chinese Academy of Medical Sciences Innovation Fund for Medical Science/ ; }, mesh = {Humans ; China/epidemiology ; *Leprosy/epidemiology ; Spatial Analysis ; Cluster Analysis ; Databases, Factual ; Spatio-Temporal Analysis ; }, abstract = {BACKGROUND: Despite many efforts to control leprosy worldwide, it is still a significant public health problem in low- and middle-income regions. It has been endemic in China for thousands of years, and southwest China has the highest leprosy burden in the country.<br><br>METHODS: This observational study was conducted with all newly detected leprosy cases in southwest China from 2010 to 2020. Data were extracted from the Leprosy Management Information System (LEPMIS) database in China. The Joinpoint model was used to determine the time trends in the study area. Spatial autocorrelation statistics was performed to understand spatial distribution of leprosy cases. Spatial scan statistics was applied to identify significant clusters with high rate.<br><br>RESULTS: A total of 4801 newly detected leprosy cases were reported in southwest China over 11 years. The temporal trends declined stably. The new case detection rate (NCDR) dropped from 4.38/1,000,000 population in 2010 to 1.25/1,000,000 population in 2020, with an average decrease of 12.24% (95% CI: -14.0 to -&#x2009;10.5; P&#x2009;<&#x2009;0.001). Results of global spatial autocorrelation showed that leprosy cases presented clustering distribution in the study area. Most likely clusters were identified during the study period and were frequently located at Yunnan or the border areas between Yunnan and Guizhou Provinces. Secondary clusters were always located in the western counties, the border areas between Yunnan and Sichuan Provinces.<br><br>CONCLUSIONS: Geographic regions characterized by clusters with high rates were considered as leprosy high-risk areas. The findings of this study could be used to design leprosy control measures and provide indications to strengthen the surveillance of high-risk areas. These areas should be prioritized in the allocation of resources.}, }
@article {pmid38355366, year = {2024}, author = {Jones, CB and Stock, K and Perkins, SE}, title = {AI-based discovery of habitats from museum collections.}, journal = {Trends in ecology &amp; evolution}, volume = {39}, number = {4}, pages = {323-327}, doi = {10.1016/j.tree.2024.01.006}, pmid = {38355366}, issn = {1872-8383}, mesh = {*Museums ; *Artificial Intelligence ; Ecosystem ; Biological Evolution ; }, abstract = {Museum collection records are a source of historic data for species occurrence, but little attention is paid to the associated descriptions of habitat at the sample locations. We propose that artificial intelligence methods have potential to use these descriptions for reconstructing past habitat, to address ecological and evolutionary questions.}, }
@article {pmid38353941, year = {2024}, author = {Iyamu, I and McKee, G and Haag, D and Gilbert, M}, title = {Defining the role of digital public health in the evolving digital health landscape: policy and practice implications in Canada.}, journal = {Health promotion and chronic disease prevention in Canada : research, policy and practice}, volume = {44}, number = {2}, pages = {66-69}, pmid = {38353941}, issn = {2368-738X}, mesh = {Humans ; *Digital Health ; *Public Health ; Canada ; Policy ; }, }
@article {pmid38350096, year = {2025}, author = {Krys, K and Kostoula, O and van Tilburg, WAP and Mosca, O and Lee, JH and Maricchiolo, F and Kosiarczyk, A and Kocimska-Bortnowska, A and Torres, C and Hitokoto, H and Liew, K and Bond, MH and Lun, VM and Vignoles, VL and Zelenski, JM and Haas, BW and Park, J and Vauclair, CM and Kwiatkowska, A and Roczniewska, M and Witoszek, N and Işık, &#x130; and Kosakowska-Berezecka, N and Domínguez-Espinosa, A and Yeung, JC and Górski, M and Adamovic, M and Albert, I and Pavlopoulos, V and Fülöp, M and Sirlopu, D and Okvitawanli, A and Boer, D and Teyssier, J and Malyonova, A and Gavreliuc, A and Serdarevich, U and Akotia, CS and Appoh, L and Mira, DMA and Baltin, A and Denoux, P and Esteves, CS and Gamsakhurdia, V and Garðarsdóttir, RB and Igbokwe, DO and Igou, ER and Kascakova, N and Klůzová Kračmárová, L and Kronberger, N and Barrientos, PE and Mohorić, T and Murdock, E and Mustaffa, NF and Nader, M and Nadi, A and van Osch, Y and Pavlović, Z and Poláčková Šolcová, I and Rizwan, M and Romashov, V and Røysamb, E and Sargautyte, R and Schwarz, B and Selecká, L and Selim, HA and Stogianni, M and Sun, CR and Wojtczuk-Turek, A and Xing, C and Uchida, Y}, title = {Happiness Maximization Is a WEIRD Way of Living.}, journal = {Perspectives on psychological science : a journal of the Association for Psychological Science}, volume = {20}, number = {5}, pages = {874-902}, pmid = {38350096}, issn = {1745-6924}, mesh = {*Happiness ; Humans ; *Personal Satisfaction ; Cross-Cultural Comparison ; }, abstract = {Psychological science tends to treat subjective well-being and happiness synonymously. We start from the assumption that subjective well-being is more than being happy to ask the fundamental question: What is the ideal level of happiness? From a cross-cultural perspective, we propose that the idealization of attaining maximum levels of happiness may be especially characteristic of Western, educated, industrial, rich, and democratic (WEIRD) societies but less so for others. Searching for an explanation for why "happiness maximization" might have emerged in these societies, we turn to studies linking cultures to their eco-environmental habitat. We discuss the premise that WEIRD cultures emerged in an exceptionally benign ecological habitat (i.e., faced relatively light existential pressures compared with other regions). We review the influence of the Gulf Stream on the Northwestern European climate as a source of these comparatively benign geographical conditions. We propose that the ecological conditions in which WEIRD societies emerged afforded them a basis to endorse happiness as a value and to idealize attaining its maximum level. To provide a nomological network for happiness maximization, we also studied some of its potential side effects, namely alcohol and drug consumption and abuse and the prevalence of mania. To evaluate our hypothesis, we reanalyze data from two large-scale studies on ideal levels of personal life satisfaction-the most common operationalization of happiness in psychology-involving respondents from 61 countries. We conclude that societies whose members seek to maximize happiness tend to be characterized as WEIRD, and generalizing this across societies can prove problematic if adopted at the ideological and policy level.}, }
@article {pmid38344693, year = {2023}, author = {Boyes, D and Gibbs, M and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Variegated Golden Tortrix, Archips xylosteana (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {538}, pmid = {38344693}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Archips xylosteana (the Variegated Golden Tortrix; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 650.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 16.39 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,861 protein coding genes.}, }
@article {pmid38343945, year = {2024}, author = {Kwon, H and Jin, BR and Kim, HJ and Kwon, J and Park, K and Kim, C and Kim, JG and Hwang, BY and Kwon, SL and Kim, JJ and Shim, SH and Guo, Y and An, HJ and Lee, D}, title = {New Pimarane Diterpenoids Isolated from EtOAc-Extract of Apiospora arundinis Culture Medium Show Antibenign Prostatic Hyperplasia Potential.}, journal = {ACS omega}, volume = {9}, number = {5}, pages = {5616-5623}, pmid = {38343945}, issn = {2470-1343}, abstract = {Three new pimarane diterpenoids, libertellenones U-W (1-3), together with libertellenone C (4) and myrocin A (5) were isolated from an EtOAc-extract of Apiospora arundinis culture medium. The chemical structures of the new compounds were elucidated using MS, NMR, and CD spectroscopic data. Benign prostatic hyperplasia (BPH), the abnormal and pathological proliferation of epithelial and stromal cells in prostatic tissues, is a common disease in middle-aged and elderly men. In this study, the anti-BPH effects of myrocin A (5) were evaluated using BPH-1 and WPMY-1 cells. Treatment with myrocin A (5) exerted antiproliferative effects in BPH-1 and dihydrotestosterone (DHT)-stimulated WPMY-1 cells. In BPH, treatment with myrocin A (5) significantly suppressed the mRNA levels of androgen receptor (AR) and its downstream targets nuclear receptor coactivator 1 (NCOA1), proliferating cell nuclear antigen (PCNA) and kallikrein-related peptidase 3 (KLK3). Additionally, DHT-stimulated WPMY-1 cells demonstrated an upregulated mRNA levels of AR, NCOA1, PCNA, and KLK3. However, treatment with myrocin A (5) resulted in suppression of the mRNA levels. Moreover, myrocin A (5) docked computationally into the binding site of the androgen receptor (-5.5 kcal/mol).}, }
@article {pmid38342840, year = {2024}, author = {Xiao, Y and Luan, H and Lu, S and Xing, M and Guo, C and Qian, R and Xiao, X}, title = {Toxic effects of atmospheric deposition in mining areas on wheat seedlings.}, journal = {Environmental geochemistry and health}, volume = {46}, number = {2}, pages = {69}, pmid = {38342840}, issn = {1573-2983}, support = {52130402//the Key Program of the National Natural Science Foundation of China/ ; DYGX-2023-035//2023 China University of Mining and Technology Large Instrument and Equipment Open Sharing Fund Project/ ; }, mesh = {Triticum ; Seedlings ; Soil ; Cadmium ; Lead ; *Soil Pollutants/toxicity/analysis ; *Metals, Heavy/analysis ; Coal ; Environmental Monitoring/methods ; China ; Risk Assessment ; }, abstract = {Storage and transportation of coal, as well as operation of coal-fired power plants, produce amounts of metallic exhaust that may lead to different atmospheric environment in the overlapped areas of farmland and coal resource (OAFCR) environment. To investigate the effects of different atmospheric environment in the OAFCR region (north of Xuzhou) on wheat seedlings (AK-58), a box experiment was conducted and compared to an area far from the OAFCR (south of Xuzhou). The study revealed that (1) compared to the southern suburb of Xuzhou, the fresh and dry weight, activities of photosynthetic enzymes and POD of wheat seedlings in the OAFCR reduced obviously. (2) Significantly higher levels of Cr, Cd, Pb, Zn, and Cu were found in the shoots and roots of wheat seedlings in the OAFCR, with lower transfer factor for heavy metals (except Cd and As) in comparison to those in the southern suburb. And the bioconcentration factors of heavy metals (except As) in wheat seedlings in the OAFCR were significantly higher. (3) Nearly 90% of heavy metals (Pb, Cu, Cd, Zn, and Cr) absorbed by wheat were stored in cell walls and soluble fractions, with significantly higher contents of Cu and Cr in wheat seedlings' cell walls and higher contents of Pb, Zn, and Cd in soluble components found in the OAFCR. Our results showed that atmospheric deposition in the mining area has a certain toxic effect on wheat seedlings, and this study provides a theoretical basis for OAFCR crop toxicity management.}, }
@article {pmid38342219, year = {2024}, author = {Lausch, A and Selsam, P and Pause, M and Bumberger, J}, title = {Monitoring vegetation- and geodiversity with remote sensing and traits.}, journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences}, volume = {382}, number = {2269}, pages = {20230058}, pmid = {38342219}, issn = {1471-2962}, mesh = {*Ecosystem ; *Remote Sensing Technology ; Phylogeny ; Biodiversity ; Phenotype ; }, abstract = {Geodiversity has shaped and structured the Earth's surface at all spatio-temporal scales, not only through long-term processes but also through medium- and short-term processes. Geodiversity is, therefore, a key control and regulating variable in the overall development of landscapes and biodiversity. However, climate change and land use intensity are leading to major changes and disturbances in bio- and geodiversity. For sustainable ecosystem management, temporal, economically viable and standardized monitoring is needed to monitor and model the effects and changes in vegetation- and geodiversity. RS approaches have been used for this purpose for decades. However, to understand in detail how RS approaches capture vegetation- and geodiversity, the aim of this paper is to describe how five features of vegetation- and geodiversity are captured using RS technologies, namely: (i) trait diversity, (ii) phylogenetic/genese diversity, (iii) structural diversity, (iv) taxonomic diversity and (v) functional diversity. Trait diversity is essential for establishing the other four. Traits provide a crucial interface between in situ, close-range, aerial and space-based RS monitoring approaches. The trait approach allows complex data of different types and formats to be linked using the latest semantic data integration techniques, which will enable ecosystem integrity monitoring and modelling in the future. This article is part of the Theo Murphy meeting issue 'Geodiversity for science and society'.}, }
@article {pmid38339498, year = {2024}, author = {Li, J and Xing, Q and Li, X and Arif, M and Li, J}, title = {Monitoring Off-Shore Fishing in the Northern Indian Ocean Based on Satellite Automatic Identification System and Remote Sensing Data.}, journal = {Sensors (Basel, Switzerland)}, volume = {24}, number = {3}, pages = {}, pmid = {38339498}, issn = {1424-8220}, support = {CAS-WX2021SF-0408//Informatization Plan of Chinese Academy of Sciences/ ; XDA19060501//International Partnership Program of Chinese Academy of Sciences, the Strategic Priority Research Program of the Chinese Academy of Sciences (Class A)/ ; }, abstract = {Satellite-derived Sea Surface Temperature (SST) and sea-surface Chlorophyll a concentration (Chl-a), along with Automatic Identification System (AIS) data of fishing vessels, were used in the examination of the correlation between fishing operations and oceanographic factors within the northern Indian Ocean from March 2020 to February 2023. Frequency analysis and the empirical cumulative distribution function (ECDF) were used to calculate the optimum ranges of two oceanographic factors for fishing operations. The results revealed a substantial influence of the northeast and southwest monsoons significantly impacting fishing operations in the northern Indian Ocean, with extensive and active operations during the period from October to March and a notable reduction from April to September. Spatially, fishing vessels were mainly concentrated between 20° N and 6° S, extending from west of 90° E to the eastern coast of Africa. Observable seasonal variations in the distribution of fishing vessels were observed in the central and southeastern Arabian Sea, along with its adjacent high sea of the Indian Ocean. Concerning the marine environment, it was observed that during the northeast monsoon, the suitable SST contributed to high CPUEs in fishing operation areas. Fishing vessels were widely distributed in the areas with both mid-range and low-range Chl-a concentrations, with a small part distributed in high-concentration areas. Moreover, the monthly numbers of fishing vessels showed seasonal fluctuations between March 2020 and February 2023, displaying a periodic pattern with an overall increasing trend. The total number of fishing vessels decreased due to the impact of the COVID-19 pandemic in 2020, but this was followed by a gradual recovery in the subsequent two years. For fishing operations in the northern Indian Ocean, the optimum ranges for SST and Chl-a concentration were 27.96 to 29.47 °C and 0.03 to 1.81 mg/m[3], respectively. The preliminary findings of this study revealed the spatial-temporal distribution characteristics of fishing vessels in the northern Indian Ocean and the suitable ranges of SST and Chl-a concentration for fishing operations. These results can serve as theoretical references for the production and resource management of off-shore fishing operations in the northern Indian Ocean.}, }
@article {pmid38337048, year = {2024}, author = {Trepel, J and le Roux, E and Abraham, AJ and Buitenwerf, R and Kamp, J and Kristensen, JA and Tietje, M and Lundgren, EJ and Svenning, JC}, title = {Meta-analysis shows that wild large herbivores shape ecosystem properties and promote spatial heterogeneity.}, journal = {Nature ecology &amp; evolution}, volume = {8}, number = {4}, pages = {705-716}, pmid = {38337048}, issn = {2397-334X}, support = {1131-00006B//Det Frie Forskningsr&#xe5;d (Danish Council for Independent Research)/ ; 0135-00225B//Det Frie Forskningsr&#xe5;d (Danish Council for Independent Research)/ ; 101062339//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; CF20-0238//Carlsbergfondet (Carlsberg Foundation)/ ; DNRF173//Danmarks Grundforskningsfond (Danish National Research Foundation)/ ; 16549//Villum Fonden (Villum Foundation)/ ; }, mesh = {Animals ; *Ecosystem ; *Herbivory ; Biodiversity ; Soil ; Biological Evolution ; }, abstract = {Megafauna (animals ≥45 kg) have probably shaped the Earth's terrestrial ecosystems for millions of years with pronounced impacts on biogeochemistry, vegetation, ecological communities and evolutionary processes. However, a quantitative global synthesis on the generality of megafauna effects on ecosystems is lacking. Here we conducted a meta-analysis of 297 studies and 5,990 individual observations across six continents to determine how wild herbivorous megafauna influence ecosystem structure, ecological processes and spatial heterogeneity, and whether these impacts depend on body size and environmental factors. Despite large variability in megafauna effects, we show that megafauna significantly alter soil nutrient availability, promote open vegetation structure and reduce the abundance of smaller animals. Other responses (14 out of 26), including, for example, soil carbon, were not significantly affected. Further, megafauna significantly increase ecosystem heterogeneity by affecting spatial heterogeneity in vegetation structure and the abundance and diversity of smaller animals. Given that spatial heterogeneity is considered an important driver of biodiversity across taxonomic groups and scales, these results support the hypothesis that megafauna may promote biodiversity at large scales. Megafauna declined precipitously in diversity and abundance since the late Pleistocene, and our results indicate that their restoration would substantially influence Earth's terrestrial ecosystems.}, }
@article {pmid38333733, year = {2023}, author = {Boyes, D and Boyes, C and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Ingrailed Clay, Diarsia mendica (Fabricius, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {448}, pmid = {38333733}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Diarsia mendica (the Ingrailed Clay; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 727.9 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.37 kilobases in length. Gene annotation of this assembly on Ensembl identified 14,077 protein coding genes.}, }
@article {pmid38332565, year = {2024}, author = {Hou, Z and Qiang, W and Wang, X and Chen, X and Hu, X and Han, X and Shen, W and Zhang, B and Xing, P and Shi, W and Dai, J and Huang, X and Zhao, G}, title = {"Cell Disk" DNA Storage System Capable of Random Reading and Rewriting.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {11}, number = {15}, pages = {e2305921}, pmid = {38332565}, issn = {2198-3844}, support = {2021YFF1201700//National Key Research and Development Program of China/ ; 2018YFA0900100//National Key Research and Development Program of China/ ; 31971340//National Natural Science Foundation of China/ ; 31800080//National Natural Science Foundation of China/ ; 32030004//National Natural Science Foundation of China/ ; 32150025//National Natural Science Foundation of China/ ; XDB0480000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2021M692645//China Postdoctoral Science Foundation/ ; 172644KYSB20180022//Bureau of International Co-operation, Chinese Academy of Sciences/ ; KQTD20180413181837372//Shenzhen Science and Technology Innovation Program/ ; RCYX20221008092950122//Shenzhen Science and Technology Innovation Program/ ; //Shenzhen Outstanding Talents Training Fund/ ; }, mesh = {*Reading ; Reproducibility of Results ; *Saccharomyces cerevisiae/genetics ; DNA/genetics ; Information Storage and Retrieval ; }, abstract = {DNA has emerged as an appealing material for information storage due to its great storage density and durability. Random reading and rewriting are essential tasks for practical large-scale data storage. However, they are currently difficult to implement simultaneously in a single DNA-based storage system, strongly limiting their practicability. Here, a "Cell Disk" storage system is presented, achieving high-density in vivo DNA data storage that enables both random reading and rewriting. In this system, each yeast cell is used as a chamber to store information, similar to a "disk block" but with the ability to self-replicate. Specifically, each genome of yeast cell has a customized CRISPR/Cas9-based "lock-and-key" module inserted, which allows selective retrieval, erasure, or rewriting of the targeted cell "block" from a pool of cells ("disk"). Additionally, a codec algorithm with lossless compression ability is developed to improve the information density of each cell "block". As a proof of concept, target-specific reading and rewriting of the compressed data from a mimic cell "disk" comprising up to 10[5] "blocks" are demonstrated and achieve high specificity and reliability. The "Cell Disk" system described here concurrently supports random reading and rewriting, and it should have great scalability for practical data storage use.}, }
@article {pmid38331396, year = {2024}, author = {Li, C and Li, X and Bank, MS and Dong, T and Fang, JK and Leusch, FDL and Rillig, MC and Wang, J and Wang, L and Xia, Y and Xu, EG and Yang, Y and Zhang, C and Zhu, D and Liu, J and Jin, L}, title = {The "Microplastome" - A Holistic Perspective to Capture the Real-World Ecology of Microplastics.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {9}, pages = {4060-4069}, pmid = {38331396}, issn = {1520-5851}, mesh = {*Microplastics ; Plastics/toxicity ; Ecosystem ; Prospective Studies ; Environmental Monitoring ; *Water Pollutants, Chemical/toxicity ; }, abstract = {Microplastic pollution, an emerging pollution issue, has become a significant environmental concern globally due to its ubiquitous, persistent, complex, toxic, and ever-increasing nature. As a multifaceted and diverse suite of small plastic particles with different physicochemical properties and associated matters such as absorbed chemicals and microbes, future research on microplastics will need to comprehensively consider their multidimensional attributes. Here, we introduce a novel, conceptual framework of the "microplastome", defined as the entirety of various plastic particles (<5 mm), and their associated matters such as chemicals and microbes, found within a sample and its overall environmental and toxicological impacts. As a novel concept, this paper aims to emphasize and call for a collective quantification and characterization of microplastics and for a more holistic understanding regarding the differences, connections, and effects of microplastics in different biotic and abiotic ecosystem compartments. Deriving from this lens, we present our insights and prospective trajectories for characterization, risk assessment, and source apportionment of microplastics. We hope this new paradigm can guide and propel microplastic research toward a more holistic era and contribute to an informed strategy for combating this globally important environmental pollution issue.}, }
@article {pmid38330650, year = {2024}, author = {Li, X and Cheng, X and Wu, J and Cai, Z and Wang, Z and Zhou, J}, title = {Multi-omics reveals different impact patterns of conventional and biodegradable microplastics on the crop rhizosphere in a biofertilizer environment.}, journal = {Journal of hazardous materials}, volume = {467}, number = {}, pages = {133709}, doi = {10.1016/j.jhazmat.2024.133709}, pmid = {38330650}, issn = {1873-3336}, mesh = {*Microplastics ; *Multiomics ; Plastics ; Rhizosphere ; Polyethylene ; Crops, Agricultural ; Polyesters ; }, abstract = {Microplastics (MPs) from the incomplete degradation of agricultural mulch can stress the effectiveness of biofertilizers and ultimately affect the rhizosphere environment of crops. Yet, the involved mechanisms are poorly known and robust empirical data is generally lacking. Here, conventional polyethylene (PE) MPs and poly(butylene adipate-co-butylene terephthalate) (PBAT) / poly(lactic acid) (PLA) biodegradable MPs (PBAT-PLA BioMPs) were investigated to assess their potential impact on the rhizosphere environment of Brassica parachinensis in the presence of Bacillus amyloliquefaciens biofertilizer. The results revealed that both MPs caused different levels of inhibited crop both above- and belowground crop biomass (up to 50.11% and 57.09%, respectively), as well as a significant decrease in plant height (up to 48.63% and 25.95%, respectively), along with an imbalance of microbial communities. Transcriptomic analyses showed that PE MPs mainly affected root's vitamin metabolism, whereas PBAT-PLA BioMPs mainly interfered with the lipid's enrichment. Metabolomic analyses further indicated that PE MPs interfered with amino acid synthesis that involved in crops' oxidative stress, and that PBAT-PLA BioMPs mainly affected the pathways associated with root growth. Additionally, PBAT-PLA BioMPs had a bigger ecological negative impact than did PE MPs, as evidenced by more pronounced alterations in root antioxidant abilities, a higher count of identified differential metabolites, more robust interrelationships among rhizosphere parameters, and a more intricate pattern of impacts on rhizosphere metrics. This study highlights the MPs' impact on crop rhizosphere in a biofertilizer environment from a rhizosphere multi-omics perspective, and has theoretical implications for scientific application of biofertilizers.}, }
@article {pmid38322859, year = {2024}, author = {Mahmoudzadeh, H and Abedini, A and Aram, F and Mosavi, A}, title = {Evaluating urban environmental quality using multi criteria decision making.}, journal = {Heliyon}, volume = {10}, number = {3}, pages = {e24921}, pmid = {38322859}, issn = {2405-8440}, abstract = {In the urban environment, the quality refers to the capacity that provides and fulfills the material and spiritual needs of inhabitants. In order to improve the quality of urban life and standard of living for their citizens, planners and managers strive to raise Urban Environmental Quality. The objective of this study is to evaluate the quality of urban environment through the spatial analysis of a multi-criteria decision making (MCDM) method utilizing CRITIC. This research is conducted in district 4 and district 2 of the Tabriz Metropolis Municipality. In order to determine the quality of an urban environment, air pollution, vegetation coverage, land surface temperature, production of waste, population density, noise pollution, health care per capita, green spaces per capita, recreational spaces per capita, and distance from fault lines are used. After evaluating and producing environmental quality maps in two separate districts, 10 indicators were tested for significance and a comparative evaluation of two districts was conducted in order to determine which district was in better condition based on a statistical analysis of the T-test results. In accordance with the CRITIC method, there are significant differences between averages of waste production, population density, noise pollution, distance from fault lines, Land Surface Temperature, Normalized difference vegetation index, and distance from fault lines between the two districts. It appears that recreational space, air pollution, health care per capita, and green space per capita are not meaningfully different on averages. The preparation of environmental quality maps reveals the importance of meaningful indicators at the neighborhood level in two urban districts. In both districts by strengthening the continuity of the landscape through the development of ecological corridors and an increase in per capita can contribute to the improvement of the quality of the urban environment.}, }
@article {pmid38322797, year = {2023}, author = {Faria, AL and Almeida, Y and Branco, D and Câmara, J and Cameirão, M and Ferreira, L and Moreira, A and Paulino, T and Rodrigues, P and Spinola, M and Vilar, M and Bermúdez I Badia, S and Simões, M and Fermé, E}, title = {NeuroAIreh@b: an artificial intelligence-based methodology for personalized and adaptive neurorehabilitation.}, journal = {Frontiers in neurology}, volume = {14}, number = {}, pages = {1258323}, pmid = {38322797}, issn = {1664-2295}, abstract = {Cognitive impairments are a prevalent consequence of acquired brain injury, dementia, and age-related cognitive decline, hampering individuals' daily functioning and independence, with significant societal and economic implications. While neurorehabilitation represents a promising avenue for addressing these deficits, traditional rehabilitation approaches face notable limitations. First, they lack adaptability, offering one-size-fits-all solutions that may not effectively meet each patient's unique needs. Furthermore, the resource-intensive nature of these interventions, often confined to clinical settings, poses barriers to widespread, cost-effective, and sustained implementation, resulting in suboptimal outcomes in terms of intervention adaptability, intensity, and duration. In response to these challenges, this paper introduces NeuroAIreh@b, an innovative cognitive profiling and training methodology that uses an AI-driven framework to optimize neurorehabilitation prescription. NeuroAIreh@b effectively bridges the gap between neuropsychological assessment and computational modeling, thereby affording highly personalized and adaptive neurorehabilitation sessions. This approach also leverages virtual reality-based simulations of daily living activities to enhance ecological validity and efficacy. The feasibility of NeuroAIreh@b has already been demonstrated through a clinical study with stroke patients employing a tablet-based intervention. The NeuroAIreh@b methodology holds the potential for efficacy studies in large randomized controlled trials in the future.}, }
@article {pmid38319551, year = {2025}, author = {Fuller, TJ and Lambert, DN and DiClemente, RJ and Wingood, GM}, title = {Reach and Capacity of Black Protestant Health Ministries as Sites of Community-Wide Health Promotion: A Qualitative Social Ecological Model Examination.}, journal = {Journal of racial and ethnic health disparities}, volume = {12}, number = {2}, pages = {887-898}, pmid = {38319551}, issn = {2196-8837}, mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Black or African American/statistics &amp; numerical data/psychology ; Georgia ; *Health Promotion/organization &amp; administration ; Interviews as Topic ; *Protestantism ; Qualitative Research ; Secondary Data Analysis ; }, abstract = {Black communities in the Southeast United States experience a disproportionate burden of illness and disease. To address this inequity, public health practitioners are partnering with Black Protestant churches to deliver health promotion interventions. Yet, the reach of these programs beyond the organizational level of the Social Ecological Model (SEM) is not well defined. Thus, the aim of this study is to understand Black Protestant church leaders' and members' perceptions about the capacity of their ministries to reach into their communities, beyond their congregations, as providers or hosts of health education or promotion interventions. From 20 Black Protestant churches in Atlanta, GA, 92 church leaders and members participated in semi-structured interviews. Grounded theory guided data analysis and a diverse team coded the interviews. Most participating churches had health ministries. Participants saw the boundaries between their churches at the organizational level of the SEM and the broader Black community to be porous. Those who described their "community" as being broader than their congregation also tended to describe community-wide health promotion their church engaged in. They described church-based health fairs as a strategy to promote engagement in their communities. Some participants, particularly those in a health-related profession, discussed visions of how to utilize their church as a site for community-wide health promotion. We suggest these participants may be boundary leaders who can build relationships between public health professionals, pastors, and congregants. Based on the findings, we suggest that church-based health fairs may be effective sites of community-wide health promotion.}, }
@article {pmid38316926, year = {2024}, author = {Zuffa, S and Schmid, R and Bauermeister, A and P Gomes, PW and Caraballo-Rodriguez, AM and El Abiead, Y and Aron, AT and Gentry, EC and Zemlin, J and Meehan, MJ and Avalon, NE and Cichewicz, RH and Buzun, E and Terrazas, MC and Hsu, CY and Oles, R and Ayala, AV and Zhao, J and Chu, H and Kuijpers, MCM and Jackrel, SL and Tugizimana, F and Nephali, LP and Dubery, IA and Madala, NE and Moreira, EA and Costa-Lotufo, LV and Lopes, NP and Rezende-Teixeira, P and Jimenez, PC and Rimal, B and Patterson, AD and Traxler, MF and Pessotti, RC and Alvarado-Villalobos, D and Tamayo-Castillo, G and Chaverri, P and Escudero-Leyva, E and Quiros-Guerrero, LM and Bory, AJ and Joubert, J and Rutz, A and Wolfender, JL and Allard, PM and Sichert, A and Pontrelli, S and Pullman, BS and Bandeira, N and Gerwick, WH and Gindro, K and Massana-Codina, J and Wagner, BC and Forchhammer, K and Petras, D and Aiosa, N and Garg, N and Liebeke, M and Bourceau, P and Kang, KB and Gadhavi, H and de Carvalho, LPS and Silva Dos Santos, M and Pérez-Lorente, AI and Molina-Santiago, C and Romero, D and Franke, R and Brönstrup, M and Vera Ponce de León, A and Pope, PB and La Rosa, SL and La Barbera, G and Roager, HM and Laursen, MF and Hammerle, F and Siewert, B and Peintner, U and Licona-Cassani, C and Rodriguez-Orduña, L and Rampler, E and Hildebrand, F and Koellensperger, G and Schoeny, H and Hohenwallner, K and Panzenboeck, L and Gregor, R and O'Neill, EC and Roxborough, ET and Odoi, J and Bale, NJ and Ding, S and Sinninghe Damsté, JS and Guan, XL and Cui, JJ and Ju, KS and Silva, DB and Silva, FMR and da Silva, GF and Koolen, HHF and Grundmann, C and Clement, JA and Mohimani, H and Broders, K and McPhail, KL and Ober-Singleton, SE and Rath, CM and McDonald, D and Knight, R and Wang, M and Dorrestein, PC}, title = {microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data.}, journal = {Nature microbiology}, volume = {9}, number = {2}, pages = {336-345}, pmid = {38316926}, issn = {2058-5276}, support = {R01 GM107550/GM/NIGMS NIH HHS/United States ; U01 DK119702/DK/NIDDK NIH HHS/United States ; R01 AI167860/AI/NIAID NIH HHS/United States ; U19 AG063744/AG/NIA NIH HHS/United States ; R35 GM142938/GM/NIGMS NIH HHS/United States ; T32 DK007202/DK/NIDDK NIH HHS/United States ; R01 GM132649/GM/NIGMS NIH HHS/United States ; DP2 GM137413/GM/NIGMS NIH HHS/United States ; R01 GM137135/GM/NIGMS NIH HHS/United States ; S10 OD021750/OD/NIH HHS/United States ; F32 AT011475/AT/NCCIH NIH HHS/United States ; U24 DK133658/DK/NIDDK NIH HHS/United States ; T32 AR064194/AR/NIAMS NIH HHS/United States ; DP1 AT010885/AT/NCCIH NIH HHS/United States ; R01 LM013115/LM/NLM NIH HHS/United States ; P 31915/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Humans ; *Tandem Mass Spectrometry ; *Metabolomics/methods ; Databases, Factual ; }, abstract = {microbeMASST, a taxonomically informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbe-derived metabolites and relative producers without a priori knowledge will vastly enhance the understanding of microorganisms' role in ecology and human health.}, }
@article {pmid38296495, year = {2024}, author = {Haga, Y and Manabe, S and Tsujino, H and Asahara, H and Higashisaka, K and Tsutsumi, Y}, title = {[Mechanisms of Cell Toxicity Caused by Degraded Microplastics].}, journal = {Yakugaku zasshi : Journal of the Pharmaceutical Society of Japan}, volume = {144}, number = {2}, pages = {177-181}, doi = {10.1248/yakushi.23-00152-3}, pmid = {38296495}, issn = {1347-5231}, mesh = {Animals ; Humans ; *Microplastics/toxicity ; Plastics/toxicity ; Ultraviolet Rays ; *Water Pollutants, Chemical/toxicity/analysis ; Fishes ; }, abstract = {Microplastics (MPs), defined as plastic particles less than 5 mm in size, are ubiquitous in the environment. The accumulation of MPs in various environmental compartments, such as the ocean, soil, and air, has raised considerable concerns regarding their impact on ecological systems, including marine life and human health. Notably, MPs have been detected in marine organisms such as shellfish and fish, and have even been found in the human body, including in the blood and placenta. Moreover, considering that MPs have been detected in drinking water, human exposure to these particles in daily life is inevitable. To assess the risk posed by MPs to human health, it is essential to consider their physiological and chemical properties, including size, shape, surface modification, and material composition. However, current risk analyses focus primarily on spherical MPs with smooth surfaces, which differ substantially from most of the MPs detected in the environment. Environmental factors, such as ocean waves and ultraviolet radiation, alter the properties of MPs, including size, shape, and surface characteristics. In this review, we summarize current research on MPs, with a particular emphasis on the effects of MP degradation on human health. Furthermore, we generated MPs with surface degradation and evaluated their impact on cell toxicity, along with the underlying biological mechanisms.}, }
@article {pmid38315121, year = {2024}, author = {Han, K and Li, J and Yang, D and Zhuang, Q and Zeng, H and Rong, C and Yue, J and Li, N and Gu, C and Chen, L and Chen, C}, title = {Detecting horizontal gene transfer with metagenomics co-barcoding sequencing.}, journal = {Microbiology spectrum}, volume = {12}, number = {3}, pages = {e0360223}, pmid = {38315121}, issn = {2165-0497}, support = {2021YFF0703805//MOST | National Key Research and Development Program of China (NKPs)/ ; 82102447//MOST | National Natural Science Foundation of China (NSFC)/ ; DFL20191801//Beijing Hospital Authority/ ; Z201100005520040//Beijing Municipal Science and Technology Commission, Adminitrative Commission of Zhongguancun Science Park/ ; QML20230701//Beijing Hospitals Authority Youth Programme/ ; }, mesh = {Animals ; Humans ; Mice ; *Gene Transfer, Horizontal ; *Metagenomics/methods ; Computational Biology/methods ; Metagenome ; Bacteria/genetics ; DNA ; }, abstract = {Horizontal gene transfer (HGT) is the process through which genetic information is transferred between different genomes and that played a crucial role in bacterial evolution. HGT can enable bacteria to rapidly acquire antibiotic resistance and bacteria that have acquired resistance is spreading within the microbiome. Conventional methods of characterizing HGT patterns include short-read metagenomic sequencing (short-reads mNGS), long-read sequencing, and single-cell sequencing. These approaches present several limitations, such as short-read fragments, high amounts of input DNA, and sequencing costs, respectively. Here, we attempt to circumvent present limitations to detect HGT by developing a metagenomics co-barcode sequencing workflow (MECOS) and applying it to the human and mouse gut microbiomes. In addition to that, we have over 10-fold increased contig length compared to short-reads mNGS; we also obtained exceeding 30 million paired reads with co-barcode information. Applying the novel bioinformatic pipeline, we integrated this co-barcoding information and the context information from long reads, and observed over 50-fold HGT events after we corrected the potential wrong HGT events. Specifically, we detected approximately 3,000 HGT blocks in individual samples, encompassing ~6,000 genes and ~100 taxonomic groups, including loci conferring tetracycline resistance through ribosomal protection. MECOS provides a valuable tool for investigating HGT and advance our understanding on the evolution of natural microbial communities within hosts.IMPORTANCEIn this study, to better identify horizontal gene transfer (HGT) in individual samples, we introduce a new co-barcoding sequencing system called metagenomics co-barcoding sequencing (MECOS), which has three significant improvements: (i) long DNA fragment extraction, (ii) a special transposome insertion, (iii) hybridization of DNA to barcode beads, and (4) an integrated bioinformatic pipeline. Using our approach, we have over 10-fold increased contig length compared to short-reads mNGS, and observed over 50-fold HGT events after we corrected the potential wrong HGT events. Our results indicate the presence of approximately 3,000 HGT blocks, involving roughly 6,000 genes and 100 taxonomic groups in individual samples. Notably, these HGT events are predominantly enriched in genes that confer tetracycline resistance via ribosomal protection. MECOS is a useful tool for investigating HGT and the evolution of natural microbial communities within hosts, thereby advancing our understanding of microbial ecology and evolution.}, }
@article {pmid38315112, year = {2024}, author = {Chandel, AS}, title = {Geo-spatial technology based on a multi-criteria evaluation technique used to find potential landfill sites in the town of Bule Hora in southern Ethiopia.}, journal = {Journal of the Air &amp; Waste Management Association (1995)}, volume = {74}, number = {4}, pages = {207-239}, doi = {10.1080/10962247.2024.2312889}, pmid = {38315112}, issn = {2162-2906}, mesh = {Humans ; *Solid Waste ; Ethiopia ; Prospective Studies ; Quality of Life ; Geographic Information Systems ; Decision Support Techniques ; *Refuse Disposal/methods ; Waste Disposal Facilities ; Technology ; }, abstract = {Solid waste has surfaced as an eminent and critical concern of environmental and social significance on a global scale, and Ethiopia, a developing country with limited income, has also encountered unfavorable outcomes due to substandard waste management practices. When pinpointing a fitting landfill location in the town of Bule Hora, various ecological, economic, and societal aspects must be considered; these may result in discord and exacerbate a multifaceted and lengthy process. Hence, this research aims to identify prospective landfill sites within the town and utilize geospatial methods, such as Multi-Criteria Evaluation and Analytic Hierarchy Process, to accomplish its objectives. The utilization of geospatial technology and multi-criteria evaluation provides an efficient manner to simultaneously address all bottlenecks involved in the selection of an appropriate landfill location. Geospatial technology evaluates and manages environmental constraints, whereas multi-criteria assessment categorizes choices based on their desirability. Furthermore, by employing a restriction map adhering to established standards, seven landfill sites have successfully been identified within the town. The Land Suitability Index assesses site suitability based on ecological factors, while the Total Hauling Distance evaluates sites within an economic framework. AHP determines weightings through 25.4 pairwise comparisons, resulting in a consistency ratio of 1.95%. The cartographic analysis is conducted using ESRI ArcGIS version 10.8 software. The findings of this study reveal that 98.69% of the area under study is subject to restrictions. The study recommends the implementation of geospatial methods for identifying suitable landfill sites, which would aid in the decision-making process and prevent hasty decisions from triggering environmental degradation. Proper waste disposal would augment the quality of life for residents by diminishing health hazards. The study endeavors to serve as a reference for other developing countries in selecting appropriate landfill sites.Implications: The town of Bule Hora also faces the problem of waste disposal; there is no scientifically selected suitable landfill. Residents of the town of Bule Hora practice waste disposal in open fields, near settlements, water bodies, roads, agricultural land, and other places. The main sources of solid waste in the town are homes, shops, hotels, restaurants, open markets, hospitals, educational institutions, private clinics, etc. Water pollution can potentially lead to the spread of waterborne diseases. According to reports from the Bule Horas Health Department, many people are affected by water-related diseases every year. These open landfill systems with no regard for settlement, topography, geology, surface, or groundwater conditions are the consequences of these unsuitable habitats and health problems. To reduce these problems, this study plays an important role in determining the suitability of landfills for the town and proposing alternative measures that can minimize negative environmental impacts from waste. This study aims to apply geospatial-based technology to a multi-criteria assessment technique to select perfectly suitable landfill sites that are environmentally friendly, economically cost-effective, and socially responsible; examine the town's current waste management system; calculate the selected parameter weights for feature ranking; and delineate solid waste landfills.}, }
@article {pmid38312217, year = {2024}, author = {Ogawa, T and Tsuzuki, S and Ohbe, H and Matsui, H and Fushimi, K and Yasunaga, H and Kutsuna, S}, title = {Analysis of Differences in Characteristics of High-Risk Endemic Areas for Contracting Japanese Spotted Fever, Tsutsugamushi Disease, and Severe Fever With Thrombocytopenia Syndrome.}, journal = {Open forum infectious diseases}, volume = {11}, number = {2}, pages = {ofae025}, pmid = {38312217}, issn = {2328-8957}, abstract = {BACKGROUND: Tick-borne infections, including tsutsugamushi disease, Japanese spotted fever, and severe fever with thrombocytopenia syndrome (SFTS), are prevalent in East Asia with varying geographic distribution and seasonality. This study aimed to investigate the differences in the characteristics among endemic areas for contracting each infection.<br><br>METHODS: We conducted an ecologic study in Japan, using data from a nationwide inpatient database and publicly available geospatial data. We identified 4493 patients who were hospitalized for tick-borne infections between July 2010 and March 2021. Mixed-effects modified Poisson regression analysis was used to identify factors associated with a higher risk of contracting each tick-borne disease (Tsutsugamushi, Japanese spotted fever, and SFTS).<br><br>RESULTS: Mixed-effects modified Poisson regression analysis revealed that environmental factors, such as temperature, sunlight duration, elevation, precipitation, and vegetation, were associated with the risk of contracting these diseases. Tsutsugamushi disease was positively associated with higher temperatures, farms, and forests, whereas Japanese spotted fever and SFTS were positively associated with higher solar radiation and forests.<br><br>CONCLUSIONS: Our findings from this ecologic study indicate that different environmental factors play a significant role in the risk of transmission of tick-borne infections. Understanding the differences can aid in identifying high-risk areas and developing public health strategies for infection prevention. Further research is needed to address causal relationships.}, }
@article {pmid38311099, year = {2024}, author = {Stanic, B and Sukur, N and Milošević, N and Markovic Filipovic, J and Pogrmic-Majkic, K and Andric, N}, title = {Differential eigengene network analysis reveals benzo[a]pyrene and 2,3,7,8-tetrachlorodibenzo-p-dioxin consensus regulatory network in human liver cell line HepG2.}, journal = {Toxicology}, volume = {502}, number = {}, pages = {153737}, doi = {10.1016/j.tox.2024.153737}, pmid = {38311099}, issn = {1879-3185}, mesh = {Humans ; *Benzo(a)pyrene/toxicity ; *Polychlorinated Dibenzodioxins/toxicity ; Consensus ; Liver/metabolism ; Cell Line, Tumor ; Receptors, Aryl Hydrocarbon/genetics/metabolism ; }, abstract = {Aryl hydrocarbon receptor (AHR) is one of the main mediators of the toxic effects of benzo[a]pyrene (BaP) and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). However, a vast number of BaP- and TCDD-affected genes may suggest a more complex transcriptional regulatory network driving common adverse effects of these two chemicals. Unlike TCDD, BaP is rapidly metabolized in the liver, yielding products with a questionable ability to bind and activate AHR. In this study, we used transcriptomics data from the BaP- and TCCD-exposed human liver cell line HepG2, and performed differential eigengene network analysis to understand the correlation among genes and to untangle the common regulatory mechanism in the action of BaP and TCDD. The genes were grouped into 11 meta-modules with an overall preservation of 0.72 and were also segregated into three consensus time clusters: 12, 24, and 48 h. The analysis showed that the consensus genes in each time cluster were either directly regulated by the AHR or the AHR-TF interactions. Some TFs form a direct physical interaction with AHR such as ESR1, FOXA1, and E2F1, whereas others, including CTCF, RXRA, FOXO1, CEBPA, CEBPB, and TP53 show an indirect interaction with AHR. The analysis of biological processes (BPs) identified unique and common BPs in BaP and TCDD samples, with DNA damage response detected in all three time points. In summary, we identified a consensus transcriptional regulatory network common for BaP and TCDD consisting of direct AHR targets and AHR-TF targets. This analysis sheds new light on the common mechanism of action of a genotoxic (BaP) and non-genotoxic (TCDD) chemical in liver cells.}, }
@article {pmid38308167, year = {2024}, author = {Wang, Y and Chen, Y and Lu, S and Guo, X}, title = {Development and trends of constructed wetland substrates over the past 30 years: a literature visualization analysis based on CiteSpace.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {10}, pages = {14537-14552}, pmid = {38308167}, issn = {1614-7499}, mesh = {Humans ; *Wetlands ; Cluster Analysis ; Databases, Factual ; *Environmental Pollutants ; Sewage ; }, abstract = {Constructed wetland substrates (CWSs) have received considerable attention owing to their importance in adsorbing and degrading pollutants, providing growth attachment points for microorganisms, and supporting wetland plants. There are differences in the configurations and functions of constructed wetlands (CWs) for treating different water bodies and sewage, resulting in a wide variety of substrates. Research on the application and mechanism of CWSs is not sufficiently systematic. Therefore, the current research advancements and hotspots must be identified. Hence, we used CiteSpace to analyze 1955 English publications from the core collection database of the Web of Science to assess the current state of the CWS research field. Based on the cooperative network analysis, the roles of various countries, institutions, and authors in research on CWSs were reviewed. Keyword co-occurrence and cluster analyses were used to discuss the transformation of CWSs from removing traditional pollutants to emerging pollutants and the transition from incorporating natural substrates to artificial substrates. Finally, we underscored the need for more emphasis to be placed on the collocation and application of the CWSs at different latitudes. Furthermore, the substrate micro-interface process and its effects on the interaction patterns of pollutants and microorganisms should be thoroughly investigated to provide theoretical guidance for the development of wetland applications and mechanisms.}, }
@article {pmid38307178, year = {2024}, author = {Fu, Y and He, Y and Chen, W and Xiao, W and Ren, H and Shi, Y and Hu, Z}, title = {Dynamics of carbon storage driven by land use/land cover transformation in coal mining areas with a high groundwater table: A case study of Yanzhou Coal Mine, China.}, journal = {Environmental research}, volume = {247}, number = {}, pages = {118392}, doi = {10.1016/j.envres.2024.118392}, pmid = {38307178}, issn = {1096-0953}, mesh = {Humans ; *Coal Mining ; Carbon ; China ; *Groundwater ; Coal ; Ecosystem ; Conservation of Natural Resources ; }, abstract = {Intensive anthropogenic activities have led to drastic changes in land use/land cover (LULC) and impacted the carbon storage in high-groundwater coal basins. In this paper, we conduct a case study on the Yanzhou Coalfield in Shandong Province of China. We further classify waterbodies by using the Google Earth Engine (GEE) to better investigate the process of LULC transformation and the forces driving it in four periods from 1985 to 2020 (i.e., 1985-1995, 1995-2005, 2005-2015, and 2015-2020). We modeled the spatiotemporal dynamics of carbon storage by using InVEST based on the transformation in LULC and its drivers, including mining (M), reclamation (R), urbanization and village relocation (U), and ecological restoration (E). The results indicate that carbon storage had depleted by 19.69 % (321099.06 Mg) owing to intensive transformations in LULC. The area of cropland shrank with the expansion of built-up land and waterbodies, and 56.31 % of the study area underwent transitions in land use in the study period. U was the primary driver of carbon loss while E was the leading driver of carbon gain. While the direct impact of M on carbon loss accounted for only 5.23 % of the total, it affected urbanization and led to village relocation. R led to the recovery of cropland and the reclamation of water for aquaculture, which in turn improved the efficiency of land use. However, it contributed only 2.09 % to the total increase in carbon storage. Numerous complicated and intertwined processes (211) drove the changes in carbon storage in the study area. The work here provides valuable information for decision-makers as well as people involved in reclamation and ecological restoration to better understand the link between carbon storage and the forces influencing it. The results can be used to integrate the goals of carbon sequestration into measures for land management.}, }
@article {pmid38305922, year = {2024}, author = {Eshetu, SB and Kipkulei, HK and Koepke, J and Kächele, H and Sieber, S and Löhr, K}, title = {Impact of forest landscape restoration in combating soil erosion in the Lake Abaya catchment, Southern Ethiopia.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {3}, pages = {228}, pmid = {38305922}, issn = {1573-2959}, mesh = {*Soil Erosion ; *Ecosystem ; Ethiopia ; Lakes ; Environmental Monitoring/methods ; Conservation of Natural Resources ; Soil ; Geographic Information Systems ; Forests ; }, abstract = {As an effect of forest degradation, soil erosion is among Ethiopia's most pressing environmental challenges and a major threat to food security where it could potentially compromise the ecosystem functions and services. As the effects of soil erosion intensify, the landscape's capacity to support ecosystem functions and services is compromised. Exploring the ecological implications of soil erosion is crucial. This study investigated the soil loss and land degradation in the Lake Abaya catchment to explore forest landscape restoration (FLR) implementation as a possible countermeasure to the effects. The study used a geographic information system (GIS)-based approach of the Revised Universal Soil Loss Equation (RUSLE) to determine the potential annual soil loss and develop an erosion risk map. Results show that 13% of the catchment, which accounts for approximately 110,000 ha, is under high erosion risk of exceeding the average annual tolerable soil loss of 10 t/ha/year. Allocation of land on steep slopes to crop production is the major reason for the calculated high erosion risk in the catchment. A scenario-based analysis was implemented following the slope-based land-use allocation proposal indicated in the Rural Land Use Proclamation 456/2005 of Ethiopia. The scenario analysis resulted in a reversal erosion effect whereby an estimated 3000 t/ha/year of soil loss in the catchment. Thus, FLR activities hold great potential for minimizing soil loss and contributing to supporting functioning and providing ecosystem services. Tree-based agroforestry systems are among the key FLR measures championed in highly degraded landscapes in Ethiopia. This study helps policymakers and FLR implementors identify erosion risk areas for future FLR activities. Thereby, it contributes to achieving the country's restoration commitment.}, }
@article {pmid38305133, year = {2024}, author = {Ramakodi, MP}, title = {Merging and concatenation of sequencing reads: a bioinformatics workflow for the comprehensive profiling of microbiome from amplicon data.}, journal = {FEMS microbiology letters}, volume = {371}, number = {}, pages = {}, doi = {10.1093/femsle/fnae009}, pmid = {38305133}, issn = {1574-6968}, mesh = {RNA, Ribosomal, 18S/genetics ; Workflow ; *Microbiota/genetics ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {A comprehensive profiling of microbial diversity is essential to understand the ecosystem functions. Universal primer sets such as the 515Y/926R could amplify a part of 16S and 18S rRNA and infer the diversity of prokaryotes and eukaryotes. However, the analyses of mixed sequencing data pose a bioinformatics challenge; the 16S and 18S rRNA sequences need to be separated first and analysed individually/independently due to variations in the amplicon length. This study describes an alternative strategy, a merging and concatenation workflow, to analyse the mixed amplicon data without separating the 16S and 18S rRNA sequences. The workflow was tested with 24 mock community (MC) samples, and the analyses resolved the composition of prokaryotes and eukaryotes adequately. In addition, there was a strong correlation (cor = 0.950; P-value = 4.754e-10) between the observed and expected abundances in the MC samples, which suggests that the computational approach could infer the microbial proportions accurately. Further, 18 samples collected from the Sundarbans mangrove region were analysed as a case study. The analyses identified Proteobacteria, Bacteroidota, Actinobacteriota, Cyanobacteria, and Crenarchaeota as dominant bacterial phyla and eukaryotic divisions such as Metazoa, Gyrista, Cryptophyta, Chlorophyta, and Dinoflagellata were found to be dominant in the samples. Thus, the results support the applicability of the method in environmental microbiome research. The merging and concatenation workflow presented here requires considerably less computational resources and uses widely/commonly used bioinformatics packages, saving researchers analyses time (for equivalent sample numbers, compared to the conventional approach) required to infer the diversity of major microbial domains from mixed amplicon data at comparable accuracy.}, }
@article {pmid38302634, year = {2024}, author = {Rajan, SC and M, V and Mitra, A and N P, S and K, A and Pillai, MS and R, J}, title = {Threshold of anthropogenic sound levels within protected landscapes in Kerala, India, for avian habitat quality and conservation.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {2701}, pmid = {38302634}, issn = {2045-2322}, mesh = {Animals ; Acoustics ; *Birds ; Conservation of Natural Resources/methods ; *Ecosystem ; India ; *Anthropogenic Effects ; *Sound ; }, abstract = {Anthrophony is an important determinant of habitat quality in the Anthropocene. Acoustic adaptation of birds at lower levels of anthrophony is known. However, threshold anthrophony, beyond which biophony starts decreasing, is less explored. Here, we present empirical results of the relationship between anthrophony and biophony in four terrestrial soundscapes. The constancy of the predicted threshold vector normalised anthropogenic power spectral density (~ 0.40 Watts/Hz) at all the study sites is intriguing. We propose the threshold value of anthropogenic power spectral density as an indicator of the avian acoustic tolerance level in the study sites. The findings pave the way to determine permissible sound levels within protected landscapes and directly contribute to conservation planning.}, }
@article {pmid38301473, year = {2024}, author = {Huang, Y and Qin, R and Wei, H and Chai, N and Yang, Y and Li, Y and Wan, P and Li, Y and Zhao, W and Lawawirojwong, S and Suepa, T and Zhang, F}, title = {Plastic film mulching application improves potato yields, reduces ammonia emissions, but boosts the greenhouse gas emissions in China.}, journal = {Journal of environmental management}, volume = {353}, number = {}, pages = {120241}, doi = {10.1016/j.jenvman.2024.120241}, pmid = {38301473}, issn = {1095-8630}, mesh = {*Greenhouse Gases/analysis ; *Solanum tuberosum ; Ammonia ; Carbon Dioxide/analysis ; Agriculture ; Soil ; China ; Methane/analysis ; Nitrous Oxide/analysis ; Fertilizers/analysis ; }, abstract = {With global population growth and climate change, food security and global warming have emerged as two major challenges to agricultural development. Plastic film mulching (PM) has long been used to improve yields in rain-fed agricultural systems, but few studies have focused on soil gas emissions from mulched rainfed potatoes on a long-term and regional scale. This study integrated field data with the Denitrification-Decomposition (DNDC) model to evaluate the impacts of PM on potato yields, greenhouse gas (GHG) and ammonia (NH3) emissions in rainfed agricultural systems in China. We found that PM increased potato yield by 39.7 % (1505 kg ha[-1]), carbon dioxide (CO2) emissions by 15.4 % (123 kg CO2 eq ha[-1]), nitrous oxide (N2O) emissions by 47.8 % (1016 kg CO2 eq ha[-1]), and global warming potential (GWP) by 38.9 % (1030 kg CO2 eq ha[-1]), while NH3 volatilization decreased by 33.9 % (8.4 kg NH3 ha[-1]), and methane (CH4) emissions were little changed compared to CK. Specifically, the yield after PM significantly increased in South China (SC), North China (NC), and Northwest China (NWC), with increases of 66.1 % (2429 kg ha[-1]), 44.1 % (1173 kg ha[-1]), and 43.6 % (956 kg ha[-1]) compared to CK, respectively. The increase in GWP and greenhouse gas emission intensity (GHGI) under PM was more pronounced in the Northeast China (NEC) and NWC regions, with respective increases of 57.1 % and 60.2 % in GWP, 16.9 % and 10.3 % in GHGI. While in the Middle and Lower reaches of the Yangtze River (MLYR) and SC, PM decreased GHGI with 10.2 % and 31.1 %, respectively. PM significantly reduced NH3 emissions in all regions and these reductions were most significant in Southwest China (SWC), SCand MLYR, which were 41 %, 38.0 %, and 38.0 % lower than CK, respectively. In addition, climatic and edaphic variables were the main contributors to GHG and NH3 emissions. In conclusion, it is appropriate to promote the use of PM in the MLYR and SC regions, because of the ability to increase yields while reducing environmental impacts (lower GHGI and NH3 emissions). The findings provide a theoretical basis for sustainable agricultural production of PM potatoes.}, }
@article {pmid38297840, year = {2024}, author = {Tian, C and Li, J and Wu, Y and Wang, G and Zhang, Y and Zhang, X and Sun, Y and Wang, Y}, title = {An integrative database and its application for plant synthetic biology research.}, journal = {Plant communications}, volume = {5}, number = {5}, pages = {100827}, pmid = {38297840}, issn = {2590-3462}, mesh = {*Synthetic Biology/methods ; Plants/genetics ; Databases, Genetic ; Nicotiana/genetics ; Computational Biology/methods ; }, abstract = {Plant synthetic biology research requires diverse bioparts that facilitate the redesign and construction of new-to-nature biological devices or systems in plants. Limited by few well-characterized bioparts for plant chassis, the development of plant synthetic biology lags behind that of its microbial counterpart. Here, we constructed a web-based Plant Synthetic BioDatabase (PSBD), which currently categorizes 1677 catalytic bioparts and 384 regulatory elements and provides information on 309 species and 850 chemicals. Online bioinformatics tools including local BLAST, chem similarity, phylogenetic analysis, and visual strength are provided to assist with the rational design of genetic circuits for manipulation of gene expression in planta. We demonstrated the utility of the PSBD by functionally characterizing taxadiene synthase 2 and its quantitative regulation in tobacco leaves. More powerful synthetic devices were then assembled to amplify the transcriptional signals, enabling enhanced expression of flavivirus non-structure 1 proteins in plants. The PSBD is expected to be an integrative and user-centered platform that provides a one-stop service for diverse applications in plant synthetic biology research.}, }
@article {pmid38297125, year = {2024}, author = {Xu, P and Li, G and Zheng, Y and Fung, JCH and Chen, A and Zeng, Z and Shen, H and Hu, M and Mao, J and Zheng, Y and Cui, X and Guo, Z and Chen, Y and Feng, L and He, S and Zhang, X and Lau, AKH and Tao, S and Houlton, BZ}, title = {Fertilizer management for global ammonia emission reduction.}, journal = {Nature}, volume = {626}, number = {8000}, pages = {792-798}, pmid = {38297125}, issn = {1476-4687}, mesh = {*Ammonia/analysis/metabolism ; *Crop Production/methods/statistics &amp; numerical data/trends ; Datasets as Topic ; Ecosystem ; *Fertilizers/adverse effects/analysis/statistics &amp; numerical data ; Machine Learning ; Nitrogen/analysis/metabolism ; Oryza/metabolism ; Soil/chemistry ; Triticum/metabolism ; Zea mays/metabolism ; Climate Change/statistics &amp; numerical data ; }, abstract = {Crop production is a large source of atmospheric ammonia (NH3), which poses risks to air quality, human health and ecosystems[1-5]. However, estimating global NH3 emissions from croplands is subject to uncertainties because of data limitations, thereby limiting the accurate identification of mitigation options and efficacy[4,5]. Here we develop a machine learning model for generating crop-specific and spatially explicit NH3 emission factors globally (5-arcmin resolution) based on a compiled dataset of field observations. We show that global NH3 emissions from rice, wheat and maize fields in 2018 were 4.3 ± 1.0 Tg N yr[-1], lower than previous estimates that did not fully consider fertilizer management practices[6-9]. Furthermore, spatially optimizing fertilizer management, as guided by the machine learning model, has the potential to reduce the NH3 emissions by about 38% (1.6 ± 0.4 Tg N yr[-1]) without altering total fertilizer nitrogen inputs. Specifically, we estimate potential NH3 emissions reductions of 47% (44-56%) for rice, 27% (24-28%) for maize and 26% (20-28%) for wheat cultivation, respectively. Under future climate change scenarios, we estimate that NH3 emissions could increase by 4.0 ± 2.7% under SSP1-2.6 and 5.5 ± 5.7% under SSP5-8.5 by 2030-2060. However, targeted fertilizer management has the potential to mitigate these increases.}, }
@article {pmid38294243, year = {2024}, author = {Omondi, VO and Bosire, GO and Onyari, JM and Kibet, C and Mwasya, S and Onyonyi, VN and Getahun, MN}, title = {Multi-omics analyses reveal rumen microbes and secondary metabolites that are unique to livestock species.}, journal = {mSystems}, volume = {9}, number = {2}, pages = {e0122823}, pmid = {38294243}, issn = {2379-5077}, support = {B1126A-185//Max Planck Institute for Chemical Ecology/ ; B1126A-185//International Centre of Insect Physiology and Ecology (ICIPE)/ ; }, mesh = {Cattle ; Humans ; Sheep ; Animals ; *Livestock/microbiology ; Rumen/metabolism ; Camelus ; Multiomics ; Ruminants/microbiology ; *Microbiota/genetics ; Goats/physiology ; Animal Feed/analysis ; }, abstract = {Ruminant livestock, including cattle, sheep, goats, and camels, possess a distinctive digestive system with complex microbiota communities critical for feed conversion and secondary metabolite production, including greenhouse gases. Yet, there is limited knowledge regarding the diversity of rumen microbes and metabolites benefiting livestock physiology, productivity, climate impact, and defense mechanisms across ruminant species. In this study, we utilized metataxonomics and metabolomics data from four evolutionarily distinct livestock species, which had fed on diverse plant materials like grass, shrubs, and acacia trees, to uncover the unique signature microbes and secondary metabolites. We established the presence of a distinctive anaerobic fungus called Oontomyces in camels, while cattle exhibited a higher prevalence of unique microbes like Psychrobacter, Anaeromyces, Cyllamyces, and Orpinomyces. Goats hosted Cleistothelebolus, and Liebetanzomyces was unique to sheep. Furthermore, we identified a set of conserved core microbes, including Prevotella, Rickenellaceae, Cladosporium, and Pecoramyces, present in all the ruminants, irrespective of host genetics and dietary composition. This underscores their indispensable role in maintaining crucial physiological functions. Regarding secondary metabolites, camel's rumen is rich in organic acids, goat's rumen is rich in alcohols and hydrocarbons, sheep's rumen is rich in indoles, and cattle's rumen is rich in sesquiterpenes. Additionally, linalool propionate and terpinolene were uniquely found in sheep rumen, while valencene was exclusive to cattle. This may suggest the existence of species-specific microbes and metabolites that require host rumen-microbes' environment balance. These results have implications for manipulating the rumen environment to target specific microbes and secondary metabolite networks, thereby enhancing livestock productivity, resilience, reducing susceptibility to vectors, and environmentally preferred livestock husbandry.IMPORTANCERumen fermentation, which depends on feed components and rumen microbes, plays a crucial role in feed conversion and the production of various metabolites important for the physiological functions, health, and environmental smartness of ruminant livestock, in addition to providing food for humans. However, given the complexity and variation of the rumen ecosystem and feed of these various livestock species, combined with inter-individual differences between gut microbial communities, how they influence the rumen secondary metabolites remains elusive. Using metagenomics and metabolomics approaches, we show that each livestock species has a signature microbe(s) and secondary metabolites. These findings may contribute toward understanding the rumen ecosystem, microbiome and metabolite networks, which may provide a gateway to manipulating rumen ecosystem pathways toward making livestock production efficient, sustainable, and environmentally friendly.}, }
@article {pmid38292065, year = {2023}, author = {Macgregor, CJ and Saccheri, IJ and ,  and ,  and ,  and , }, title = {The genome sequence of the Rock Grayling, Hipparchia semele (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {495}, pmid = {38292065}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Hipparchia semele (the Rock Grayling; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 403.4 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.22 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,540 protein coding genes.}, }
@article {pmid38285940, year = {2024}, author = {Long, C and Deng, J and Nguyen, J and Liu, YY and Alm, EJ and Solé, R and Saavedra, S}, title = {Structured community transitions explain the switching capacity of microbial systems.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {6}, pages = {e2312521121}, pmid = {38285940}, issn = {1091-6490}, support = {R01 AI141529/AI/NIAID NIH HHS/United States ; }, mesh = {*Microbiota ; *Environment ; *Ecology ; }, abstract = {Microbial systems appear to exhibit a relatively high switching capacity of moving back and forth among few dominant communities (taxon memberships). While this switching behavior has been mainly attributed to random environmental factors, it remains unclear the extent to which internal community dynamics affect the switching capacity of microbial systems. Here, we integrate ecological theory and empirical data to demonstrate that structured community transitions increase the dependency of future communities on the current taxon membership, enhancing the switching capacity of microbial systems. Following a structuralist approach, we propose that each community is feasible within a unique domain in environmental parameter space. Then, structured transitions between any two communities can happen with probability proportional to the size of their feasibility domains and inversely proportional to their distance in environmental parameter space-which can be treated as a special case of the gravity model. We detect two broad classes of systems with structured transitions: one class where switching capacity is high across a wide range of community sizes and another class where switching capacity is high only inside a narrow size range. We corroborate our theory using temporal data of gut and oral microbiota (belonging to class 1) as well as vaginal and ocean microbiota (belonging to class 2). These results reveal that the topology of feasibility domains in environmental parameter space is a relevant property to understand the changing behavior of microbial systems. This knowledge can be potentially used to understand the relevant community size at which internal dynamics can be operating in microbial systems.}, }
@article {pmid38284174, year = {2024}, author = {Challa, A and Maras, JS and Nagpal, S and Tripathi, G and Taneja, B and Kachhawa, G and Sood, S and Dhawan, B and Acharya, P and Upadhyay, AD and Yadav, M and Sharma, R and Bajpai, M and Gupta, S}, title = {Multi-omics analysis identifies potential microbial and metabolite diagnostic biomarkers of bacterial vaginosis.}, journal = {Journal of the European Academy of Dermatology and Venereology : JEADV}, volume = {38}, number = {6}, pages = {1152-1165}, doi = {10.1111/jdv.19805}, pmid = {38284174}, issn = {1468-3083}, support = {8-06/AC-06/2018-RS//All India Institute of Medical Sciences/ ; }, mesh = {Humans ; Female ; *Vaginosis, Bacterial/diagnosis/microbiology ; *Biomarkers/metabolism ; Adult ; *Machine Learning ; *Microbiota ; Metabolomics/methods ; Young Adult ; Vagina/microbiology ; Metabolome ; RNA, Ribosomal, 16S/genetics ; Multiomics ; }, abstract = {BACKGROUND: Bacterial vaginosis (BV) is a common clinical manifestation of a perturbed vaginal ecology associated with adverse sexual and reproductive health outcomes if left untreated. The existing diagnostic modalities are either cumbersome or require skilled expertise, warranting alternate tests. Application of machine-learning tools to heterogeneous and high-dimensional multi-omics datasets finds promising potential in data integration and may aid biomarker discovery.<br><br>OBJECTIVES: The present study aimed to evaluate the potential of the microbiome and metabolome-derived biomarkers in BV diagnosis. Interpretable machine-learning algorithms were used to evaluate the utility of an integrated-omics-derived classification model.<br><br>METHODS: Vaginal samples obtained from reproductive-age group women with (n&#x2009;=&#x2009;40) and without BV (n&#x2009;=&#x2009;40) were subjected to 16S rRNA amplicon sequencing and LC-MS-based metabolomics. The vaginal microbiome and metabolome were characterized, and machine-learning analysis was performed to build a classification model using biomarkers with the highest diagnostic accuracy.<br><br>RESULTS: Microbiome-based diagnostic model exhibited a ROC-AUC (10-fold CV) of 0.84&#x2009;&#xb1;&#x2009;0.21 and accuracy of 0.79&#x2009;&#xb1;&#x2009;0.18, and important features were Aerococcus spp., Mycoplasma hominis, Sneathia spp., Lactobacillus spp., Prevotella spp., Gardnerella spp. and Fannyhessea vaginae. The metabolome-derived model displayed superior performance with a ROC-AUC of 0.97&#x2009;&#xb1;&#x2009;0.07 and an accuracy of 0.92&#x2009;&#xb1;&#x2009;0.08. Beta-leucine, methylimidazole acetaldehyde, dimethylethanolamine, L-arginine and beta cortol were among key predictive metabolites for BV. A predictive model combining both microbial and metabolite features exhibited a high ROC-AUC of 0.97&#x2009;&#xb1;&#x2009;0.07 and accuracy of 0.94&#x2009;&#xb1;&#x2009;0.08 with diagnostic performance only slightly superior to the metabolite-based model.<br><br>CONCLUSION: Application of machine-learning tools to multi-omics datasets aid biomarker discovery with high predictive performance. Metabolome-derived classification models were observed to have superior diagnostic performance in predicting BV than microbiome-based biomarkers.}, }
@article {pmid38283543, year = {2024}, author = {Wang, H and Chen, Z and Li, Z and He, X and Subramanian, SV}, title = {How economic development affects healthcare access for people with disabilities: A multilevel study in China.}, journal = {SSM - population health}, volume = {25}, number = {}, pages = {101594}, pmid = {38283543}, issn = {2352-8273}, abstract = {Meeting the healthcare needs of people with disabilities is an important challenge in achieving the central promise of "leave no one behind" during the Sustainable Development Goals era. In this study, we describe the accessibility of healthcare for people living with disabilities, as well as the potential influences of individuals' socioeconomic status and regional economic development. Our data covered 324 prefectural cities in China in 2019 and captured the access to healthcare services for people with disabilities. First, we used linear probability regression models to investigate the association between individual socioeconomic status, including residence, poverty status, education, and healthcare access. Second, we conducted an ecological analysis to test the association between prefectural economic indicators, including GDP (gross domestic product) per capita, urbanization ratio, average years of education, Engel's coefficient, and the overall prevalence of access to healthcare for people with disabilities within prefectures. Third, we used multilevel regression models to explore the association between the individual's socio-economic status, prefectural economic indicators, and access to healthcare at the individual level for people with disabilities. The results showed, first, that higher individual socioeconomic status (urban residence or higher educational level) was associated with better access to healthcare for people with disabilities. Second, regional economic indicators were positively associated with access to healthcare at the aggregate and individual levels. This study suggests that local governments, particularly in low- and middle-income countries, should promote economic development and conduct poverty alleviation policies to improve healthcare access for disadvantaged groups.}, }
@article {pmid38279205, year = {2024}, author = {Reuber, VM and Westbury, MV and Rey-Iglesia, A and Asefa, A and Farwig, N and Miehe, G and Opgenoorth, L and Šumbera, R and Wraase, L and Wube, T and Lorenzen, ED and Schabo, DG}, title = {Topographic barriers drive the pronounced genetic subdivision of a range-limited fossorial rodent.}, journal = {Molecular ecology}, volume = {33}, number = {5}, pages = {e17271}, doi = {10.1111/mec.17271}, pmid = {38279205}, issn = {1365-294X}, support = {FOR 2358//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Animals ; *Ecosystem ; *Rodentia/genetics ; Ethiopia ; Gene Flow ; Microsatellite Repeats ; Genetic Variation/genetics ; Genetics, Population ; }, abstract = {Due to their limited dispersal ability, fossorial species with predominantly belowground activity usually show increased levels of population subdivision across relatively small spatial scales. This may be exacerbated in harsh mountain ecosystems, where landscape geomorphology limits species' dispersal ability and leads to small effective population sizes, making species relatively vulnerable to environmental change. To better understand the environmental drivers of species' population subdivision in remote mountain ecosystems, particularly in understudied high-elevation systems in Africa, we studied the giant root-rat (Tachyoryctes macrocephalus), a fossorial rodent confined to the afro-alpine ecosystem of the Bale Mountains in Ethiopia. Using mitochondrial and low-coverage nuclear genomes, we investigated 77 giant root-rat individuals sampled from nine localities across its entire ~1000 km[2] range. Our data revealed a distinct division into a northern and southern group, with no signs of gene flow, and higher nuclear genetic diversity in the south. Landscape genetic analyses of the mitochondrial and nuclear genomes indicated that population subdivision was driven by slope and elevation differences of up to 500 m across escarpments separating the north and south, potentially reinforced by glaciation of the south during the Late Pleistocene (~42,000-16,000 years ago). Despite this landscape-scale subdivision between the north and south, weak geographic structuring of sampling localities within regions indicated gene flow across distances of at least 16 km at the local scale, suggesting high, aboveground mobility for relatively long distances. Our study highlights that despite the potential for local-scale gene flow in fossorial species, topographic barriers can result in pronounced genetic subdivision. These factors can reduce genetic variability, which should be considered when developing conservation strategies.}, }
@article {pmid38278971, year = {2024}, author = {Larivière, D and Abueg, L and Brajuka, N and Gallardo-Alba, C and Grüning, B and Ko, BJ and Ostrovsky, A and Palmada-Flores, M and Pickett, BD and Rabbani, K and Antunes, A and Balacco, JR and Chaisson, MJP and Cheng, H and Collins, J and Couture, M and Denisova, A and Fedrigo, O and Gallo, GR and Giani, AM and Gooder, GM and Horan, K and Jain, N and Johnson, C and Kim, H and Lee, C and Marques-Bonet, T and O'Toole, B and Rhie, A and Secomandi, S and Sozzoni, M and Tilley, T and Uliano-Silva, M and van den Beek, M and Williams, RW and Waterhouse, RM and Phillippy, AM and Jarvis, ED and Schatz, MC and Nekrutenko, A and Formenti, G}, title = {Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy.}, journal = {Nature biotechnology}, volume = {42}, number = {3}, pages = {367-370}, pmid = {38278971}, issn = {1546-1696}, support = {U24 HG010263/HG/NHGRI NIH HHS/United States ; U24 CA231877/CA/NCI NIH HHS/United States ; R01 HG011649/HG/NHGRI NIH HHS/United States ; U41 HG006620/HG/NHGRI NIH HHS/United States ; U01 CA253481/CA/NCI NIH HHS/United States ; U24 HG006620/HG/NHGRI NIH HHS/United States ; }, mesh = {*Computational Biology ; *Software ; }, }
@article {pmid38278172, year = {2024}, author = {, }, title = {Effects of education on adult mortality: a global systematic review and meta-analysis.}, journal = {The Lancet. Public health}, volume = {9}, number = {3}, pages = {e155-e165}, pmid = {38278172}, issn = {2468-2667}, mesh = {Adult ; Humans ; Databases, Factual ; Educational Status ; *Life Expectancy ; Norway ; *Mortality ; }, abstract = {BACKGROUND: The positive effect of education on reducing all-cause adult mortality is known; however, the relative magnitude of this effect has not been systematically quantified. The aim of our study was to estimate the reduction in all-cause adult mortality associated with each year of schooling at a global level.<br><br>METHODS: In this systematic review and meta-analysis, we assessed the effect of education on all-cause adult mortality. We searched PubMed, Web of Science, Scopus, Embase, Global Health (CAB), EconLit, and Sociology Source Ultimate databases from Jan 1, 1980, to May 31, 2023. Reviewers (LD, TM, HDV, CW, IG, AG, CD, DS, KB, KE, and AA) assessed each record for individual-level data on educational attainment and mortality. Data were extracted by a single reviewer into a standard template from the Global Burden of Diseases, Injuries, and Risk Factors Study. We excluded studies that relied on case-crossover or ecological study designs to reduce the risk of bias from unlinked data and studies that did not report key measures of interest (all-cause adult mortality). Mixed-effects meta-regression models were implemented to address heterogeneity in referent and exposure measures among studies and to adjust for study-level covariates. This study was registered with PROSPERO (CRD42020183923).<br><br>FINDINGS: 17&#x2009;094 unique records were identified, 603 of which were eligible for analysis and included data from 70 locations in 59 countries, producing a final dataset of 10&#x2009;355 observations. Education showed a dose-response relationship with all-cause adult mortality, with an average reduction in mortality risk of 1&#xb7;9% (95% uncertainty interval 1&#xb7;8-2&#xb7;0) per additional year of education. The effect was greater in younger age groups than in older age groups, with an average reduction in mortality risk of 2&#xb7;9% (2&#xb7;8-3&#xb7;0) associated with each additional year of education for adults aged 18-49 years, compared with a 0&#xb7;8% (0&#xb7;6-1&#xb7;0) reduction for adults older than 70 years. We found no differential effect of education on all-cause mortality by sex or Socio-demographic Index level. We identified publication bias (p<0&#xb7;0001) and identified and reported estimates of between-study heterogeneity.<br><br>INTERPRETATION: To our knowledge, this is the first systematic review and meta-analysis to quantify the importance of years of schooling in reducing adult mortality, the benefits of which extend into older age and are substantial across sexes and economic contexts. This work provides compelling evidence of the importance of education in improving life expectancy and supports calls for increased investment in education as a crucial pathway for reducing global inequities in mortality.<br><br>FUNDING: Research Council of Norway and the Bill &amp; Melinda Gates Foundation.}, }
@article {pmid38277106, year = {2024}, author = {Shen, Z and Shi, H and Jiang, Y and Sun, Z}, title = {Diurnal variation in the urban thermal environment and its relationship to human activities in China: a Tencent location-based service geographic big data perspective.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {9}, pages = {14218-14228}, pmid = {38277106}, issn = {1614-7499}, mesh = {Humans ; *Hot Temperature ; Cities ; *Big Data ; Environmental Monitoring/methods ; Temperature ; China ; }, abstract = {The main factor of the formation and deterioration in China's urban thermal environment is human activity, which is difficult to describe and measure. A new perspective on the effect of human activity on the urban thermal environment can be obtained by examining the interaction between location-based service (LBS) data and the urban thermal environment in China. However, relevant research is still limited. In this study, we used Tencent LBS data, Terra/Aqua MODIS land surface temperature (LST) data, and land use data to investigate the relationship between LBS and the urban thermal environment, specifically the LST and surface urban heat island intensity (SUHII) across China and its provinces. Our results showed that (1) in summer, the heat island effect was an issue in 94% of the urban areas in China, which was worse during the day. The high- and low-value periods of LBS data on a given day coincided with the acquisition times of MODIS LST products during the day and at night, respectively. (2) During both the day and at night, there was a significant connection between LBS data and the urban thermal environment in China. The highest correlation coefficient (r) between LBS data and the LST could reach 0.55 (p < 0.01) at the provincial level, and the highest correlation coefficient (r) between LBS data and the SUHII could reach 0.78 (p < 0.01) at the provincial level. (3) The urban thermal environment diurnal difference and LBS data exhibited a significant relationship. The ΔLBS diurnal differences were significantly positively related to the SUHII diurnal differences in China. The overall study findings revealed that LBS data constitute an important parameter to represent the human activity intensity when investigating the formation of the urban thermal environment in China.}, }
@article {pmid38274410, year = {2023}, author = {Boyes, D and Mulley, JF and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Common Pug, Eupithecia vulgata (Haworth, 1809).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {129}, pmid = {38274410}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Eupithecia vulgata (the Common Pug; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 454.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 17.1 kilobases in length.}, }
@article {pmid38273575, year = {2024}, author = {Augustine, SP and Bailey-Marren, I and Charton, KT and Kiel, NG and Peyton, MS}, title = {Improper data practices erode the quality of global ecological databases and impede the progress of ecological research.}, journal = {Global change biology}, volume = {30}, number = {1}, pages = {e17116}, doi = {10.1111/gcb.17116}, pmid = {38273575}, issn = {1365-2486}, mesh = {*Plant Leaves ; *Plants ; Big Data ; Databases, Factual ; Phenotype ; }, abstract = {The scientific community has entered an era of big data. However, with big data comes big responsibilities, and best practices for how data are contributed to databases have not kept pace with the collection, aggregation, and analysis of big data. Here, we rigorously assess the quantity of data for specific leaf area (SLA) available within the largest and most frequently used global plant trait database, the TRY Plant Trait Database, exploring how much of the data were applicable (i.e., original, representative, logical, and comparable) and traceable (i.e., published, cited, and consistent). Over three-quarters of the SLA data in TRY either lacked applicability or traceability, leaving only 22.9% of the original data usable compared with the 64.9% typically deemed usable by standard data cleaning protocols. The remaining usable data differed markedly from the original for many species, which led to altered interpretation of ecological analyses. Though the data we consider here make up only 4.5% of SLA data within TRY, similar issues of applicability and traceability likely apply to SLA data for other species as well as other commonly measured, uploaded, and downloaded plant traits. We end with suggested steps forward for global ecological databases, including suggestions for both uploaders to and curators of databases with the hope that, through addressing the issues raised here, we can increase data quality and integrity within the ecological community.}, }
@article {pmid38273562, year = {2024}, author = {Ross, SRP and Friedman, NR and Dudley, KL and Yoshida, T and Yoshimura, M and Economo, EP and Armitage, DW and Donohue, I}, title = {Divergent ecological responses to typhoon disturbance revealed via landscape-scale acoustic monitoring.}, journal = {Global change biology}, volume = {30}, number = {1}, pages = {e17067}, doi = {10.1111/gcb.17067}, pmid = {38273562}, issn = {1365-2486}, support = {//Canon Foundation in Europe/ ; GOIPG/2018/3023//Irish Research Council/ ; //Okinawa Institute of Science and Technology Graduate University/ ; }, mesh = {Animals ; *Cyclonic Storms ; Ecosystem ; Climate Change ; Birds/physiology ; Acoustics ; }, abstract = {Climate change is increasing the frequency, intensity, and duration of extreme weather events across the globe. Understanding the capacity for ecological communities to withstand and recover from such events is critical. Typhoons are extreme weather events that are expected to broadly homogenize ecological dynamics through structural damage to vegetation and longer-term effects of salinization. Given their unpredictable nature, monitoring ecological responses to typhoons is challenging, particularly for mobile animals such as birds. Here, we report spatially variable ecological responses to typhoons across terrestrial landscapes. Using a high temporal resolution passive acoustic monitoring network across 24 sites on the subtropical island of Okinawa, Japan, we found that typhoons elicit divergent ecological responses among Okinawa's diverse terrestrial habitats, as indicated by increased spatial variability of biological sound production (biophony) and individual species detections. This suggests that soniferous communities are capable of a diversity of different responses to typhoons. That is, spatial insurance effects among local ecological communities provide resilience to typhoons at the landscape scale. Even though site-level typhoon impacts on soundscapes and bird detections were not particularly strong, monitoring at scale with high temporal resolution across a broad spatial extent nevertheless enabled detection of spatial heterogeneity in typhoon responses. Further, species-level responses mirrored those of acoustic indices, underscoring the utility of such indices for revealing insight into fundamental questions concerning disturbance and stability. Our findings demonstrate the significant potential of landscape-scale acoustic sensor networks to capture the understudied ecological impacts of unpredictable extreme weather events.}, }
@article {pmid38273542, year = {2024}, author = {Zeuss, D and Bald, L and Gottwald, J and Becker, M and Bellafkir, H and Bendix, J and Bengel, P and Beumer, LT and Brandl, R and Brändle, M and Dahlke, S and Farwig, N and Freisleben, B and Friess, N and Heidrich, L and Heuer, S and Höchst, J and Holzmann, H and Lampe, P and Leberecht, M and Lindner, K and Masello, JF and Mielke Möglich, J and Mühling, M and Müller, T and Noskov, A and Opgenoorth, L and Peter, C and Quillfeldt, P and Rösner, S and Royauté, R and Mestre-Runge, C and Schabo, D and Schneider, D and Seeger, B and Shayle, E and Steinmetz, R and Tafo, P and Vogelbacher, M and Wöllauer, S and Younis, S and Zobel, J and Nauss, T}, title = {Nature 4.0: A networked sensor system for integrated biodiversity monitoring.}, journal = {Global change biology}, volume = {30}, number = {1}, pages = {e17056}, doi = {10.1111/gcb.17056}, pmid = {38273542}, issn = {1365-2486}, support = {519/03/04.001 - (0006)//Hessian state research programme for the development of scientific-economic excellence (LOEWE, Germany)/ ; }, mesh = {Animals ; *Ecosystem ; *Conservation of Natural Resources ; Biodiversity ; Plants ; }, abstract = {Ecosystem functions and services are severely threatened by unprecedented global loss in biodiversity. To counteract these trends, it is essential to develop systems to monitor changes in biodiversity for planning, evaluating, and implementing conservation and mitigation actions. However, the implementation of monitoring systems suffers from a trade-off between grain (i.e., the level of detail), extent (i.e., the number of study sites), and temporal repetition. Here, we present an applied and realized networked sensor system for integrated biodiversity monitoring in the Nature 4.0 project as a solution to these challenges, which considers plants and animals not only as targets of investigation, but also as parts of the modular sensor network by carrying sensors. Our networked sensor system consists of three main closely interlinked components with a modular structure: sensors, data transmission, and data storage, which are integrated into pipelines for automated biodiversity monitoring. We present our own real-world examples of applications, share our experiences in operating them, and provide our collected open data. Our flexible, low-cost, and open-source solutions can be applied for monitoring individual and multiple terrestrial plants and animals as well as their interactions. Ultimately, our system can also be applied to area-wide ecosystem mapping tasks, thereby providing an exemplary cost-efficient and powerful solution for biodiversity monitoring. Building upon our experiences in the Nature 4.0 project, we identified ten key challenges that need to be addressed to better understand and counteract the ongoing loss of biodiversity using networked sensor systems. To tackle these challenges, interdisciplinary collaboration, additional research, and practical solutions are necessary to enhance the capability and applicability of networked sensor systems for researchers and practitioners, ultimately further helping to ensure the sustainable management of ecosystems and the provision of ecosystem services.}, }
@article {pmid38273499, year = {2024}, author = {Liang, C and Zhang, M and Wang, Z and Xiang, X and Gong, H and Wang, K and Liu, H}, title = {The strengthened impact of water availability at interannual and decadal time scales on vegetation GPP.}, journal = {Global change biology}, volume = {30}, number = {1}, pages = {e17138}, doi = {10.1111/gcb.17138}, pmid = {38273499}, issn = {1365-2486}, support = {164320H116//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; CAS-WX2021SF-0305//Special application demonstration project of network security and informatization of Chinese Academy of Sciences/ ; 41971382//National Natural Science Foundation of China/ ; 32271663//National Natural Science Foundation of China/ ; 41930652//National Natural Science Foundation of China/ ; U19A2051//National Natural Science Foundation of China/ ; U20A2048//National Natural Science Foundation of China/ ; KYCX22_1593//Postgraduate Research amp; Practice Innovation Program of Jiangsu Province/ ; KYCX23_1712//Postgraduate Research amp; Practice Innovation Program of Jiangsu Province/ ; }, mesh = {*Ecosystem ; *Water ; Forests ; Carbon Cycle ; Climate Change ; }, abstract = {Water availability (WA) is a key factor influencing the carbon cycle of terrestrial ecosystems under climate warming, but its effects on gross primary production (EWA-GPP) at multiple time scales are poorly understood. We used ensemble empirical mode decomposition (EEMD) and partial correlation analysis to assess the WA-GPP relationship (RWA-GPP) at different time scales, and geographically weighted regression (GWR) to analyze their temporal dynamics from 1982 to 2018 with multiple GPP datasets, including near-infrared radiance of vegetation GPP, FLUXCOM GPP, and eddy covariance-light-use efficiency GPP. We found that the 3- and 7-year time scales dominated global WA variability (61.18% and 11.95%), followed by the 17- and 40-year time scales (7.28% and 8.23%). The long-term trend also influenced 10.83% of the regions, mainly in humid areas. We found consistent spatiotemporal patterns of the EWA-GPP and RWA-GPP with different source products: In high-latitude regions, RWA-GPP changed from negative to positive as the time scale increased, while the opposite occurred in mid-low latitudes. Forests had weak RWA-GPP at all time scales, shrublands showed negative RWA-GPP at long time scales, and grassland (GL) showed a positive RWA-GPP at short time scales. Globally, the EWA-GPP , whether positive or negative, enhanced significantly at 3-, 7-, and 17-year time scales. For arid and humid zones, the semi-arid and sub-humid zones experienced a faster increase in the positive EWA-GPP , whereas the humid zones experienced a faster increase in the negative EWA-GPP . At the ecosystem types, the positive EWA-GPP at a 3-year time scale increased faster in GL, deciduous broadleaf forest, and savanna (SA), whereas the negative EWA-GPP at other time scales increased faster in evergreen needleleaf forest, woody savannas, and SA. Our study reveals the complex and dynamic EWA-GPP at multiple time scales, which provides a new perspective for understanding the responses of terrestrial ecosystems to climate change.}, }
@article {pmid38272936, year = {2024}, author = {Gnacek, M and Quintero, L and Mavridou, I and Balaguer-Ballester, E and Kostoulas, T and Nduka, C and Seiss, E}, title = {AVDOS-VR: Affective Video Database with Physiological Signals and Continuous Ratings Collected Remotely in VR.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {132}, pmid = {38272936}, issn = {2052-4463}, support = {EP/L016540/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; }, abstract = {Investigating emotions relies on pre-validated stimuli to evaluate induced responses through subjective self-ratings and physiological changes. The creation of precise affect models necessitates extensive datasets. While datasets related to pictures, words, and sounds are abundant, those associated with videos are comparatively scarce. To overcome this challenge, we present the first virtual reality (VR) database with continuous self-ratings and physiological measures, including facial EMG. Videos were rated online using a head-mounted VR device (HMD) with attached emteqPRO mask and a cinema VR environment in remote home and laboratory settings with minimal setup requirements. This led to an affective video database with continuous valence and arousal self-rating measures and physiological responses (PPG, facial-EMG (7x), IMU). The AVDOS-VR database includes data from 37 participants who watched 30 randomly ordered videos (10 positive, neutral, and negative). Each 30-second video was assessed with two-minute relaxation between categories. Validation results suggest that remote data collection is ecologically valid, providing an effective strategy for future affective study designs. All data can be accessed via: www.gnacek.com/affective-video-database-online-study .}, }
@article {pmid38272335, year = {2024}, author = {Chen, Y and Shi, Y and Liang, C and Min, Z and Deng, Q and Yu, R and Zhang, J and Chang, K and Chen, L and Yan, K and Wang, C and Tan, Y and Wang, X and Chen, J and Hua, Q}, title = {MicrobeTCM: A comprehensive platform for the interactions of microbiota and traditional Chinese medicine.}, journal = {Pharmacological research}, volume = {201}, number = {}, pages = {107080}, doi = {10.1016/j.phrs.2024.107080}, pmid = {38272335}, issn = {1096-1186}, mesh = {*Medicine, Chinese Traditional ; Medicine, Traditional ; *Microbiota ; Computational Biology ; Databases, Factual ; }, abstract = {Thanks to the advancements in bioinformatics, drugs, and other interventions that modulate microbes to treat diseases have been emerging continuously. In recent years, an increasing number of databases related to traditional Chinese medicine (TCM) or gut microbes have been established. However, a database combining the two has not yet been developed. To accelerate TCM research and address the traditional medicine and micro ecological system connection between short board, we have developed the most comprehensive micro-ecological database of TCM. This initiative includes the standardization of the following advantages: (1) A repeatable process achieved through the standardization of a retrieval strategy to identify literature. This involved identifying 419 experiment articles from PubMed and six authoritative databases; (2) High-quality data integration achieved through double-entry extraction of literature, mitigating uncertainties associated with natural language extraction; (3) Implementation of a similar strategy aiding in the prediction of mechanisms of action. Leveraging drug similarity, target entity similarity, and known drug-target entity association, our platform enables the prediction of the effects of a new herb or acupoint formulas using the existing data. In total, MicrobeTCM includes 171 diseases, 725 microbes, 1468 herb-formulas, 1032 herbs, 15780 chemical compositions, 35 acupoint-formulas, and 77 acupoints. For further exploration, please visit https://www.microbetcm.com.}, }
@article {pmid38271874, year = {2024}, author = {Ren, XY and Zheng, YL and Liu, ZL and Duan, GL and Zhu, D and Ding, LJ}, title = {Exploring ecological effects of arsenic and cadmium combined exposure on cropland soil: from multilevel organisms to soil functioning by multi-omics coupled with high-throughput quantitative PCR.}, journal = {Journal of hazardous materials}, volume = {466}, number = {}, pages = {133567}, doi = {10.1016/j.jhazmat.2024.133567}, pmid = {38271874}, issn = {1873-3336}, mesh = {Cadmium/metabolism ; *Arsenic/toxicity/analysis ; Soil ; Multiomics ; *Microbiota/genetics ; *Environmental Pollutants/analysis ; Crops, Agricultural/metabolism ; Polymerase Chain Reaction ; *Soil Pollutants/metabolism ; }, abstract = {Arsenic (As) and cadmium (Cd) pose potential ecological threats to cropland soils; however, few studies have investigated their combined effects on multilevel organisms and soil functioning. Here, we used collembolans and soil microbiota as test organisms to examine their responses to soil As and Cd co-contamination at the gene, individual, and community levels, respectively, and further uncovered ecological relationships between pollutants, multilevel organisms, and soil functioning. At the gene level, collembolan transcriptome revealed that elevated As concentrations stimulated As-detoxifying genes AS3MT and GST, whereas the concurrent Cd restrained GST gene expression. At the individual level, collembolan reproduction was sensitive to pollutants while collembolan survival wasn't. At the community level, significant but inconsistent correlations were observed between the biodiversity of different soil keystone microbial clusters and soil As levels. Moreover, soil functioning related to nutrient (e.g., carbon, nitrogen, phosphorus, and sulfur) cycles was inhibited under As and Cd co-exposure only through the mediation of plant pathogens. Overall, these findings suggested multilevel bioindicators (i.e., AS3MT gene expression in collembolans, collembolan reproduction, and biodiversity of soil keystone microbial clusters) in cropland soils co-contaminated with As and Cd, thus improving the understanding of the ecotoxicological impact of heavy metal co-contamination on soil ecosystems.}, }
@article {pmid38271521, year = {2024}, author = {Couce, A and Limdi, A and Magnan, M and Owen, SV and Herren, CM and Lenski, RE and Tenaillon, O and Baym, M}, title = {Changing fitness effects of mutations through long-term bacterial evolution.}, journal = {Science (New York, N.Y.)}, volume = {383}, number = {6681}, pages = {eadd1417}, doi = {10.1126/science.add1417}, pmid = {38271521}, issn = {1095-9203}, support = {R35 GM133700/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Physiological/genetics ; *Escherichia coli/genetics ; *Evolution, Molecular ; *Genetic Fitness ; Mutagenesis, Insertional ; Mutation ; Selection, Genetic ; }, abstract = {The distribution of fitness effects of new mutations shapes evolution, but it is challenging to observe how it changes as organisms adapt. Using Escherichia coli lineages spanning 50,000 generations of evolution, we quantify the fitness effects of insertion mutations in every gene. Macroscopically, the fraction of deleterious mutations changed little over time whereas the beneficial tail declined sharply, approaching an exponential distribution. Microscopically, changes in individual gene essentiality and deleterious effects often occurred in parallel; altered essentiality is only partly explained by structural variation. The identity and effect sizes of beneficial mutations changed rapidly over time, but many targets of selection remained predictable because of the importance of loss-of-function mutations. Taken together, these results reveal the dynamic-but statistically predictable-nature of mutational fitness effects.}, }
@article {pmid38269820, year = {2024}, author = {Andison, M}, title = {Digital Health Safety Matters: A Promising Practice Study into the Adoption of Patient Safety Guidelines in Australia.}, journal = {Studies in health technology and informatics}, volume = {310}, number = {}, pages = {334-338}, doi = {10.3233/SHTI230982}, pmid = {38269820}, issn = {1879-8365}, mesh = {Humans ; *Digital Health ; *Patient Safety ; Australia ; Artifacts ; Data Mining ; }, abstract = {A foundation for digitally enabling healthier living is the safe development and use of technology. The practice of digital health safety has emerged from patient harm attributed to failing technologies. The study aimed to investigate how to adopt and implement digital health safety guidelines at scale. Data was collected through an online survey, semi-structured interviews, focus groups, document review, and data mining of artefacts. The findings of this study capture the emerging practice from Australia in a way that offers insights into the problem of practice, patient safety practice, safety culture, and socio-technical factors. The research findings contribute to better understanding of the complexities of balancing digital innovation with patient safety. The four recommendations from the study and the provision of a logic model will support the audience to implement actions toward a safer digital health ecology.}, }
@article {pmid38268612, year = {2023}, author = {Boyes, D and Holland, PWH and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Muslin moth, Diaphora mendica (Clerck, 1759).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {257}, pmid = {38268612}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Diaphora mendica (the Muslin moth; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 748.7 megabases in span. Most of the assembly is scaffolded into 26 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.41 kilobases in length.}, }
@article {pmid38263406, year = {2024}, author = {Ismaeel, A and Tai, APK and Santos, EG and Maraia, H and Aalto, I and Altman, J and Doležal, J and Lembrechts, JJ and Camargo, JL and Aalto, J and Sam, K and Avelino do Nascimento, LC and Kopecký, M and Svátek, M and Nunes, MH and Matula, R and Plichta, R and Abera, T and Maeda, EE}, title = {Patterns of tropical forest understory temperatures.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {549}, pmid = {38263406}, issn = {2041-1723}, support = {319905//Academy of Finland (Suomen Akatemia)/ ; 345472//Academy of Finland (Suomen Akatemia)/ ; }, mesh = {*Ecosystem ; Temperature ; *Forests ; Climate Change ; Computer Systems ; }, abstract = {Temperature is a fundamental driver of species distribution and ecosystem functioning. Yet, our knowledge of the microclimatic conditions experienced by organisms inside tropical forests remains limited. This is because ecological studies often rely on coarse-gridded temperature estimates representing the conditions at 2 m height in an open-air environment (i.e., macroclimate). In this study, we present a high-resolution pantropical estimate of near-ground (15 cm above the surface) temperatures inside forests. We quantify diurnal and seasonal variability, thus revealing both spatial and temporal microclimate patterns. We find that on average, understory near-ground temperatures are 1.6 °C cooler than the open-air temperatures. The diurnal temperature range is on average 1.7 °C lower inside the forests, in comparison to open-air conditions. More importantly, we demonstrate a substantial spatial variability in the microclimate characteristics of tropical forests. This variability is regulated by a combination of large-scale climate conditions, vegetation structure and topography, and hence could not be captured by existing macroclimate grids. Our results thus contribute to quantifying the actual thermal ranges experienced by organisms inside tropical forests and provide new insights into how these limits may be affected by climate change and ecosystem disturbances.}, }
@article {pmid38262510, year = {2024}, author = {Sajjad, W and Ilahi, N and Haq, A and Shang, Z and Nabi, G and Rafiq, M and Bahadur, A and Banerjee, A and Kang, S}, title = {Bacteria populating freshly appeared supraglacial lake possess metals and antibiotic-resistant genes.}, journal = {Environmental research}, volume = {247}, number = {}, pages = {118288}, doi = {10.1016/j.envres.2024.118288}, pmid = {38262510}, issn = {1096-0953}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Lakes/microbiology ; Metals ; }, abstract = {Antibiotic resistance (AR) has been extensively studied in natural habitats and clinical applications. AR is mainly reported with the use and misuse of antibiotics; however, little is known about its presence in antibiotic-free remote supraglacial lake environments. This study evaluated bacterial strains isolated from supraglacial lake debris and meltwater in Dook Pal Glacier, northern Pakistan, for antibiotic-resistant genes (ARGs) and metal-tolerant genes (MTGs) using conventional PCR. Several distinct ARGs were reported in the bacterial strains isolated from lake debris (92.5%) and meltwater (100%). In lake debris, 57.5% of isolates harbored the blaTEM gene, whereas 58.3% of isolates in meltwater possessed blaTEM and qnrA each. Among the ARGs, qnrA was dominant in debris isolates (19%), whereas in meltwater isolates, qnrA (15.2%) and blaTEM (15.2%) were dominant. ARGs were widely distributed among the bacterial isolates and different bacteria shared similar types of ARGs. Relatively greater number of ARGs were reported in Gram-negative bacterial strains. In addition, 92.5% of bacterial isolates from lake debris and 83.3% of isolates from meltwater harbored MTGs. Gene copA was dominant in meltwater isolates (50%), whereas czcA was greater in debris bacterial isolates (45%). Among the MTGs, czcA (18.75%) was dominant in debris strains, whereas copA (26.0%) was greater in meltwater isolates. This presents the co-occurrence and co-selection of MTGs and ARGs in a freshly appeared supraglacial lake. The same ARGs and MTGs were present in different bacteria, exhibiting horizontal gene transfer (HGT). Both positive and negative correlations were determined between ARGs and MTGs. The research provides insights into the existence of MTGs and ARGs in bacterial strains isolated from remote supraglacial lake environments, signifying the need for a more detailed study of bacteria harboring ARGs and MTGs in supraglacial lakes.}, }
@article {pmid38259099, year = {2024}, author = {Caesar, L and Rice, DW and McAfee, A and Underwood, R and Ganote, C and Tarpy, DR and Foster, LJ and Newton, ILG}, title = {Metagenomic analysis of the honey bee queen microbiome reveals low bacterial diversity and Caudoviricetes phages.}, journal = {mSystems}, volume = {9}, number = {2}, pages = {e0118223}, pmid = {38259099}, issn = {2379-5077}, support = {2005306//National Science Foundation (NSF)/ ; 2022049//National Science Foundation (NSF)/ ; //L'Oreal USA (L'Or&#xe9;al)/ ; //Project Apis m. (PAm)/ ; 2017-51300-26814//U.S. Department of Agriculture (USDA)/ ; }, mesh = {Bees ; Female ; Animals ; *Bacteriophages/genetics ; *Microbiota/genetics ; Reproduction ; Metagenome ; }, abstract = {In eusocial insects, the health of the queens-the colony founders and sole reproductive females-is a primary determinant for colony success. Queen failure in the honey bee Apis mellifera, for example, is a major concern of beekeepers who annually suffer colony losses, necessitating a greater knowledge of queen health. Several studies on the microbiome of honey bees have characterized its diversity and shown its importance for the health of worker bees, the female non-reproductive caste. However, the microbiome of workers differs from that of queens, which, in comparison, is still poorly studied. Thus, direct investigations of the queen microbiome are required to understand colony-level microbiome assembly, functional roles, and evolution. Here, we used metagenomics to comprehensively characterize the honey bee queen microbiome. Comparing samples from different geographic locations and breeder sources, we show that the microbiome of queens is mostly shaped by the environment experienced since early life and is predicted to play roles in the breakdown of the diet and protection from pathogens and xenobiotics. We also reveal that the microbiome of queens comprises only four candidate core bacterial species, Apilactobacillus kunkeei, Lactobacillus apis, Bombella apis, and Commensalibacter sp. Interestingly, in addition to bacteria, we show that bacteriophages infect the queen microbiome, for which Lactobacillaceae are predicted to be the main reservoirs. Together, our results provide the basis to understand the honey bee colony microbiome assemblage, can guide improvements in queen-rearing processes, and highlight the importance of considering bacteriophages for queen microbiome health and microbiome homeostasis in eusocial insects.IMPORTANCEThe queen caste plays a central role in colony success in eusocial insects, as queens lay eggs and regulate colony behavior and development. Queen failure can cause colonies to collapse, which is one of the major concerns of beekeepers. Thus, understanding the biology behind the queen's health is a pressing issue. Previous studies have shown that the bee microbiome plays an important role in worker bee health, but little is known about the queen microbiome and its function in vivo. Here, we characterized the queen microbiome, identifying for the first time the present species and their putative functions. We show that the queen microbiome has predicted nutritional and protective roles in queen association and comprises only four consistently present bacterial species. Additionally, we bring to attention the spread of phages in the queen microbiome, which increased in abundance in failing queens and may impact the fate of the colony.}, }
@article {pmid38259095, year = {2024}, author = {Wang, C and Ma, A and Li, Y and McNutt, ME and Zhang, S and Zhu, J and Hoyd, R and Wheeler, CE and Robinson, LA and Chan, CHF and Zakharia, Y and Dodd, RD and Ulrich, CM and Hardikar, S and Churchman, ML and Tarhini, AA and Singer, EA and Ikeguchi, AP and McCarter, MD and Denko, N and Tinoco, G and Husain, M and Jin, N and Osman, AEG and Eljilany, I and Tan, AC and Coleman, SS and Denko, L and Riedlinger, G and Schneider, BP and Spakowicz, D and Ma, Q and , }, title = {A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset.}, journal = {Cancer research communications}, volume = {4}, number = {2}, pages = {293-302}, pmid = {38259095}, issn = {2767-9764}, support = {UL1 TR000090/TR/NCATS NIH HHS/United States ; U01 CA206110/CA/NCI NIH HHS/United States ; K07 CA222060/CA/NCI NIH HHS/United States ; P30 CA016058/CA/NCI NIH HHS/United States ; AS1695/AS/Autism Speaks/United States ; P30 CA042014/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; Phylogeny ; *Microbiota/genetics ; Computational Biology ; High-Throughput Nucleotide Sequencing ; }, abstract = {UNLABELLED: Evidence supports significant interactions among microbes, immune cells, and tumor cells in at least 10%-20% of human cancers, emphasizing the importance of further investigating these complex relationships. However, the implications and significance of tumor-related microbes remain largely unknown. Studies have demonstrated the critical roles of host microbes in cancer prevention and treatment responses. Understanding interactions between host microbes and cancer can drive cancer diagnosis and microbial therapeutics (bugs as drugs). Computational identification of cancer-specific microbes and their associations is still challenging due to the high dimensionality and high sparsity of intratumoral microbiome data, which requires large datasets containing sufficient event observations to identify relationships, and the interactions within microbial communities, the heterogeneity in microbial composition, and other confounding effects that can lead to spurious associations. To solve these issues, we present a bioinformatics tool, microbial graph attention (MEGA), to identify the microbes most strongly associated with 12 cancer types. We demonstrate its utility on a dataset from a consortium of nine cancer centers in the Oncology Research Information Exchange Network. This package has three unique features: species-sample relations are represented in a heterogeneous graph and learned by a graph attention network; it incorporates metabolic and phylogenetic information to reflect intricate relationships within microbial communities; and it provides multiple functionalities for association interpretations and visualizations. We analyzed 2,704 tumor RNA sequencing samples and MEGA interpreted the tissue-resident microbial signatures of each of 12 cancer types. MEGA can effectively identify cancer-associated microbial signatures and refine their interactions with tumors.<br><br>SIGNIFICANCE: Studying the tumor microbiome in high-throughput sequencing data is challenging because of the extremely sparse data matrices, heterogeneity, and high likelihood of contamination. We present a new deep learning tool, MEGA, to refine the organisms that interact with tumors.}, }
@article {pmid38258939, year = {2024}, author = {Mori, K and Odagami, K and Inagaki, M and Moriya, K and Fujiwara, H and Eguchi, H}, title = {Work engagement among older workers: a systematic review.}, journal = {Journal of occupational health}, volume = {66}, number = {1}, pages = {}, pmid = {38258939}, issn = {1348-9585}, mesh = {Humans ; Adult ; Middle Aged ; *Work Engagement ; *Aging ; Databases, Factual ; Employment ; Europe ; Observational Studies as Topic ; }, abstract = {OBJECTIVES: Given current labor force conditions, including population aging, keeping older workers engaged in work and motivated is important. Aging may alter the effects that psychological and environmental factors have on work engagement. We conducted a systematic review to understand the features of work engagement among older workers.<br><br>METHODS: A systematic search was conducted in July 2022 using 4 databases. The review included relevant articles that focused on participants aged 40&#xa0;years and older.<br><br>RESULTS: Fifty articles were selected for our review, which were grouped into 5 categories: (1) studies examining the relationship between chronological age and work engagement, (2) studies investigating the moderating effects of age on the relationship between job-related psychological factors and work environment factors and work engagement, (3) studies comparing the relationship of job-related psychological factors and work environment factors with work engagement across different age groups, (4) studies exploring the relationship between work engagement and retirement intentions or continued employment beyond retirement age, and (5) other studies discussing work engagement in the context of older workers. Most articles focused on workers in Europe and the United States and used observational study designs.<br><br>CONCLUSIONS: Work engagement increases with age, and is mainly mediated by increased emotional regulation. In addition, age moderates the relationships between various job-related psychological and work-environmental factors and work engagement. Work engagement is associated with working beyond retirement age. Organizations should understand the characteristics of work engagement among older workers and make age-conscious efforts to support them in adapting to social changes.}, }
@article {pmid38258936, year = {2024}, author = {Tani, N and Fujihara, H and Ishii, K and Kamakura, Y and Tsunemi, M and Yamaguchi, C and Eguchi, H and Imamura, K and Kanamori, S and Kojimahara, N and Ebara, T}, title = {What digital health technology types are used in mental health prevention and intervention? Review of systematic reviews for systematization of technologies.}, journal = {Journal of occupational health}, volume = {66}, number = {1}, pages = {}, pmid = {38258936}, issn = {1348-9585}, support = {JP22rea522006//Japan Agency for Medical Research and Development (AMED)/ ; }, mesh = {Humans ; *Digital Health ; *Mental Health ; Systematic Reviews as Topic ; Technology ; Avatar ; }, abstract = {Digital health technology has been widely applied to mental health interventions worldwide. Using digital phenotyping to identify an individual's mental health status has become particularly important. However, many technologies other than digital phenotyping are expected to become more prevalent in the future. The systematization of these technologies is necessary to accurately identify trends in mental health interventions. However, no consensus on the technical classification of digital health technologies for mental health interventions has emerged. Thus, we conducted a review of systematic review articles on the application of digital health technologies in mental health while attempting to systematize the technology using the Delphi method. To identify technologies used in digital phenotyping and other digital technologies, we included 4 systematic review articles that met the inclusion criteria, and an additional 8 review articles, using a snowballing approach, were incorporated into the comprehensive review. Based on the review results, experts from various disciplines participated in the Delphi process and agreed on the following 11 technical categories for mental health interventions: heart rate estimation, exercise or physical activity, sleep estimation, contactless heart rate/pulse wave estimation, voice and emotion analysis, self-care/cognitive behavioral therapy/mindfulness, dietary management, psychological safety, communication robots, avatar/metaverse devices, and brain wave devices. The categories we defined intentionally included technologies that are expected to become widely used in the future. Therefore, we believe these 11 categories are socially implementable and useful for mental health interventions.}, }
@article {pmid38258809, year = {2024}, author = {Viera, A and Ondrusek, A and Tengatenga, C and McBurney, E and Lauckner, J and Tran, E and Muilenburg, J and Kershaw, T and Lauckner, C}, title = {A Qualitative Exploration of Attitudes Toward Global Positioning System Tracking and Ecological Momentary Assessment Among Individuals in Substance Use Treatment.}, journal = {Substance use &amp; addiction journal}, volume = {45}, number = {2}, pages = {260-267}, doi = {10.1177/29767342231218514}, pmid = {38258809}, issn = {2976-7350}, support = {R01 AA025954/AA/NIAAA NIH HHS/United States ; F31 AA028992/AA/NIAAA NIH HHS/United States ; }, mesh = {Humans ; *Ecological Momentary Assessment ; Geographic Information Systems ; *Substance-Related Disorders ; Craving ; Georgia ; }, abstract = {BACKGROUND: The use of tracking technology in substance use research can uncover the role of contextual factors, such as social networks and environmental cues, in triggering cravings and precipitating return to use. Few studies have explored the opinions of individuals in substance use treatment related to tracking technology.<br><br>METHODS: We conducted 30 semi-structured interviews with individuals in substance use treatment facilities in Connecticut and Georgia. Interviews were not limited to individuals with any specific substance use disorder. Interviewers described a hypothetical study involving ecological momentary assessment and global positioning system tracking to examine place-based predictors of substance use. Participants were invited to share reactions to this description. We used thematic analysis to identify themes in participant perceptions of this hypothetical research study.<br><br>RESULTS: Most participants shared positive opinions about study participation and expressed little to no concern about the tracking components. Participant concerns focused on the security of their information and the potential burden of responding to study questions. Participants largely understood the importance of study participation for promoting greater understanding of substance use and identified potential therapeutic effects of study participation on their own recovery.<br><br>CONCLUSIONS: Individuals in substance use treatment expressed little concern with research studies or interventions incorporating mobile-tracking elements. Future studies should explore the responsible use of tracking elements in recovery support interventions.}, }
@article {pmid38257567, year = {2024}, author = {Kraft, R and Reichert, M and Pryss, R}, title = {Mobile Crowdsensing in Ecological Momentary Assessment mHealth Studies: A Systematic Review and Analysis.}, journal = {Sensors (Basel, Switzerland)}, volume = {24}, number = {2}, pages = {}, pmid = {38257567}, issn = {1424-8220}, mesh = {Humans ; *Ecological Momentary Assessment ; Computers, Handheld ; Data Collection ; Databases, Factual ; *Telemedicine ; }, abstract = {As mobile devices have become a central part of our daily lives, they are also becoming increasingly important in research. In the medical context, for example, smartphones are used to collect ecologically valid and longitudinal data using Ecological Momentary Assessment (EMA), which is mostly implemented through questionnaires delivered via smart notifications. This type of data collection is intended to capture a patient's condition on a moment-to-moment and longer-term basis. To collect more objective and contextual data and to understand patients even better, researchers can not only use patients' input via EMA, but also use sensors as part of the Mobile Crowdsensing (MCS) approach. In this paper, we examine how researchers have embraced the topic of MCS in the context of EMA through a systematic literature review. This PRISMA-guided review is based on the databases PubMed, Web of Science, and EBSCOhost. It is shown through the results that both EMA research in general and the use of sensors in EMA research are steadily increasing. In addition, most of the studies reviewed used mobile apps to deliver EMA to participants, used a fixed-time prompting strategy, and used signal-contingent or interval-contingent self-assessment as sampling/assessment strategies. The most commonly used sensors in EMA studies are the accelerometer and GPS. In most studies, these sensors are used for simple data collection, but sensor data are also commonly used to verify study participant responses and, less commonly, to trigger EMA prompts. Security and privacy aspects are addressed in only a subset of mHealth EMA publications. Moreover, we found that EMA adherence was negatively correlated with the total number of prompts and was higher in studies using a microinteraction-based EMA (μEMA) approach as well as in studies utilizing sensors. Overall, we envision that the potential of the technological capabilities of smartphones and sensors could be better exploited in future, more automated approaches.}, }
@article {pmid38256741, year = {2024}, author = {Hanazaki, N}, title = {Brazilian Environment and Plants as Seen by Japanese Eyes Two Hundred and Twenty Years Ago.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {2}, pages = {}, pmid = {38256741}, issn = {2223-7747}, support = {305789/2022-1//National Council for Scientific and Technological Development/ ; }, abstract = {In 2023, the Japanese migration to Brazil completed 115 years. However, the first time Japanese people arrived in Brazil and left a testimony of their experience was about two centuries ago. Their reports were registered in a historical document, handwritten during the Edo period when Japan was adopting a closed-door policy. The episode of their visit to Brazil is only a small part of the odyssey of these four Japanese sailors who departed from Ishinomiya to Tokyo at the end of the 18th century, but unexpectedly traveled around the globe. After a storm, they were adrift for six months until shipwrecking on the Aleutian Islands; from the Russian Aleutian Islands, they crossed the whole of Russia and boarded, in Saint Petersburg, on the first Russian expedition to circumnavigate the world. Their only stop in South America was at Santa Catarina Island, southern Brazil, and this is the first analysis of this episode from an ethnobiological perspective. Their reports described both the forest environment and the plants they observed and included at least 23 taxa of plants, mostly cultivated. These descriptions of plants and the environment are in contrast with other reports from the same period and to the current environment found in Santa Catarina Island, inspiring reflections on the construction of Brazil's image in Japan before the 20th century.}, }
@article {pmid38256002, year = {2024}, author = {Han, S and Han, X and Qi, C and Guo, F and Yin, J and Liu, Y and Zhu, Y}, title = {Genome-Wide Identification of DUF668 Gene Family and Expression Analysis under F. solani, Chilling, and Waterlogging Stresses in Zingiber officinale.}, journal = {International journal of molecular sciences}, volume = {25}, number = {2}, pages = {}, pmid = {38256002}, issn = {1422-0067}, support = {CARS-24-G-17//Fengling Guo/ ; }, mesh = {*Zingiber officinale/genetics ; Amino Acid Sequence ; Cold-Shock Response/genetics ; Computational Biology ; *Fusariosis ; *MicroRNAs/genetics ; }, abstract = {The domains of unknown function (DUF) superfamilies contain proteins with conserved amino acid sequences without known functions. Among them, DUF668 was indicated widely involving the stress response of plants. However, understanding ZoDUF668 is still lacking. Here, 12 ZoDUF668 genes were identified in ginger by the bioinformatics method and unevenly distributed on six chromosomes. Conserved domain analysis showed that members of the same subfamily had similar conserved motifs and gene structures. The promoter region of ZoDUF668s contained the light, plant hormone and stress-responsive elements. The prediction of miRNA targeting relationship showed that nine ginger miRNAs targeted four ZoDUF668 genes through cleavage. The expression patterns of 12 ZoDUF668 genes under biotic and abiotic stress were analyzed using RT-qPCR. The results showed that the expression of seven ZoDUF668 genes was significantly downregulated under Fusarium solani infection, six ZoDUF668 genes were upregulated under cold stress, and five ZoDUF668 genes were upregulated under waterlogging stress. These results indicate that the ZoDUF668 gene has different expression patterns under different stress conditions. This study provides excellent candidate genes and provides a reference for stress-resistance research in ginger.}, }
@article {pmid38254931, year = {2023}, author = {Yang, D and Zhang, X and Cao, M and Yin, L and Gao, A and An, K and Gao, S and Guo, S and Yin, H}, title = {Genome-Wide Identification, Expression and Interaction Analyses of PP2C Family Genes in Chenopodium quinoa.}, journal = {Genes}, volume = {15}, number = {1}, pages = {}, pmid = {38254931}, issn = {2073-4425}, support = {2022SZX17//Science &amp; Technology Specific Projects in Agricultural High-tech Industrial Demonstration Area of the Yellow River Delta/ ; 2019BHLC001//the "Bohai Sea Granary" Science and Technology Demonstration Project of Shandong Provincial/ ; }, mesh = {Humans ; *Chenopodium quinoa/genetics ; Genome-Wide Association Study ; Phylogeny ; Biological Evolution ; Data Interpretation, Statistical ; Phosphoric Monoester Hydrolases ; }, abstract = {Plant protein phosphatase 2Cs (PP2Cs) function as inhibitors in protein kinase cascades involved in various processes and are crucial participants in both plant development and signaling pathways activated by abiotic stress. In this study, a genome-wide study was conducted on the CqPP2C gene family. A total of putative 117 CqPP2C genes were identified. Comprehensive analyses of physicochemical properties, chromosome localization and subcellular localization were conducted. According to phylogenetic analysis, CqPP2Cs were divided into 13 subfamilies. CqPP2Cs in the same subfamily had similar gene structures, and conserved motifs and all the CqPP2C proteins had the type 2C phosphatase domains. The expansion of CqPP2Cs through gene duplication was primarily driven by segmental duplication, and all duplicated CqPP2Cs underwent evolutionary changes guided by purifying selection. The expression of CqPP2Cs in various tissues under different abiotic stresses was analyzed using RNA-seq data. The findings indicated that CqPP2C genes played a role in regulating both the developmental processes and stress responses of quinoa. Real-time quantitative reverse transcription PCR (qRT-PCR) analysis of six CqPP2C genes in subfamily A revealed that they were up-regulated or down-regulated under salt and drought treatments. Furthermore, the results of yeast two-hybrid assays revealed that subfamily A CqPP2Cs interacted not only with subclass III CqSnRK2s but also with subclass II CqSnRK2s. Subfamily A CqPP2Cs could interact with CqSnRK2s in different combinations and intensities in a variety of biological processes and biological threats. Overall, our results will be useful for understanding the functions of CqPP2C in regulating ABA signals and responding to abiotic stress.}, }
@article {pmid38251877, year = {2024}, author = {Schloss, PD}, title = {Rarefaction is currently the best approach to control for uneven sequencing effort in amplicon sequence analyses.}, journal = {mSphere}, volume = {9}, number = {2}, pages = {e0035423}, pmid = {38251877}, issn = {2379-5042}, support = {R01 CA215574/CA/NCI NIH HHS/United States ; U01 CA264071/CA/NCI NIH HHS/United States ; U01 AI124255/AI/NIAID NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; }, mesh = {RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; }, abstract = {UNLABELLED: Considering it is common to find as much as 100-fold variation in the number of 16S rRNA gene sequences across samples in a study, researchers need to control for the effect of uneven sequencing effort. How to do this has become a contentious question. Some have argued that rarefying or rarefaction is "inadmissible" because it omits valid data. A number of alternative approaches have been developed to normalize and rescale the data that purport to be invariant to the number of observations. I generated community distributions based on 12 published data sets where I was able to assess the ability of multiple methods to control for uneven sequencing effort. Rarefaction was the only method that could control for variation in uneven sequencing effort when measuring commonly used alpha and beta diversity metrics. Next, I compared the false detection rate and power to detect true differences between simulated communities with a known effect size using various alpha and beta diversity metrics. Although all methods of controlling for uneven sequencing effort had an acceptable false detection rate when samples were randomly assigned to two treatment groups, rarefaction was consistently able to control for differences in sequencing effort when sequencing depth was confounded with treatment group. Finally, the statistical power to detect differences in alpha and beta diversity metrics was consistently the highest when using rarefaction. These simulations underscore the importance of using rarefaction to normalize the number of sequences across samples in amplicon sequencing analyses.<br><br>IMPORTANCE: Sequencing 16S rRNA gene fragments has become a fundamental tool for understanding the diversity of microbial communities and the factors that affect their diversity. Due to technical challenges, it is common to observe wide variation in the number of sequences that are collected from different samples within the same study. However, the diversity metrics used by microbial ecologists are sensitive to differences in sequencing effort. Therefore, tools are needed to control for the uneven levels of sequencing. This simulation-based analysis shows that despite a longstanding controversy, rarefaction is the most robust approach to control for uneven sequencing effort. The controversy started because of confusion over the definition of rarefaction and violation of assumptions that are made by methods that have been borrowed from other fields. Microbial ecologists should use rarefaction.}, }
@article {pmid38250723, year = {2024}, author = {Abdullah, NI and Elias, NA and Ohte, N and Vincenot, C}, title = {Resource partitioning among bat species in Peninsular Malaysia rice fields.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e16657}, pmid = {38250723}, issn = {2167-8359}, mesh = {Humans ; Pregnancy ; Animals ; Female ; Male ; *Oryza ; *Chiroptera ; Lactation ; Malaysia ; *Coleoptera ; *Lepidoptera ; }, abstract = {Resource partitioning among tropical bats in agricultural areas of Peninsular Malaysia remains unclear. This study was conducted to evaluate resource partitioning among bats by examining their fecal samples. The main bat species sampled included: Rhinolophus coelophyllus, Rhinolophus malayanus, Rhinolophus pusillus, Rhinolophus refulgens, Taphozous melanopogon and Hipposideros larvatus. Two harp traps were set at different elevations on a hilltop (Gunung Keriang) and two high nets were used in neighboring rice fields at three sites, for three consecutive nights per sampling from April 2021 to February 2022. A total of 301 bats and 1,505 pellets were analyzed using a conventional approach which examined the fecal sample under the microscope. All of the bat species within the study had insects from the order Coleoptera, Lepidoptera, Diptera and Hemiptera in their diet. Larger bats exhibited a greater variety of prey consumption. Male individuals were observed to be generalists while female individuals were specialists, particularly during pregnancy and lactating reproductive stages. Bat species and insect order had a significant impact on the percentage fragment frequency of the insects consumed. Rhinolophus coelophyllus specialized in feeding on Coleoptera and Diptera, H. larvatus fed on Coleoptera, R. malayanus fed on Hemiptera, R. pusillus and T. melanopogon fed on Lepidoptera. Future molecular analysis can be carried out to further identify the insect pests consumed by these bats up to species level. These findings enhance our understanding of bats' ecological roles in agricultural landscapes and contribute to conservation and pest management strategies.}, }
@article {pmid38249959, year = {2023}, author = {Blaxter, ML and Spurgeon, D and Kille, P and ,  and ,  and ,  and , }, title = {The genome sequence of the common earthworm, Lumbricus terrestris (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {500}, pmid = {38249959}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual Lumbricus terrestris (the common earthworm; Annelida; Clitellata; Haplotaxida; Lumbricidae). The genome sequence is 1,056.5 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.93 kilobases in length.}, }
@article {pmid38249957, year = {2023}, author = {Boyes, D and Eagles, M and Holland, PWH and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Willow Beauty, Peribatodes rhomboidaria (Denis &amp; Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {233}, pmid = {38249957}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Peribatodes rhomboidaria (the Willow Beauty; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 499.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.7 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,486 protein coding genes.}, }
@article {pmid38248287, year = {2024}, author = {Sokołowska, B}, title = {Being in Virtual Reality and Its Influence on Brain Health-An Overview of Benefits, Limitations and Prospects.}, journal = {Brain sciences}, volume = {14}, number = {1}, pages = {}, pmid = {38248287}, issn = {2076-3425}, abstract = {BACKGROUND: Dynamic technological development and its enormous impact on modern societies are posing new challenges for 21st-century neuroscience. A special place is occupied by technologies based on virtual reality (VR). VR tools have already played a significant role in both basic and clinical neuroscience due to their high accuracy, sensitivity and specificity and, above all, high ecological value.<br><br>OBJECTIVE: Being in a digital world affects the functioning of the body as a whole and its individual systems. The data obtained so far, both from experimental and modeling studies, as well as (clinical) observations, indicate their great and promising potential, but apart from the benefits, there are also losses and negative consequences for users.<br><br>METHODS: This review was conducted according to the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) framework across electronic databases (such as Web of Science Core Collection; PubMed; and Scopus, Taylor &amp; Francis Online and Wiley Online Library) to identify beneficial effects and applications, as well as adverse impacts, especially on brain health in human neuroscience.<br><br>RESULTS: More than half of these articles were published within the last five years and represent state-of-the-art approaches and results (e.g., 54.7% in Web of Sciences and 63.4% in PubMed), with review papers accounting for approximately 16%. The results show that in addition to proposed novel devices and systems, various methods or procedures for testing, validation and standardization are presented (about 1% of articles). Also included are virtual developers and experts, (bio)(neuro)informatics specialists, neuroscientists and medical professionals.<br><br>CONCLUSIONS: VR environments allow for expanding the field of research on perception and cognitive and motor imagery, both in healthy and patient populations. In this context, research on neuroplasticity phenomena, including mirror neuron networks and the effects of applied virtual (mirror) tasks and training, is of interest in virtual prevention and neurogeriatrics, especially in neurotherapy and neurorehabilitation in basic/clinical and digital neuroscience.}, }
@article {pmid38247366, year = {2024}, author = {Erickson, BA and Griffith, JW and Wensheng, G and Mengying, Y and Herman, T and Bradley, CS and Quentin Clemens, J and Farrar, JT and Gupta, P and Kreder, KJ and Henry Lai, H and Naliboff, BD and Newman, DK and Rodriguez, LV and Spitznagle, T and Sutcliffe, S and Sutherland, SE and Taple, BJ and Richard Landis, J}, title = {Ecological momentary assessment of pelvic pain and urinary urgency variability in urologic chronic pelvic pain syndrome and their association with illness impact and quality of life: Findings from the multidisciplinary approach to the study of chronic pelvic pain symptom patterns study.}, journal = {Neurourology and urodynamics}, volume = {43}, number = {4}, pages = {893-901}, pmid = {38247366}, issn = {1520-6777}, support = {U01 DK082345/DK/NIDDK NIH HHS/United States ; U01 DK082315/DK/NIDDK NIH HHS/United States ; U01 DK082316/DK/NIDDK NIH HHS/United States ; U01 DK082344/DK/NIDDK NIH HHS/United States ; U01 DK082333/DK/NIDDK NIH HHS/United States ; U24 DK082316/DK/NIDDK NIH HHS/United States ; R01 DK117208/DK/NIDDK NIH HHS/United States ; U24 DK082333/DK/NIDDK NIH HHS/United States ; U01 DK082325/DK/NIDDK NIH HHS/United States ; U01 DK082370/DK/NIDDK NIH HHS/United States ; U01 DK082342/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; Female ; Male ; *Quality of Life ; Ecological Momentary Assessment ; *Chronic Pain/diagnosis ; Pelvic Pain/diagnosis ; Pain Measurement ; }, abstract = {PURPOSE: This study tested the hypothesis that ecological momentary assessment (EMA) of pelvic pain (PP) and urinary urgency (UU) would reveal unique Urologic Chronic Pelvic Pain Syndrome (UCPPS) phenotypes that would be associated with disease specific quality of life (QOL) and illness impact metrics (IIM).<br><br>MATERIALS AND METHODS: A previously validated smart phone app (M-app) was provided to willing Multidisciplinary Approach to the Study of Chronic Pelvic Pain (MAPP) participants. M-app notifications were sent 4-times daily for 14 days inquiring about PP and UU severity. A clustering algorithm that accounted for variance placed participants into PP and UU variability? clusters. Associations between clusters and QOL and IIM were then determined.<br><br>RESULTS: A total of 204 participants enrolled in the M-app study (64% female). M-app compliance was high (median 63% of surveys). Cluster analysis revealed k&#x2009;=&#x2009;3 (high, low, none) PP clusters and k&#x2009;=&#x2009;2 (high, low) UU clusters. When adjusting for baseline pain severity, high PP variability, but not UU variability, was strongly associated with QOL and IIM; specifically worse mood, worse sleep and higher anxiety. UU and PP clusters were associated with each other (p&#x2009;<&#x2009;0.0001), but a large percentage (33%) of patients with high PP variability had low UU variability.<br><br>CONCLUSIONS: PP variability is an independent predictor of worse QOL and more severe IIM in UCPPS participants after controlling for baseline pain severity and UU. These findings suggest alternative pain indices, such as pain variability and unpredictability, may be useful adjuncts to traditional measures of worst and average pain when assessing UCPPS treatment responses.}, }
@article {pmid38246154, year = {2024}, author = {McConnell, RJ and Kamysh, O and O'Kane, PL and Greenebaum, E and Rozhko, AV and Yauseyenka, VV and Minenko, VF and Drozdovitch, V and Yarets, Y and Kukhta, T and Mabuchi, K and Little, MP and Cahoon, EK and Zablotska, LB}, title = {Radiation Dose Does Not Affect the Predictive Value of Thyroid Biopsy for Diagnosing Papillary Thyroid Cancer in a Belarusian Cohort Exposed to Chernobyl Fallout.}, journal = {Acta cytologica}, volume = {68}, number = {1}, pages = {34-44}, pmid = {38246154}, issn = {1938-2650}, support = {N01 CP021178/CP/NCI NIH HHS/United States ; ZIA CP010132/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Adolescent ; Child ; Humans ; Biopsy ; *Carcinoma, Papillary/pathology ; *Chernobyl Nuclear Accident ; *Eastern European People ; Radiation Dosage ; Thyroid Cancer, Papillary/diagnosis ; *Thyroid Neoplasms/diagnosis/epidemiology/pathology ; Adult ; }, abstract = {INTRODUCTION: The Chernobyl nuclear accident exposed residents of contaminated territories to substantial quantities of radioiodines and was followed by an increase in thyroid cancer, primarily papillary thyroid cancer (PTC), among exposed children and adolescents. Although thyroid biopsy is an essential component of screening programs following accidental exposure to radioiodines, it is unknown whether the predictive value of biopsy is affected by different levels of environmental exposure.<br><br>METHODS: A cohort of 11,732 Belarusians aged &#x2264;18 years at the time of the Chernobyl accident with individual thyroid radiation dose estimates was screened at least once 11-22 years later. Paired cytologic conclusions and histopathologic diagnoses were possible for 258 thyroid nodules from 238 cohort members. Cytologic conclusions were divided into five reporting categories, with all follicular lesion aspirates combined into a single indeterminate category. Standard performance indicators, risk of malignancy (ROM), and odds ratios for a correct cytologic conclusion were calculated, both overall and according to quintile of thyroid radiation dose.<br><br>RESULTS: The arithmetic mean thyroid dose estimate for the study group was 1.73 Gy (range: 0.00-23.64 Gy). The final histopathologic diagnosis was cancer for 136 of 258 biopsies (52.7%; 135 papillary and 1 follicular). The overall ROM was 96.7% for cytologies definite for PTC, 83.7% for suspicious for PTC, 33.0% for indeterminate, 8.1% for benign, and 31.0% for non-diagnostic. The ROM showed little change according to level of radiation exposure. Overall, there was no association between thyroid radiation dose and the odds ratio for a correct cytologic conclusion (p = 0.24). When analyzed according to dose quintile, the odds ratio for a correct conclusion increased two-fold at 0.10-0.29 Gy compared to a dose of 0.00-0.09 Gy and decreased at doses of 0.3-24 Gy (p value for linear trend = 0.99).<br><br>CONCLUSIONS: At radiation doses received by a cohort of young Belarusians exposed to radioiodines by the Chernobyl accident, the predictive value of thyroid biopsy for diagnosing PTC was not significantly affected by level of radiation exposure.}, }
@article {pmid38246125, year = {2024}, author = {Mahony, J}, title = {Biological and bioinformatic tools for the discovery of unknown phage-host combinations.}, journal = {Current opinion in microbiology}, volume = {77}, number = {}, pages = {102426}, doi = {10.1016/j.mib.2024.102426}, pmid = {38246125}, issn = {1879-0364}, mesh = {*Bacteriophages/genetics ; Artificial Intelligence ; Computational Biology ; *Microbiota ; Metagenomics ; }, abstract = {The field of microbial ecology has been transformed by metagenomics in recent decades and has culminated in vast datasets that facilitate the bioinformatic dissection of complex microbial communities. Recently, attention has turned from defining the microbiota composition to the interactions and relationships that occur between members of the microbiota. Within complex microbiota, the identification of bacteriophage-host combinations has been a major challenge. Recent developments in artificial intelligence tools to predict protein structure and function as well as the relationships between bacteria and their infecting bacteriophages allow a strategic approach to identifying and validating phage-host relationships. However, biological validation of these predictions remains essential and will serve to improve the existing predictive tools. In this review, I provide an overview of the most recent developments in both bioinformatic and experimental approaches to predicting and experimentally validating unknown phage-host combinations.}, }
@article {pmid38245889, year = {2024}, author = {Schlapbach, LJ and Watson, RS and Sorce, LR and Argent, AC and Menon, K and Hall, MW and Akech, S and Albers, DJ and Alpern, ER and Balamuth, F and Bembea, M and Biban, P and Carrol, ED and Chiotos, K and Chisti, MJ and DeWitt, PE and Evans, I and Flauzino de Oliveira, C and Horvat, CM and Inwald, D and Ishimine, P and Jaramillo-Bustamante, JC and Levin, M and Lodha, R and Martin, B and Nadel, S and Nakagawa, S and Peters, MJ and Randolph, AG and Ranjit, S and Rebull, MN and Russell, S and Scott, HF and de Souza, DC and Tissieres, P and Weiss, SL and Wiens, MO and Wynn, JL and Kissoon, N and Zimmerman, JJ and Sanchez-Pinto, LN and Bennett, TD and , }, title = {International Consensus Criteria for Pediatric Sepsis and Septic Shock.}, journal = {JAMA}, volume = {331}, number = {8}, pages = {665-674}, pmid = {38245889}, issn = {1538-3598}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; Child ; *Shock, Septic/mortality ; Multiple Organ Failure/diagnosis/etiology ; *Sepsis/mortality ; Systemic Inflammatory Response Syndrome/diagnosis ; Organ Dysfunction Scores ; }, abstract = {IMPORTANCE: Sepsis is a leading cause of death among children worldwide. Current pediatric-specific criteria for sepsis were published in 2005 based on expert opinion. In 2016, the Third International Consensus Definitions for Sepsis and Septic Shock (Sepsis-3) defined sepsis as life-threatening organ dysfunction caused by a dysregulated host response to infection, but it excluded children.<br><br>OBJECTIVE: To update and evaluate criteria for sepsis and septic shock in children.<br><br>EVIDENCE REVIEW: The Society of Critical Care Medicine (SCCM) convened a task force of 35 pediatric experts in critical care, emergency medicine, infectious diseases, general pediatrics, nursing, public health, and neonatology from 6 continents. Using evidence from an international survey, systematic review and meta-analysis, and a new organ dysfunction score developed based on more than 3 million electronic health record encounters from 10 sites on 4 continents, a modified Delphi consensus process was employed to develop criteria.<br><br>FINDINGS: Based on survey data, most pediatric clinicians used sepsis to refer to infection with life-threatening organ dysfunction, which differed from prior pediatric sepsis criteria that used systemic inflammatory response syndrome (SIRS) criteria, which have poor predictive properties, and included the redundant term, severe sepsis. The SCCM task force recommends that sepsis in children be identified by a Phoenix Sepsis Score of at least 2 points in children with suspected infection, which indicates potentially life-threatening dysfunction of the respiratory, cardiovascular, coagulation, and/or neurological systems. Children with a Phoenix Sepsis Score of at least 2 points had in-hospital mortality of 7.1% in higher-resource settings and 28.5% in lower-resource settings, more than 8 times that of children with suspected infection not meeting these criteria. Mortality was higher in children who had organ dysfunction in at least 1 of 4-respiratory, cardiovascular, coagulation, and/or neurological-organ systems that was not the primary site of infection. Septic shock was defined as children with sepsis who had cardiovascular dysfunction, indicated by at least 1 cardiovascular point in the Phoenix Sepsis Score, which included severe hypotension for age, blood lactate exceeding 5 mmol/L, or need for vasoactive medication. Children with septic shock had an in-hospital mortality rate of 10.8% and 33.5% in higher- and lower-resource settings, respectively.<br><br>CONCLUSIONS AND RELEVANCE: The Phoenix sepsis criteria for sepsis and septic shock in children were derived and validated by the international SCCM Pediatric Sepsis Definition Task Force using a large international database and survey, systematic review and meta-analysis, and modified Delphi consensus approach. A Phoenix Sepsis Score of at least 2 identified potentially life-threatening organ dysfunction in children younger than 18 years with infection, and its use has the potential to improve clinical care, epidemiological assessment, and research in pediatric sepsis and septic shock around the world.}, }
@article {pmid38244396, year = {2024}, author = {Sakamoto, Y and Miyoshi, K}, title = {A confidence framing effect: Flexible use of evidence in metacognitive monitoring.}, journal = {Consciousness and cognition}, volume = {118}, number = {}, pages = {103636}, doi = {10.1016/j.concog.2024.103636}, pmid = {38244396}, issn = {1090-2376}, mesh = {Humans ; *Decision Making ; Choice Behavior ; *Metacognition ; }, abstract = {Human behavior is flexibly regulated by specific goals of cognitive tasks. One notable example is goal-directed modulation of metacognitive behavior, where logically equivalent decision-making problems can yield different patterns of introspective confidence depending on the frame in which they are presented. While this observation highlights the important heuristic nature of metacognitive monitoring, computational mechanisms underlying this phenomenon remain elusive. We confirmed the confidence framing effect in two-alternative dot-number discrimination and in previously published preference-choice data, demonstrating distinctive confidence patterns between "choose more" or "choose less" frames. Formal model comparisons revealed a simple confidence heuristic behind this phenomenon, which assigns greater weight to chosen than unchosen stimulus evidence. This computation appears to be based on internal evidence constituted under specific task demands rather than physical stimulus intensity itself, a view justified in terms of ecological rationality. These results shed light on the adaptive nature of human decision-making and metacognitive monitoring.}, }
@article {pmid38243062, year = {2024}, author = {Kwon, H and Ann, HW and Park, S and Kwon, J and Park, K and Ryu, SM and Guo, Y and Kim, JJ and Yim, JH and Kim, IC and Shim, SH and Lee, S and Lee, D}, title = {Mass spectrometry-guided isolation of thiodiketopiperazines from an EtOAc-extract of Setosphaeria rostrata culture medium and their anti-skin aging effects on TNF-α-induced human dermal fibroblasts.}, journal = {The Journal of antibiotics}, volume = {77}, number = {4}, pages = {257-263}, pmid = {38243062}, issn = {1881-1469}, support = {PE23150//Korea Polar Research Institute (KOPRI)/ ; NRF-2022R1A4A3022401//National Research Foundation of Korea (NRF)/ ; NRF-2019R1A2C1006226//National Research Foundation of Korea (NRF)/ ; }, mesh = {Humans ; *Tumor Necrosis Factor-alpha ; *Matrix Metalloproteinase 1/pharmacology ; Reactive Oxygen Species ; Fibroblasts ; *Ascomycota ; }, abstract = {Using mass spectrometry (MS)-guided isolation methods, a new thiodiketopiperazine derivative (1) and exserohilone (2) were isolated from an EtOAc-extract of Setosphaeria rostrata culture medium. The chemical structure of the new compound was elucidated by MS and NMR spectroscopy, and the absolute configurations were established by the quantum mechanical calculations of electronic circular dichroism. All isolated compounds were examined for their effects on reactive oxygen species (ROS) production, matrix metalloproteinase 1 (MMP-1) secretion, and procollagen type I α1 secretion in tumor necrosis factor (TNF)-α-induced human dermal fibroblasts. Compound 1 and exserohilone (2) exhibited the inhibition of TNF-α-induced ROS generation and MMP-1 secretion. Additionally, compound 1 and exserohilone (2) increased the procollagen type I α1 secretion. Compound 1 docked computationally into the active site of MMP-1 (-6.0 kcal/mol).}, }
@article {pmid38242303, year = {2024}, author = {Rojo, J and Cervigón, P and Ferencova, Z and Cascón, &#xc1; and Galán Díaz, J and Romero-Morte, J and Sabariego, S and Torres, M and Gutiérrez-Bustillo, AM}, title = {Assessment of environmental risk areas based on airborne pollen patterns as a response to land use and land cover distribution.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {344}, number = {}, pages = {123385}, doi = {10.1016/j.envpol.2024.123385}, pmid = {38242303}, issn = {1873-6424}, mesh = {Cluster Analysis ; Databases, Factual ; *Pollen ; Public Health ; *Respiratory Tract Diseases ; }, abstract = {Allergic respiratory diseases are considered to be among the most important public health concerns, and pollen is the main cause of allergic respiratory diseases worldwide. However, the biological component of air quality is largely underestimated, and there is an important gap in the legislation in this area. The aims of this study were to characterise the occurrence and incidence of pollen exposure in relation to potential pollen sources and to delineate the main areas of aerobiological risk in the Madrid Autonomous Region based on homogeneous patterns of pollen exposure. This study uses the historical aerobiological database of the Madrid Region Palynological Network (central Spain) from ten pollen stations from 1994 to 2022, and the land-use information from the Corine Land Cover. Multiple clustering approaches were followed to group the sampling stations and subsequently all the 1 × 1km pixels for the Madrid Autonomous Region. The clustering dendrogram for land-use distribution was compared to the dendrogram for historical airborne pollen data. The two dendrograms showed a good alignment with a very high correlation (0.95) and very low entanglement (0.15), which indicates a close correspondence between the distribution of the potential pollen sources and the airborne pollen dynamics. Based on this knowledge, the Madrid Autonomous Region was divided into six aerobiological risk areas following a clear anthropogenic gradient in terms of the potential pollen sources that determine pollen exposure in the Madrid Region. Spatial regionalisation is a common practice in environmental risk assessment to improve the application of management plans and optimise the air quality monitoring networks. The risk areas proposed by scientific criteria in the Madrid Autonomous Region can be adjusted to other operational criteria following a framework equivalent to other air quality networks.}, }
@article {pmid38236268, year = {2024}, author = {Rogoza, R and Krammer, G and Jauk, E and Flakus, M and Baran, L and Di Sarno, M and Di Pierro, R and Zajenkowski, M and Dufner, M and Fatfouta, R}, title = {The peaks and valleys of narcissism: The factor structure of narcissistic states and their relations to trait measures.}, journal = {Psychological assessment}, volume = {36}, number = {2}, pages = {147-161}, doi = {10.1037/pas0001295}, pmid = {38236268}, issn = {1939-134X}, support = {//National Science Centre/ ; //Austrian Science Fund (FWF)/ ; }, mesh = {Humans ; *Narcissism ; Databases, Factual ; *Ecological Momentary Assessment ; Phenotype ; }, abstract = {Although interindividual differences in narcissism are well studied, little is known about assessing narcissism at the within-person level. To fill this research gap, we investigated whether the narcissism construct is represented in the same way at the between- and within-person levels. We analyzed four established narcissism measures across multiple studies. In each of the studies, participants completed narcissism measures in ecological momentary assessment or daily diary studies. Equivalent construct representation across between- and within-person narcissism (i.e., cross-level measurement invariance) was found. State narcissism measures showed convergent validities for the trait narcissism scales. Moreover, we also found that antagonistic narcissism was most strongly related to within-person variability in narcissism. Our investigation sheds new light on the structure and assessment of narcissism on the within-person level by providing a comprehensive examination of its measurement. (PsycInfo Database Record (c) 2024 APA, all rights reserved).}, }
@article {pmid38235411, year = {2024}, author = {Coury, SM and López, V and Bajwa, Z and Garcia, JM and Teresi, GI and Kuhlman, KR and Li, Y and Cole, S and Miklowitz, DJ and Pappas, I and Ho, TC}, title = {Protocol for teen inflammation glutamate emotion research (TIGER): Toward predictors of treatment response and clinical course in depressed adolescents.}, journal = {Brain, behavior, &amp; immunity - health}, volume = {35}, number = {}, pages = {100718}, pmid = {38235411}, issn = {2666-3546}, support = {K01 MH117442/MH/NIMH NIH HHS/United States ; P30 AG066530/AG/NIA NIH HHS/United States ; R01 MH127176/MH/NIMH NIH HHS/United States ; }, abstract = {Adolescent-onset depression is a prevalent and debilitating condition commonly associated with treatment refractory depression and non-response to first-line antidepressants. There are, however, no objective tests to determine who may or may not respond to antidepressants. As depressed adolescents are especially vulnerable to the lifelong consequences of ineffectively-treated depression, it is critical to identify neurobiological predictors of treatment non-response in this population. Here, we describe the scientific rationale and protocol for the Teen Inflammation Glutamate Emotion Research (TIGER) study, a prospective 18-month investigation of 160 depressed adolescents who will be assessed before and after treatment with selective serotonin reuptake inhibitors. TIGER will be using ultra-high field imaging to test the effects of acute stress and antidepressant treatment on inflammatory and glutamatergic processes hypothesized to underlie depression maintenance. Results from this work will motivate future studies testing alternative therapeutics for depressed adolescents at risk for treatment resistant depression. ClinicalTrials.gov Identifier: NCT05329441.}, }
@article {pmid38232851, year = {2024}, author = {Liu, YE and Luo, XJ and Huang, CC and Lu, Q and Wang, S and Mai, BX}, title = {Insights into the occurrence, spatial distribution, and ecological implications of organophosphate triesters in surface sediments from polluted urban rivers across China.}, journal = {The Science of the total environment}, volume = {915}, number = {}, pages = {170108}, doi = {10.1016/j.scitotenv.2024.170108}, pmid = {38232851}, issn = {1879-1026}, abstract = {Organophosphate triesters (tri-OPEs) are a kind of widespread contaminants in the world, particularly in China, which is a major producer and user of tri-OPEs. However, tri-OPE pollution in urban river sediments in China remains unclear. In current work, we carried out the first nationwide investigation to comprehensively monitor 10 conventional and five emerging tri-OPEs in sediments of 173 black-odorous urban rivers throughout China. Concentrations of 10 conventional and five emerging tri-OPEs were 3.8-1240 ng/g dw (mean: 253 ng/g dw) and 0.21-1107 ng/g dw (68 ng/g dw), respectively, and significantly differed among the cities sampled but generally decreased from Northeast and East China to Central and West China. These spatial patterns suggest that tri-OPE pollution was mainly from local sources and was controlled by the industrial and economic development levels in these four areas, as indicated by the significant correlations between tri-OPE concentrations and gross domestic production, gross industrial output, and daily wastewater treatment capacity. Although the tri-OPE composition varied spatially at different sites, which indicated different tri-OPE input patterns, it was commonly dominated by tris(2-chloroethyl) phosphate, tris(2-ethylhexyl) phosphate, and tris(1-chloro-2-propyl) phosphate (conventional tri-OPEs) and bisphenol A-bis(diphenyl phosphate) and isodecyl diphenyl phosphate (emerging tri-OPEs). A risk assessment indicated that tri-OPEs in most sampling sediments had a low to moderate risk to aquatic organisms.}, }
@article {pmid38231860, year = {2024}, author = {Grones, C and Eekhout, T and Shi, D and Neumann, M and Berg, LS and Ke, Y and Shahan, R and Cox, KL and Gomez-Cano, F and Nelissen, H and Lohmann, JU and Giacomello, S and Martin, OC and Cole, B and Wang, JW and Kaufmann, K and Raissig, MT and Palfalvi, G and Greb, T and Libault, M and De Rybel, B}, title = {Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics.}, journal = {The Plant cell}, volume = {36}, number = {4}, pages = {812-828}, pmid = {38231860}, issn = {1532-298X}, support = {F32 GM136030/GM/NIGMS NIH HHS/United States ; /ERC_/European Research Council/International ; }, mesh = {Reproducibility of Results ; *Gene Expression Profiling ; *Plants/genetics ; Stress, Physiological/genetics ; Information Storage and Retrieval ; }, abstract = {Single-cell and single-nucleus RNA-sequencing technologies capture the expression of plant genes at an unprecedented resolution. Therefore, these technologies are gaining traction in plant molecular and developmental biology for elucidating the transcriptional changes across cell types in a specific tissue or organ, upon treatments, in response to biotic and abiotic stresses, or between genotypes. Despite the rapidly accelerating use of these technologies, collective and standardized experimental and analytical procedures to support the acquisition of high-quality data sets are still missing. In this commentary, we discuss common challenges associated with the use of single-cell transcriptomics in plants and propose general guidelines to improve reproducibility, quality, comparability, and interpretation and to make the data readily available to the community in this fast-developing field of research.}, }
@article {pmid38229583, year = {2024}, author = {Devine, K and Russell, CD and Blanco, GR and Walker, BR and Homer, NZM and Denham, SG and Simpson, JP and Leavy, OC and Elneima, O and McAuley, HJC and Shikotra, A and Singapuri, A and Sereno, M and Saunders, RM and Harris, VC and Houchen-Wolloff, L and Greening, NJ and Lone, NI and Thorpe, M and Greenhalf, W and Chalmers, JD and Ho, LP and Horsley, A and Marks, M and Raman, B and Moore, SC and Dunning, J and Semple, MG and Andrew, R and Wain, LV and Evans, RA and Brightling, CE and Kenneth Baillie, J and Reynolds, RM and , }, title = {Plasma steroid concentrations reflect acute disease severity and normalise during recovery in people hospitalised with COVID-19.}, journal = {Clinical endocrinology}, volume = {100}, number = {4}, pages = {317-327}, doi = {10.1111/cen.15012}, pmid = {38229583}, issn = {1365-2265}, support = {MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; Male ; Female ; *COVID-19 ; Hydrocortisone ; Acute Disease ; Aftercare ; Patient Discharge ; Glucocorticoids/therapeutic use ; Steroids/therapeutic use ; Patient Acuity ; Testosterone ; }, abstract = {OBJECTIVE: Endocrine systems are disrupted in acute illness, and symptoms reported following coronavirus disease 2019 (COVID-19) are similar to those found with clinical hormone deficiencies. We hypothesised that people with severe acute COVID-19 and with post-COVID symptoms have glucocorticoid and sex hormone deficiencies.<br><br>DESIGN/PATIENTS: Samples were obtained for analysis from two UK multicentre cohorts during hospitalisation with COVID-19 (International Severe Acute Respiratory Infection Consortium/World Health Organisation [WHO] Clinical Characterization Protocol for Severe Emerging Infections in the UK study), and at follow-up 5 months after hospitalisation (Post-hospitalisation COVID-19 study).<br><br>MEASUREMENTS: Plasma steroids were quantified by liquid chromatography-mass spectrometry. Steroid concentrations were compared against disease severity (WHO ordinal scale) and validated symptom scores. Data are presented as geometric mean (SD).<br><br>RESULTS: In the acute cohort (n&#x2009;=&#x2009;239, 66.5% male), plasma cortisol concentration increased with disease severity (cortisol 753.3 [1.6] vs. 429.2 [1.7]&#x2009;nmol/L in fatal vs. least severe, p&#x2009;<&#x2009;.001). In males, testosterone concentrations decreased with severity (testosterone 1.2 [2.2] vs. 6.9 [1.9]&#x2009;nmol/L in fatal vs. least severe, p&#x2009;<&#x2009;.001). In the follow-up cohort (n&#x2009;=&#x2009;198, 62.1% male, 68.9% ongoing symptoms, 165 [121-192] days postdischarge), plasma cortisol concentrations (275.6 [1.5]&#x2009;nmol/L) did not differ with in-hospital severity, perception of recovery, or patient-reported symptoms. Male testosterone concentrations (12.6 [1.5]&#x2009;nmol/L) were not related to in-hospital severity, perception of recovery or symptom scores.<br><br>CONCLUSIONS: Circulating glucocorticoids in patients hospitalised with COVID-19 reflect acute illness, with a marked rise in cortisol and fall in male testosterone. These findings are not observed 5 months from discharge. The lack of association between hormone concentrations and common post-COVID symptoms suggests steroid insufficiency does not play a causal role in this condition.}, }
@article {pmid38229470, year = {2024}, author = {Wondimagegnehu, A and Assefa, M and Teferra, S and Kantelhardt, EJ and Zebrack, B and Addissie, A}, title = {A Qualitative Study on Psychosocial Challenges of Patients With Cancer in Ethiopia Using the Social-Ecological Model.}, journal = {Qualitative health research}, volume = {34}, number = {8-9}, pages = {828-841}, doi = {10.1177/10497323231219409}, pmid = {38229470}, issn = {1552-7557}, mesh = {Humans ; Ethiopia ; *Neoplasms/psychology/therapy ; *Qualitative Research ; Female ; Male ; Adult ; *Social Support ; Middle Aged ; *Focus Groups ; Interviews as Topic ; Young Adult ; Family/psychology ; Aged ; Stress, Psychological/psychology ; Depression/psychology/therapy ; }, abstract = {Cancer diagnosis and treatment can be physically arduous, disrupting patients' social and work lives. Understanding the extent of these problems is key to addressing patients' needs, but specific psychosocial challenges have not yet been well studied in resource-limited settings. A qualitative study was conducted in the capital and two regions of Ethiopia with the aim of exploring psychosocial challenges among cancer patients. A total of 14 in-depth interviews (IDIs) and 16 focus group discussions (FGDs) were done with cancer patients, health professionals, community representatives, and religious leaders. Four separate interview guides were used to facilitate the interviews and discussions. All transcribed documents, field notes, and reflexive memos were entered into NVivo 12 software, and deductive thematic analysis using the social-ecological model was applied to summarize the main findings. At an individual level, emotional distress, suicidal risk, denial, and refusal of treatment were identified immediately after diagnosis while hopelessness, feeling depressed, and fear of death were commonly reported psychosocial challenges during the course of treatment. Involvement of family members in major treatment decisions was recognized at an interpersonal level. Our result also revealed that cancer patients had strong social support from family members and close friends. In the community, traditional medicine and religious rituals were considered an alternative treatment for cancer. The findings indicate that counselling and psychoeducation are crucial for cancer patients, family members, and close friends. Awareness creation programmes should be delivered through collaboration with religious leaders and traditional healers.}, }
@article {pmid38225503, year = {2024}, author = {Gubó, E and Plutzer, J and Molnár, T and Pordán-Háber, D and Szabó, L and Szalai, Z and Gubó, R and Szakál, P and Szakál, T and Környei, L and Bede-Fazekas, &#xc1; and Kalocsai, R}, title = {Correction to: A 4‑year study of bovine reproductive hormones that are induced by pharmaceuticals and appear as steroid estrogenic pollutants in the resulting slurry, using in vitro and instrumental analytical methods.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {6}, pages = {9868}, doi = {10.1007/s11356-024-31992-0}, pmid = {38225503}, issn = {1614-7499}, }
@article {pmid38218164, year = {2024}, author = {Pérez, G and O'Leary, BC and Allegri, E and Casal, G and Cornet, CC and de Juan, S and Failler, P and Fredriksen, S and Fonseca, C and Furlan, E and Gil, A and Hawkins, JP and Maréchal, JP and McCarthy, T and Roberts, CM and Trégarot, E and van der Geest, M and Simide, R}, title = {A conceptual framework to help choose appropriate blue nature-based solutions.}, journal = {Journal of environmental management}, volume = {352}, number = {}, pages = {119936}, doi = {10.1016/j.jenvman.2023.119936}, pmid = {38218164}, issn = {1095-8630}, mesh = {Humans ; *Ecosystem ; *Biodiversity ; Climate Change ; }, abstract = {Biodiversity loss and climate change have severely impacted ecosystems and livelihoods worldwide, compromising access to food and water, increasing disaster risk, and affecting human health globally. Nature-based Solutions (NbS) have gained interest in addressing these global societal challenges. Although much effort has been directed to NbS in urban and terrestrial environments, the implementation of NbS in marine and coastal environments (blue NbS) lags. The lack of a framework to guide decision-makers and practitioners through the initial planning stages appears to be one of the main obstacles to the slow implementation of blue NbS. To address this, we propose an integrated conceptual framework, built from expert knowledge, to inform the selection of the most appropriate blue NbS based on desired intervention objectives and social-ecological context. Our conceptual framework follows a four incremental steps structure: Step 1 aims to identify the societal challenge(s) to address; Step 2 highlights ecosystem services and the underlying biodiversity and ecological functions that could contribute to confronting the societal challenge(s); Step 3 identify the specific environmental context the intervention needs to be set within (e.g. the spatial scale the intervention will operate within, the ecosystem's vulnerability to stressors, and its ecological condition); and Step 4 provides a selection of potential blue NbS interventions that would help address the targeted societal challenge(s) considering the context defined through Step 3. Designed to maintain, enhance, recover, rehabilitate, or create ecosystem services by supporting biodiversity, the blue NbS intervention portfolio includes marine protection (i.e., fully, highly, lightly, and minimally protected areas), restorative activities (i.e., active, passive, and partial restoration; rehabilitation of ecological function and ecosystem creation), and other management measures (i.e., implementation and enforcement of regulation). Ultimately, our conceptual framework guides decision-makers toward a versatile portfolio of interventions that cater to the specific needs of each ecosystem rather than imposing a rigid, one-size-fits-all model. In the future, this framework needs to integrate socio-economic considerations more comprehensively and be kept up-to-date by including the latest scientific information.}, }
@article {pmid38215805, year = {2024}, author = {Lacson, R and Pianykh, O and Hartmann, S and Johnston, H and Daye, D and Flores, E and Kapoor, N and Khorasani, R}, title = {Factors Associated With Timeliness and Equity of Access to Outpatient MRI Examinations.}, journal = {Journal of the American College of Radiology : JACR}, volume = {21}, number = {7}, pages = {1049-1057}, pmid = {38215805}, issn = {1558-349X}, support = {R18 HS029348/HS/AHRQ HHS/United States ; }, mesh = {Humans ; Female ; Male ; *Magnetic Resonance Imaging ; *Health Services Accessibility ; Middle Aged ; Adult ; Time Factors ; Aged ; Ambulatory Care/statistics &amp; numerical data ; Outpatients ; }, abstract = {OBJECTIVE: The role of MRI in guiding patients' diagnosis and treatment is increasing. Therefore, timely MRI performance prevents delays that can impact patient care. We assessed the timeliness of performing outpatient MRIs using the socio-ecological model approach and evaluated multilevel factors associated with delays.<br><br>METHODS: This institutional review board-approved study included outpatient MRI examinations ordered between October 1, 2021, and December 31, 2022, for performance at a large quaternary care health system. Mean order-to-performed (OtoP) interval (in days) and prolonged OtoP interval (defined as >10 days) for MRI orders with an expected date of 1 day to examination performance were measured. Logistic regression was used to assess patient-level (demographic and social determinants of health), radiology practice-level, and community-level factors associated with prolonged OtoP interval.<br><br>RESULTS: There were 126,079 MRI examination orders with expected performance within 1 day placed during the study period (56% of all MRI orders placed). After excluding duplicates, there were 97,160 orders for unique patients. Of the MRI orders, 48% had a prolonged OtoP interval, and mean OtoP interval was 18.5 days. Factors significantly associated with delay in MRI performance included public insurance (odds ratio [OR]&#xa0;= 1.11, P < .001), female gender (OR&#xa0;= 1.11, P < .001), radiology subspecialty (ie, cardiac, OR&#xa0;= 1.71, P < .001), and patients from areas that are most deprived (ie, highest Area Deprivation Index quintile, OR&#xa0;= 1.70, P < .001).<br><br>DISCUSSION: Nearly half of outpatient MRI orders were delayed, performed >10 days from the expected date selected by the ordering provider. Addressing multilevel factors associated with such delays may help enhance timeliness and equity of access to MRI examinations, potentially reducing diagnostic errors and treatment delays.}, }
@article {pmid38215053, year = {2024}, author = {Ho, PC and Yu, WH and Tee, BL and Lee, WP and Li, C and Gu, Y and Yokoyama, JS and Reyes-Dumeyer, D and Choi, YB and Yang, HS and Vardarajan, BN and Tzuang, M and Lieu, K and Lu, A and Faber, KM and Potter, ZD and Revta, C and Kirsch, M and McCallum, J and Mei, D and Booth, B and Cantwell, LB and Chen, F and Chou, S and Clark, D and Deng, M and Hong, TH and Hwang, LJ and Jiang, L and Joo, Y and Kang, Y and Kim, ES and Kim, H and Kim, K and Kuzma, AB and Lam, E and Lanata, SC and Lee, K and Li, D and Li, M and Li, X and Liu, CL and Liu, C and Liu, L and Lupo, JL and Nguyen, K and Pfleuger, SE and Qian, J and Qian, W and Ramirez, V and Russ, KA and Seo, EH and Song, YE and Tartaglia, MC and Tian, L and Torres, M and Vo, N and Wong, EC and Xie, Y and Yau, EB and Yi, I and Yu, V and Zeng, X and St George-Hyslop, P and Au, R and Schellenberg, GD and Dage, JL and Varma, R and Hsiung, GR and Rosen, H and Henderson, VW and Foroud, T and Kukull, WA and Peavy, GM and Lee, H and Feldman, HH and Mayeux, R and Chui, H and Jun, GR and Ta Park, VM and Chow, TW and Wang, LS}, title = {Asian Cohort for Alzheimer's Disease (ACAD) pilot study on genetic and non-genetic risk factors for Alzheimer's disease among Asian Americans and Canadians.}, journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association}, volume = {20}, number = {3}, pages = {2058-2071}, pmid = {38215053}, issn = {1552-5279}, support = {R01 AG080469/AG/NIA NIH HHS/United States ; U24 AG021886/AG/NIA NIH HHS/United States ; P30 AG062429/AG/NIA NIH HHS/United States ; U19AG068753/AG/NIA NIH HHS/United States ; K23AG062750/AG/NIA NIH HHS/United States ; UH2 AG083258/AG/NIA NIH HHS/United States ; U19 AG068753/AG/NIA NIH HHS/United States ; R01 AG072562/AG/NIA NIH HHS/United States ; R21 AG068757/AG/NIA NIH HHS/United States ; P30AG062422/AG/NIA NIH HHS/United States ; K24 AG045333/AG/NIA NIH HHS/United States ; R56 AG069130/AG/NIA NIH HHS/United States ; R24 AG063718/AG/NIA NIH HHS/United States ; R01 AG062588/AG/NIA NIH HHS/United States ; U19 AG079774/AG/NIA NIH HHS/United States ; ALZ-NAN-22-928181/ALZ/Alzheimer's Association/United States ; R01AG080469/AG/NIA NIH HHS/United States ; P30 AG062422/AG/NIA NIH HHS/United States ; R01 AG083840/AG/NIA NIH HHS/United States ; P01 AG019724/AG/NIA NIH HHS/United States ; P30 AG066462/AG/NIA NIH HHS/United States ; R03 AG061439/AG/NIA NIH HHS/United States ; R24AG063718/AG/NIA NIH HHS/United States ; UH2AG083258/AG/NIA NIH HHS/United States ; P30 AG066530/AG/NIA NIH HHS/United States ; R01 AG083926/AG/NIA NIH HHS/United States ; AACSFD-22-972143/ALZ/Alzheimer's Association/United States ; R61 AG083582/AG/NIA NIH HHS/United States ; U19AG079774/AG/NIA NIH HHS/United States ; R01AG083926/AG/NIA NIH HHS/United States ; K23 AG062750/AG/NIA NIH HHS/United States ; U10EY017337/EY/NEI NIH HHS/United States ; R01AG083840/AG/NIA NIH HHS/United States ; R21AG077649/AG/NIA NIH HHS/United States ; R21 AG077649/AG/NIA NIH HHS/United States ; R21AG068757/AG/NIA NIH HHS/United States ; R61AG083582/AG/NIA NIH HHS/United States ; U10 EY017337/EY/NEI NIH HHS/United States ; U24AG021886/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; *Alzheimer Disease/genetics ; Pilot Projects ; Asian/genetics ; Canada ; Risk Factors ; *North American People ; }, abstract = {INTRODUCTION: Clinical research in Alzheimer's disease (AD) lacks cohort diversity despite being a global health crisis. The Asian Cohort for Alzheimer's Disease (ACAD) was formed to address underrepresentation of Asians in research, and limited understanding of how genetics and non-genetic/lifestyle factors impact this multi-ethnic population.<br><br>METHODS: The ACAD started fully recruiting in October 2021 with one central coordination site, eight recruitment sites, and two analysis sites. We developed a comprehensive study protocol for outreach and recruitment, an extensive data collection packet, and a centralized data management system, in English, Chinese, Korean, and Vietnamese.<br><br>RESULTS: ACAD has recruited 606 participants with an additional 900 expressing interest in enrollment since program inception.<br><br>DISCUSSION: ACAD's traction indicates the feasibility of recruiting Asians for clinical research to enhance understanding of AD risk factors. ACAD will recruit&#xa0;>&#xa0;5000 participants to identify genetic and non-genetic/lifestyle AD risk factors, establish blood biomarker levels for AD diagnosis, and facilitate clinical trial readiness.<br><br>HIGHLIGHTS: The Asian Cohort for Alzheimer's Disease (ACAD) promotes awareness of under-investment in clinical research for Asians. We are recruiting Asian Americans and Canadians for novel insights into Alzheimer's disease. We describe culturally appropriate recruitment strategies and data collection protocol. ACAD addresses challenges of recruitment from heterogeneous Asian subcommunities. We aim to implement a successful recruitment program that enrolls across three Asian subcommunities.}, }
@article {pmid38212658, year = {2024}, author = {Ning, D and Wang, Y and Fan, Y and Wang, J and Van Nostrand, JD and Wu, L and Zhang, P and Curtis, DJ and Tian, R and Lui, L and Hazen, TC and Alm, EJ and Fields, MW and Poole, F and Adams, MWW and Chakraborty, R and Stahl, DA and Adams, PD and Arkin, AP and He, Z and Zhou, J}, title = {Environmental stress mediates groundwater microbial community assembly.}, journal = {Nature microbiology}, volume = {9}, number = {2}, pages = {490-501}, pmid = {38212658}, issn = {2058-5276}, support = {DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; EF-2025558//National Science Foundation (NSF)/ ; DEB-2129235//National Science Foundation (NSF)/ ; }, mesh = {Phylogeny ; *Microbiota ; *Groundwater ; Stochastic Processes ; }, abstract = {Community assembly describes how different ecological processes shape microbial community composition and structure. How environmental factors impact community assembly remains elusive. Here we sampled microbial communities and >200 biogeochemical variables in groundwater at the Oak Ridge Field Research Center, a former nuclear waste disposal site, and developed a theoretical framework to conceptualize the relationships between community assembly processes and environmental stresses. We found that stochastic assembly processes were critical (>60% on average) in shaping community structure, but their relative importance decreased as stress increased. Dispersal limitation and 'drift' related to random birth and death had negative correlations with stresses, whereas the selection processes leading to dissimilar communities increased with stresses, primarily related to pH, cobalt and molybdenum. Assembly mechanisms also varied greatly among different phylogenetic groups. Our findings highlight the importance of microbial dispersal limitation and environmental heterogeneity in ecosystem restoration and management.}, }
@article {pmid38204360, year = {2024}, author = {Kiran, A and Hanachi, M and Alsayed, N and Fassatoui, M and Oduaran, OH and Allali, I and Maslamoney, S and Meintjes, A and Zass, L and Rocha, JD and Kefi, R and Benkahla, A and Ghedira, K and Panji, S and Mulder, N and Fadlelmola, FM and Souiai, O}, title = {The African Human Microbiome Portal: a public web portal of curated metagenomic metadata.}, journal = {Database : the journal of biological databases and curation}, volume = {2024}, number = {}, pages = {}, pmid = {38204360}, issn = {1758-0463}, support = {U24 HG006941/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; *Metadata ; Metagenome ; Databases, Factual ; Metagenomics ; *Microbiota/genetics ; }, abstract = {There is growing evidence that comprehensive and harmonized metadata are fundamental for effective public data reusability. However, it is often challenging to extract accurate metadata from public repositories. Of particular concern is the metagenomic data related to African individuals, which often omit important information about the particular features of these populations. As part of a collaborative consortium, H3ABioNet, we created a web portal, namely the African Human Microbiome Portal (AHMP), exclusively dedicated to metadata related to African human microbiome samples. Metadata were collected from various public repositories prior to cleaning, curation and harmonization according to a pre-established guideline and using ontology terms. These metadata sets can be accessed at https://microbiome.h3abionet.org/. This web portal is open access and offers an interactive visualization of 14 889 records from 70 bioprojects associated with 72 peer reviewed research articles. It also offers the ability to download harmonized metadata according to the user's applied filters. The AHMP thereby supports metadata search and retrieve operations, facilitating, thus, access to relevant studies linked to the African Human microbiome. Database URL: https://microbiome.h3abionet.org/.}, }
@article {pmid38203410, year = {2023}, author = {Di Martino, J and Arcieri, M and Madeddu, F and Pieroni, M and Carotenuto, G and Bottoni, P and Botta, L and Castrignanò, T and Gabellone, S and Saladino, R}, title = {Molecular Dynamics Investigations of Human DNA-Topoisomerase I Interacting with Novel Dewar Valence Photo-Adducts: Insights into Inhibitory Activity.}, journal = {International journal of molecular sciences}, volume = {25}, number = {1}, pages = {}, pmid = {38203410}, issn = {1422-0067}, mesh = {Humans ; *Molecular Dynamics Simulation ; *DNA Topoisomerases, Type I ; Biomimetics ; DNA Adducts ; Data Interpretation, Statistical ; Pyrimidine Dimers ; }, abstract = {Chronic exposure to ultraviolet (UV) radiation is known to induce the formation of DNA photo-adducts, including cyclobutane pyrimidine dimers (CPDs) and Dewar valence derivatives (DVs). While CPDs usually occur at higher frequency than DVs, recent studies have shown that the latter display superior selectivity and significant stability in interaction with the human DNA/topoisomerase 1 complex (TOP1). With the aim to deeply investigate the mechanism of interaction of DVs with TOP1, we report here four all-atom molecular dynamic simulations spanning one microsecond. These simulations are focused on the stability and conformational changes of two DNA/TOP1-DV complexes in solution, the data being compared with the biomimetic thymine dimer counterparts. Results from root-mean-square deviation (RMSD) and root-mean-square fluctuation (RMSF) analyses unequivocally confirmed increased stability of the DNA/TOP1-DV complexes throughout the simulation duration. Detailed interaction analyses, uncovering the presence of salt bridges, hydrogen bonds, water-mediated interactions, and hydrophobic interactions, as well as pinpointing the non-covalent interactions within the complexes, enabled the identification of specific TOP1 residues involved in the interactions over time and suggested a potential TOP1 inhibition mechanism in action.}, }
@article {pmid38196369, year = {2024}, author = {Hauber, ME and Nagy, J and Sheard, C and Antonson, ND and Street, SE and Healy, SD and Lala, KN and Mainwaring, MC}, title = {Nest architecture influences host use by avian brood parasites and is shaped by coevolutionary dynamics.}, journal = {Proceedings. Biological sciences}, volume = {291}, number = {2014}, pages = {20231734}, pmid = {38196369}, issn = {1471-2954}, mesh = {Animals ; Biological Evolution ; *Birds ; Databases, Factual ; Host Specificity ; *Nesting Behavior ; }, abstract = {Brood (social) parasites and their hosts exhibit a wide range of adaptations and counter-adaptations as part of their ongoing coevolutionary arms races. Obligate avian brood parasites are expected to use potential host species with more easily accessible nests, while potential hosts are expected to evade parasitism by building more concealed nests that are difficult for parasites to enter and in which to lay eggs. We used phylogenetically informed comparative analyses, a global database of the world's brood parasites, their host species, and the design of avian host and non-host nests (approx. 6200 bird species) to examine first, whether parasites preferentially target host species that build open nests and, second, whether host species that build enclosed nests are more likely to be targeted by specialist parasites. We found that species building more accessible nests are more likely to serve as hosts, while host species with some of the more inaccessible nests are targeted by more specialist brood parasites. Furthermore, evolutionary-transition analyses demonstrate that host species building enclosed nests frequently evolve to become non-hosts. We conclude that nest architecture and the accessibility of nests for parasitism represent a critical stage of the ongoing coevolutionary arms race between avian brood parasites and their hosts.}, }
@article {pmid38195441, year = {2024}, author = {Rádai, Z and Váradi, A and Takács, P and Nagy, NA and Schmitt, N and Prépost, E and Kardos, G and Laczkó, L}, title = {An overlooked phenomenon: complex interactions of potential error sources on the quality of bacterial de novo genome assemblies.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {45}, pmid = {38195441}, issn = {1471-2164}, support = {GINOP-2.3.4-15-2020-00008//European Regional Development Fund/ ; GINOP-2.3.4-15-2020-00008//European Regional Development Fund/ ; GINOP-2.3.4-15-2020-00008//European Regional Development Fund/ ; GINOP-2.3.4-15-2020-00008//European Regional Development Fund/ ; GINOP-2.3.4-15-2020-00008//European Regional Development Fund/ ; GINOP-2.3.4-15-2020-00008//European Regional Development Fund/ ; GINOP-2.3.4-15-2020-00008//European Regional Development Fund/ ; }, mesh = {*Research Design ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Parameters adversely affecting the contiguity and accuracy of the assemblies from Illumina next-generation sequencing (NGS) are well described. However, past studies generally focused on their additive effects, overlooking their potential interactions possibly exacerbating one another's effects in a multiplicative manner. To investigate whether or not they act interactively on de novo genome assembly quality, we simulated sequencing data for 13 bacterial reference genomes, with varying levels of error rate, sequencing depth, PCR and optical duplicate ratios.<br><br>RESULTS: We assessed the quality of assemblies from the simulated sequencing data with a number of contiguity and accuracy metrics, which we used to quantify both additive and multiplicative effects of the four parameters. We found that the tested parameters are engaged in complex interactions, exerting multiplicative, rather than additive, effects on assembly quality. Also, the ratio of non-repeated regions and GC% of the original genomes can shape how the four parameters affect assembly quality.<br><br>CONCLUSIONS: We provide a framework for consideration in future studies using de novo genome assembly of bacterial genomes, e.g. in choosing the optimal sequencing depth, balancing between its positive effect on contiguity and negative effect on accuracy due to its interaction with error rate. Furthermore, the properties of the genomes to be sequenced also should be taken into account, as they might influence the effects of error sources themselves.}, }
@article {pmid38194414, year = {2024}, author = {Terpstra, S and Marquitti, FMD and Vasconcelos, VV}, title = {Adaptive foraging of pollinators fosters gradual tipping under resource competition and rapid environmental change.}, journal = {PLoS computational biology}, volume = {20}, number = {1}, pages = {e1011762}, pmid = {38194414}, issn = {1553-7358}, mesh = {Humans ; *Pollination/physiology ; *Models, Biological ; Models, Theoretical ; Plants ; Food Chain ; }, abstract = {Plant and pollinator communities are vital for transnational food chains. Like many natural systems, they are affected by global change: rapidly deteriorating conditions threaten their numbers. Previous theoretical studies identified the potential for community-wide collapse above critical levels of environmental stressors-so-called bifurcation-induced tipping points. Fortunately, even as conditions deteriorate, individuals have some adaptive capacity, potentially increasing the boundary for a safe operating space where changes in ecological processes are reversible. Our study considers this adaptive capacity of pollinators to resource availability and identifies a new threat to disturbed pollinator communities. We model the adaptive foraging of pollinators in changing environments. Pollinator's adaptive foraging alters the dynamical responses of species, to the advantage of some-typically generalists-and the disadvantage of others, with systematic non-linear and non-monotonic effects on the abundance of particular species. We show that, in addition to the extent of environmental stress, the pace of change of environmental stress can also lead to the early collapse of both adaptive and nonadaptive pollinator communities. Specifically, perturbed communities exhibit rate-induced tipping points at stress levels within the safe boundary defined for constant stressors. With adaptive foraging, tipping is a more asynchronous collapse of species compared to nonadaptive pollinator communities, meaning that not all pollinator species reach a tipping event simultaneously. These results suggest that it is essential to consider the adaptive capacity of pollinator communities for monitoring and conservation. Both the extent and the rate of stress change relative to the ability of communities to recover are critical environmental boundaries.}, }
@article {pmid38188173, year = {2024}, author = {Lizardo, V and García Trejo, EA and Morrone, JJ}, title = {Niche conservatism and convergence in birds of three cenocrons in the Mexican Transition Zone.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e16664}, pmid = {38188173}, issn = {2167-8359}, mesh = {Animals ; Phylogeny ; *Biological Evolution ; *Biota ; Birds ; }, abstract = {BACKGROUND: The niche conservatism hypothesis postulates that physiological and phylogenetic factors constrain species distributions, creating richness hotspots with older lineages in ancestral climatic conditions. Conversely, niche convergence occurs when species successfully disperse to novel environments, diversifying and resulting in areas with high phylogenetic clustering and endemism, low diversity, and lower clade age. The Mexican Transition Zone exhibits both patterns as its biotic assembly resulted from successive dispersal events of different biotic elements called cenocrons. We test the hypothesis that biogeographic transitionallity in the area is a product of niche conservatism in the Nearctic and Typical Neotropical cenocrons and niche convergence in the Mountain Mesoamerican cenocron.<br><br>METHODS: We split the avifauna into three species sets representing cenocrons (sets of taxa that share the same biogeographic history, constituting an identifiable subset within a biota by their common biotic origin and evolutionary history). Then, we correlated richness, endemism, phylogenetic diversity, number of nodes, and crowning age with environmental and topographic variables. These correlations were then compared with the predictions of niche conservatism versus niche convergence. We also detected areas of higher species density in environmental space and interpreted them as an environmental transition zone where birds' niches converge.<br><br>RESULTS: Our findings support the expected predictions on how niches evolved. Nearctic and Typical Neotropical species behaved as predicted by niche conservatism, whereas Mountain Mesoamerican species and the total of species correlations indicated niche convergence. We also detected distinct ecological and evolutionary characteristics of the cenocrons on a macroecological scale and the environmental conditions where the three cenocrons overlap in the Mesoamerican region.}, }
@article {pmid38184954, year = {2024}, author = {Loo, SL and Howerton, E and Contamin, L and Smith, CP and Borchering, RK and Mullany, LC and Bents, S and Carcelen, E and Jung, SM and Bogich, T and van Panhuis, WG and Kerr, J and Espino, J and Yan, K and Hochheiser, H and Runge, MC and Shea, K and Lessler, J and Viboud, C and Truelove, S}, title = {The US COVID-19 and Influenza Scenario Modeling Hubs: Delivering long-term projections to guide policy.}, journal = {Epidemics}, volume = {46}, number = {}, pages = {100738}, pmid = {38184954}, issn = {1878-0067}, support = {R24 GM153920/GM/NIGMS NIH HHS/United States ; U24 GM132013/GM/NIGMS NIH HHS/United States ; Z99 TW999999/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Humans ; *COVID-19/epidemiology ; *Influenza, Human/epidemiology ; Pandemics ; Policy ; Public Health ; }, abstract = {Between December 2020 and April 2023, the COVID-19 Scenario Modeling Hub (SMH) generated operational multi-month projections of COVID-19 burden in the US to guide pandemic planning and decision-making in the context of high uncertainty. This effort was born out of an attempt to coordinate, synthesize and effectively use the unprecedented amount of predictive modeling that emerged throughout the COVID-19 pandemic. Here we describe the history of this massive collective research effort, the process of convening and maintaining an open modeling hub active over multiple years, and attempt to provide a blueprint for future efforts. We detail the process of generating 17 rounds of scenarios and projections at different stages of the COVID-19 pandemic, and disseminating results to the public health community and lay public. We also highlight how SMH was expanded to generate influenza projections during the 2022-23 season. We identify key impacts of SMH results on public health and draw lessons to improve future collaborative modeling efforts, research on scenario projections, and the interface between models and policy.}, }
@article {pmid38182924, year = {2024}, author = {Brodie, JF and Mohd-Azlan, J and Chen, C and Wearn, OR and Deith, MCM and Ball, JGC and Slade, EM and Burslem, DFRP and Teoh, SW and Williams, PJ and Nguyen, A and Moore, JH and Goetz, SJ and Burns, P and Jantz, P and Hakkenberg, CR and Kaszta, ZM and Cushman, S and Coomes, D and Helmy, OE and Reynolds, G and Rodríguez, JP and Jetz, W and Luskin, MS}, title = {Publisher Correction: Landscape-scale benefits of protected areas for tropical biodiversity.}, journal = {Nature}, volume = {625}, number = {7996}, pages = {E28}, doi = {10.1038/s41586-023-07007-2}, pmid = {38182924}, issn = {1476-4687}, }
@article {pmid38182741, year = {2024}, author = {Ryu, H and Kinoshita, K and Joo, S and Choi, YS and Kim, SS}, title = {Increased urinary creatinine during hibernation and day roosting in the Eastern bent-winged bat (Miniopterus fuliginosus) in Korea.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {42}, pmid = {38182741}, issn = {2399-3642}, mesh = {Animals ; *Hibernation ; *Chiroptera ; Creatinine ; *Torpor ; Republic of Korea ; }, abstract = {Torpor and arousal cycles, both daily and seasonal (e.g. hibernation), are crucial for small mammals, including bats, to maintain the energy and water balance. The alternation between torpor and arousal leads to metabolic changes, leaving traceable evidence of metabolic wastes in urine. In this study we investigated urinary creatinine and acetoacetate (a ketone body) in the Eastern bent-wing bat (Miniopterus fuliginosus) in Mungyeong, South Korea. We found an increase in urinary creatinine during torpor in summer, indicating changes in renal water reabsorption rates during the active season. Although we could not confirm ketonuria in hibernating bats due to a methodological limitation caused by the small amount of urine, we verified an increase in urinary creatinine concentration during hibernation. This finding suggests that managing water stress resulting from evaporative water loss is one of key reasons for arousal during hibernation in Eastern bent-wing bats.}, }
@article {pmid38175682, year = {2024}, author = {Henry, LM and Hansen, E and Chimoff, J and Pokstis, K and Kiderman, M and Naim, R and Kossowsky, J and Byrne, ME and Lopez-Guzman, S and Kircanski, K and Pine, DS and Brotman, MA}, title = {Selecting an Ecological Momentary Assessment Platform: Tutorial for Researchers.}, journal = {Journal of medical Internet research}, volume = {26}, number = {}, pages = {e51125}, pmid = {38175682}, issn = {1438-8871}, support = {K01 DA057374/DA/NIDA NIH HHS/United States ; ZIA MH002969/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Adolescent ; Child ; Humans ; *Ecological Momentary Assessment ; Data Management ; Digital Technology ; Laboratories ; *Medicine ; }, abstract = {BACKGROUND: Although ecological momentary assessment (EMA) has been applied in psychological research for decades, delivery methods have evolved with the proliferation of digital technology. Technological advances have engendered opportunities for enhanced accessibility, convenience, measurement precision, and integration with wearable sensors. Notwithstanding, researchers must navigate novel complexities in EMA research design and implementation.<br><br>OBJECTIVE: In this paper, we aimed to provide guidance on platform selection for clinical scientists launching EMA studies.<br><br>METHODS: Our team includes diverse specialties in child and adolescent behavioral and mental health with varying expertise on EMA platforms (eg, users and developers). We (2 research sites) evaluated EMA platforms with the goal of identifying the platform or platforms with the best fit for our research. We created a list of extant EMA platforms; conducted a web-based review; considered institutional security, privacy, and data management requirements; met with developers; and evaluated each of the candidate EMA platforms for 1 week.<br><br>RESULTS: We selected 2 different EMA platforms, rather than a single platform, for use at our 2 research sites. Our results underscore the importance of platform selection driven by individualized and prioritized laboratory needs; there is no single, ideal platform for EMA researchers. In addition, our project generated 11 considerations for researchers in selecting an EMA platform: (1) location; (2) developer involvement; (3) sample characteristics; (4) onboarding; (5) survey design features; (6) sampling scheme and scheduling; (7) viewing results; (8) dashboards; (9) security, privacy, and data management; (10) pricing and cost structure; and (11) future directions. Furthermore, our project yielded a suggested timeline for the EMA platform selection process.<br><br>CONCLUSIONS: This study will guide scientists initiating studies using EMA, an in vivo, real-time research tool with tremendous promise for facilitating advances in psychological assessment and intervention.}, }
@article {pmid38173562, year = {2023}, author = {Boyes, D and Boyes, C and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Pine Hawkmoth, Sphinx pinastri (Linneaus 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {312}, pmid = {38173562}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Sphinx pinastri (the Pine Hawkmoth; Arthropoda; Insecta; Lepidoptera; Sphingidae). The genome sequence is 509.2 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length.}, }
@article {pmid38172362, year = {2024}, author = {Paolo, FS and Kroodsma, D and Raynor, J and Hochberg, T and Davis, P and Cleary, J and Marsaglia, L and Orofino, S and Thomas, C and Halpin, P}, title = {Satellite mapping reveals extensive industrial activity at sea.}, journal = {Nature}, volume = {625}, number = {7993}, pages = {85-91}, pmid = {38172362}, issn = {1476-4687}, mesh = {Humans ; COVID-19/epidemiology ; Deep Learning ; Energy-Generating Resources/statistics &amp; numerical data ; Food Supply/statistics &amp; numerical data ; Geographic Information Systems ; Geographic Mapping ; *Human Activities/economics/statistics &amp; numerical data ; Hunting/statistics &amp; numerical data ; *Industry/economics/statistics &amp; numerical data ; *Oceans and Seas ; *Satellite Imagery ; Ships/statistics &amp; numerical data ; Wind ; }, abstract = {The world's population increasingly relies on the ocean for food, energy production and global trade[1-3], yet human activities at sea are not well quantified[4,5]. We combine satellite imagery, vessel GPS data and deep-learning models to map industrial vessel activities and offshore energy infrastructure across the world's coastal waters from 2017 to 2021. We find that 72-76% of the world's industrial fishing vessels are not publicly tracked, with much of that fishing taking place around South Asia, Southeast Asia and Africa. We also find that 21-30% of transport and energy vessel activity is missing from public tracking systems. Globally, fishing decreased by 12 ± 1% at the onset of the COVID-19 pandemic in 2020 and had not recovered to pre-pandemic levels by 2021. By contrast, transport and energy vessel activities were relatively unaffected during the same period. Offshore wind is growing rapidly, with most wind turbines confined to small areas of the ocean but surpassing the number of oil structures in 2021. Our map of ocean industrialization reveals changes in some of the most extensive and economically important human activities at sea.}, }
@article {pmid38172330, year = {2024}, author = {Gong, Y and Zha, J and Guo, Q and Guo, G}, title = {A new indicator for estimating the degree of mining-induced land subsidence: the overburden's average GSI value.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {332}, pmid = {38172330}, issn = {2045-2322}, support = {2023YFC3804200//National Key Research and Development Program of China/ ; 2023YFC3804200//National Key Research and Development Program of China/ ; 2023YFC3804200//National Key Research and Development Program of China/ ; U21A20109, 4227040173, 52274164, 42174048//National Natural Science Foundation of China/ ; U21A20109, 4227040173, 52274164, 42174048//National Natural Science Foundation of China/ ; U21A20109, 4227040173, 52274164, 42174048//National Natural Science Foundation of China/ ; }, abstract = {Underground coal mining leads to land subsidence, which, in turn, results in damage to buildings and infrastructure, disturbs the original ecological environment, and hinders the sustainable development of coal mining cities. A reasonable estimation of land subsidence, on the other hand, is the foundation for building protection, land reclamation, and ecological environment reconstruction. However, when we applied the existing land subsidence estimation theory to the deep mining areas of the Ordos coalfield in western China, there was a significant deviation between the estimations and the measurements. To explain such unusual case, we propose using the overburden's average GSI (Geological Strength Index) value instead of the compressive strength (UCS) of rock specimens for a better representation of the overburden's overall properties. By using on-site subsidence monitoring results and historical data, we provided evidence which supports that the overburden's average GSI value has a much greater impact on subsidence rates than the UCS. Subsequently, we investigated the relationship between three typical overburden's GSI values and the subsidence rates via a calibrated numerical model, revealing the variation patterns of maximum surface subsidence when the overburden's average GSI value is set at 30, 50, and 75, respectively. Finally, on the basis of the measured and simulated results, we discussed a non-conventional strip mining method for mining subsidence control in the deep mining areas of the Ordos coalfield in western China, and explained why it is possible and what are the significant advantages behind. The proposed methods, findings, and suggestions in this paper are therefore quite helpful for researchers and engineers who wish to estimate and control the mining-induced land subsidence, as well as for those who are particularly interested in the study of environment science related to land subsidence.}, }
@article {pmid38172116, year = {2024}, author = {Külling, N and Adde, A and Fopp, F and Schweiger, AK and Broennimann, O and Rey, PL and Giuliani, G and Goicolea, T and Petitpierre, B and Zimmermann, NE and Pellissier, L and Altermatt, F and Lehmann, A and Guisan, A}, title = {SWECO25: a cross-thematic raster database for ecological research in Switzerland.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {21}, pmid = {38172116}, issn = {2052-4463}, abstract = {Standard and easily accessible cross-thematic spatial databases are key resources in ecological research. In Switzerland, as in many other countries, available data are scattered across computer servers of research institutions and are rarely provided in standard formats (e.g., different extents or projections systems, inconsistent naming conventions). Consequently, their joint use can require heavy data management and geomatic operations. Here, we introduce SWECO25, a Swiss-wide raster database at 25-meter resolution gathering 5,265 layers. The 10 environmental categories included in SWECO25 are: geologic, topographic, bioclimatic, hydrologic, edaphic, land use and cover, population, transportation, vegetation, and remote sensing. SWECO25 layers were standardized to a common grid sharing the same resolution, extent, and geographic coordinate system. SWECO25 includes the standardized source data and newly calculated layers, such as those obtained by computing focal or distance statistics. SWECO25 layers were validated by a data integrity check, and we verified that the standardization procedure had a negligible effect on the output values. SWECO25 is available on Zenodo and is intended to be updated and extended regularly.}, }
@article {pmid38167330, year = {2024}, author = {Li, M and Liang, H and Yang, H and Ding, Q and Xia, R and Chen, J and Zhou, W and Yang, Y and Zhang, Z and Yao, Y and Ran, C and Zhou, Z}, title = {Deciphering the gut microbiome of grass carp through multi-omics approach.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {2}, pmid = {38167330}, issn = {2049-2618}, support = {31925038//National Natural Science Foundation of China/ ; 31925038//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Carps ; Multiomics ; *Microbiota ; Proteobacteria/genetics ; Fusobacteria/genetics ; Bacteroidetes/genetics ; Bacillota/genetics ; Fusobacterium/genetics ; RNA, Ribosomal, 16S/genetics ; Mammals/genetics ; }, abstract = {BACKGROUND: Aquaculture plays an important role in global protein supplies and food security. The ban on antibiotics as feed additive proposes urgent need to develop alternatives. Gut microbiota plays important roles in the metabolism and immunity of fish and has the potential to give rise to novel solutions for challenges confronted by fish culture. However, our understanding of fish gut microbiome is still lacking.<br><br>RESULTS: We identified 575,856 non-redundant genes by metagenomic sequencing of the intestinal content samples of grass carp. Taxonomic and functional annotation of the gene catalogue revealed specificity of the gut microbiome of grass carp compared with mammals. Co-occurrence analysis indicated exclusive relations between the genera belonging to Proteobacteria and Fusobacteria/Firmicutes/Bacteroidetes, suggesting two independent ecological groups of the microbiota. The association pattern of Proteobacteria with the gene expression modules of fish gut and the liver was consistently opposite to that of Fusobacteria, Firmicutes, and Bacteroidetes, implying differential functionality of Proteobacteria and Fusobacteria/Firmicutes/Bacteroidetes. Therefore, the two ecological groups were considered as two functional groups, i.e., Functional Group 1: Proteobacteria and Functional Group 2: Fusobacteria/Firmicutes/Bacteroidetes. Further analysis revealed that the two functional groups differ in genetic capacity for carbohydrate utilization, virulence factors, and antibiotic resistance. Finally, we proposed that the ratio of "Functional Group 2/Functional Group 1" can be used as a biomarker that efficiently reflects the structural and functional characteristics of the microbiota of grass carp.<br><br>CONCLUSIONS: The gene catalogue is an important resource for investigating the gut microbiome of grass carp. Multi-omics analysis provides insights into functional implications of the main phyla that comprise the fish microbiota and shed lights on targets for microbiota regulation. Video Abstract.}, }
@article {pmid38166118, year = {2024}, author = {Muraleedharan, V and Rajan, SC and R, J}, title = {Geometric entropy of plant leaves: A measure of morphological complexity.}, journal = {PloS one}, volume = {19}, number = {1}, pages = {e0293596}, pmid = {38166118}, issn = {1932-6203}, mesh = {Entropy ; *Plants ; *Biological Evolution ; Physical Phenomena ; Plant Leaves/anatomy &amp; histology ; }, abstract = {Shape is an objective characteristic of an object. A boundary separates a physical object from its surroundings. It defines the shape and regulates energy flux into and from an object. Visual perception of a definite shape (geometry) of physical objects is an abstraction. While the perceived geometry at an object's sharp interface (macro) creates a Euclidian illusion of actual shape, the notion of diffuse interfaces (micro) allows an understanding of the realistic form of objects. Here, we formulate a dimensionless geometric entropy of plant leaves (SL) by a 2-D description of a phase-field function. We applied this method to 112 tropical plant leaf images. SL was estimated from the leaf perimeter (P) and leaf area (A). It correlates positively with a fractal dimensional measure of leaf complexity, viz., segmental fractal complexity. Leaves with a higher P: A ratio have higher SL and possess complex morphology. The univariate cluster analysis of SL reveals the taxonomic relationship among the leaf shapes at the genus level. An increase in SL of plant leaves could be an evolutionary strategy. The results of morphological complexity presented in this paper will trigger discussion on the causal links between leaf adaptive stability/efficiency and complexity. We present SL as a derived plant trait to describe plant leaf complexity and adaptive stability. Integrating SL into other leaf physiological measures will help to understand the dynamics of energy flow between plants and their environment.}, }
@article {pmid38163964, year = {2025}, author = {Bhardwaj, N and S, S and Tripathi, N and Kumar, S and Lal, UR and G, R and Guru, SK and Jain, SK}, title = {Mahamanalactone A, a new triterpenoid from Dysoxylum malabaricum bark: a case study for rapid identification of new metabolites via LC-HRMS profiling and database mining strategy.}, journal = {Natural product research}, volume = {39}, number = {9}, pages = {2438-2443}, doi = {10.1080/14786419.2023.2298721}, pmid = {38163964}, issn = {1478-6427}, mesh = {Humans ; *Triterpenes/chemistry/isolation &amp; purification/pharmacology ; *Plant Bark/chemistry ; Cell Line, Tumor ; *Antineoplastic Agents, Phytogenic/chemistry/pharmacology/isolation &amp; purification ; Chromatography, Liquid ; Molecular Structure ; Mass Spectrometry ; *Meliaceae/chemistry ; Data Mining ; Plant Extracts/chemistry ; }, abstract = {In this recent investigation, the focus centred on exploring the potential phytoconstituents within the bark of Dysoxylum malabaricum. A profiling strategy employing LC-HRMS (Liquid Chromatography-High Resolution Mass Spectrometry) was implemented for the rapid identification of compounds from the bark extract. The crude extract underwent fractionation, resulting in the isolation of four previously known compounds (1-4) and a novel cycloartane triterpenoid named Mahamanalactone A (5). Compound 5 represents a cycloartane triterpenoid with a modified ring-A, featuring £-caprolactone fusion at positions 4 and 5, distinguishing it from other reported compounds where £-caprolactone is typically fused at positions 3 and 4. Cytotoxicity assessment revealed that the newly identified compound 5 exhibited a moderate cytotoxic profile (IC50 29 to 78 µM) against a panel of cancer cell lines.}, }
@article {pmid38160970, year = {2024}, author = {Thenmozhi, M and Sujatha, M and Kavitha, M and Senthilraja, S and Babu, M and Priya, V}, title = {Assessment of cyclone risk and case study of Gaja cyclone using GIS techniques and machine learning algorithms in coastal zone of Tamil Nadu, India.}, journal = {Environmental research}, volume = {246}, number = {}, pages = {118089}, doi = {10.1016/j.envres.2023.118089}, pmid = {38160970}, issn = {1096-0953}, mesh = {*Cyclonic Storms ; India ; Geographic Information Systems ; *Disasters ; Algorithms ; }, abstract = {Cyclones can cause devastating impacts, including strong winds, heavy rainfall, storm surges, and flooding. The aftermath includes infrastructure damage, loss of life, displacement of communities, and ecological disruptions. Timely response and recovery efforts are crucial to minimize the socio-economic and environmental consequences of cyclones. To accelerate the time-consuming risk assessment process, particularly in geographically diverse regions, a blend of multi-criteria decision-making and machine learning models was utilized. This novel approach swiftly assessed cyclone risk and the impact of the Gaja cyclone in Nagapattinam, India. The method involved assigning weights to distinct criteria, unveiling notable vulnerability aspects like elevation, slope, proximity to the coast, distance from cyclone tracts, Lu/Lc, population density, proximity to cyclone shelters, household density, accessibility to healthcare facilities, NDVI, and levels of awareness. Daddavari, Ettugudi, Kodikarai, Vedharanyam, Velankanni, and Thirupoondi face high/ex